ctakes fhir

Collection Readers
Output Writers

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Collection Readers

FhirJsonFileReader

Reads fhir information from json.

Source class: FhirJsonFileReader
Source package: org.apache.ctakes.fhir.cr
Parent class: org.apache.ctakes.core.cr.AbstractFileTreeReader

Parameter	Description	Class	Required	Default
InputDirectory	Directory for all input files.	String	Yes
CRtoSpace	Change windows-format CR + LF character sequences to LF + .	boolean	No
Encoding	The character encoding used by the input files.	String	No
Extensions	The extensions of the files that the collection reader will read.	String[]	No	*
KeepCR	Keep windows-format carriage return characters at line endings. This will only keep existing characters, it will not add them.	boolean	No
PatientLevel	The level in the directory hierarchy at which patient identifiers exist.Default value is 1; directly under root input directory.	int	No
StripQuotes	Replace document-enclosing quote characters with space characters.	boolean	No
WriteBanner	Write a large banner at each major step of the pipeline.	String	No	no

FhirXmlFileReader

Reads fhir information from xml.

Source class: FhirXmlFileReader
Source package: org.apache.ctakes.fhir.cr
Parent class: org.apache.ctakes.core.cr.AbstractFileTreeReader

Parameter	Description	Class	Required	Default
InputDirectory	Directory for all input files.	String	Yes
CRtoSpace	Change windows-format CR + LF character sequences to LF + .	boolean	No
Encoding	The character encoding used by the input files.	String	No
Extensions	The extensions of the files that the collection reader will read.	String[]	No	*
KeepCR	Keep windows-format carriage return characters at line endings. This will only keep existing characters, it will not add them.	boolean	No
PatientLevel	The level in the directory hierarchy at which patient identifiers exist.Default value is 1; directly under root input directory.	int	No
StripQuotes	Replace document-enclosing quote characters with space characters.	boolean	No
WriteBanner	Write a large banner at each major step of the pipeline.	String	No	no

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Output Writers

FHIR JSON File Writer (Dir Tree)

Writes Json files with full representation of input text and all extracted information.

Source class: FhirJsonFileWriter
Source package: org.apache.ctakes.fhir.cc
Parent class: org.apache.ctakes.core.cc.AbstractJCasFileWriter
Dependencies: Document Id
Usables: Document Id Prefix

Parameter	Description	Class	Required	Default
OutputDirectory	Directory for all output files.	File	Yes
SubDirectory	SubDirectory for files.	String	No
WriteNlpFhir	Write all nlp information (paragraph, sentence, base annotations) to FHIR.	boolean	No	false

FHIR JSON Writer

Writes Json to standard output with full representation of input text and all extracted information.

Source class: FhirJsonWriter
Source package: org.apache.ctakes.fhir.cc
Parent class: org.apache.uima.fit.component.JCasAnnotator_ImplBase

Parameter	Description	Class	Required	Default
WriteNlpFhir	Write all nlp information (paragraph, sentence, base annotations) to FHIR.	boolean	No	false