org.apache.ctakes.padtermspotter.cr
Class RadiologyRecordsCollectionReader

java.lang.Object
  org.apache.uima.resource.Resource_ImplBase
      org.apache.uima.resource.ConfigurableResource_ImplBase
          org.apache.uima.collection.CollectionReader_ImplBase
              org.apache.ctakes.padtermspotter.cr.RadiologyRecordsCollectionReader

All Implemented Interfaces:

org.apache.uima.collection.base_cpm.BaseCollectionReader, org.apache.uima.collection.CollectionReader, org.apache.uima.resource.ConfigurableResource, org.apache.uima.resource.Resource

public class RadiologyRecordsCollectionReader
extends org.apache.uima.collection.CollectionReader_ImplBase

The original code was copied from org.apache.uima.examples.cpe.FileSystemCollectionReader and modified for Mayo use. This collection reader facilitates reading "documents" from a single file. Each line in the document will be considered an entity to be analyzed by the CPE. That is each line will be treated as a "document" and will have its own CAS. Extremely large files will require large memory resources as each line is read into memory upon initialization. This was done to simplify implementation.

Author:

Mayo Clinic

Field Summary

(package private) java.lang.Integer	filterColunmNumber
(package private) java.lang.String	filterExamTypes
(package private) int	iv_currentIndex
(package private) java.lang.String	iv_delimeter
(package private) java.lang.String	iv_language
(package private) java.util.List	iv_linesFromFile
(package private) java.lang.Integer	numberOfColumns
static java.lang.String	PARAM_COMMENT_STRING Optional parameter specifies a comment string.
static java.lang.String	PARAM_EXAM_COLUMN The column number of the input file that contains the compare string to parse applicable exam types.
static java.lang.String	PARAM_FILTER_EXAMS Specifies the file which contains the valid types of exams which will be processed by the pipeline.
static java.lang.String	PARAM_ID_DELIMETER Name of optional configuration parameter that specifies a character (or string) that delimits the id of the document from the text of the document.
static java.lang.String	PARAM_IGNORE_BLANK_LINES Optional parameter determines whether a blank line will be processed as a document or will be ignored.
static java.lang.String	PARAM_INPUT_FILE_NAME This parameter will be used the descriptor file to specify the location of the file that will be run through this collection reader.
static java.lang.String	PARAM_LANGUAGE Name of optional configuration parameter that contains the language of the documents in the input directory.
static java.lang.String	PARAM_TOTAL_COLUMNS Number of columns contained in the radiology record.

Fields inherited from interface org.apache.uima.resource.Resource

PARAM_AGGREGATE_SOFA_MAPPINGS, PARAM_CONFIG_MANAGER, PARAM_CONFIG_PARAM_SETTINGS, PARAM_PERFORMANCE_TUNING_SETTINGS, PARAM_RESOURCE_MANAGER, PARAM_UIMA_CONTEXT

Constructor Summary

RadiologyRecordsCollectionReader()

Method Summary

void	close()
void	getNext(org.apache.uima.cas.CAS cas)
int	getNumberOfDocuments() Gets the total number of documents that will be returned by this collection reader.
org.apache.uima.util.Progress[]	getProgress()
boolean	hasNext()
void	initialize()

Methods inherited from class org.apache.uima.collection.CollectionReader_ImplBase

destroy, getCasInitializer, getProcessingResourceMetaData, initialize, isConsuming, reconfigure, setCasInitializer, typeSystemInit

Methods inherited from class org.apache.uima.resource.ConfigurableResource_ImplBase

getConfigParameterValue, getConfigParameterValue, setConfigParameterValue, setConfigParameterValue

Methods inherited from class org.apache.uima.resource.Resource_ImplBase

getCasManager, getLogger, getMetaData, getResourceManager, getUimaContext, getUimaContextAdmin, setLogger, setMetaData

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.apache.uima.resource.ConfigurableResource

getConfigParameterValue, getConfigParameterValue, setConfigParameterValue, setConfigParameterValue

Methods inherited from interface org.apache.uima.resource.Resource

getLogger, getMetaData, getResourceManager, getUimaContext, getUimaContextAdmin, setLogger

Field Detail

PARAM_INPUT_FILE_NAME

public static final java.lang.String PARAM_INPUT_FILE_NAME

This parameter will be used the descriptor file to specify the location of the file that will be run through this collection reader.

See Also:

Constant Field Values

PARAM_COMMENT_STRING

public static final java.lang.String PARAM_COMMENT_STRING

Optional parameter specifies a comment string. Any line that begins with the string will be ignored and not be added as a "document" to the CPE.

See Also:

Constant Field Values

PARAM_IGNORE_BLANK_LINES

public static final java.lang.String PARAM_IGNORE_BLANK_LINES

Optional parameter determines whether a blank line will be processed as a document or will be ignored. The default will be set to 'true'.

See Also:

Constant Field Values

PARAM_LANGUAGE

public static final java.lang.String PARAM_LANGUAGE

Name of optional configuration parameter that contains the language of the documents in the input directory. If specified this information will be added to the CAS.

See Also:

Constant Field Values

PARAM_ID_DELIMETER

public static final java.lang.String PARAM_ID_DELIMETER

Name of optional configuration parameter that specifies a character (or string) that delimits the id of the document from the text of the document. For example, if the parameter is set to '|' then the following line from a file: 1234|this is some text would have an id of 1234 and text this is some text. If this parameter is not set, then the id of a document will be its line number in the file.

See Also:

Constant Field Values

PARAM_TOTAL_COLUMNS

public static final java.lang.String PARAM_TOTAL_COLUMNS

Number of columns contained in the radiology record. Typically, all the columns will be skipped for actual annotation except the final column which contains the details of the examination.

See Also:

Constant Field Values

PARAM_FILTER_EXAMS

public static final java.lang.String PARAM_FILTER_EXAMS

Specifies the file which contains the valid types of exams which will be processed by the pipeline.

See Also:

Constant Field Values

PARAM_EXAM_COLUMN

public static final java.lang.String PARAM_EXAM_COLUMN

The column number of the input file that contains the compare string to parse applicable exam types.

See Also:

Constant Field Values

iv_linesFromFile

java.util.List iv_linesFromFile

iv_currentIndex

int iv_currentIndex

iv_language

java.lang.String iv_language

iv_delimeter

java.lang.String iv_delimeter

numberOfColumns

java.lang.Integer numberOfColumns

filterExamTypes

java.lang.String filterExamTypes

filterColunmNumber

java.lang.Integer filterColunmNumber

Constructor Detail

RadiologyRecordsCollectionReader

public RadiologyRecordsCollectionReader()

Method Detail

initialize

public void initialize()
                throws org.apache.uima.resource.ResourceInitializationException

Overrides:

initialize in class org.apache.uima.collection.CollectionReader_ImplBase

Throws:

org.apache.uima.resource.ResourceInitializationException

getNext

public void getNext(org.apache.uima.cas.CAS cas)
             throws java.io.IOException,
                    org.apache.uima.collection.CollectionException

Throws:

java.io.IOException

org.apache.uima.collection.CollectionException

hasNext

public boolean hasNext()
                throws java.io.IOException,
                       org.apache.uima.collection.CollectionException

Throws:

java.io.IOException

org.apache.uima.collection.CollectionException

getProgress

public org.apache.uima.util.Progress[] getProgress()

getNumberOfDocuments

public int getNumberOfDocuments()

Gets the total number of documents that will be returned by this collection reader.

Returns:

the number of documents in the collection

close

public void close()
           throws java.io.IOException

Throws:

java.io.IOException