https://github.com/gyorilab/trialsynth
TrialSynth interprets and integrates clinical trials data from multiple registries in a computable form
https://github.com/gyorilab/trialsynth
Last synced: 2 months ago
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TrialSynth interprets and integrates clinical trials data from multiple registries in a computable form
- Host: GitHub
- URL: https://github.com/gyorilab/trialsynth
- Owner: gyorilab
- License: bsd-2-clause
- Created: 2024-04-17T17:36:33.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2024-10-01T17:04:16.000Z (8 months ago)
- Last Synced: 2024-11-17T12:19:50.381Z (6 months ago)
- Language: Python
- Size: 301 KB
- Stars: 0
- Watchers: 3
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Trial Synth
Interpretation and integration of clinical trials data from multiple registries in a computable form
## Adding registries and processors
Getting data of each registry happens via a corresponding `Processor` object, its components, and relevant methods and functions.
Users create a `Processor` by composition; some require different work than others.
Some common components include:
- Fetcher: get raw data from a source (e.g. a REST API)
- Transformer: change the data into a desired format for downstream use
- Storer: save the data to some location(s)
- Validator: check the data for quality
- Configuration: management of processor behaviors
- CLI: entrypoint for downstream use
A user can add a registry and `Processor` by test-driven development. A pattern for doing this looks like:
- Get a sample response from the API and save it to a file
- Write the test for API stability
- This can detect unexpected API behavior (e.g. changes or outages)
- Add the file to the imposter to use as a stubbed response
- Add a new port for the stubbed service to the imposter and compose files
- Write the test for the processor's end-to-end behaviors
- The input is the sample response
- Write the components and functions to make the test pass
- Set the `url` environment variable for the `Processor` to the stub's port
## Installation
Run the following to install this repository's package in editable mode:
```bash
$ git clone https://github.com/gyorilab/trialsynth
$ cd trialsynth
$ pip install -e
```
## Local run
Users can run all system components on their computers via the compose stack, wrapped by a shell script:
```bash
./run_e2e.sh
```
## Testing
Users can run all the suite of full system tests on their computers via the compose stack, wrapped by a shell script:
```bash
./test_e2e.sh
```
## References
[Test-driven development](https://tidyfirst.substack.com/p/canon-tdd)
[Mountebank](https://www.mbtest.org/)