Download FHIR Patient IDs

Before we can query a FHIR server for patients, we need to know what patients exist on the server. This tool will query a FHIR server and extract patient IDs from that server. By default ALL patient IDs are downloaded for a given server. A parameter can be passed to this tool that will limit the number of patients downloaded. This is often useful for testing, validation, demos, etc.

Prerequisites

Before running the Download Patient IDs Tool you will need the following

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 downloaded from here. For this example we are using Miter's SyntheticMass FHIR Patient Server. 
# ---
# DOWNLOAD STUFF
# ---

httpClientAuthenticatorClass=org.nachc.tools.fhirtoomop.fhir.util.server.auth.impl.HeaderTokenAuthenticator

fhirPatientServerUrl=https://syntheticmass.mitre.org/v1/fhir

headerTokenAuthenticatorApiId=<your_value_goes_here>
headerTokenAuthenticatorApiKey=<your_value_goes_here>
headerTokenAuthenticatorSecret=<your_value_goes_here>
headerTokenAuthenticatorUrl=https://syntheticmass.mitre.org/oauth2/accesstoken
downloadPatientIdDir=D:\\NACHC\\SYNTHEA\\TEST\\patient-ids-test

Running the Application

The Download Patient IDs Tool can be run from the Standalone application as shown below by entering the command shown below. The second screen shot shows what the application should look like when it has finished. This tool will accept a second parameter. The second parameter is the maximum number of patients to download. In this example we are limiting the number of patient ids to 1000. This max is only approximate. Because of the way some FHIR servers implement paging the actual max number of patients down loaded can be slightly different. 

fhir-to-omop.bat ids 1000

Results

The results of running the application is the creation of a series of files in the directory specified in the app.properties file. In this example we used "D:\NACHC\SYNTHEA\TEST\patient-ids-test" as the directory. After running the application the directory looks like this:
Each of the files in this directory contains 100 patient IDs. These IDs can then be used to query the FHIR Patient Server for information about that patient. This includes the /Patient[id]/$everything resource. The contents of synthea-patient-ids-1.txt is shown below. This file can be downloaded here. 

6f7acde5-db81-4361-82cf-886893a3280c
728b270d-d7de-4143-82fe-d3ccd92cebe4
5acc8bb4-2d14-4461-a560-228d96459cc3
78b28fcd-c455-4da1-81c5-ba94c1f3f5b6
933c5ad6-11aa-4228-a5ae-72f075aa4681
d819cfa2-c349-4920-94ab-dc244da43c50
0cd47600-e7d5-426a-9320-b1d817e8a73a
7e38c1b6-0b23-486c-b497-08902390a31d
b24efd46-fae3-47e5-97a5-a1545da053fe
f6d2bf6d-5c91-40b6-ba88-9bcbca6ebfbd
db252ad1-7748-4b86-bac7-61184decb0ae
69639ae1-8cf3-4112-9097-6ad93a5997dc
f9501d43-81e0-4c40-8306-9f9cb1769b3d
570cbad5-a727-4720-9a97-b46088196cd7
580625f2-cb5f-4d81-87d2-0f1e66862969
167d8dd6-7ecd-4ad5-8e7a-63a6d6f077da
b83daa26-3eea-41a0-be57-74beb42f6504
05306f3b-c7c3-4f9a-a441-87feb2ec6a66
871c83f5-5674-450b-a3b6-be3bbcf8a095
995a1c0f-b6bc-4d16-b6b0-b8a6597c6e1d
b6ab974a-0cd3-4a45-9c8f-0543b79a007d
b2360a02-ec1b-4463-b5e8-0996f7b6a4ac
615c67c5-5ac0-4538-84ae-bd8d4e19dc5d
81471da3-aaab-458a-bae3-c71525fe7415
6c1c89d0-27fc-4289-ba21-ed79a200ebe6
789fce0b-d5a5-4d8b-9fa9-070ccfb7d474
326299d1-23d8-46bf-8266-e58efe60c0ea
c0c6a188-d377-413e-8dc7-6ded539c96d9
155835fd-7f1d-414b-94d2-41d44adcf250
ef25ddf1-615e-43d5-b539-6af200ae7da4
fde02360-8b61-40c1-b5c9-e686627d8207
d41ef714-15e0-44d3-afe3-3be47689f873
89645076-a956-485d-9de0-bef62b10daa6
0d28e708-12c0-4282-ab1f-831599e61792
c3e58176-8e84-4721-a6b9-0d7eea88d109
03a27898-d209-48aa-a2ec-a03f6fdaf1fe
47fc4fcb-2862-406c-9931-929fc1892ca2
d02546e8-aa0a-4b24-97a4-b6147a599478
fd71330e-ebd7-4e86-a43c-39ea210caf5c
c784b280-c6e9-4205-975e-b89057e23a2e
326c4936-086b-4967-9970-4db1d7a169c9
57091303-30fb-4bcc-a4e6-1f76dc7993a7
245c115e-eeba-4d79-88fb-9ff7029cc662
2cd701bf-b781-493c-ab3c-30a8603015df
a29211ce-0014-43f5-a103-6368fa664749
a28cfad3-f1da-421e-91e2-0f16f1d7253d
5294faca-cba1-4606-a079-23539a3e26e2
78226741-3095-42a9-87e2-9a18604edb7d
bbb2ec77-c5cf-408f-aab8-3f1496334617
770a1931-b6d8-485e-8da8-9256f3208c27
aaae7cd0-c632-4b28-8aa7-c5ae41e4753d
fe8a77cd-facf-471d-97ad-6a7a7cf6561d
4fdb156f-e87a-4f69-bca2-d8d61e595ce9
ef59d34d-e132-4bca-9246-d2efc1df73da
dcf240d2-ad7d-4bd2-8952-cebd9ebc6003
41d0b3e0-264a-41d7-9370-84a1521ec505
81fdf5bf-e03f-4662-a727-6804a7870021
9b84f3aa-1ac8-4a74-b07b-f5853a365494
ed011cc9-cf28-4234-bc62-e96ad02d06bf
fc0b3924-0ca8-424f-81b0-08f7f37b6e9b
4dafccb6-7548-43f4-b394-39170367f1ef
772fe3d7-c13c-4f24-bf0f-fc714cbf98b1
9958eb49-ff3b-4797-b720-52a32d0fc7d0
9e87ed0a-d759-4407-a0dc-c629fc102c89
a490a01b-4d69-4498-8ef3-caa8ed5ea3ba
3ee3e7f0-bfeb-476b-abc2-eb6517d2d0b2
9bcf15aa-c5cc-4d5d-b16b-325eef407f9f
d82dd97f-b76e-4d49-bae7-38f3d3bef190
46b6a07a-2e13-4460-85a5-cc9c63747c73
8e43e552-17d9-406d-9a5b-250c3c33ce83
818cf547-5821-46eb-b2f2-14e2a46fccbb
67cf4015-f9fc-4e22-bc90-b40e17442039
9ee5abef-b073-4926-8cf1-6b0c7caf31ac
67fc74cc-7e9b-4eb8-9ad6-47dfe73121e1
dbef14f5-f48e-458e-9a2a-5479db87db38
ffdaff70-25f4-419b-a55e-f718a8c3efc3
b93f0e35-b955-49f2-807d-187788137edf
142149fa-b73b-4466-9eb8-d88af9eb5448
80c54830-4add-48fd-b9f6-a76020b0570a
474a5860-bbac-4101-8890-10ad29351845
07605caa-9b62-4c90-a939-5fb630cab028
b6e5a598-87a8-43f7-9677-dc51ca76b72a
e7190189-9c85-497d-a7b5-3972ca3c0ecb
a91c0655-0f40-4253-864e-2f9a77d37667
673c9383-9b88-4a28-a4d0-4c6df1190690
4323f5df-289a-4aa5-8795-b048f8c8fdf8
46f99b9f-ab88-40d6-a3a2-24adec933bb3
6064dd35-f93a-4fba-902b-2f92191554c3
7e866b75-a36d-4531-b1e3-57aae634ae04
6a49d9e8-6c8b-4326-80dc-bb54856b07f2
6f526a1e-eae2-4583-bb15-856d7b2d9289
f7b6050c-2986-4175-8026-688ca4062543
088828a0-7ef6-43a5-aa4e-0c6292e59389
7da4a2c2-144f-46a6-bba0-78c384efae03
fda8df83-a8d9-4c5c-bc5b-e7b294889414
22b0e94a-c395-4c38-ab65-7b34084e15dc
d59c197a-0115-47c0-ad90-01799d32e01e
ea39dc3c-1e38-484f-b6db-c03d5e96347a
0e0d36f4-6653-4ae0-b83d-2530f90deff5
52e68ec6-3662-4d7a-b612-dff264d7f071