Patient de-identification Process API - Implementation Template

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Developer guide

This document provides information generated from the DataWeave scripts included in the project, such as function definitions, variable definitions, and data mapping tables.

Module	Description
createDeIdentifiedResources	This module defines functions that are used to generate De-Identified resources based on original resource, rules, and De-Identified Resource IDs. This module require changes if any new fields need to be included in a specific resource.
fhirTools	This module defines a number of common functions that are used to generate De-Identified values for the fields of a resource based on original value and Rule. Introducing new rules may require modifications to the functions.
export-config-request-to-db-mapping	Create an Export Configuration
export-config-get-response-mapping	Returns Transaction Details along with Export Configuration details for a specific Export Configuration

createDeIdentifiedResources

This module defines functions that are used to generate De-Identified resources
based on original resource, rules, and De-Identified Resource IDs.
This module require changes if any new fields need to be included in a specific
resource.

Source: ./src/main/resources/dwl/createDeIdentifiedResources.dwl

Variables

var observationResourceType

Variable to hold the Resource Types that has Observation, used for filtering references

var patientResourceType

Variable to hold the Resource Types that has Patient, used for filtering references

var supportedResourceTypes

Variable to hold the supported Resource Types, used for filtering references

Functions

fun getPatientBirthDate (item, format)

This function takes a patient object that need to be De-Identified and validates the age to produced a De-Identified date of birth.

param item Patient object that need to be De-Identified.
param format date format to be used to produce De-Identified date of birth.
return datetime which is the De-Identified date of birth of the patient.

fun getDeIdentifiedContainedResources (containedArray, muleIds, rules, resourceTypes, zipCodeToPopulation)

This function takes an array of resources to De-Identify and returns an array of De-Identified resources based on rules,supported resource types and De-Identified resource ids. This function is mainly used to De-Identify the resources in the 'contained' field of the top level resource.

param containedArray an array of resources that are to be De-Identified from the contained field.
param muleIds an object that has IDs of resources as a key and De-Identified IDs as value.
param rules an array of rules to apply to De-Identify the resource.
param resourceTypeArray an array of resource types that are to be retained if reference exists.
return resource Array with De-Identified objects.

fun createDeIdentifiedPatient (data, muleIds, rules, zipCodeToPopulation, metaTag)

This function takes a Patient Resource Object to De-Identify and returns the De-Identified resources based on rules and De-Identified resource ids provided. Only a specific set of fields are retained in the De-Identified object.

param data Patient resource object that is to be De-Identified.
param muleIds an object that has IDs of resources as a key and De-Identified IDs as value.
param rules an array of rules to apply to De-Identify the resource.
param zipCodeToPopulation an array of Zip Codes and population to De-Identify Zip Codes based on rules.
param metaTag a tag applied to search De-Identified resources based on export configuration id.

Field Name	Type(s)	Min	Max	Default retain in the output	User determined	Options presented to user	Comments
Patient.id	id	0	1	YES	NO		The application will generate a unique ID for each FHIR resource instance and substitute the source system resource identifier with it. Both the source system and the application-generated resource instance identifiers will be stored in a data store
Patient.implicitRules	uri	0	1	NO	NO		If implicitRules are detected; the application will not process the record and log that it was not processed
Patient.contained	Resource	0	*	YES	NO		Retained if the reference to the contained resource is retained
Patient.modifierExtension	Extension	0	*	NO	NO		If modifierExtensions are detected; the application will not process the record and log that it was not processed
Patient.active	boolean	0	1	YES	NO		Actual value will be returned
Patient.gender	code	0	1	YES	NO		Actual value will be returned
Patient.birthDate	date	0	1	NO	YES	Keep the birthdate in output? Options: 1. Do not retain 2. YYYY 3. YYYY-MM 4. YYYY-MM-DD	If the patient age is 89 or older then default to 90 years and set the year accordingly
Patient.deceased[x]	boolean dateTime	0	1	NO	YES	Keep the deceased date in output? Options: 1. Do not retain 2. YYYY 3. YYYY-MM 4. YYYY-MM-DD 5. YYYY-MM-DDThh:mm:ss+zz:zz
Patient.address	Address	0	*	NO	YES	Keep the address or geographic identifiers in output? 1. Do not retain 2. Truncate to the first 3 characters of zip code 3. Truncate to the first 5 characters of zip code 4. Do not truncate	If postal code is not found or population is less than 20K include default capability to modify output to 000 or 00000 or 00000-0000
Patient.maritalStatus	CodeableConcept	0	1	NO	YES	Keep the marital status in output? 1. Do not retain 2. Yes
Patient.multipleBirth[x]	boolean integer	0	1	NO	YES	Keep multiple birth information in output? 1. Do not retain 2. Convert to boolean if numeric 3. Yes
Patient.communication.language	CodeableConcept	1	1	NO	YES	Keep patient language in output? 1. Do not retain 2. Yes

fun createDeIdentifiedCondition (data, muleIds, rules, zipCodeToPopulation, metaTag)

This function takes a Condition Resource Object to De-Identify and returns the De-Identified resources based on rules and De-Identified resource ids provided. Only a specific set of fields are retained in the De-Identified object.

param data Condition resource object that is to be De-Identified.
param muleIds an object that has IDs of resources as a key and De-Identified IDs as value.
param rules an array of rules to apply to De-Identify the resource.
param zipCodeToPopulation an array of Zip Codes and population to De-Identify Zip Codes based on rules.
param metaTag a tag applied to search De-Identified resources based on export configuration id.
return Condition resource object with De-Identified fields based on rules.

Field Name	Type(s)	Min	Max	Default retain in the output	User determined	Options presented to user	Comments
Condition.id	id	0	1	YES	NO		The application will generate a unique ID for each FHIR resource instance and substitute the source system resource identifier with it. Both the source system and the application-generated resource instance identifiers will be stored in a data store
Condition.implicitRules	uri	0	1	NO	NO		If Application detects implicitRules; it will not process the record and log that it was not processed
Condition.contained	Resource	0	*	YES	NO		Retained if the reference to the contained resource is retained
Condition.modifierExtension	Extension	0	*	NO	NO		If modifierExtensions are detected; the application will not process the record and log that it was not processed
Condition.clinicalStatus	CodeableConcept	1	1	YES	NO		CodeableConcept.text is removed
Condition.verificationStatus	CodeableConcept	0	1	YES	NO		CodeableConcept.text is removed
Condition.category	CodeableConcept	0	*	YES	NO		CodeableConcept.text is removed
Condition.severity	CodeableConcept	0	1	YES	NO		CodeableConcept.text is removed
Condition.code	CodeableConcept	0	1	NO	YES	Filter by condition codes 1. Include all conditions 2. Filter by selected codes	CodeableConcept.text is removed; If the condition code filter yields no results then do not process the condition resource instance itself. Assumptions: If the source record does not include system and code then filter the condition resource instance.
Condition.bodySite	CodeableConcept	0	*	YES	NO		CodeableConcept.text is removed
Condition.bodyStructure	Reference(BodyStructure)	0	1	NO	YES	Keep the Body Structure details in output? 1. Do not retain 2. Retain
Condition.subject	Reference(Patient or Group)	1	1	YES	NO		Only need to support Patient and not Group
Condition.onset[x]	dateTime	0	1	NO	YES	Keep the condition onset date in output? Options: 1. Do not retain 2. YYYY 3. YYYY-MM 4. YYYY-MM-DD 5. YYYY-MM-DDThh:mm:ss+zz:zz
Condition.onset[x]	Age	0	1	YES	NO		Actual value will be returned
Condition.onset[x]	Period	0	1	NO	YES	Keep the condition onset period in output? Options: 1. Do not retain 2. YYYY 3. YYYY-MM
Condition.onset[x]	Range	0	1	NO	YES	Keep the condition onset range in output? Options: 1. Do not retain 2. YYYY 3. YYYY-MM
Condition.abatement[x]	dateTime	0	1	NO	YES	Keep the condition abatement date in output? Options: 1. Do not retain 2. YYYY 3. YYYY-MM 4. YYYY-MM-DD 5. YYYY-MM-DDThh:mm:ss+zz:zz
Condition.abatement[x]	Age	0	1	YES	NO		Actual value will be returned
Condition.abatement[x]	Period	0	1	NO	YES	Keep the condition abatement period in output? Options: 1. Do not retain 2. YYYY 3. YYYY-MM
Condition.abatement[x]	Range	0	1	NO	YES	Keep the condition abatement range in output? Options: 1. Do not retain 2. YYYY 3. YYYY-MM
Condition.recordedDate	dateTime	0	1	NO	YES	Keep the condition recorded date in output? Options: 1. Do not retain 2. YYYY 3. YYYY-MM 4. YYYY-MM-DD 5. YYYY-MM-DDThh:mm:ss+zz:zz
Condition.stage	BackboneElement	0	*	YES	NO		Actual value will be returned
Condition.stage.summary	CodeableConcept	0	1	YES	NO		CodeableConcept.text is removed
Condition.stage.type	CodeableConcept	0	1	YES	NO		CodeableConcept.text is removed

fun createDeIdentifiedObservation (data, muleIds, rules, zipCodeToPopulation, metaTag)

This function takes a Observation Resource Object to De-Identify and returns the De-Identified resources based on rules and De-Identified resource ids provided. Only a specific set of fields are retained in the De-Identified object.

param data Observation resource object that is to be De-Identified.
param muleIds an object that has IDs of resources as a key and De-Identified IDs as value.
param rules an array of rules to apply to De-Identify the resource.
param zipCodeToPopulation an array of Zip Codes and population to De-Identify Zip Codes based on rules.
param metaTag a tag applied to search De-Identified resources based on export configuration id.
return Observation resource object with De-Identified fields based on rules.

Field Name	Type(s)	Min	Max	Default retain in the output	User determined	Options presented to user	Comments
Observation.id	id	0	1	YES	NO		The application will generate a unique ID for each FHIR resource instance and substitute the source system resource identifier with it. Both the source system and the application-generated resource instance identifiers will be stored in a data store
Observation.implicitRules	uri	0	1	NO	YES		If implicitRules are detected; the application will not process the record and log that it was not processed
Observation.contained	Resource	0	*	YES	NO		Retained if the reference to the contained resource is retained
Observation.modifierExtension	Extension	0	*	NO	YES		If modifierExtensions are detected; the application will not process the record and log that it was not processed
Observation.status	code	1	1	YES	NO		Actual value will be returned
Observation.category	CodeableConcept	0	*	YES	NO		CodeableConcept.text is removed
Observation.code	CodeableConcept	1	1	YES	NO		CodeableConcept.text is removed
Observation.subject	Reference(Patient or Group or Device or Location or Organization or Procedure or Practitioner or Medication or Substance or BiologicallyDerivedProduct or NutritionProduct)	0	1	YES	NO		Retains the value when the Reference is a Patient
Observation.focus	Reference(Any)	0	*	YES	NO		Retains if Reference is to a supported resource (Patient or Condition or BodyStructure)
Observation.effective[x]	dateTime	0	1	NO	YES	Keep the observation effective date in output? Options: 1. Do not retain 2. YYYY 3. YYYY-MM 4. YYYY-MM-DD 5. YYYY-MM-DDThh:mm:ss+zz:zz
Observation.effective[x]	Period	0	1	NO	YES	Keep the observation effective period in output? Options: 1. Do not retain 2. YYYY 3. YYYY-MM
Observation.effective[x]	instant	0	1	NO	YES	Keep the observation effective instant in output? Options: 1. Do not retain 2. Retain
Observation.issued	instant	0	1	NO	YES	Keep the observation issued instant in output? Options: 1. Do not retain 2. Retain
Observation.value[x]	Quantity CodeableConcept string boolean integer Range Ratio SampledData time dateTime Period Attachment Reference(MolecularSequence)	0	1	YES	NO		Actual value will be returned
Observation.dataAbsentReason	CodeableConcept	0	1	YES	NO		CodeableConcept.text is removed
Observation.interpretation	CodeableConcept	0	*	YES	NO		CodeableConcept.text is removed
Observation.bodySite	CodeableConcept	0	1	YES	NO		CodeableConcept.text is removed
Observation.bodyStructure	Reference(BodyStructure)	0	1	YES	NO		Actual value will be returned
Observation.method	CodeableConcept	0	1	YES	NO		CodeableConcept.text is removed
Observation.referenceRange	BackboneElement	0	*	YES	NO		Actual value will be returned
Observation.referenceRange.low	Quantity {SimpleQuantity}	0	1	YES	NO		Actual value will be returned
Observation.referenceRange.high	Quantity {SimpleQuantity}	0	1	YES	NO		Actual value will be returned
Observation.referenceRange.normalValue	CodeableConcept	0	1	YES	NO		CodeableConcept.text is removed
Observation.referenceRange.type	CodeableConcept	0	1	YES	NO		CodeableConcept.text is removed
Observation.referenceRange.appliesTo	CodeableConcept	0	*	YES	NO		CodeableConcept.text is removed
Observation.referenceRange.age	Range	0	1	YES	NO		Actual value will be returned
Observation.hasMember	Reference(Observation or QuestionnaireResponse or MolecularSequence)	0	*	YES	NO		Retains if a Reference is to a supported resource (currently just Observation)
Observation.derivedFrom	Reference(DocumentReference or ImagingStudy or ImagingSelection or QuestionnaireResponse or Observation or MolecularSequence or GenomicStudy)	0	*	YES	NO		Retains if a Reference is to a supported resource (currently just Observation)
Observation.component	BackboneElement	0	*	YES	NO		Actual value will be returned
Observation.component.code	CodeableConcept	1	1	YES	NO		CodeableConcept.text is removed

fun getBodyStructure (bodyStructure, muleIds, rules, metaTag)

This function takes a BodyStructure Resource Object to De-Identify and returns the De-Identified resources based on rules and De-Identified resource ids provided. Fields in Body Structure vary from FHIR R4 and R5 versions and both scenarios are handled. Only a specific set of fields are retained in the De-Identified object.

param bodyStructure BodyStructure resource object that is to be De-Identified.
param muleIds an object that has IDs of resources as a key and De-Identified IDs as value.
param rules an array of rules to apply to De-Identify the resource.
param zipCodeToPopulation an array of Zip Codes and population to De-Identify Zip Codes based on rules.
param metaTag a tag applied to search De-Identified resources based on export configuration id.
return BodyStructure resource object with De-Identified fields based on rules.

Field Name	Type(s)	Min	Max	Default retain in the output	User determined	Comments
BodyStructure.id	id	0	1	YES	NO	The application will generate a unique ID for each FHIR resource instance and substitute the source system resource identifier with it. Both the source system and the application-generated resource instance identifiers will be stored in a data store
BodyStructure.implicitRules	uri	0	1	NO	NO	If implicitRules are detected; the application will not process the record and log that it was not processed
BodyStructure.modifierExtension	Extension	0	*	NO	NO	If modifierExtensions are detected; the application will not process the record and log that it was not processed
BodyStructure.active	boolean	0	1	YES	NO	Actual value will be returned
BodyStructure.includedStructure	BackboneElement	1	*	YES	NO	Actual value will be returned
BodyStructure.includedStructure.structure	CodeableConcept	1	1	YES	NO	Actual value will be returned
BodyStructure.includedStructure.laterality	CodeableConcept	0	1	YES	NO	Actual value will be returned
BodyStructure.patient	Reference(Patient)	1	1	YES	NO	Actual value will be returned

fun getIncludedStructure (includedStructure)

This function takes a includedStructure field of BodyStructure Resource Object to De-Identify and returns the De-Identified structure and laterality fields.

param includedStructure includedStructure object of BodyStructure resource object that is to be De-Identified.
return includedStructure resource object with De-Identified fields.

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fhirTools

This module defines a number of common functions that are used to generate
De-Identified values for the fields of a resource based on original value and Rule.
Introducing new rules may require modifications to the functions.

Source: ./src/main/resources/dwl/fhirTools.dwl

Functions

fun getRuleValue (rules, name)

This function takes an array of rules and name of the rule to filter the value to apply.

param rules an array of rules defined as a name and value object.
param name filters the value based on the matched name from the rules.
return The value of the corresponding rule that matched the name.

fun getDeIdentifiedCodeableConcept (data)

This function takes an array or object of CodeadbaleConcept and returns a De-Identified CodeadbaleConcept.

param data an array or object of CodeadbaleConcept to De-Identify.
return CodeadbaleConcept array or object that has been De-Identified.

fun getDeIdentifiedCodeableConceptFiltered (data, format)

This function takes an array of CodeadbaleConcept along with a string of of filters (system|code) csv to and returns a filtered De-Identified CodeadbaleConcept that matches the filters.

param data an array or object of CodeadbaleConcept to De-Identify.
param format string data in format of (system|code) csv to match and retain.
return CodeadbaleConcept array that has been De-Identified.

fun getDeIdentifiedDateTime (dateTime, format)

This function takes date and time along with a string to format as De-Identified date and time.

param dateTime Date and Time to De-Identify.
param format string format of date and time to retain.
return dateTime De-Identified date and time based on format.

fun getDeIdentifiedPostalCode (postalCode, format, zipCodeToPopulation)

This function takes postal code along with a string to format as De-Identified postal code.

param postalCode postal code to De-Identify.
param format string format of postal code to retain.
param zipCodeToPopulation an array of Zip Codes and population to De-Identify Zip Codes based on rules.
return postalCode De-Identified postal code based on format.

fun getDeIdentifiedMaritalStatus (maritalStatus, format)

This function takes marital status along with a string to format as De-Identified marital status.

param maritalStatus marital status to De-Identify.
param format string format of date and time to retain.
return maritalStatus De-Identified marital status on format.

fun getDeIdentifiedBoolean (bool, format)

This function takes a boolean along with a string to format as De-Identified boolean status.

param bool boolean to De-Identify.
param format string format of date and time to retain.
return boolean De-Identified boolean on format.

fun filterNoImplictRulesandModifiedExtension (data)

This function takes an array of resources and ignores any resource that has implicitRules or modifiedExtension fields. It returns an array of filtered resources.

param data an array of resources.
return data an array of filtered resources.

fun getDeIdentifiedReferencesArray (referencesArray, resourceTypeArray, muleIds)

This function takes an array of references that needs to be De-Identified along with an array of resource types to retain and an object that holds resource IDs that are De-Identified. The De-Identified ids are used for mapping references. If there is no De-Identified id for a given resource, the reference is null and will be excluded from the list.

param referencesArray an array of references that are to be De-Identified.
param resourceTypeArray an array of resource types that are to be retained if reference exists.
param muleIds an object that has IDs of resources as a key and De-Identified IDs as value.
return references array that is De-Identified.

fun getDeIdentifiedReferenceObject (referenceObj, resourceTypeArray, muleIds)

This function takes a reference object that needs to be De-Identified along with an array of resource types to retain and an object that holds resource IDs that are De-Identified. The De-Identified ids are used for mapping references. If there is no De-Identified id for a given resource, the reference is not returned.

param referencesArray an array of references that are to be De-Identified.
param resourceTypeArray an array of resource types that are to be retained if reference exists.
param muleIds an object that has IDs of resources as a key and De-Identified IDs as value.
return references object that is De-Identified.

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export-config-request-to-db-mapping

Create an Export Configuration

Source: ./src/main/resources/dwl/export-config-request-to-db-mapping.dwl

Mapping Tables

Create an Export Configuration. Mapping from API Field to DB field to create an Export Configuration

API Field	DB Field Name	Description
name	NAME	Name of the Export Configuration
description	DESCRIPTION	Description about Export Configuration
resources	RESOURCES	Resources that need to be exported from EHR.
fhirGroupId	FHIR_GROUP_ID	Group Id of EHR Bulk Export
earliestRecordDate	EARLIEST_RECORD_DATE	Data to be retrieved from EHR Bulk export APIS using `sinceDate`
frequency	FREQUENCY	Frequency when the Job should run based on Export Configuration
dayOfWeek	DAY_OF_WEEK	Day of the week when the Job should run based on Export Configuration
weekOfMonth	WEEK_OF_MONTH	Week of the month when the Job should run based on Export Configuration
status	STATUS	Status of the Job based on the Export Configuration.
rules	RULES	JSON Array that hold the ruleName and rule Values for Export Configuration
isDeleted	IS_DELETED	Soft deletion of Export Configuration

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export-config-get-response-mapping

Returns Transaction Details along with Export Configuration details for a specific Export Configuration

Source: ./src/main/resources/dwl/export-config-get-response-mapping.dwl

Mapping Tables

Returns Transaction Details along with Export Configuration details for a specific Export Configuration

API Field	DB Field Name	Description
id	ID	Unique Auto Generated Id of the Export Configuration
name	NAME	Name of the Export Configuration
description	DESCRIPTION	Description about Export Configuration
resources	RESOURCES	Resources that need to be exported from EHR.
fhirGroupId	FHIR_GROUP_ID	Group Id of EHR Bulk Export
earliestRecordDate	EARLIEST_RECORD_DATE	Data to be retrieved from EHR Bulk export APIS using `sinceDate`
lastRunEndTime	LAST_RUN	Last Successful Job Run based on Export Configuration
frequency	FREQUENCY	Frequency when the Job should run based on Export Configuration
dayOfWeek	DAY_OF_WEEK	Day of the week when the Job should run based on Export Configuration
weekOfMonth	WEEK_OF_MONTH	Week of the month when the Job should run based on Export Configuration
status	STATUS	Status of the Job based on the Export Configuration.
rules	RULES	JSON Array that hold the ruleName and rule Values for Export Configuration
isDeleted	IS_DELETED	Soft deletion of Export Configuration
createdDateTime	CREATED_DATE	Date when the Export Configuration has been created
runHistory	JOB_END	Only last 10 records with status as `completed` will be returned
initialSucessfulRunTime	JOB_END	Mapped with first record that has `completed` status for the Export Configuration Id

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Type	Template
Organization	Mulesoft Inc.
Published by	MuleSoft Solutions
Published on	May 30, 2024

Patient de-identification Process API - Implementation Template

Developer guide

createDeIdentifiedResources

Variables

Functions

fhirTools

Functions

export-config-request-to-db-mapping

Mapping Tables

export-config-get-response-mapping

Mapping Tables

Reviews

Asset versions for 1.0.x