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# Copyright (c) 2014 The MITRE Corporation
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
# * Neither the name of HL7 nor the names of its contributors may be used to
# endorse or promote products derived from this software without specific
# prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
# IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
# INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
# NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
DT = require '../cql-datatypes'
CORE = require('./core')
Element = CORE.Element
Resource = CORE.Resource
Timing = CORE.Timing
Period = CORE.Period
Parameters = CORE.Parameters
Coding = CORE.Coding
Resource = CORE.Resource
Range = CORE.Range
Quantity = CORE.Quantity
Attachment = CORE.Attachment
BackboneElement = CORE.BackboneElement
DomainResource = CORE.DomainResource
ContactPoint = CORE.ContactPoint
ElementDefinition = CORE.ElementDefinition
Extension = CORE.Extension
HumanName = CORE.HumanName
Address = CORE.Address
Ratio = CORE.Ratio
SampledData = CORE.SampledData
Reference = CORE.Reference
CodeableConcept = CORE.CodeableConcept
Identifier = CORE.Identifier
Narrative = CORE.Narrative
Element = CORE.Element
###*
Embedded class
@class SpecimenSourceComponent
@exports SpecimenSourceComponent as SpecimenSourceComponent
###
class SpecimenSourceComponent extends BackboneElement
constructor: (@json) ->
super(@json)
###*
Whether this relationship is to a parent or to a child.
@returns {Array} an array of {@link String} objects
###
relationship:-> @json['relationship']
###*
The specimen resource that is the target of this relationship.
@returns {Array} an array of {@link Reference} objects
###
target: ->
if @json['target']
for item in @json['target']
new Reference(item)
###*
Embedded class
@class SpecimenCollectionComponent
@exports SpecimenCollectionComponent as SpecimenCollectionComponent
###
class SpecimenCollectionComponent extends BackboneElement
constructor: (@json) ->
super(@json)
###*
Person who collected the specimen.
@returns {Reference}
###
collector: -> if @json['collector'] then new Reference(@json['collector'])
###*
To communicate any details or issues encountered during the specimen collection procedure.
@returns {Array} an array of {@link String} objects
###
comment:-> @json['comment']
###*
Time when specimen was collected from subject - the physiologically relevant time.
@returns {Array} an array of {@link Date} objects
###
collectedDateTime:-> if @json['collectedDateTime'] then DT.DateTime.parse(@json['collectedDateTime'])
###*
Time when specimen was collected from subject - the physiologically relevant time.
@returns {Period}
###
collectedPeriod: -> if @json['collectedPeriod'] then new Period(@json['collectedPeriod'])
###*
The quantity of specimen collected; for instance the volume of a blood sample, or the physical measurement of an anatomic pathology sample.
@returns {Quantity}
###
quantity: -> if @json['quantity'] then new Quantity(@json['quantity'])
###*
A coded value specifying the technique that is used to perform the procedure.
@returns {CodeableConcept}
###
method: -> if @json['method'] then new CodeableConcept(@json['method'])
###*
Anatomical location from which the specimen should be collected (if subject is a patient). This element is not used for environmental specimens.
@returns {CodeableConcept}
###
sourceSite: -> if @json['sourceSite'] then new CodeableConcept(@json['sourceSite'])
###*
Embedded class
@class SpecimenTreatmentComponent
@exports SpecimenTreatmentComponent as SpecimenTreatmentComponent
###
class SpecimenTreatmentComponent extends BackboneElement
constructor: (@json) ->
super(@json)
###*
Textual description of procedure.
@returns {Array} an array of {@link String} objects
###
description:-> @json['description']
###*
A coded value specifying the procedure used to process the specimen.
@returns {CodeableConcept}
###
procedure: -> if @json['procedure'] then new CodeableConcept(@json['procedure'])
###*
Material used in the processing step.
@returns {Array} an array of {@link Reference} objects
###
additive: ->
if @json['additive']
for item in @json['additive']
new Reference(item)
###*
Embedded class
@class SpecimenContainerComponent
@exports SpecimenContainerComponent as SpecimenContainerComponent
###
class SpecimenContainerComponent extends BackboneElement
constructor: (@json) ->
super(@json)
###*
Id for container. There may be multiple; a manufacturer's bar code, lab assigned identifier, etc. The container ID may differ from the specimen id in some circumstances.
@returns {Array} an array of {@link Identifier} objects
###
identifier: ->
if @json['identifier']
for item in @json['identifier']
new Identifier(item)
###*
Textual description of the container.
@returns {Array} an array of {@link String} objects
###
description:-> @json['description']
###*
The type of container associated with the specimen (e.g. slide, aliquot, etc).
@returns {CodeableConcept}
###
type: -> if @json['type'] then new CodeableConcept(@json['type'])
###*
The capacity (volume or other measure) the container may contain.
@returns {Quantity}
###
capacity: -> if @json['capacity'] then new Quantity(@json['capacity'])
###*
The quantity of specimen in the container; may be volume, dimensions, or other appropriate measurements, depending on the specimen type.
@returns {Quantity}
###
specimenQuantity: -> if @json['specimenQuantity'] then new Quantity(@json['specimenQuantity'])
###*
Introduced substance to preserve, maintain or enhance the specimen. examples: Formalin, Citrate, EDTA.
@returns {CodeableConcept}
###
additiveCodeableConcept: -> if @json['additiveCodeableConcept'] then new CodeableConcept(@json['additiveCodeableConcept'])
###*
Introduced substance to preserve, maintain or enhance the specimen. examples: Formalin, Citrate, EDTA.
@returns {Reference}
###
additiveReference: -> if @json['additiveReference'] then new Reference(@json['additiveReference'])
###*
Sample for analysis.
@class Specimen
@exports Specimen as Specimen
###
class Specimen extends DomainResource
constructor: (@json) ->
super(@json)
###*
Id for specimen.
@returns {Array} an array of {@link Identifier} objects
###
identifier: ->
if @json['identifier']
for item in @json['identifier']
new Identifier(item)
###*
Kind of material that forms the specimen.
@returns {CodeableConcept}
###
type: -> if @json['type'] then new CodeableConcept(@json['type'])
###*
Parent specimen from which the focal specimen was a component.
@returns {Array} an array of {@link SpecimenSourceComponent} objects
###
source: ->
if @json['source']
for item in @json['source']
new SpecimenSourceComponent(item)
###*
Where the specimen came from. This may be the patient(s) or from the environment or a device.
@returns {Reference}
###
subject: -> if @json['subject'] then new Reference(@json['subject'])
###*
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.
@returns {Identifier}
###
accessionIdentifier: -> if @json['accessionIdentifier'] then new Identifier(@json['accessionIdentifier'])
###*
Time when specimen was received for processing or testing.
@returns {Array} an array of {@link Date} objects
###
receivedTime:-> if @json['receivedTime'] then DT.DateTime.parse(@json['receivedTime'])
###*
Details concerning the specimen collection.
@returns {SpecimenCollectionComponent}
###
collection: -> if @json['collection'] then new SpecimenCollectionComponent(@json['collection'])
###*
Details concerning treatment and processing steps for the specimen.
@returns {Array} an array of {@link SpecimenTreatmentComponent} objects
###
treatment: ->
if @json['treatment']
for item in @json['treatment']
new SpecimenTreatmentComponent(item)
###*
The container holding the specimen. The recursive nature of containers; i.e. blood in tube in tray in rack is not addressed here.
@returns {Array} an array of {@link SpecimenContainerComponent} objects
###
container: ->
if @json['container']
for item in @json['container']
new SpecimenContainerComponent(item)
module.exports.Specimen = Specimen
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