Specimen

@POJOBoilerplate
class Specimen(val id: Option[String], val meta: Option[Meta], val text: Option[Narrative], `type`: Option[CodeableConcept], val note: LitSeq[Annotation], val status: Option[SPECIMEN_STATUS], val parent: LitSeq[Reference], val subject: Option[Reference], val request: LitSeq[Reference], val language: Option[LANGUAGES], val contained: LitSeq[Resource], val extension: LitSeq[Extension], val condition: LitSeq[CodeableConcept], val identifier: LitSeq[Identifier], val receivedTime: Option[FHIRDateTime], val implicitRules: Option[UriStr], val modifierExtension: LitSeq[Extension], val accessionIdentifier: Option[Identifier], val container: LitSeq[Container], val collection: Option[Collection], val processing: LitSeq[Processing], val primitiveAttributes: TreeMap[FHIRComponentFieldMeta[_], PrimitiveElementInfo]) extends DomainResource

A sample to be used for analysis.

Subclass of hl7.model.DomainResource (A resource that includes narrative, extensions, and contained resources.)

Value parameters:
`type`
  • The kind of material that forms the specimen.
accessionIdentifier
  • The identifier assigned by the lab when accessioning specimen(s). This is not necessarily the same as the specimen identifier, depending on local lab procedures.
collection
  • Details concerning the specimen collection.
condition
  • A mode or state of being that describes the nature of the specimen.
contained
  • These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope.
container
  • The container holding the specimen. The recursive nature of containers; i.e. blood in tube in tray in rack is not addressed here.
extension
  • May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.
id
  • The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.
identifier
  • Id for specimen.
implicitRules
  • A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc.
language
  • The base language in which the resource is written.
meta
  • The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource.
modifierExtension
  • May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).
note
  • To communicate any details or issues about the specimen or during the specimen collection. (for example: broken vial, sent with patient, frozen).
parent
  • Reference to the parent (source) specimen which is used when the specimen was either derived from or a component of another specimen.
processing
  • Details concerning processing and processing steps for the specimen.
receivedTime
  • Time when specimen was received for processing or testing.
request
  • Details concerning a service request that required a specimen to be collected.
status
  • The availability of the specimen.
subject
  • Where the specimen came from. This may be from patient(s), from a location (e.g., the source of an environmental sample), or a sampling of a substance or a device.
text
  • A human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it "clinically safe" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety.
Constructor:

Introduces the fields type, note, status, parent, subject, request, condition, identifier, receivedTime, accessionIdentifier, container, collection, processing.

Companion:
object
class Resource
class FHIRObject
trait FHIRComponent
trait Utils
class Object
trait Matchable
class Any

Type members

Inherited classlikes

object extensions
Inherited from:
FHIRObject
object ids
Inherited from:
FHIRObject

Inherited types

type FieldToElementLookup = TreeMap[FHIRComponentFieldMeta[_], PrimitiveElementInfo]
Inherited from:
FHIRObject

Value members

Inherited methods

final def >>[T](fn: T => T)(implicit tt: LTag[T]): Specimen

Slower than nodalMap, but should work with subtypes (e.g. PositiveInt). If you must use it, then:

Slower than nodalMap, but should work with subtypes (e.g. PositiveInt). If you must use it, then:

  • T should not be a Choice[_], a LitSeq[_] or an Option[_]
  • It may require a type parameter sometimes (e.g. sampleResource >>[BUNDLE_TYPE] { (_: BUNDLE_TYPE) => BUNDLE_TYPE.SEARCHSET } )
Inherited from:
FHIRObject
final def >>=[T, F[_] : Monad](fn: T => F[T])(implicit evidence$7: Monad[F], tt: LTag[T]): F[Specimen]
Inherited from:
FHIRObject
final def ^^[From, To](fn: From => To)(implicit tt: LTag[From]): LitSeq[To]

Extract values of type From, and map to LitSeq[To] using fn: From => To. Unlike >>, this is safe even if From is a Choice[], a LitSeq[] or an Option[_] Quite slow, slower than nodalExtract

Extract values of type From, and map to LitSeq[To] using fn: From => To. Unlike >>, this is safe even if From is a Choice[], a LitSeq[] or an Option[_] Quite slow, slower than nodalExtract

Inherited from:
FHIRObject
final def ^^^[T](implicit tt: LTag[T]): LitSeq[T]
Inherited from:
FHIRObject
def companionClassName[T](tag: LTag[T]): String
Inherited from:
Utils
def companionOf[T <: FHIRObject : ClassTag](implicit evidence$1: ClassTag[T], tag: LTag[T]): CompanionFor[T]
Inherited from:
Utils
def constructor: Constructor[_]
Inherited from:
FHIRComponent
def decodeMethodFor[T <: FHIRObject : ClassTag](implicit evidence$2: ClassTag[T], tag: LTag[T], params: DecoderParams): HCursor => Try[T]
Inherited from:
Utils
override def equals(obj: Any): Boolean
Definition Classes
FHIRObject -> Any
Inherited from:
FHIRObject
def fields: Seq[FHIRComponentField[_]]
Inherited from:
FHIRObject
def getFieldByClass[T](name: String, clazz: Class[T]): LitSeq[T]
Inherited from:
FHIRComponent
def getFieldByType[T : LTag](name: String): LitSeq[T]
Inherited from:
FHIRComponent
def getIdentifier: Option[String]
Inherited from:
Resource
def getMostSpecificIdentifier: Option[String]
Inherited from:
Resource
def getVersionedIdentifier: Option[String]
Inherited from:
Resource
override def hashCode(): Int
Definition Classes
FHIRObject -> Any
Inherited from:
FHIRObject
def modifyField[T : LTag, Up >: Specimen <: FHIRObject](fieldName: String, modify: T => T)(implicit evidence$5: LTag[T], ct: ClassTag[Up], tt: LTag[Up]): Up
Inherited from:
FHIRObject
def modifyFieldUnsafe[T, Up >: Specimen <: FHIRObject](fieldName: String, modify: T => T)(implicit ct: ClassTag[Up], tt: LTag[Up]): Up
Inherited from:
FHIRObject
final def nodalExtract[From, To](klass: Class[From], fn: From => To): LitSeq[To]

Convenience alias for nodalGetByClass andThen map to LitSeq[To] using fn: From => To.

Convenience alias for nodalGetByClass andThen map to LitSeq[To] using fn: From => To.

Inherited from:
FHIRObject
final def nodalGetByClass[Target](klass: Class[Target]): LitSeq[Target]

Extract values of type From Unlike nodalMap, this is safe even if From is a Choice[_], a LitSeq[_] or an Option[_], however there remains a caveat with 'subtyped' types (eg PositiveInt), in that we can't differentiate them from the parent class Quite slow but faster than ^^

Extract values of type From Unlike nodalMap, this is safe even if From is a Choice[_], a LitSeq[_] or an Option[_], however there remains a caveat with 'subtyped' types (eg PositiveInt), in that we can't differentiate them from the parent class Quite slow but faster than ^^

Inherited from:
FHIRObject
final def nodalMap[T](klass: Class[T], fn: T => T): Specimen

Bit faster than >>, but still much slower than using update$foo when possible. If you must use it, then:

Bit faster than >>, but still much slower than using update$foo when possible. If you must use it, then:

  • T should not be a Choice[_], a LitSeq[_], an Option[_], or any 'subtyped' type (eg PositiveInt). You should ensure, if T is a supertype of multiple valid choice values (e.g. T =:= Object), that the return value of fn retains the same type as the input value.
Inherited from:
FHIRObject
def setFromField[T, UpType >: Specimen <: FHIRObject : LTag](field: FHIRComponentFieldMeta[T])(newVal: T): UpType
Inherited from:
FHIRObject
def thisClassName: String
Inherited from:
FHIRObject
def toClass[T](klass: Class[T]): Option[T]
Inherited from:
FHIRObject
override def toString: String
Definition Classes
FHIRObject -> Any
Inherited from:
FHIRObject
def toType[T](implicit ct: ClassTag[T]): Option[T]
Inherited from:
FHIRObject
def updateFromField[T, UpType >: Specimen <: FHIRObject : LTag](field: FHIRComponentFieldMeta[T])(fn: T => T): UpType
Inherited from:
FHIRObject
def updatePrimitiveAttributes(fn: FieldToElementLookup => FieldToElementLookup): Specimen
Inherited from:
FHIRObject
def withField[T : LTag, Up >: Specimen <: FHIRObject](fieldName: String, value: T)(implicit evidence$6: LTag[T], ct: ClassTag[Up], tt: LTag[Up]): Up
Inherited from:
FHIRObject
def withFieldUnsafe[T, Up >: Specimen <: FHIRObject](fieldName: String, value: T)(implicit ct: ClassTag[Up], tt: LTag[Up]): Up
Inherited from:
FHIRObject
def withFields[Up >: Specimen <: FHIRObject](replacementFields: (String, Any)*)(implicit ct: ClassTag[Up], tt: LTag[Up]): Up
Inherited from:
FHIRObject
def withPrimitiveAttributes(a: FieldToElementLookup): Specimen
Inherited from:
FHIRObject

Concrete fields

val `type`: Option[CodeableConcept]
val accessionIdentifier: Option[Identifier]
val collection: Option[Collection]
val condition: LitSeq[CodeableConcept]
override val contained: LitSeq[Resource]
val container: LitSeq[Container]
override val extension: LitSeq[Extension]
override val id: Option[String]
val identifier: LitSeq[Identifier]
override val implicitRules: Option[UriStr]
override val language: Option[LANGUAGES]
override val meta: Option[Meta]
override val modifierExtension: LitSeq[Extension]
val note: LitSeq[Annotation]
val parent: LitSeq[Reference]
override val primitiveAttributes: TreeMap[FHIRComponentFieldMeta[_], PrimitiveElementInfo]
val processing: LitSeq[Processing]
val receivedTime: Option[FHIRDateTime]
val request: LitSeq[Reference]
val status: Option[SPECIMEN_STATUS]
val subject: Option[Reference]
override val text: Option[Narrative]
override val thisTypeName: String

Inherited fields

val companion: CompanionFor[Specimen]
Inherited from:
FHIRObject