org.apache.ctakes.preprocessor

Class ClinicalNotePreProcessor

java.lang.Object

org.xml.sax.helpers.DefaultHandler

org.apache.ctakes.preprocessor.ClinicalNotePreProcessor

All Implemented Interfaces:

PreProcessor, ContentHandler, DTDHandler, EntityResolver, ErrorHandler

public class ClinicalNotePreProcessor
extends org.xml.sax.helpers.DefaultHandler
implements PreProcessor

Given an HL7 document, the text contained inside a section is extracted.

Author:

Mayo

Field Summary

Fields

Modifier and Type	Field and Description
static String	MD_KEY_ADMIT_DATE
static String	MD_KEY_CUSTOMER_ID
static String	MD_KEY_DISCHARGE_DATE
static String	MD_KEY_DOC_CONFIDENTIAL_IND
static String	MD_KEY_DOC_ID
static String	MD_KEY_DOC_LINK_ID
static String	MD_KEY_DOC_REVISION_ID
static String	MD_KEY_DOC_STATUS_CODE
static String	MD_KEY_EVENT_TYPE_CODE
static String	MD_KEY_FACILITY_CODE
static String	MD_KEY_HISTORY_SECTION
static String	MD_KEY_LOCATION
static String	MD_KEY_MINUTES_COUNSELING
static String	MD_KEY_NOTE_DATE
static String	MD_KEY_PATIENT_CITY
static String	MD_KEY_PATIENT_CNT
static String	MD_KEY_PATIENT_STATE
static String	MD_KEY_PATIENT_STREET_ADDR
static String	MD_KEY_PATIENT_ZIP
static String	MD_KEY_PROVIDER_ID
static String	MD_KEY_PROVIDER2_ID
static String	MD_KEY_PT_BILLING_CODE
static String	MD_KEY_PT_BIRTH_DATE
static String	MD_KEY_PT_BMI
static String	MD_KEY_PT_BSA
static String	MD_KEY_PT_GENDER
static String	MD_KEY_PT_HEAD_CIRCUMFERENCE
static String	MD_KEY_PT_HEIGHT
static String	MD_KEY_PT_RESPIRATORY_RATE
static String	MD_KEY_PT_TEMPERATURE
static String	MD_KEY_PT_WEIGHT
static String	MD_KEY_REV_DATE
static String	MD_KEY_SERVICE_CODE
static String	MD_KEY_SIGNATURE_DATE
static String	MD_KEY_SIGNATURE_ID
static String	MD_KEY_SITE_CODE
static String	MD_KEY_TOTAL_TIME
static String	MD_KEY_TRANSCRIBER_ID
static String	MD_KEY_TRANSCRIPTION_DATE
static int	UNKNOWN_TABLE_TYPE

Constructor Summary

Constructors

Constructor and Description
ClinicalNotePreProcessor(InputStream dtdFile, boolean includeSectionMarkers) Constructor

Method Summary

Modifier and Type	Method and Description
void	characters(char[] ch, int start, int length)
void	endDocument()
void	endElement(String uri, String localName, String qName)
DocumentMetaData	process(String xml) Process a document to retrieve meta data about the document.
void	startDocument()
void	startElement(String uri, String localName, String qName, Attributes attributes)

Methods inherited from class org.xml.sax.helpers.DefaultHandler

endPrefixMapping, error, fatalError, ignorableWhitespace, notationDecl, processingInstruction, resolveEntity, setDocumentLocator, skippedEntity, startPrefixMapping, unparsedEntityDecl, warning

Methods inherited from class java.lang.Object

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

Field Detail

MD_KEY_PATIENT_STREET_ADDR

public static final String MD_KEY_PATIENT_STREET_ADDR

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Constant Field Values

MD_KEY_PATIENT_CITY

public static final String MD_KEY_PATIENT_CITY

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Constant Field Values

MD_KEY_PATIENT_STATE

public static final String MD_KEY_PATIENT_STATE

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Constant Field Values

MD_KEY_PATIENT_ZIP

public static final String MD_KEY_PATIENT_ZIP

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Constant Field Values

MD_KEY_PATIENT_CNT

public static final String MD_KEY_PATIENT_CNT

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Constant Field Values

MD_KEY_DOC_ID

public static final String MD_KEY_DOC_ID

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Constant Field Values

MD_KEY_DOC_LINK_ID

public static final String MD_KEY_DOC_LINK_ID

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Constant Field Values

MD_KEY_DOC_REVISION_ID

public static final String MD_KEY_DOC_REVISION_ID

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Constant Field Values

MD_KEY_NOTE_DATE

public static final String MD_KEY_NOTE_DATE

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Constant Field Values

MD_KEY_REV_DATE

public static final String MD_KEY_REV_DATE

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Constant Field Values

MD_KEY_ADMIT_DATE

public static final String MD_KEY_ADMIT_DATE

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Constant Field Values

MD_KEY_DISCHARGE_DATE

public static final String MD_KEY_DISCHARGE_DATE

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Constant Field Values

MD_KEY_SERVICE_CODE

public static final String MD_KEY_SERVICE_CODE

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Constant Field Values

MD_KEY_SITE_CODE

public static final String MD_KEY_SITE_CODE

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Constant Field Values

MD_KEY_FACILITY_CODE

public static final String MD_KEY_FACILITY_CODE

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Constant Field Values

MD_KEY_PT_BIRTH_DATE

public static final String MD_KEY_PT_BIRTH_DATE

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Constant Field Values

MD_KEY_PT_HEIGHT

public static final String MD_KEY_PT_HEIGHT

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Constant Field Values

MD_KEY_PT_WEIGHT

public static final String MD_KEY_PT_WEIGHT

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Constant Field Values

MD_KEY_PT_HEAD_CIRCUMFERENCE

public static final String MD_KEY_PT_HEAD_CIRCUMFERENCE

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Constant Field Values

MD_KEY_PT_GENDER

public static final String MD_KEY_PT_GENDER

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Constant Field Values

MD_KEY_PT_BMI

public static final String MD_KEY_PT_BMI

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Constant Field Values

MD_KEY_PT_BSA

public static final String MD_KEY_PT_BSA

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Constant Field Values

MD_KEY_PT_TEMPERATURE

public static final String MD_KEY_PT_TEMPERATURE

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Constant Field Values

MD_KEY_PT_BILLING_CODE

public static final String MD_KEY_PT_BILLING_CODE

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Constant Field Values

MD_KEY_PT_RESPIRATORY_RATE

public static final String MD_KEY_PT_RESPIRATORY_RATE

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Constant Field Values

MD_KEY_EVENT_TYPE_CODE

public static final String MD_KEY_EVENT_TYPE_CODE

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Constant Field Values

MD_KEY_DOC_CONFIDENTIAL_IND

public static final String MD_KEY_DOC_CONFIDENTIAL_IND

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Constant Field Values

MD_KEY_DOC_STATUS_CODE

public static final String MD_KEY_DOC_STATUS_CODE

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Constant Field Values

MD_KEY_HISTORY_SECTION

public static final String MD_KEY_HISTORY_SECTION

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Constant Field Values

MD_KEY_LOCATION

public static final String MD_KEY_LOCATION

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Constant Field Values

MD_KEY_MINUTES_COUNSELING

public static final String MD_KEY_MINUTES_COUNSELING

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Constant Field Values

MD_KEY_TOTAL_TIME

public static final String MD_KEY_TOTAL_TIME

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Constant Field Values

MD_KEY_PROVIDER_ID

public static final String MD_KEY_PROVIDER_ID

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Constant Field Values

MD_KEY_PROVIDER2_ID

public static final String MD_KEY_PROVIDER2_ID

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Constant Field Values

MD_KEY_SIGNATURE_ID

public static final String MD_KEY_SIGNATURE_ID

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Constant Field Values

MD_KEY_SIGNATURE_DATE

public static final String MD_KEY_SIGNATURE_DATE

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Constant Field Values

MD_KEY_TRANSCRIBER_ID

public static final String MD_KEY_TRANSCRIBER_ID

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Constant Field Values

MD_KEY_TRANSCRIPTION_DATE

public static final String MD_KEY_TRANSCRIPTION_DATE

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Constant Field Values

MD_KEY_CUSTOMER_ID

public static final String MD_KEY_CUSTOMER_ID

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Constant Field Values

UNKNOWN_TABLE_TYPE

public static final int UNKNOWN_TABLE_TYPE

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Constant Field Values

Constructor Detail

ClinicalNotePreProcessor

public ClinicalNotePreProcessor(InputStream dtdFile,
                                boolean includeSectionMarkers)
                         throws SAXException,
                                FileNotFoundException

Constructor

Parameters:

dtdFile - File object pointing to DTD.

includeSectionMarkers - Flag that determines whether the section markers are included as part of the section.

Throws:

SAXException

FileNotFoundException

Method Detail

process

public DocumentMetaData process(String xml)
                         throws Exception

Description copied from interface: PreProcessor

Process a document to retrieve meta data about the document.

Specified by:

process in interface PreProcessor

Returns:

Throws:

Exception

startElement

public void startElement(String uri,
                         String localName,
                         String qName,
                         Attributes attributes)
                  throws SAXException

Specified by:

startElement in interface ContentHandler

Overrides:

startElement in class org.xml.sax.helpers.DefaultHandler

Throws:

SAXException

See Also:

ContentHandler.startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)

characters

public void characters(char[] ch,
                       int start,
                       int length)
                throws SAXException

Specified by:

characters in interface ContentHandler

Overrides:

characters in class org.xml.sax.helpers.DefaultHandler

Throws:

SAXException

endElement

public void endElement(String uri,
                       String localName,
                       String qName)
                throws SAXException

Specified by:

endElement in interface ContentHandler

Overrides:

endElement in class org.xml.sax.helpers.DefaultHandler

Throws:

SAXException

See Also:

ContentHandler.endElement(java.lang.String, java.lang.String, java.lang.String)

startDocument

public void startDocument()
                   throws SAXException

Specified by:

startDocument in interface ContentHandler

Overrides:

startDocument in class org.xml.sax.helpers.DefaultHandler

Throws:

SAXException

See Also:

ContentHandler.startDocument()

endDocument

public void endDocument()
                 throws SAXException

Specified by:

endDocument in interface ContentHandler

Overrides:

endDocument in class org.xml.sax.helpers.DefaultHandler

Throws:

SAXException

See Also:

ContentHandler.endDocument()