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S4S FHIR Image Broker

The broker requires a WADO RS Image source and an introspection server for testing. You can provide these yourself, or use the test setups here:

Set up a dcm4chee image archive for testing

A dockerized dcm4chee is used for testing. Setting it up involves three containers. I found that running each container in a separate terminal window and leaving the "-d" parameter off allowed me to see logs readily.

  1. dcm4che/slapd-dcm4chee

Ref: https://hub.docker.com/r/dcm4che/slapd-dcm4chee/

docker run --name slapd \
   -p 389:389 \
   -v /etc/localtime:/etc/localtime \
   -v /var/local/dcm4chee-arc/ldap:/var/lib/ldap \
   -v /var/local/dcm4chee-arc/slapd.d:/etc/ldap/slapd.d \
   dcm4che/slapd-dcm4chee:2.4.44-10.5
  1. dcm4che/postgres-dcm4chee

Ref: https://hub.docker.com/r/dcm4che/postgres-dcm4chee/

docker run --name postgres \
   -p 5432:5432 \
   -v /etc/localtime:/etc/localtime \
   -e POSTGRES_DB=pacsdb \
   -e POSTGRES_USER=pacs\
   -e POSTGRES_PASSWORD=pacs \
   -v /var/local/dcm4chee-arc/db:/var/lib/postgresql/data \
   dcm4che/postgres-dcm4chee:9.6-10
  1. dcm4che/dcm4chee-arc-psql

Ref: https://hub.docker.com/r/dcm4che/dcm4chee-arc-psql/

I used the non-secured version, tag 5.10.5, ignored the option to use Elasticsearch, and moved the Wildfly port to 9090.

docker run --name dcm4chee-arc \
   -p 9090:8080 \
   -p 9990:9990 \
   -p 11112:11112 \
   -p 2575:2575 \
   -v /var/local/dcm4chee-arc/wildfly:/opt/wildfly/standalone \
   -v /var/local/dcm4chee-arc/storage:/storage \
   --link slapd:ldap \
   --link postgres:db \
   dcm4che/dcm4chee-arc-psql:5.10.5

The reference page gives more details, but this setup provides a dcm4chee server with:

Load test images into dcm4chee server

There is a docker image which contains dicom test images which can be loaded into the test archive. At present it contains one set of images, named "smart-1288992", which contains an anonymized Chest CR. It can be run as follows:

docker run \
   -e DEST_PACS="DCM4CHEE@<your host>:11112" \
   -e IMAGE_SET="smart-1288992" \
    rsna/load-images

using information for your own test PACS archive and the name of the image set you want to load. The above environment values are the defaults. Note: It is important to put the actual IP address of the PACS archive, not "localhost", even if that is the case.

The "smart-1288992" data set image has these tags:

  • (0x0008,0x0016) SOP Class UID = 1.2.840.10008.5.1.4.1.1.1
  • (0x0008,0x0018) SOPInstanceUID = 1.3.6.1.4.1.14519.5.2.1.6279.6001.270617793.1.1
  • (0x0008,0x0020) StudyDate = 20000101
  • (0x0008,0x0030) StudyTime = empty
  • (0x0008,0x0050) AccessionNumber = 2819497684894126
  • (0x0010,0x0030) PatientBirthDate = 19251223
  • (0x0010,0x0020) PatientID = smart-1288992
  • (0x0012,0x0062) PatientIdentityRemoved = YES
  • (0x0010,0x0010) PatientName = Adams^Daniel
  • (0x0020,0x000d) StudyInstanceUID = 1.3.6.1.4.1.14519.5.2.1.6279.6001.270617793
  • (0x0020,0x000e) SeriesInstanceUID = 1.3.6.1.4.1.14519.5.2.1.6279.6001.270617793

Run RSNA DICOM-RS Broker

docker run \
    -p 4567:4567 \
    -p 11122:11112 \
    -e QIDO_REMOTE_AE="DCM4CHEE" \
    -e QIDO_REMOTE_HOST="<your host>" \
    -e QIDO_REMOTE_PORT="11112" \
    -e QIDO_LOCAL_AE="QIDO-TESTING" \
    -e WADO_REMOTE_AE="DCM4CHEE" \
    -e WADO_REMOTE_HOST="<your host>" \
    -e WADO_REMOTE_PORT="11112"  \
    -e WADO_LOCAL_AE="WADO-TESTING" \
    -e SCP_LOCAL_AE="PACS-SCP" \
    -e SCP_CACHE_DIR_PATH=/dcmrs-broker/cache \
    rsna/dcmrs-broker

Note: The AE titles do not have to be set up in the dcm4che3e archive. However, it is important to use the actual IP address for the remote host. Do not use "localhost" or "127.0.0.1", even if the containers are on the same system.

Add the PACS SCP Application entity to the dcm4chee LDAP server

There is a docker image which will add an application entity to the LDAP server. Run it using:

docker run \
   -e AE_TITLE="PACS-SCP" \
   -e DEVICE_NAME="DCM-BROKER-SCP" \
   -e DEVICE_HOST="<host SCP is on>" \
   -e DEVICE_PORT="11122" \
   -e LDAP_HOST="<ldap server host>" \
   -e LDAP_PORT="389" \
   rsna/load-ldap

Note: If you are using the dcm4chee archive console, you will have to reload (menu>Control>Reload), to see the change.

Run introspection service

There is a docker image which will run the introspection service for testing. Run it using: Clone the Introspection Service application from github:

docker run \
   -p 9004:5000 \
   rsna/introspection-service

This brings up an introspection endpoint at: http://localhost:9004/api/introspect which handles tokens by requests to: https://portal.demo.syncfor.science/api/fhir.

run the S4S RSNA Edge server test database

There is a docker image which will run the S4S RSNA Edge server test database testing. Run it using (for example):

docker run --name rsnadb \
   -p 5433:5432 \
   -v /etc/localtime:/etc/localtime \
   -e POSTGRES_DB=rsnadb \
   -e POSTGRES_USER=edge \
   -e POSTGRES_PASSWORD=psword \
   rsna/s4s-edgeserverdb

run the s4s FHIR Broker service

There is a docker image which will run the S4S FHIR Broker service for testing. Run it using (for example):

docker run -p 8080:8080 \
   -e DICOM_RS_BROKER_QIDO_URL="http://<dicomrs broker host>:4567/qido-rs" \
   -e DICOM_RS_BROKER_WADO_URL="http://<dicomrs broker host>:4567/wado-rs" \
   -e INTROSPECTION_SERVICE_URL="http://<introspection service host>:9004/api/introspect" \
   -e IMAGE_ARCHIVE_WADO_RS_URL="http://<dcm4chee arc host>:9090/dcm4chee-arc/aets/DCM4CHEE/rs" \
   -e PID_LOOKUP_DB_URL="jdbc:derby:directory:/data/pidLookup;create=true" \
   -e DIAGNOSTIC_REPORT_DB_URL="jdbc:postgresql://localhost:5433/rsnadb" \
   -e DIAGNOSTIC_REPORT_PERFORMER_REFERENCE="Organization/57" \
   rsna/s4s-fhir-broker

This brings up the FHIR broker service at: http://localhost:8080/baseDstu3. The environment variables point to the dicom rs broker and the introspection service.

Running tests

Use the Restful client of your choice to run tests.

Test ImageStudy query

GET http://localhost:8080/baseDstu3/ImagingStudy?patient=smart-1288992
Authorization: Bearer authorizationTokenGoesHere

Here is one example using curl:

curl -H "Authorization: Bearer X3BreWfdBTWo4vwcQvxTF4pnHF6UPG" \
     -H "Accept: application/json" \
	  http://localhost:8080/baseDstu3/ImagingStudy?patient=smart-1288992

GET Test WADO Study request (include Authorization header for authentication)

GET http://localhost:8080/baseDstu3/studies/1.3.6.1.4.1.14519.5.2.1.6279.6001.270617793
Authorization: Bearer authorizationTokenGoesHere

Here is a curl example to retrieve the image data. Note the use of a log file to record the header response

curl -H "Authorization: Bearer X3BreWfdBTWo4vwcQvxTF4pnHF6UPG" \
     -H "Accept: multipart/related; type=\"application/dicom\"" \
     -D study-retrieve.log \
	  http://localhost:8080/baseDstu3/studies/1.3.6.1.4.1.14519.5.2.1.6279.6001.270617793

Test DiagnosticReport query

GET http://localhost:8080/baseDstu3/DiagnosticReport?patient=smart-1288992
Accept-Charset: utf-8
Accept-Encoding: deflate, sdch
Accept: Application/json
Authorization: Bearer X3BreWfdBTWo4vwcQvxTF4pnHF6UPG

Here is a curl example to retrieve diagnostic report resource(s).

curl -H "Accept-Charset: utf-8" \
     -H "Accept-Encoding: deflate, sdch" \
     -H "Accept: Application/json" \
     -H "Authorization: Bearer X3BreWfdBTWo4vwcQvxTF4pnHF6UPG" \
     http://localhost:8080/baseDstu3/DiagnosticReport?patient=smart-1288992

Notes:

  1. When running tests, a successful ImageStudy query for a patient must be run before running study requests for studies for that patient, so that the fhir broker will 'known' the patient MRN. If this is not done the study request will result in an Authorization failure.
  2. Running a study request will result in an http 503 response code if the image(s) are not already in the cache - the archive will be loading them into the cache. This is normal behavior. Rerun the request after the images have had time to load and it will should return the images.

To Test introspection service directly

POST http://localhost:9004/api/introspect
Content-Type: application/x-www-form-urlencoded
Accept-Charset: utf-8
and, in the request body:
?token=authorizationTokenGoesHere$patient=smart-1288992

How to generate an authentication token for testing

  1. Navigate to https://tests.demo.syncfor.science

s4s-1

  1. Select Vendor: SMART-EHR-STU3
  2. Click on "Show more options"

s4s-1

  1. Next to "Tags", click on "None"
  2. then click on "patient-demographics"

s4s-1

  1. Click on the "Run tests" button.
  2. A "Tests complete!" dialog will display; click on its "x" to dismiss it.
  3. On the right panel, click on "Feature: Patient demographics". A "Method URL" table with two http GET requests should appear.

s4s-1

  1. Click on the first URL, which should read:
https://portal-stu3.demo.syncfor.science/api/fhir/Patient/smart-1288992
  1. A new tab or window should open, showing an http Request and Response beginning:
Request
-------
GET https://portal.demo.syncfor.science/api/fhir/Patient/smart-1288992
Accept-Encoding: deflate,sdch
User-Agent: python-requests/2.10.0
Accept: application/json
Connection: keep-alive
Authorization: Bearer Y4ljzndNNkvayLME2HphxBJTs08SUo
  1. Copy the bearer token to your http Request Authorization header. Not sure how long the tokens remain valid.