DAFNI Workflow Enhancements

.github/workflows/publish-to-dafni.yaml

@@ -38,14 +38,25 @@ jobs:
         with:
           python-version: '3.10'
 
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install causal-testing-framework -e .[dev]
+          python -m pip install dafni-cli
+
+      - name: Run tests before uploading
+        id: tests
+        run: |
+          python -m pytest ./dafni/tests 
+
       - name: Build the container
+        if: steps.tests.outcome == 'success'
         run: |
           docker build -t ctf:${{ env.VERSION }} -f ./dafni/Dockerfile .
           docker save ctf:${{ env.VERSION }} | gzip > ctf-dafni-${{ env.VERSION }}.tar.gz
 
-      - name: Install DAFNI-CLI and log in
+      - name: Log into DAFNI
         run: |
-          python -m pip install dafni-cli
           dafni login
 
       - name: Upload to DAFNI

dafni/Dockerfile

@@ -8,26 +8,23 @@ ENV PYTHONDONTWRITEBYTECODE=1
 ## from crashing without emitting any logs due to buffering
 ENV PYTHONUNBUFFERED=1
 
-#Label maintainer
+# Label maintainer
 LABEL maintainer="Dr. Farhad Allian - The University of Sheffield"
 
 # Create a folder for the source code/outputs
 RUN mkdir -p ./causal_testing
 RUN mkdir -p ./data/outputs
 
-# Copy the source code and test files from build into the container
-COPY --chown=nobody  ../causal_testing ./causal_testing
-COPY --chown=nobody ./dafni/main_dafni.py ./
+# Copy the source code from local root and test files from build into the container
+COPY --chown=nobody  ./causal_testing ./causal_testing
+COPY --chown=nobody ./dafni/src/ ./src
 COPY --chown=nobody ./dafni/data/inputs ./data/inputs
 
 # Install core dependencies using PyPi
 RUN pip install causal-testing-framework --no-cache-dir
 
-#For local testing purposes
-ENV VARIABLES_PATH=./data/inputs/variables.json \
-    CAUSAL_TESTS=./data/inputs/causal_tests.json \
-    DATA_PATH=./data/inputs/runtime_data.csv \
-    DAG_PATH=./data/inputs/dag.dot
+# Set the PYTHONPATH environment variable to include the /src directory
+ENV PYTHONPATH="/src:${PYTHONPATH}"
 
 # Define the entrypoint/commands
-CMD python main_dafni.py --variables_path $VARIABLES_PATH --dag_path $DAG_PATH --data_path $DATA_PATH --tests_path $CAUSAL_TESTS
+CMD python -m main_dafni --dag_path $DAG_PATH --data_path $DATA_PATH --tests_path $TESTS_PATH

dafni/README.md

@@ -10,8 +10,8 @@ to upload the framework onto [DAFNI](https://www.dafni.ac.uk).
 - `data` contains two sub-folders (the structure is important for DAFNI).
   - `inputs` is a folder that contains the input files that are (separately) uploaded to DAFNI.
     - `causal_tests.json` is a JSON file that contains the causal tests.
-    - `variables.json` is a JSON file that contains the variables and constraints to be used.
-    - `dag.dot` is a dot file that contains the directed acyclc graph (dag) file.
+    - `dag.dot` is a dot file that contains the directed acyclc graph (dag) file, 
+       including the variables (and constraints if necessary) as node attributes.
     - `runtime_data.csv` is a csv file that contains the runtime data.
 
   - `outputs` is a folder where the `causal_tests_results.json` output file is created.

dafni/data/inputs/dag.dot

@@ -1,7 +1,12 @@
 digraph CausalDAG {
     rankdir=LR;
-    "vaccine" -> "cum_vaccinations";
-    "vaccine" -> "cum_vaccinated";
-    "vaccine" -> "cum_infections";
-    "max_doses";
+    vaccine [datatype="int", typestring="input"];
+    cum_vaccinations [datatype="int", typestring="output"];
+    cum_vaccinated [datatype="int", typestring="output"];
+    cum_infections [datatype="int", typestring="output"];
+    max_doses [datatype="int", typestring="output"];
+    vaccine -> cum_vaccinations;
+    vaccine -> cum_vaccinated;
+    vaccine -> cum_infections;
+    max_doses;
 }

dafni/data/outputs/causal_tests_results.json

@@ -18,9 +18,15 @@
       "outcome": "cum_vaccinations",
       "adjustment_set": [],
       "effect_measure": "coefficient",
-      "effect_estimate": 252628.1066666667,
-      "ci_low": 252271.33332001517,
-      "ci_high": 252984.8800133182
+      "effect_estimate": {
+        "max_doses": 252628.1066666667
+      },
+      "ci_low": [
+        252271.33332001517
+      ],
+      "ci_high": [
+        252984.8800133182
+      ]
     }
   },
   {
@@ -42,9 +48,15 @@
       "outcome": "cum_vaccinated",
       "adjustment_set": [],
       "effect_measure": "coefficient",
-      "effect_estimate": 213111.93333333335,
-      "ci_low": 212755.15056812647,
-      "ci_high": 213468.71609854023
+      "effect_estimate": {
+        "max_doses": 213111.93333333335
+      },
+      "ci_low": [
+        212755.15056812647
+      ],
+      "ci_high": [
+        213468.71609854023
+      ]
     }
   },
   {
@@ -66,9 +78,15 @@
       "outcome": "cum_infections",
       "adjustment_set": [],
       "effect_measure": "coefficient",
-      "effect_estimate": 2666.3066666666664,
-      "ci_low": 2619.972040648758,
-      "ci_high": 2712.6412926845746
+      "effect_estimate": {
+        "max_doses": 2666.3066666666664
+      },
+      "ci_low": [
+        2619.972040648758
+      ],
+      "ci_high": [
+        2712.6412926845746
+      ]
     }
   },
   {
@@ -89,9 +107,15 @@
       "outcome": "cum_vaccinations",
       "adjustment_set": [],
       "effect_measure": "coefficient",
-      "effect_estimate": 315785.1333333332,
-      "ci_low": 315339.1666500188,
-      "ci_high": 316231.1000166476
+      "effect_estimate": {
+        "vaccine": 315785.1333333332
+      },
+      "ci_low": [
+        315339.1666500188
+      ],
+      "ci_high": [
+        316231.1000166476
+      ]
     }
   },
   {
@@ -112,9 +136,15 @@
       "outcome": "cum_vaccinated",
       "adjustment_set": [],
       "effect_measure": "coefficient",
-      "effect_estimate": 266389.91666666657,
-      "ci_low": 265943.93821015797,
-      "ci_high": 266835.89512317517
+      "effect_estimate": {
+        "vaccine": 266389.91666666657
+      },
+      "ci_low": [
+        265943.93821015797
+      ],
+      "ci_high": [
+        266835.89512317517
+      ]
     }
   },
   {
@@ -135,9 +165,15 @@
       "outcome": "cum_infections",
       "adjustment_set": [],
       "effect_measure": "coefficient",
-      "effect_estimate": 3332.883333333332,
-      "ci_low": 3274.9650508109467,
-      "ci_high": 3390.801615855717
+      "effect_estimate": {
+        "vaccine": 3332.883333333332
+      },
+      "ci_low": [
+        3274.9650508109467
+      ],
+      "ci_high": [
+        3390.801615855717
+      ]
     }
   },
   {
@@ -159,9 +195,15 @@
       "outcome": "cum_vaccinated",
       "adjustment_set": [],
       "effect_measure": "coefficient",
-      "effect_estimate": 0.9998656401531605,
-      "ci_low": 0.9929245394499968,
-      "ci_high": 1.0068067408563242
+      "effect_estimate": {
+        "cum_vaccinations": 0.9998656401531605
+      },
+      "ci_low": [
+        0.9929245394499968
+      ],
+      "ci_high": [
+        1.0068067408563242
+      ]
     }
   },
   {
@@ -183,9 +225,15 @@
       "outcome": "cum_infections",
       "adjustment_set": [],
       "effect_measure": "coefficient",
-      "effect_estimate": -0.006416682407515084,
-      "ci_low": -0.05663010083886572,
-      "ci_high": 0.043796736023835554
+      "effect_estimate": {
+        "cum_vaccinations": -0.006416682407515084
+      },
+      "ci_low": [
+        -0.05663010083886572
+      ],
+      "ci_high": [
+        0.043796736023835554
+      ]
     }
   },
   {
@@ -207,9 +255,15 @@
       "outcome": "cum_infections",
       "adjustment_set": [],
       "effect_measure": "coefficient",
-      "effect_estimate": -0.006176900588291234,
-      "ci_low": -0.05639349612119588,
-      "ci_high": 0.04403969494461341
+      "effect_estimate": {
+        "cum_vaccinated": -0.006176900588291234
+      },
+      "ci_low": [
+        -0.05639349612119588
+      ],
+      "ci_high": [
+        0.04403969494461341
+      ]
     }
   }
 ]

dafni/docker-compose.yaml

@@ -3,8 +3,8 @@ services:
   causal-testing-framework:
     build:
       context: ../
-      dockerfile: ./dafni/Dockerfile
+      dockerfile: dafni/Dockerfile
     env_file:
       - .env
     volumes:
-      - .:/usr/src/app
+      - ./dafni:/usr/src/

dafni/model_definition.yaml

@@ -49,14 +49,6 @@ spec:
         path: inputs/
         required: true
 
-      - name: Variables
-        description: >
-          A .JSON file containing the input variables to be used
-        default:
-          - 02e755c8-952b-461a-a914-4f4ffbe2edf1
-        path: inputs/
-        required: true
-
   outputs:
       datasets:
         - name: causal_test_results.json