Packages

class DrugNormalizer extends AnnotatorModel[DrugNormalizer] with HasSimpleAnnotate[DrugNormalizer]

Annotator which normalizes raw text from clinical documents, e.g. scraped web pages or xml documents, from document type columns into Sentence. Removes all dirty characters from text following one or more input regex patterns. Can apply non wanted character removal which a specific policy. Can apply lower case normalization.

See Spark NLP Workshop for more examples of usage.

Example

val data = Seq(
  ("Sodium Chloride/Potassium Chloride 13bag"),
  ("interferon alfa-2b 10 million unit ( 1 ml ) injec"),
  ("aspirin 10 meq/ 5 ml oral sol")
).toDF("text")
val document = new DocumentAssembler().setInputCol("text").setOutputCol("document")
val drugNormalizer = new DrugNormalizer().setInputCols("document").setOutputCol("document_normalized")

val trainingPipeline = new Pipeline().setStages(Array(document, drugNormalizer))
val result = trainingPipeline.fit(data).transform(data)

result.selectExpr("explode(document_normalized.result) as normalized_text").show(false)
+----------------------------------------------------+
|normalized_text                                     |
+----------------------------------------------------+
|Sodium Chloride / Potassium Chloride 13 bag         |
|interferon alfa - 2b 10000000 unt ( 1 ml ) injection|
|aspirin 2 meq/ml oral solution                      |
+----------------------------------------------------+
Linear Supertypes
HasSimpleAnnotate[DrugNormalizer], AnnotatorModel[DrugNormalizer], CanBeLazy, RawAnnotator[DrugNormalizer], HasOutputAnnotationCol, HasInputAnnotationCols, HasOutputAnnotatorType, ParamsAndFeaturesWritable, HasFeatures, DefaultParamsWritable, MLWritable, Model[DrugNormalizer], Transformer, PipelineStage, Logging, Params, Serializable, Serializable, Identifiable, AnyRef, Any
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Inherited
  1. DrugNormalizer
  2. HasSimpleAnnotate
  3. AnnotatorModel
  4. CanBeLazy
  5. RawAnnotator
  6. HasOutputAnnotationCol
  7. HasInputAnnotationCols
  8. HasOutputAnnotatorType
  9. ParamsAndFeaturesWritable
  10. HasFeatures
  11. DefaultParamsWritable
  12. MLWritable
  13. Model
  14. Transformer
  15. PipelineStage
  16. Logging
  17. Params
  18. Serializable
  19. Serializable
  20. Identifiable
  21. AnyRef
  22. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new DrugNormalizer()
  2. new DrugNormalizer(uid: String)

    uid

    required uid for storing annotator to disk

Type Members

  1. type AnnotationContent = Seq[Row]
    Attributes
    protected
    Definition Classes
    AnnotatorModel
  2. type AnnotatorType = String
    Definition Classes
    HasOutputAnnotatorType

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def $[T](param: Param[T]): T
    Attributes
    protected
    Definition Classes
    Params
  4. def $$[T](feature: StructFeature[T]): T
    Attributes
    protected
    Definition Classes
    HasFeatures
  5. def $$[K, V](feature: MapFeature[K, V]): Map[K, V]
    Attributes
    protected
    Definition Classes
    HasFeatures
  6. def $$[T](feature: SetFeature[T]): Set[T]
    Attributes
    protected
    Definition Classes
    HasFeatures
  7. def $$[T](feature: ArrayFeature[T]): Array[T]
    Attributes
    protected
    Definition Classes
    HasFeatures
  8. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  9. def _transform(dataset: Dataset[_], recursivePipeline: Option[PipelineModel]): DataFrame
    Attributes
    protected
    Definition Classes
    AnnotatorModel
  10. val abbreviations: MapFeature[String, String]

    abbreviation regex patterns which match will be extended in document

  11. def afterAnnotate(dataset: DataFrame): DataFrame
    Attributes
    protected
    Definition Classes
    AnnotatorModel
  12. def annotate(annotations: Seq[Annotation]): Seq[Annotation]
    Definition Classes
    DrugNormalizer → HasSimpleAnnotate
  13. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  14. def beforeAnnotate(dataset: Dataset[_]): Dataset[_]
    Attributes
    protected
    Definition Classes
    AnnotatorModel
  15. final def checkSchema(schema: StructType, inputAnnotatorType: String): Boolean
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  16. final def clear(param: Param[_]): DrugNormalizer.this.type
    Definition Classes
    Params
  17. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  18. def copy(extra: ParamMap): DrugNormalizer
    Definition Classes
    RawAnnotator → Model → Transformer → PipelineStage → Params
  19. def copyValues[T <: Params](to: T, extra: ParamMap): T
    Attributes
    protected
    Definition Classes
    Params
  20. final def defaultCopy[T <: Params](extra: ParamMap): T
    Attributes
    protected
    Definition Classes
    Params
  21. def dfAnnotate: UserDefinedFunction
    Definition Classes
    HasSimpleAnnotate
  22. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  23. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  24. def explainParam(param: Param[_]): String
    Definition Classes
    Params
  25. def explainParams(): String
    Definition Classes
    Params
  26. def extraValidate(structType: StructType): Boolean
    Attributes
    protected
    Definition Classes
    RawAnnotator
  27. def extraValidateMsg: String
    Attributes
    protected
    Definition Classes
    RawAnnotator
  28. final def extractParamMap(): ParamMap
    Definition Classes
    Params
  29. final def extractParamMap(extra: ParamMap): ParamMap
    Definition Classes
    Params
  30. val features: ArrayBuffer[Feature[_, _, _]]
    Definition Classes
    HasFeatures
  31. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  32. def get[T](feature: StructFeature[T]): Option[T]
    Attributes
    protected
    Definition Classes
    HasFeatures
  33. def get[K, V](feature: MapFeature[K, V]): Option[Map[K, V]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  34. def get[T](feature: SetFeature[T]): Option[Set[T]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  35. def get[T](feature: ArrayFeature[T]): Option[Array[T]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  36. final def get[T](param: Param[T]): Option[T]
    Definition Classes
    Params
  37. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  38. final def getDefault[T](param: Param[T]): Option[T]
    Definition Classes
    Params
  39. def getInputCols: Array[String]
    Definition Classes
    HasInputAnnotationCols
  40. def getLazyAnnotator: Boolean
    Definition Classes
    CanBeLazy
  41. def getLowercase: Boolean

    Lowercase tokens, default false

  42. final def getOrDefault[T](param: Param[T]): T
    Definition Classes
    Params
  43. final def getOutputCol: String
    Definition Classes
    HasOutputAnnotationCol
  44. def getParam(paramName: String): Param[Any]
    Definition Classes
    Params
  45. def getPolicy: String

    Policy to remove patterns from text.

    Policy to remove patterns from text. Defaults "all".

  46. final def hasDefault[T](param: Param[T]): Boolean
    Definition Classes
    Params
  47. def hasParam(paramName: String): Boolean
    Definition Classes
    Params
  48. def hasParent: Boolean
    Definition Classes
    Model
  49. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  50. def initializeLogIfNecessary(isInterpreter: Boolean, silent: Boolean): Boolean
    Attributes
    protected
    Definition Classes
    Logging
  51. def initializeLogIfNecessary(isInterpreter: Boolean): Unit
    Attributes
    protected
    Definition Classes
    Logging
  52. val inputAnnotatorTypes: Array[AnnotatorType]

    Input annotator type : DOCUMENT

    Input annotator type : DOCUMENT

    Definition Classes
    DrugNormalizer → HasInputAnnotationCols
  53. final val inputCols: StringArrayParam
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  54. final def isDefined(param: Param[_]): Boolean
    Definition Classes
    Params
  55. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  56. final def isSet(param: Param[_]): Boolean
    Definition Classes
    Params
  57. def isTraceEnabled(): Boolean
    Attributes
    protected
    Definition Classes
    Logging
  58. val lazyAnnotator: BooleanParam
    Definition Classes
    CanBeLazy
  59. def log: Logger
    Attributes
    protected
    Definition Classes
    Logging
  60. def logDebug(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  61. def logDebug(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  62. def logError(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  63. def logError(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  64. def logInfo(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  65. def logInfo(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  66. def logName: String
    Attributes
    protected
    Definition Classes
    Logging
  67. def logTrace(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  68. def logTrace(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  69. def logWarning(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  70. def logWarning(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  71. val lowercase: BooleanParam

    whether to convert strings to lowercase (Default: false)

  72. def msgHelper(schema: StructType): String
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  73. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  74. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  75. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  76. def onWrite(path: String, spark: SparkSession): Unit
    Attributes
    protected
    Definition Classes
    ParamsAndFeaturesWritable
  77. val outputAnnotatorType: AnnotatorType

    Output annotator type : DOCUMENT

    Output annotator type : DOCUMENT

    Definition Classes
    DrugNormalizer → HasOutputAnnotatorType
  78. final val outputCol: Param[String]
    Attributes
    protected
    Definition Classes
    HasOutputAnnotationCol
  79. lazy val params: Array[Param[_]]
    Definition Classes
    Params
  80. var parent: Estimator[DrugNormalizer]
    Definition Classes
    Model
  81. val patterns: MapFeature[String, String]

    normalization regex patterns which match will be normalized document

  82. val policy: Param[String]

    removalPolicy to remove patterns from text (Default: 'all')

  83. def save(path: String): Unit
    Definition Classes
    MLWritable
    Annotations
    @Since( "1.6.0" ) @throws( ... )
  84. def set[T](feature: StructFeature[T], value: T): DrugNormalizer.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  85. def set[K, V](feature: MapFeature[K, V], value: Map[K, V]): DrugNormalizer.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  86. def set[T](feature: SetFeature[T], value: Set[T]): DrugNormalizer.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  87. def set[T](feature: ArrayFeature[T], value: Array[T]): DrugNormalizer.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  88. final def set(paramPair: ParamPair[_]): DrugNormalizer.this.type
    Attributes
    protected
    Definition Classes
    Params
  89. final def set(param: String, value: Any): DrugNormalizer.this.type
    Attributes
    protected
    Definition Classes
    Params
  90. final def set[T](param: Param[T], value: T): DrugNormalizer.this.type
    Definition Classes
    Params
  91. def setDefault[T](feature: StructFeature[T], value: () ⇒ T): DrugNormalizer.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  92. def setDefault[K, V](feature: MapFeature[K, V], value: () ⇒ Map[K, V]): DrugNormalizer.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  93. def setDefault[T](feature: SetFeature[T], value: () ⇒ Set[T]): DrugNormalizer.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  94. def setDefault[T](feature: ArrayFeature[T], value: () ⇒ Array[T]): DrugNormalizer.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  95. final def setDefault(paramPairs: ParamPair[_]*): DrugNormalizer.this.type
    Attributes
    protected
    Definition Classes
    Params
  96. final def setDefault[T](param: Param[T], value: T): DrugNormalizer.this.type
    Attributes
    protected
    Definition Classes
    Params
  97. final def setInputCols(value: String*): DrugNormalizer.this.type
    Definition Classes
    HasInputAnnotationCols
  98. final def setInputCols(value: Array[String]): DrugNormalizer.this.type
    Definition Classes
    HasInputAnnotationCols
  99. def setLazyAnnotator(value: Boolean): DrugNormalizer.this.type
    Definition Classes
    CanBeLazy
  100. def setLowercase(value: Boolean): DrugNormalizer.this.type

    Lower case tokens, default false

  101. final def setOutputCol(value: String): DrugNormalizer.this.type
    Definition Classes
    HasOutputAnnotationCol
  102. def setParent(parent: Estimator[DrugNormalizer]): DrugNormalizer
    Definition Classes
    Model
  103. def setPolicy(value: String): DrugNormalizer.this.type

    Removal policy to apply.

    Removal policy to apply. Valid policy values are: "all", "abbreviations", "dosages"

  104. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  105. def toString(): String
    Definition Classes
    Identifiable → AnyRef → Any
  106. final def transform(dataset: Dataset[_]): DataFrame
    Definition Classes
    AnnotatorModel → Transformer
  107. def transform(dataset: Dataset[_], paramMap: ParamMap): DataFrame
    Definition Classes
    Transformer
    Annotations
    @Since( "2.0.0" )
  108. def transform(dataset: Dataset[_], firstParamPair: ParamPair[_], otherParamPairs: ParamPair[_]*): DataFrame
    Definition Classes
    Transformer
    Annotations
    @Since( "2.0.0" ) @varargs()
  109. final def transformSchema(schema: StructType): StructType
    Definition Classes
    RawAnnotator → PipelineStage
  110. def transformSchema(schema: StructType, logging: Boolean): StructType
    Attributes
    protected
    Definition Classes
    PipelineStage
    Annotations
    @DeveloperApi()
  111. val uid: String
    Definition Classes
    DrugNormalizer → Identifiable
  112. def validate(schema: StructType): Boolean
    Attributes
    protected
    Definition Classes
    RawAnnotator
  113. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  114. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  115. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  116. def wrapColumnMetadata(col: Column): Column
    Attributes
    protected
    Definition Classes
    RawAnnotator
  117. def write: MLWriter
    Definition Classes
    ParamsAndFeaturesWritable → DefaultParamsWritable → MLWritable

Inherited from HasSimpleAnnotate[DrugNormalizer]

Inherited from AnnotatorModel[DrugNormalizer]

Inherited from CanBeLazy

Inherited from RawAnnotator[DrugNormalizer]

Inherited from HasOutputAnnotationCol

Inherited from HasInputAnnotationCols

Inherited from HasOutputAnnotatorType

Inherited from ParamsAndFeaturesWritable

Inherited from HasFeatures

Inherited from DefaultParamsWritable

Inherited from MLWritable

Inherited from Model[DrugNormalizer]

Inherited from Transformer

Inherited from PipelineStage

Inherited from Logging

Inherited from Params

Inherited from Serializable

Inherited from Serializable

Inherited from Identifiable

Inherited from AnyRef

Inherited from Any

Parameters

Annotator types

Required input and expected output annotator types

Members

Parameter setters

Parameter getters