Download FHIR Patients
The Download FHIR Patient tool will download a set of patients using the /Patient/[ID]/$everything FHIR resource. The set of patients that are downloaded is defined by the patient ids found in the directory created by the Download FHIR Patient IDs tool (or any dir that contains files similar to those created by the Download FHIR Patient IDs tool).Prerequisites
Before running the Download FHIR Patients tool you will need the following- An app.properties file that contains the information needed to connect to the FHIR Patient server you will be using, etc.
- A dir that contains the files with the patient IDs for the patients to be downloaded
- Java
The app.properties File
The following shows the settings in the app.properties file used for this example. A complete app.properties file can be down loaded from here. For this example we are using Miter's SyntheticMass FHIR Patient Server. To use this service you will need to get your own credentials and replace the <your_info_goes_here> values. (as described here). The properties required for this tool are essentially the same as those for the Download Patient IDs tool, with the addition of the dir where the down loaded patients will be stored and some parameters that define the number of threads that will be used for the process. There are three threading parameters. The number of patients per thread (this should probably always be 1). The number of workers, and the number of workers per thread. For each worker, the tool creates a thread for each patient. A constant pool of workers is maintained by the tool. Thereby, there is a relatively constant number of downloads occurring during the entire process (except at the very end when the final stragglers are finishing up).# --- # DOWNLOAD STUFF # --- httpClientAuthenticatorClass=org.nachc.tools.fhirtoomop.fhir.util.server.auth.impl.HeaderTokenAuthenticator fhirPatientServerUrl=https://syntheticmass.mitre.org/v1/fhir headerTokenAuthenticatorApiId=<your_info_goes_here> headerTokenAuthenticatorApiKey=<your_info_goes_here> headerTokenAuthenticatorSecret=<your_info_goes_here> headerTokenAuthenticatorUrl=https://syntheticmass.mitre.org/oauth2/accesstoken downloadPatientIdDir=D:\\NACHC\\SYNTHEA\\TEST\\patient-ids-test downloadNumberOfPatientsPerThread=1 downloadMaxNumberOfActiveWorkers=20 downloadNumberOfPatientsPerWorker=100 downloadRetryCount=5 downloadOutputDir=D:\\NACHC\\SYNTHEA\\TEST\\patients-test
Running the Application
The Patient Download tool can be run from the Standalone Application as shown below. The second screen shot shows what the application should look like when it has completed.
fhir-to-omop.bat d
Results
After the application has run, the down load directory specified in the app.parameters file will contain a set of directory. Each directory represents a single patient. Each directory will have one or more files that represent the /Patient/[ID]/$everything resource. The directory can contain multiple files as the Patient/[ID]/$everything resource is allowed to be paged. The down load directory should look something like what is shown below.
Each folder will contain json files for an individual patient as shown below.
Each file will have the json for the patient resource as shown below. This resource has been pretty printed so it is human readable. The actual resource will have all of the information on a singele line.
{
"resourceType": "Bundle",
"type": "searchset",
"entry": [
{
"resource": {
"address": [
{
"city": "Mashpee",
"country": "US",
"extension": [
{
"extension": [
{
"url": "latitude",
"valueDecimal": 41.617623
},
{
"url": "longitude",
"valueDecimal": -70.492713
}
],
"url": "http://hl7.org/fhir/StructureDefinition/geolocation"
}
],
"line": [
"213 Watsica Ranch Apt 9"
],
"postalCode": "02649",
"state": "Massachusetts"
}
],
"birthDate": "1924-02-19",
"communication": [
{
"language": {
"coding": [
{
"code": "ru-RU",
"display": "Russian (Russia)",
"system": "urn:ietf:bcp:47"
}
],
"text": "Russian (Russia)"
}
}
],
"deceasedDateTime": "2005-01-22T12:01:28-05:00",
"extension": [
{
"extension": [
{
"url": "ombCategory",
"valueCoding": {
"code": "2106-3",
"display": "White",
"system": "urn:oid:2.16.840.1.113883.6.238"
}
},
{
"url": "text",
"valueString": "White"
}
],
"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race"
},
{
"extension": [
{
"url": "ombCategory",
"valueCoding": {
"code": "2186-5",
"display": "Not Hispanic or Latino",
"system": "urn:oid:2.16.840.1.113883.6.238"
}
},
{
"url": "text",
"valueString": "Not Hispanic or Latino"
}
],
"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity"
},
{
"url": "http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName",
"valueString": "June482 Weimann465"
},
{
"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex",
"valueCode": "M"
},
{
"url": "http://hl7.org/fhir/StructureDefinition/birthPlace",
"valueAddress": {
"city": "Moscow",
"country": "RU",
"state": "Moscow"
}
},
{
"url": "http://synthetichealth.github.io/synthea/disability-adjusted-life-years",
"valueDecimal": 1.5127317395301776
},
{
"url": "http://synthetichealth.github.io/synthea/quality-adjusted-life-years",
"valueDecimal": 78.48726826046982
}
],
"gender": "male",
"id": "0b3ede79-49be-42b4-961e-a0e99e52b473",
"identifier": [
{
"system": "https://github.com/synthetichealth/synthea",
"value": "213f7a06-ece7-4874-b6e9-dba8126d91ad"
},
{
"system": "http://hospital.smarthealthit.org",
"type": {
"coding": [
{
"code": "MR",
"display": "Medical Record Number",
"system": "http://hl7.org/fhir/v2/0203"
}
],
"text": "Medical Record Number"
},
"value": "213f7a06-ece7-4874-b6e9-dba8126d91ad"
},
{
"system": "http://hl7.org/fhir/sid/us-ssn",
"type": {
"coding": [
{
"code": "SB",
"display": "Social Security Number",
"system": "http://hl7.org/fhir/identifier-type"
}
],
"text": "Social Security Number"
},
"value": "999-92-4155"
},
{
"system": "urn:oid:2.16.840.1.113883.4.3.25",
"type": {
"coding": [
{
"code": "DL",
"display": "Driver's License",
"system": "http://hl7.org/fhir/v2/0203"
}
],
"text": "Driver's License"
},
"value": "S99988556"
},
{
"system": "http://standardhealthrecord.org/fhir/StructureDefinition/passportNumber",
"type": {
"coding": [
{
"code": "PPN",
"display": "Passport Number",
"system": "http://hl7.org/fhir/v2/0203"
}
],
"text": "Passport Number"
},
"value": "X63811569X"
}
],
"maritalStatus": {
"coding": [
{
"code": "M",
"display": "M",
"system": "http://hl7.org/fhir/v3/MaritalStatus"
}
],
"text": "M"
},
"meta": {
"lastUpdated": "2019-04-09T12:04:02.359213+00:00",
"versionId": "MTU1NDgxMTQ0MjM1OTIxMzAwMA"
},
"multipleBirthBoolean": false,
"name": [
{
"family": "Schmidt332",
"given": [
"Dong972"
],
"prefix": [
"Mr."
],
"use": "official"
}
],
"resourceType": "Patient",
"telecom": [
{
"system": "phone",
"use": "home",
"value": "555-598-2659"
}
],
"text": {
"div": "Generated by Synthea.Version identifier: v2.2.0-56-g113d8a2d\n . Person seed: 1696807339395505153 Population seed: 9",
"status": "generated"
}
}
},
{
"resource": {
"activity": [
{
"detail": {
"code": {
"coding": [
{
"code": "850261000000100",
"display": "Education about dementia",
"system": "http://snomed.info/sct"
}
],
"text": "Education about dementia"
},
"status": "in-progress"
}
},
{
"detail": {
"code": {
"coding": [
{
"code": "710125008",
"display": "Promotion of use of memory skills",
"system": "http://snomed.info/sct"
}
],
"text": "Promotion of use of memory skills"
},
"status": "in-progress"
}
},
{
"detail": {
"code": {
"coding": [
{
"code": "315043002",
"display": "Long term social support",
"system": "http://snomed.info/sct"
}
],
"text": "Long term social support"
},
"status": "in-progress"
}
}
],
"addresses": [
{
"reference": "Condition/cbd9b36a-6667-4687-805a-7c8815109db3"
}
],
"category": [
{
"coding": [
{
"code": "386257007",
"display": "Demential management",
"system": "http://snomed.info/sct"
}
],
"text": "Demential management"
}
],
"context": {
"reference": "Encounter/2c46a9c2-3d4e-4037-aab1-89910b37c929"
},
"id": "9e1c6e8a-48f7-457f-8a21-9c134b1d9f9c",
"intent": "order",
"meta": {
"lastUpdated": "2019-04-09T12:04:02.414600+00:00",
"versionId": "MTU1NDgxMTQ0MjQxNDYwMDAwMA"
},
"period": {
"start": "1997-08-26T13:01:28-04:00"
},
"resourceType": "CarePlan",
"status": "active",
"subject": {
"reference": "Patient/0b3ede79-49be-42b4-961e-a0e99e52b473"
}
}
},
{
"resource": {
"activity": [
{
"detail": {
"code": {
"coding": [
{
"code": "872781000000100",
"display": "Joint mobility exercises",
"system": "http://snomed.info/sct"
}
],
"text": "Joint mobility exercises"
},
"status": "in-progress"
}
},
{
"detail": {
"code": {
"coding": [
{
"code": "266694003",
"display": "Heat therapy",
"system": "http://snomed.info/sct"
}
],
"text": "Heat therapy"
},
"status": "in-progress"
}
}
],
"addresses": [
{
"reference": "Condition/63f2e619-0189-4451-ab0b-182299be7ca6"
}
],
"category": [
{
"coding": [
{
"code": "872781000000100",
"display": "Musculoskeletal care",
"system": "http://snomed.info/sct"
}
],
"text": "Musculoskeletal care"
}
],
"context": {
"reference": "Encounter/e3a63385-7b88-487b-b022-1fb9cf971993"
},
"id": "e22f55df-1ac5-4af3-86d9-7de98a3d429c",
"intent": "order",
"meta": {
"lastUpdated": "2019-04-09T12:04:02.384203+00:00",
"versionId": "MTU1NDgxMTQ0MjM4NDIwMzAwMA"
},
"period": {
"start": "1975-02-06T12:01:28-05:00"
},
"resourceType": "CarePlan",
"status": "active",
"subject": {
"reference": "Patient/0b3ede79-49be-42b4-961e-a0e99e52b473"
}
}
},
{
"resource": {
"billablePeriod": {
"end": "2003-03-04T12:31:28-05:00",
"start": "2003-03-04T12:01:28-05:00"
},
"id": "02a37210-e9af-4c01-a118-0651cfa0d408",
"information": [
{
"category": {
"coding": [
{
"code": "info",
"system": "http://hl7.org/fhir/claiminformationcategory"
}
]
},
"sequence": 1,
"valueReference": {
"reference": "Immunization/bbef024e-36d3-4157-8994-229e26a26788"
}
}
],
"item": [
{
"encounter": [
{
"reference": "Encounter/1eea8843-1bd6-4676-b0cd-b386a565660c"
}
],
"sequence": 1
},
{
"informationLinkId": [
1
],
"net": {
"code": "USD",
"system": "urn:iso:std:iso:4217",
"value": 140.52
},
"sequence": 2
},
{
"net": {
"code": "USD",
"system": "urn:iso:std:iso:4217",
"value": 584.35
},
"procedureLinkId": [
1
],
"sequence": 3,
"service": {
"coding": [
{
"code": "428191000124101",
"system": "http://snomed.info/sct",
"version": "v1"
}
]
}
}
],
"meta": {
"lastUpdated": "2019-04-09T12:04:03.461052+00:00",
"versionId": "MTU1NDgxMTQ0MzQ2MTA1MjAwMA"
},
"organization": {
"reference": "Organization/fea46cf5-78cb-45ba-a53c-1889a8b8ee75"
},
"patient": {
"reference": "Patient/0b3ede79-49be-42b4-961e-a0e99e52b473"
},
"procedure": [
{
"procedureReference": {
"reference": "Procedure/fbdca0d1-fc7f-43cc-9452-86b831d46ae0"
},
"sequence": 1
}
],
"resourceType": "Claim",
"status": "active",
"total": {
"code": "USD",
"system": "urn:iso:std:iso:4217",
"value": 849.87
},
"use": "complete"
}
},
{
"resource": {
"billablePeriod": {
"end": "1995-08-15T13:16:28-04:00",
"start": "1995-08-15T13:01:28-04:00"
},
"id": "03137beb-28f5-44af-af31-fb4749ca8534",
"item": [
{
"encounter": [
{
"reference": "Encounter/c4c77f57-0b5f-4c3e-8a2b-66d1190f51cb"
}
],
"sequence": 1
}
],
"meta": {
"lastUpdated": "2019-04-09T12:04:02.389735+00:00",
"versionId": "MTU1NDgxMTQ0MjM4OTczNTAwMA"
},
"organization": {
"reference": "Organization/fea46cf5-78cb-45ba-a53c-1889a8b8ee75"
},
"patient": {
"reference": "Patient/0b3ede79-49be-42b4-961e-a0e99e52b473"
},
"resourceType": "Claim",
"status": "active",
"total": {
"code": "USD",
"system": "urn:iso:std:iso:4217",
"value": 125
},
"use": "complete"
}
},
{
"resource": {
"billablePeriod": {
"end": "2003-01-27T12:16:28-05:00",
"start": "2003-01-27T12:01:28-05:00"
},
"id": "0650594e-f9f1-468e-b1c9-4fff390dc9e9",
"item": [
{
"encounter": [
{
"reference": "Encounter/cb78356f-1126-4f79-ad0a-7cfff5df4cda"
}
],
"sequence": 1
}
],
"meta": {
"lastUpdated": "2019-04-09T12:04:03.446437+00:00",
"versionId": "MTU1NDgxMTQ0MzQ0NjQzNzAwMA"
},
"organization": {
"reference": "Organization/fea46cf5-78cb-45ba-a53c-1889a8b8ee75"
},
"patient": {
"reference": "Patient/0b3ede79-49be-42b4-961e-a0e99e52b473"
},
"resourceType": "Claim",
"status": "active",
"total": {
"code": "USD",
"system": "urn:iso:std:iso:4217",
"value": 125
},
"use": "complete"
}
},
{
"resource": {
"billablePeriod": {
"end": "1999-05-18T13:16:28-04:00",
"start": "1999-05-18T13:01:28-04:00"
},
"id": "094bb710-c8fa-4720-9e32-6f9cd3ff274c",
"item": [
{
"encounter": [
{
"reference": "Encounter/0a79db40-56b8-4d3d-afee-aa0703b9c371"
}
],
"sequence": 1
}
],
"meta": {
"lastUpdated": "2019-04-09T12:04:03.444828+00:00",
"versionId": "MTU1NDgxMTQ0MzQ0NDgyODAwMA"
},
"organization": {
"reference": "Organization/fea46cf5-78cb-45ba-a53c-1889a8b8ee75"
},
"patient": {
"reference": "Patient/0b3ede79-49be-42b4-961e-a0e99e52b473"
},
"prescription": {
"reference": "MedicationRequest/24a41fc1-d706-4d13-adb9-de0debfc6a57"
},
"resourceType": "Claim",
"status": "active",
"total": {
"code": "USD",
"system": "urn:iso:std:iso:4217",
"value": 255
},
"use": "complete"
}
},
{
"resource": {
"billablePeriod": {
"end": "1998-02-03T12:31:28-05:00",
"start": "1998-02-03T12:01:28-05:00"
},
"id": "0d40fc8b-5ae9-4f3c-8a9a-b16ccab1db43",
"information": [
{
"category": {
"coding": [
{
"code": "info",
"system": "http://hl7.org/fhir/claiminformationcategory"
}
]
},
"sequence": 1,
"valueReference": {
"reference": "Immunization/a3e3f5df-ae48-4399-b4ac-ee28f99dfc7b"
}
}
],
"item": [
{
"encounter": [
{
"reference": "Encounter/bc5202fe-0320-418f-8829-0f345b2b8c1c"
}
],
"sequence": 1
},
{
"informationLinkId": [
1
],
"net": {
"code": "USD",
"system": "urn:iso:std:iso:4217",
"value": 140.52
},
"sequence": 2
},
{
"net": {
"code": "USD",
"system": "urn:iso:std:iso:4217",
"value": 810.5
},
"procedureLinkId": [
1
],
"sequence": 3,
"service": {
"coding": [
{
"code": "428191000124101",
"system": "http://snomed.info/sct",
"version": "v1"
}
]
}
}
],
"meta": {
"lastUpdated": "2019-04-09T12:04:02.411506+00:00",
"versionId": "MTU1NDgxMTQ0MjQxMTUwNjAwMA"
},
"organization": {
"reference": "Organization/fea46cf5-78cb-45ba-a53c-1889a8b8ee75"
},
"patient": {
"reference": "Patient/0b3ede79-49be-42b4-961e-a0e99e52b473"
},
"procedure": [
{
"procedureReference": {
"reference": "Procedure/705d70bf-bb48-4267-8dca-da6dea2f51c5"
},
"sequence": 1
}
],
"resourceType": "Claim",
"status": "active",
"total": {
"code": "USD",
"system": "urn:iso:std:iso:4217",
"value": 1076.02
},
"use": "complete"
}
},
{
"resource": {
"billablePeriod": {
"end": "1925-11-19T12:16:28-05:00",
"start": "1925-11-19T12:01:28-05:00"
},
"diagnosis": [
{
"diagnosisReference": {
"reference": "Condition/2fa3c99d-f2da-44a6-a22a-de63605bce59"
},
"sequence": 1
}
],
"id": "0e39b999-4daa-48c2-9b27-4b3b3a10b019",
"item": [
{
"encounter": [
{
"reference": "Encounter/b2849afc-0754-4019-94cc-772bccd21576"
}
],
"sequence": 1
},
{
"diagnosisLinkId": [
1
],
"sequence": 2
}
],
"meta": {
"lastUpdated": "2019-04-09T12:04:02.376300+00:00",
"versionId": "MTU1NDgxMTQ0MjM3NjMwMDAwMA"
},
"organization": {
"reference": "Organization/fea46cf5-78cb-45ba-a53c-1889a8b8ee75"
},
"patient": {
"reference": "Patient/0b3ede79-49be-42b4-961e-a0e99e52b473"
},
"resourceType": "Claim",
"status": "active",
"total": {
"code": "USD",
"system": "urn:iso:std:iso:4217",
"value": 125
},
"use": "complete"
}
},
{
"resource": {
"billablePeriod": {
"end": "1999-02-09T12:31:28-05:00",
"start": "1999-02-09T12:01:28-05:00"
},
"id": "17946f2e-f65c-4d24-a8b2-b54e0ce2badd",
"information": [
{
"category": {
"coding": [
{
"code": "info",
"system": "http://hl7.org/fhir/claiminformationcategory"
}
]
},
"sequence": 1,
"valueReference": {
"reference": "Immunization/34aec705-252d-4ee4-8d4a-748f2034ef5b"
}
}
],
"item": [
{
"encounter": [
{
"reference": "Encounter/c87473d8-d9fd-41e3-add3-1b8fea20b3f0"
}
],
"sequence": 1
},
{
"informationLinkId": [
1
],
"net": {
"code": "USD",
"system": "urn:iso:std:iso:4217",
"value": 140.52
},
"sequence": 2
},
{
"net": {
"code": "USD",
"system": "urn:iso:std:iso:4217",
"value": 372.98
},
"procedureLinkId": [
1
],
"sequence": 3,
"service": {
"coding": [
{
"code": "428191000124101",
"system": "http://snomed.info/sct",
"version": "v1"
}
]
}
}
],
"meta": {
"lastUpdated": "2019-04-09T12:04:03.448310+00:00",
"versionId": "MTU1NDgxMTQ0MzQ0ODMxMDAwMA"
},
"organization": {
"reference": "Organization/fea46cf5-78cb-45ba-a53c-1889a8b8ee75"
},
"patient": {
"reference": "Patient/0b3ede79-49be-42b4-961e-a0e99e52b473"
},
"procedure": [
{
"procedureReference": {
"reference": "Procedure/9f084e7c-ff24-408b-8634-2f49240402d4"
},
"sequence": 1
}
],
"resourceType": "Claim",
"status": "active",
"total": {
"code": "USD",
"system": "urn:iso:std:iso:4217",
"value": 638.5
},
"use": "complete"
}
},
{
"resource": {
"billablePeriod": {
"end": "2001-02-20T12:16:28-05:00",
"start": "2001-02-20T12:01:28-05:00"
},
"id": "1da28e66-42c0-422b-a3f2-7f8588b22ca9",
"information": [
{
"category": {
"coding": [
{
"code": "info",
"system": "http://hl7.org/fhir/claiminformationcategory"
}
]
},
"sequence": 1,
"valueReference": {
"reference": "Immunization/e02defc2-e578-476e-a524-9fba1c7992ec"
}
}
],
"item": [
{
"encounter": [
{
"reference": "Encounter/2557a148-bd62-44f1-9ef9-7a3506e6860d"
}
],
"sequence": 1
},
{
"informationLinkId": [
1
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