hdsfhir

package module
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 Go to latest Published: Aug 10, 2016 License: Apache-2.0 Imports: 12 Imported by: 0

README

HDS to FHIR Build Status

This project converts JSON data for a patient in the structure used byhealth-data-standards into the HL7 FHIR DSTU2 models defined in the Intervention Engine fhir project.

NOTE: The HDS-to-FHIR conversion focuses only on those data elements that are needed by Intervention Engine. It is not a complete and robust conversion.

Building hdsfhir Locally

For information on installing and running the full Intervention Engine stack, please see Building and Running the Intervention Engine Stack in a Development Environment.

The hdsfhir project is a Go library. For information related specifically to building the code in this repository (hdsfhir), please refer to the following sections in the above guide:

To build the hdsfhir library, you must install its dependencies via go get first, and then build it:

$ cd $GOPATH/src/github.com/intervention-engine/hdsfhir
$ go get
$ go build

For information on using the uploadhds tool to convert HDS patients to FHIR and upload them to a FHIR server, please refer to the uploadhds section of the tools repository README.

Using hdsfhir as a library

The following is a simple example of converting a HDS patient to the corresponding slice of FHIR models:

import (
	"encoding/json"
	"io/ioutil"
	"github.com/intervention-engine/hdsfhir"
)

func ExampleConversion(pathToHdsPatient string) ([]interface{}, error) {
	data, err := ioutil.ReadFile(pathToHdsPatient)
	if err != nil {
		return nil, err
	}

	p := &hdsfhir.Patient{}
	err = json.Unmarshal(data, p)
	if err != nil {
		return nil, err
	}

	return p.FHIRModels(), nil
}

License

Copyright 2016 The MITRE Corporation

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

Documentation

Index

Constants

This section is empty.

Variables

View Source 
var CodeSystemMap = map[string]string{
	"CPT":                             "http://www.ama-assn.org/go/cpt",
	"LOINC":                           "http://loinc.org",
	"SNOMED-CT":                       "http://snomed.info/sct",
	"RxNorm":                          "http://www.nlm.nih.gov/research/umls/rxnorm",
	"ICD-9-CM":                        "http://hl7.org/fhir/sid/icd-9",
	"ICD-10-CM":                       "http://hl7.org/fhir/sid/icd-10",
	"ICD-9-PCS":                       "http://hl7.org/fhir/sid/icd-9",
	"ICD-10-PCS":                      "http://hl7.org/fhir/sid/icd-10",
	"NDC":                             "http://www.fda.gov/Drugs/InformationOnDrugs",
	"CVX":                             "http://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=cvx",
	"HCP":                             "urn:oid:2.16.840.1.113883.6.14",
	"HCPCS":                           "urn:oid:2.16.840.1.113883.6.285",
	"HL7 Marital Status":              "http://hl7.org/fhir/ValueSet/v3-MaritalStatus",
	"HITSP C80 Observation Status":    "http://hl7.org/fhir/ValueSet/v3-ObservationInterpretation",
	"NCI Thesaurus":                   "urn:oid:2.16.840.1.113883.3.26.1.1",
	"FDA SPL":                         "urn:oid:2.16.840.1.113883.3.26.1.1",
	"FDA":                             "urn:oid:2.16.840.1.113883.3.88.12.80.20",
	"UNII":                            "http://fdasis.nlm.nih.gov",
	"HL7 ActStatus":                   "http://hl7.org/fhir/ValueSet/v3-ActStatus",
	"HL7 Healthcare Service Location": "urn:oid:2.16.840.1.113883.6.259",
	"HSLOC":                           "urn:oid:2.16.840.1.113883.6.259",
	"DischargeDisposition":            "urn:oid:2.16.840.1.113883.12.112",
	"HL7 Act Code":                    "http://hl7.org/fhir/ValueSet/v3-ActCode",
	"HL7 Relationship Code":           "urn:oid:2.16.840.1.113883.1.11.18877",
	"CDC Race":                        "urn:oid:2.16.840.1.113883.6.238",
	"NLM Mesh":                        "urn:oid:2.16.840.1.113883.6.177",
	"Religious Affiliation":           "http://hl7.org/fhir/ValueSet/v3-ReligiousAffiliation",
	"HL7 ActNoImmunicationReason":     "urn:oid:2.16.840.1.113883.1.11.19717",
	"NUBC":                            "urn:oid:2.16.840.1.113883.3.88.12.80.33",
	"HL7 Observation Interpretation":  "urn:oid:2.16.840.1.113883.1.11.78",
	"Source of Payment Typology":      "urn:oid:2.16.840.1.113883.3.221.5",
	"SOP":                             "urn:oid:2.16.840.1.113883.3.221.5",
	"CDT":                             "urn:oid:2.16.840.1.113883.6.13",
	"AdministrativeSex":               "urn:oid:2.16.840.1.113883.18.2",
}

Functions

func ConvertToConditionalUpdates 

func ConvertToConditionalUpdates(bundle *models.Bundle) error

ConvertToConditionalUpdates converts a bundle containing POST requests to a bundle with PUT requests using conditional updates. For patient resources, the update is based on the Medical Record Number. For all other resources it is based on reasonable indicators of sameness (such as equal dates and codes).

Types

type Allergy 

type Allergy struct {
	Entry
	Reaction *CodeObject `json:"reaction"`
	Severity *CodeObject `json:"severity"`
}

func (*Allergy) FHIRModels 

func (a *Allergy) FHIRModels() []interface{}

type CodeMap 

type CodeMap map[string][]string

func (*CodeMap) FHIRCodeableConcept 

func (c *CodeMap) FHIRCodeableConcept(text string) *fhir.CodeableConcept

type CodeObject 

type CodeObject struct {
	Code       string `json:"code"`
	CodeSystem string `json:"codeSystem"`
}

func (*CodeObject) FHIRCodeableConcept 

func (c *CodeObject) FHIRCodeableConcept(text string) *fhir.CodeableConcept

type CodedResult 

type CodedResult struct {
	Codes       CodeMap `json:"codes"`
	Description string  `json:"description"`
}

type Condition 

type Condition struct {
	Entry
	// NOTE: HDS has inconsistent representations of severity, but the only working importer (cat1)
	// models it like a CodeMap -- so that's what we assume.  Note the difference from Allergy.
	Severity CodeMap `json:"severity"`
}

func (*Condition) FHIRModels 

func (c *Condition) FHIRModels() []interface{}

type Encounter 

type Encounter struct {
	Entry
	Reason               *Entry      `json:"reason"`
	DischargeDisposition *CodeObject `json:"dischargeDisposition"`
}

func (*Encounter) FHIRModels 

func (e *Encounter) FHIRModels() []interface{}

type Entry 

type Entry struct {
	TemporallyIdentified
	Patient        *Patient    `json:"-"`
	StartTime      *UnixTime   `json:"start_time"`
	EndTime        *UnixTime   `json:"end_time"`
	Time           *UnixTime   `json:"time"`
	Oid            string      `json:"oid"`
	Codes          CodeMap     `json:"codes"`
	MoodCode       string      `json:"mood_code"`
	NegationInd    bool        `json:"negationInd"`
	NegationReason *CodeObject `json:"negationReason"`
	StatusCode     CodeMap     `json:"status_code"`
	Description    string      `json:"description"`
}

func (*Entry) GetFHIRPeriod 

func (e *Entry) GetFHIRPeriod() *fhir.Period

type Immunization 

type Immunization struct {
	Entry
	SeriesNumber *uint32 `json:"seriesNumber"`
}

func (*Immunization) FHIRModels 

func (i *Immunization) FHIRModels() []interface{}

type Medication 

type Medication struct {
	Entry
}

func (*Medication) FHIRModels 

func (m *Medication) FHIRModels() []interface{}

type Patient 

type Patient struct {
	TemporallyIdentified
	MedicalRecordNumber string          `json:"medical_record_number"`
	FirstName           string          `json:"first"`
	LastName            string          `json:"last"`
	BirthTime           *UnixTime       `json:"birthdate"`
	Gender              string          `json:"gender"`
	Encounters          []*Encounter    `json:"encounters"`
	Conditions          []*Condition    `json:"conditions"`
	VitalSigns          []*VitalSign    `json:"vital_signs"`
	Procedures          []*Procedure    `json:"procedures"`
	Medications         []*Medication   `json:"medications"`
	Immunizations       []*Immunization `json:"immunizations"`
	Allergies           []*Allergy      `json:"allergies"`
}

func (*Patient) FHIRModel 

func (p *Patient) FHIRModel() *fhir.Patient

func (*Patient) FHIRModels 

func (p *Patient) FHIRModels() []interface{}

func (*Patient) FHIRTransactionBundle 

func (p *Patient) FHIRTransactionBundle(conditionalUpdate bool) *fhir.Bundle

FHIRTransactionBundle returns a FHIR bundle representing a transaction to post all patient data to a server

func (*Patient) MatchingEncounterReference 

func (p *Patient) MatchingEncounterReference(entry Entry) *fhir.Reference

func (*Patient) UnmarshalJSON 

func (p *Patient) UnmarshalJSON(data []byte) (err error)

type PhysicalQuantityResult 

type PhysicalQuantityResult struct {
	Unit   string `json:"unit"`
	Scalar string `json:"scalar"`
}

Result Types

type Procedure 

type Procedure struct {
	Entry
	AnatomicalTarget *CodeObject   `json:"anatomical_target"`
	Values           []ResultValue `json:"values"`
}

func (*Procedure) FHIRModels 

func (p *Procedure) FHIRModels() []interface{}

type ResultValue 

type ResultValue struct {
	TemporallyIdentified
	Physical *PhysicalQuantityResult
	Coded    *CodedResult
}

func (*ResultValue) FHIRModels 

func (v *ResultValue) FHIRModels() []interface{}

func (*ResultValue) UnmarshalJSON 

func (v *ResultValue) UnmarshalJSON(data []byte) (err error)

type TemporallyIdentified 

type TemporallyIdentified struct {
	// contains filtered or unexported fields
}

func (*TemporallyIdentified) FHIRReference 

func (t *TemporallyIdentified) FHIRReference() *fhir.Reference

func (*TemporallyIdentified) GetTempID 

func (t *TemporallyIdentified) GetTempID() string

type UnixTime 

type UnixTime int64

func NewUnixTime 

func NewUnixTime(offset int64) *UnixTime

func (*UnixTime) FHIRDate 

func (t *UnixTime) FHIRDate() *fhir.FHIRDateTime

func (*UnixTime) FHIRDateTime 

func (t *UnixTime) FHIRDateTime() *fhir.FHIRDateTime

func (*UnixTime) Time 

func (t *UnixTime) Time() time.Time

type VitalSign 

type VitalSign struct {
	Entry
	Description    string        `json:"description"`
	Interpretation *CodeObject   `json:"interpretation"`
	Values         []ResultValue `json:"values"`
}

func (*VitalSign) FHIRModels 

func (v *VitalSign) FHIRModels() []interface{}

Source Files

View all Source files

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