Inferno mCODE Edition performs API conformance testing for the Minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU1 Implementation Guide.
Inferno mCODE Edition is a pre-configured and customized version of the open source Inferno FHIR testing tool, and only contains tests and functionality relevant to the mCODE Implementation Guide. Users interested in extending or reusing this open testing capability to meet their own needs are encouraged to visit the Inferno GitHub repository.
Docker is the recommended installation method for Windows devices and can also be used on Linux and MacOS hosts.
- Install Docker for the host platform as well as the docker-compose tool (which may be included in the distribution, as is the case for Windows and MacOS).
- Download the latest release of the
infernoproject to your local computer on a directory of your choice. - Open a terminal in the directory where the project was downloaded (above).
- Run the command
docker-compose upto start the server. This will automatically build the Docker image and launch both the ruby server (using unicorn) and an NGINX web server. - Navigate to http://localhost:4567 to find the running application.
If the docker image gets out of sync with the underlying system, such as when
new dependencies are added to the application, you need to run docker-compose up --build to rebuild the containers.
Check out the Troubleshooting Documentation for help.
Inferno can installed and run locally on your machine. Install the following dependencies first:
And run the following commands from the terminal:
# MacOS or Linux
git clone https://github.com/onc-healthit/inferno
cd inferno
bundle install
bundle exec rackupInferno can then be accessed at http://localhost:4567 in a web browser.
If you would like to use a different port it can be specified when calling
rackup. For example, the following command would host Inferno on port 3000:
rackup -p 3000Inferno can also be deployed onto a server to test many different instances of the FHIR Servers by multiple users. Test results are kept private at a unique, unguessable URI that can be saved for future reference or shared.
Deployment on a remote server can be done by using a modified form of the Docker containers provided (see above) or by direct installation on the remote host.
Please see the file deployment-configuration.md for details.
In order to validate terminologies, Inferno must be loaded with files generated from the Unified Medical Language System (UMLS). The UMLS is distributed by the National Library of Medicine (NLM) and requires an account to access.
Inferno provides some rake tasks which may make this process easier, as well as a Dockerfile and docker-compose file that will create the validators in a self-contained environment.
Prerequisites:
- A UMLS account
- A working Docker toolchain, which has been assigned at least 10GB of RAM (The Metathesaurus step requires 8GB of RAM for the Java process)
- A copy of the Inferno repository, which contains the required Docker and Ruby files
You can prebuild the terminology docker container by running the following command:
docker-compose -f terminology_compose.yml buildOnce the container is built, you can run the terminology creation task by using the following commands, in order:
export UMLS_USERNAME=<your UMLS username>
export UMLS_PASSWORD=<your UMLS password>
docker-compose -f terminology_compose.yml upThis will run the terminology creation steps in order, using the UMLS credentials supplied. These tasks may take several hours. If the creation task is cancelled in progress and restarted, it will restart after the last completed step. Intermediate files are saved to tmp/terminology in the Inferno repository that the Docker Compose job is run from, and the validators are saved to resources/terminology/validators/bloom, where Inferno can use them for validation.
If this Docker-based method does not work based on your architecture, manual setup and creation of the terminology validators is documented on this wiki page
Some material in the UMLS Metathesaurus is from copyrighted sources of the respective copyright holders. Users of the UMLS Metathesaurus are solely responsible for compliance with any copyright, patent or trademark restrictions and are referred to the copyright, patent or trademark notices appearing in the original sources, all of which are hereby incorporated by reference.
Bodenreider O. The Unified Medical Language System (UMLS): integrating biomedical terminology.
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D267-70. doi: 10.1093/nar/gkh061.
PubMed PMID: 14681409; PubMed Central PMCID: PMC308795.
While it is recommended that users install Inferno locally, a reference implementation of Inferno is hosted at https://inferno.healthit.gov
Users that would like to try out Inferno before installing locally can use that reference implementation, but should be forewarned that the database will be periodically refreshed and there is no guarantee that previous test runs will be available in perpetuity.
Inferno has been tested on the latest versions of Chrome, Firefox, Safari, and Edge. Internet Explorer is not supported at this time.
To generate the inferno test sequences run the following command:
bundle exec rake "inferno:generate[mcode]"Inferno contains a robust set of self-tests to ensure that the test clients conform to the specification and performs as intended. To run these tests, execute the following command:
bundle exec rake testTests are written to be easily understood, even by those who aren't familiar with Ruby. They can be viewed directly in this repository.
Tests contain metadata that provide additional details and traceability to
standards. The active tests and related metadata can be exported into CSV
format and saved to a file named testlist.csv with the following command:
bundle exec rake inferno:tests_to_csvArguments can be provided to the task in order to export a specific set of tests or to specify the output file.
bundle exec rake inferno:tests_to_csv[onc,all_tests.csv]To just choose the module and use the default groups and filename:
bundle exec rake inferno:tests_to_csv[onc]
Inferno provides two methods of running tests via the command line: by directly providing the sequences or running automated scripts
Note: This feature is still in development and we are looking for feedback on features and improvements in ways it can be used
Testing sequences can be run from the command line via a rake task which takes the sequence (or sequences) to be run and server url as arguments:
bundle exec rake inferno:execute[https://my-server.org/data,onc,ArgonautConformance]For more complicated testing where passing arguments is unwieldy, Inferno
provides the ability to use a script containing parameters to drive test
execution. The provided example_script.json shows an example of this script
and how it can be used. The execute_batch task runs the script:
bundle exec rake inferno:execute_batch[script.json]Inferno also provides a generate_script rake task which prompts the user for
a series of inputs which are then used to generate a script. The user is
expected to provide a url for the FHIR Server to be tested and the module name
from which sequences will be pulled.
bundle exec rake inferno:generate_script[https://my-server.org/data,onc]- For
DynamicRegistrationusers must provide instructions similar to that provided inexample_script.jsonto automate the webdriver. - The
confidential_clientfield is a boolean and must be provided astrueorfalse
Instructions and examples are available in the Continuous Integration Section of the Wiki.
The Inferno development team can be reached by email at inferno@groups.mitre.org. Inferno also has a dedicated HL7 FHIR chat channel.
Copyright 2020 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.