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Fix: structure and files uploaded to dafni.
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‎dafni/.dockerignore

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../*
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../!causal_testing
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../!LICENSE
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./!inputs
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./!main_dafni.py
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./!main_dafni.py
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./!data/

‎dafni/.env

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#.env
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VARIABLES_PATH=./data/inputs/variables.json
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CAUSAL_TESTS=./data/inputs/causal_tests.json
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DATA_PATH=./data/inputs/runtime_data.csv
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DAG_PATH=./data/inputs/dag.dot

‎dafni/Dockerfile

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#Label maintainer
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LABEL maintainer="Dr. Farhad Allian - The University of Sheffield"
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# Copy the source code and test files from build into the container
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COPY --chown=nobody ./causal_testing /usr/src/app/
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COPY --chown=nobody ./dafni/inputs /usr/src/app/inputs/
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COPY --chown=nobody ./dafni/main_dafni.py /usr/src/app/
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# Create a folder for the source code/outputs
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RUN mkdir -p ./causal_testing
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RUN mkdir -p ./data/outputs
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# Change the working directory
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WORKDIR /usr/src/app/
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# Copy the source code and test files from build into the container
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COPY --chown=nobody ../causal_testing ./causal_testing
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COPY --chown=nobody ./dafni/main_dafni.py ./
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COPY --chown=nobody ./dafni/data/inputs ./data/inputs
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# Install core dependencies using PyPi
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RUN pip install causal-testing-framework --no-cache-dir
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# Use the necessaary environment variables for the script's inputs
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ENV VARIABLES=./inputs/variables.json \
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CAUSAL_TESTS=./inputs/causal_tests.json \
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DATA_PATH=./inputs/simulated_data.csv \
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DAG_PATH=./inputs/dag.dot
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#For local testing purposes
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ENV VARIABLES_PATH=./data/inputs/variables.json \
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CAUSAL_TESTS=./data/inputs/causal_tests.json \
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DATA_PATH=./data/inputs/runtime_data.csv \
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DAG_PATH=./data/inputs/dag.dot
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# Define the entrypoint/commands
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CMD python main_dafni.py --variables_path $VARIABLES_PATH --dag_path $DAG_PATH --data_path $DATA_PATH --tests_path $CAUSAL_TESTS

‎dafni/README.md

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# Causal Testing Framework on DAFNI
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- This directory contains the containerisation files of the causal testing framework using Docker, which is used
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to upload the framework onto [DAFNI](https://www.dafni.ac.uk).
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- It is **not** recommended to install the causal testing framework using Docker, and should only be installed
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using [PyPI](https://pypi.org/project/causal-testing-framework/).
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### Folders
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- `data` contains two sub-folders (the structure is important for DAFNI).
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- `inputs` is a folder that contains the input files that are (separately) uploaded to DAFNI.
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- `causal_tests.json` is a JSON file that contains the causal tests.
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- `variables.json` is a JSON file that contains the variables and constraints to be used.
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- `dag.dot` is a dot file that contains the directed acyclc graph (dag) file.
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- `runtime_data.csv` is a csv file that contains the runtime data.
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- `outputs` is a folder where the `causal_tests_results.json` output file is created.
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### Docker files
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- `main_dafni.py` is the entry-point to the causal testing framework that is used by Docker.
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- `model_definition.yaml` is the model metadata that is required to be uploaded to DAFNI.
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- `.env` is an example of a configuration file containing the environment variables. This is only required
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if using `docker-compose` to build the image.
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- `Dockerfile` is the main blueprint that builds the image.
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- `.dockerignore` tells the Dockerfile which files to not include in the image.
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- `docker-compose.yaml` is another method of building the image and running the container in one line.
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Note: the `.env` file that contains the environment variables for `main_dafni.py` is only used here.
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‎dafni/inputs/causal_tests.json renamed to ‎dafni/data/inputs/causal_tests.json

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‎dafni/inputs/dag.dot renamed to ‎dafni/data/inputs/dag.dot

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‎dafni/inputs/simulated_data.csv renamed to ‎dafni/data/inputs/runtime_data.csv

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‎dafni/inputs/variables.json renamed to ‎dafni/data/inputs/variables.json

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‎dafni/data/outputs/causal_tests_results.json

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[
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{
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"name": "max_doses _||_ cum_vaccinations",
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"estimate_type": "coefficient",
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"effect": "direct",
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"mutations": [
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"max_doses"
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],
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"expected_effect": {
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"cum_vaccinations": "NoEffect"
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},
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"formula": "cum_vaccinations ~ max_doses",
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"alpha": 0.05,
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"skip": false,
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"failed": true,
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"result": {
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"treatment": "max_doses",
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"outcome": "cum_vaccinations",
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"adjustment_set": [],
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"effect_measure": "coefficient",
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"effect_estimate": 252628.1066666667,
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"ci_low": 252271.33332001517,
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"ci_high": 252984.8800133182
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}
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},
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{
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"name": "max_doses _||_ cum_vaccinated",
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"estimate_type": "coefficient",
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"effect": "direct",
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"mutations": [
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"max_doses"
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],
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"expected_effect": {
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"cum_vaccinated": "NoEffect"
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},
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"formula": "cum_vaccinated ~ max_doses",
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"alpha": 0.05,
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"skip": false,
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"failed": true,
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"result": {
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"treatment": "max_doses",
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"outcome": "cum_vaccinated",
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"adjustment_set": [],
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"effect_measure": "coefficient",
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"effect_estimate": 213111.93333333335,
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"ci_low": 212755.15056812647,
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"ci_high": 213468.71609854023
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}
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},
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{
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"name": "max_doses _||_ cum_infections",
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"estimate_type": "coefficient",
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"effect": "direct",
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"mutations": [
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"max_doses"
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],
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"expected_effect": {
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"cum_infections": "NoEffect"
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},
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"formula": "cum_infections ~ max_doses",
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"alpha": 0.05,
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"skip": false,
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"failed": true,
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"result": {
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"treatment": "max_doses",
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"outcome": "cum_infections",
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"adjustment_set": [],
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"effect_measure": "coefficient",
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"effect_estimate": 2666.3066666666664,
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"ci_low": 2619.972040648758,
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"ci_high": 2712.6412926845746
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}
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},
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{
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"name": "vaccine --> cum_vaccinations",
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"estimate_type": "coefficient",
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"effect": "direct",
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"mutations": [
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"vaccine"
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],
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"expected_effect": {
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"cum_vaccinations": "SomeEffect"
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},
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"formula": "cum_vaccinations ~ vaccine",
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"skip": false,
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"failed": false,
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"result": {
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"treatment": "vaccine",
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"outcome": "cum_vaccinations",
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"adjustment_set": [],
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"effect_measure": "coefficient",
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"effect_estimate": 315785.1333333332,
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"ci_low": 315339.1666500188,
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"ci_high": 316231.1000166476
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}
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},
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{
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"name": "vaccine --> cum_vaccinated",
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"estimate_type": "coefficient",
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"effect": "direct",
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"mutations": [
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"vaccine"
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],
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"expected_effect": {
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"cum_vaccinated": "SomeEffect"
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},
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"formula": "cum_vaccinated ~ vaccine",
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"skip": false,
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"failed": false,
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"result": {
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"treatment": "vaccine",
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"outcome": "cum_vaccinated",
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"adjustment_set": [],
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"effect_measure": "coefficient",
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"effect_estimate": 266389.91666666657,
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"ci_low": 265943.93821015797,
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"ci_high": 266835.89512317517
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}
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},
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{
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"name": "vaccine --> cum_infections",
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"estimate_type": "coefficient",
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"effect": "direct",
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"mutations": [
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"vaccine"
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],
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"expected_effect": {
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"cum_infections": "SomeEffect"
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},
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"formula": "cum_infections ~ vaccine",
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"skip": false,
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"failed": false,
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"result": {
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"treatment": "vaccine",
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"outcome": "cum_infections",
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"adjustment_set": [],
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"effect_measure": "coefficient",
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"effect_estimate": 3332.883333333332,
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"ci_low": 3274.9650508109467,
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"ci_high": 3390.801615855717
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}
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},
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{
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"name": "cum_vaccinations _||_ cum_vaccinated | ['vaccine']",
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"estimate_type": "coefficient",
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"effect": "direct",
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"mutations": [
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"cum_vaccinations"
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],
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"expected_effect": {
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"cum_vaccinated": "NoEffect"
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},
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"formula": "cum_vaccinated ~ cum_vaccinations + vaccine",
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"alpha": 0.05,
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"skip": false,
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"failed": true,
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"result": {
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"treatment": "cum_vaccinations",
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"outcome": "cum_vaccinated",
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"adjustment_set": [],
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"effect_measure": "coefficient",
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"effect_estimate": 0.9998656401531605,
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"ci_low": 0.9929245394499968,
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"ci_high": 1.0068067408563242
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}
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},
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{
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"name": "cum_vaccinations _||_ cum_infections | ['vaccine']",
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"estimate_type": "coefficient",
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"effect": "direct",
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"mutations": [
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"cum_vaccinations"
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],
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"expected_effect": {
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"cum_infections": "NoEffect"
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},
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"formula": "cum_infections ~ cum_vaccinations + vaccine",
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"alpha": 0.05,
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"skip": false,
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"failed": false,
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"result": {
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"treatment": "cum_vaccinations",
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"outcome": "cum_infections",
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"adjustment_set": [],
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"effect_measure": "coefficient",
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"effect_estimate": -0.006416682407515084,
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"ci_low": -0.05663010083886572,
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"ci_high": 0.043796736023835554
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}
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},
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{
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"name": "cum_vaccinated _||_ cum_infections | ['vaccine']",
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"estimate_type": "coefficient",
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"effect": "direct",
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"mutations": [
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"cum_vaccinated"
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],
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"expected_effect": {
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"cum_infections": "NoEffect"
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},
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"formula": "cum_infections ~ cum_vaccinated + vaccine",
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"alpha": 0.05,
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"skip": false,
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"failed": false,
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"result": {
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"treatment": "cum_vaccinated",
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"outcome": "cum_infections",
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"adjustment_set": [],
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"effect_measure": "coefficient",
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"effect_estimate": -0.006176900588291234,
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"ci_low": -0.05639349612119588,
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"ci_high": 0.04403969494461341
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}
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}
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]

‎dafni/docker-compose.yaml

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- .env
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volumes:
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- .:/usr/src/app
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- ./inputs:/usr/src/app/inputs/
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- ./outputs:/usr/src/app/outputs/

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