ctakes fhir - apache/ctakes GitHub Wiki
Collection Readers
Output Writers
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 |
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 |
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 |
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 |