Packages

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

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
CheckLicense, 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. CheckLicense
  3. HasSimpleAnnotate
  4. AnnotatorModel
  5. CanBeLazy
  6. RawAnnotator
  7. HasOutputAnnotationCol
  8. HasInputAnnotationCols
  9. HasOutputAnnotatorType
  10. ParamsAndFeaturesWritable
  11. HasFeatures
  12. DefaultParamsWritable
  13. MLWritable
  14. Model
  15. Transformer
  16. PipelineStage
  17. Logging
  18. Params
  19. Serializable
  20. Serializable
  21. Identifiable
  22. AnyRef
  23. 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. def checkValidEnvironment(spark: Option[SparkSession], scopes: Seq[String]): Unit
    Definition Classes
    CheckLicense
  17. def checkValidScope(scope: String): Unit
    Definition Classes
    CheckLicense
  18. def checkValidScopeAndEnvironment(scope: String, spark: Option[SparkSession], checkLp: Boolean): Unit
    Definition Classes
    CheckLicense
  19. def checkValidScopesAndEnvironment(scopes: Seq[String], spark: Option[SparkSession], checkLp: Boolean): Unit
    Definition Classes
    CheckLicense
  20. final def clear(param: Param[_]): DrugNormalizer.this.type
    Definition Classes
    Params
  21. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  22. def copy(extra: ParamMap): DrugNormalizer
    Definition Classes
    RawAnnotator → Model → Transformer → PipelineStage → Params
  23. def copyValues[T <: Params](to: T, extra: ParamMap): T
    Attributes
    protected
    Definition Classes
    Params
  24. final def defaultCopy[T <: Params](extra: ParamMap): T
    Attributes
    protected
    Definition Classes
    Params
  25. def dfAnnotate: UserDefinedFunction
    Definition Classes
    HasSimpleAnnotate
  26. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  27. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  28. def explainParam(param: Param[_]): String
    Definition Classes
    Params
  29. def explainParams(): String
    Definition Classes
    Params
  30. def extraValidate(structType: StructType): Boolean
    Attributes
    protected
    Definition Classes
    RawAnnotator
  31. def extraValidateMsg: String
    Attributes
    protected
    Definition Classes
    RawAnnotator
  32. final def extractParamMap(): ParamMap
    Definition Classes
    Params
  33. final def extractParamMap(extra: ParamMap): ParamMap
    Definition Classes
    Params
  34. val features: ArrayBuffer[Feature[_, _, _]]
    Definition Classes
    HasFeatures
  35. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  36. def get[T](feature: StructFeature[T]): Option[T]
    Attributes
    protected
    Definition Classes
    HasFeatures
  37. def get[K, V](feature: MapFeature[K, V]): Option[Map[K, V]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  38. def get[T](feature: SetFeature[T]): Option[Set[T]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  39. def get[T](feature: ArrayFeature[T]): Option[Array[T]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  40. final def get[T](param: Param[T]): Option[T]
    Definition Classes
    Params
  41. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  42. final def getDefault[T](param: Param[T]): Option[T]
    Definition Classes
    Params
  43. def getInputCols: Array[String]
    Definition Classes
    HasInputAnnotationCols
  44. def getLazyAnnotator: Boolean
    Definition Classes
    CanBeLazy
  45. def getLowercase: Boolean

    Lowercase tokens, default false

  46. final def getOrDefault[T](param: Param[T]): T
    Definition Classes
    Params
  47. final def getOutputCol: String
    Definition Classes
    HasOutputAnnotationCol
  48. def getParam(paramName: String): Param[Any]
    Definition Classes
    Params
  49. def getPolicy: String

    Policy to remove patterns from text.

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

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

    Input annotator type : DOCUMENT

    Input annotator type : DOCUMENT

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

    whether to convert strings to lowercase (Default: false)

  76. def msgHelper(schema: StructType): String
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  77. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  78. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  79. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  80. def onWrite(path: String, spark: SparkSession): Unit
    Attributes
    protected
    Definition Classes
    ParamsAndFeaturesWritable
  81. val optionalInputAnnotatorTypes: Array[String]
    Definition Classes
    HasInputAnnotationCols
  82. val outputAnnotatorType: AnnotatorType

    Output annotator type : DOCUMENT

    Output annotator type : DOCUMENT

    Definition Classes
    DrugNormalizer → HasOutputAnnotatorType
  83. final val outputCol: Param[String]
    Attributes
    protected
    Definition Classes
    HasOutputAnnotationCol
  84. lazy val params: Array[Param[_]]
    Definition Classes
    Params
  85. var parent: Estimator[DrugNormalizer]
    Definition Classes
    Model
  86. val patterns: MapFeature[String, String]

    normalization regex patterns which match will be normalized document

  87. val policy: Param[String]

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

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

    Lower case tokens, default false

  106. final def setOutputCol(value: String): DrugNormalizer.this.type
    Definition Classes
    HasOutputAnnotationCol
  107. def setParent(parent: Estimator[DrugNormalizer]): DrugNormalizer
    Definition Classes
    Model
  108. def setPolicy(value: String): DrugNormalizer.this.type

    Removal policy to apply.

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

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

Inherited from CheckLicense

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