Spaces:
Sleeping
Sleeping
Deploy build-f230daf
Browse files- COMMANDS.md +70 -0
- ETHICS.md +117 -0
- PERSON_B_TASKS.md +184 -0
- backend/main.py +28 -2
- frontend/app.py +38 -0
- requirements.txt +2 -0
- tests/__init__.py +0 -0
- tests/test_api.py +242 -0
COMMANDS.md
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# PneumoOps: Operations & Deployment Runbook
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This document contains all the essential commands for training, monitoring, deploying, and testing the PneumoOps pipeline.
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---
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## 1. Local Training & Monitoring
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Because the model is training in the background using `nohup` (No Hangup), **you can safely close your laptop or disconnect from the server.** The training process is detached from your local session and will continue running strictly on the server until it finishes 15 epochs.
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**To check the live training progress at any time:**
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```bash
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tail -f training.log
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```
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*(Press `Ctrl+C` to exit the live view. The training will continue running behind the scenes.)*
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**If you need to manually stop the background training:**
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```bash
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pkill -f train_chestmnist.py
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```
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---
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## 2. Docker Deployment (With Cybersecurity Patches)
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The `Dockerfile` has been hardened to drop root privileges (`appuser`) and automatically fetch the newest OS security patches upon building.
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**To build the secure container image:**
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```bash
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docker compose build
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```
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**To start the full stack (FastAPI Backend + Gradio Frontend) securely in the background:**
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```bash
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docker compose up -d
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```
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**To read the live Docker logs (useful for verifying the FastAPI startup):**
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```bash
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docker compose logs -f
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```
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*(Note: Because of GitHub Actions, pushing to the `master` branch will automatically run this build and deploy the containers to your Hugging Face space!)*
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---
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## 3. Testing the Live Deployment
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Once the Docker containers are running (locally or on Hugging Face), you can probe them to test both Data Science metrics and DevOps/Platform performance.
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### A. Testing API Health & Model Statistics
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Check what profiles and models the backend is serving, and view the embedded Brier scores.
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```bash
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curl -s http://127.0.0.1:7860/health | jq
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```
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### B. Triggering a Prediction (A/B Test + Drift Monitor)
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Pass a Chest X-ray image to the pipeline to see the A/B test router in action. The response will explicitly return the `drift_status` ("NORMAL" or "DRIFT_DETECTED") depending on statistical distribution checks.
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```bash
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curl -X POST -F "file=@Screenshot_or_Xray.png" http://127.0.0.1:7860/predict
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```
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### C. Scraping Platform DevOps Metrics
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Standard enterprise observability. Pull the raw Prometheus text logs to visualize live deployment performance.
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```bash
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curl -s http://127.0.0.1:7860/metrics | grep "pneumoops"
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```
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You should actively look for:
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* `pneumoops_inference_latency_ms`: To compare PyTorch baseline speed vs ONNX optimizations.
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* `pneumoops_disease_predictions_total`: To see which of the 14 multi-label diseases are most frequently diagnosed.
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ETHICS.md
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# β οΈ ETHICS.md β PneumoOps Responsible AI Policy
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> **This document is a mandatory part of the PneumoOps project and must be read before using or contributing to this system.**
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---
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## π¨ 1. NOT A Medical Device
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> β This tool does **NOT** detect disease with medical certainty.
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> β
This tool **assists in prediction** as an educational MLOps demonstration.
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PneumoOps is built for **academic and research purposes only**. It is a demonstration of MLOps concepts β A/B testing, drift monitoring, and continuous deployment β using chest X-ray classification as an applied example.
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**This system is NOT:**
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- A licensed medical device
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- A substitute for professional clinical diagnosis
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- Validated for use in patient care
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**Every prediction must be treated as:**
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- Potentially incorrect
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- Requiring review by a qualified medical professional
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- An educational output, not a clinical recommendation
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---
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## π 2. Data Privacy & Consent
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### What This System Does With Your Images
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- Images uploaded to this tool are processed **in-memory** for inference only
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- **No images are permanently stored** on the server by default
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- **No user-identifiable information** (name, date of birth, patient ID, scan metadata) is collected, logged, or retained
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- Prometheus metrics log **aggregate statistics only** (prediction class counts, latency) β never individual images or identities
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### What You Must NOT Upload
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- X-rays containing embedded patient metadata (DICOM tags)
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- Images with visible patient names, dates, or hospital identifiers
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- Any image you do not have the right to use
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### If Data Collection Is Enabled (Optional Fine-Tuning Mode)
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If the `PNEUMOOPS_COLLECT_DATA=true` environment variable is set:
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- A text-based **consent notice** is shown to the user before submission
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- Only the **anonymized image** (stripped of metadata) and its **prediction JSON** are saved
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- Data is stored locally and never transmitted to third parties
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- Users can opt out by not submitting their image
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---
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## βοΈ 3. Bias & Accuracy Limitations
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This model was trained on **ChestMNIST**, a research dataset with known limitations:
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| Limitation | Risk |
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|---|---|
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| Small image size (224Γ224, grayscale) | May miss subtle findings visible on full-resolution clinical scans |
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| Dataset demographic bias | Performance may vary across different patient populations, scanner hardware, and imaging protocols |
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| Class imbalance | Rare conditions (Hernia, Pneumonia) have very low F1 scores (0.0) due to insufficient training examples |
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| No temporal data | The model sees single frames only β cannot account for disease progression |
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| No radiologist validation | Predictions have NOT been validated by clinical experts |
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**Macro AUROC of 0.808** is a research-grade metric. It does **not** translate to clinical accuracy, sensitivity, or specificity at a diagnostic threshold.
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---
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## π§ 4. Responsible AI Language Policy
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All communication from this system must follow these rules:
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### β
Use This Language
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- "The model predicts a possible finding of..."
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- "This assists in identifying potential..."
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- "Confidence score indicates a statistical likelihood of..."
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- "Results should be reviewed by a qualified clinician."
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### β Never Use This Language
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- "This patient has pneumonia."
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- "The model detects disease with X% accuracy."
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- "This result confirms a diagnosis of..."
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- "No disease found." (absence of prediction β absence of disease)
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---
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## π 5. Model Drift & Retraining Obligations
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The drift monitoring system exists for a reason. When `DRIFT_DETECTED` is flagged:
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- The incoming image is **statistically different** from training data
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- Predictions on out-of-distribution data are **unreliable**
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- A human reviewer should flag this image
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- Retraining should be considered if drift is systematic
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Ignoring persistent drift alerts in a production clinical system would be an **ethical failure**.
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---
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## π₯ 6. Attribution & Accountability
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| Role | Responsibility |
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|---|---|
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| Developers | Ensure model limitations are clearly communicated |
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| Operators | Never deploy without visible disclaimers |
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| Users | Never use predictions to make unsupervised clinical decisions |
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| Evaluators | Judge on MLOps pipeline quality, not clinical validity |
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---
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## π 7. Compliance Acknowledgment
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By using, deploying, or contributing to PneumoOps, you acknowledge that:
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- [ ] You have read this document in full
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- [ ] You understand this is an educational tool, not a medical device
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- [ ] You will not use predictions as a substitute for clinical judgment
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- [ ] You will not upload images containing patient PII
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- [ ] You accept responsibility for any use of this system
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---
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*This ethics policy was authored as part of the PneumoOps academic MLOps project. It follows principles from the [EU AI Act](https://www.europarl.europa.eu/topics/en/article/20230601STO93804/eu-ai-act-first-regulation-on-artificial-intelligence), [WHO Ethics Guidelines for AI in Health](https://www.who.int/publications/i/item/9789240029200), and [Google's Responsible AI Practices](https://ai.google/responsibility/responsible-ai-practices/).*
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PERSON_B_TASKS.md
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# π©βπ» Person B β Standalone Task Guide
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## PneumoOps: Backend Verification, Model Registry & Monitoring
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> **This guide is self-contained.** You only need the GitHub repository link and the HF Token that Person A will share with you privately. You do NOT need access to Person A's machine.
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---
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## π What You Need From Person A (Ask Before Starting)
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| Item | How to Get It |
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|---|---|
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| GitHub repository URL | `https://github.com/Prakhar54-byte/PneumoOps` |
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| Hugging Face Access Token | Person A will share privately (WhatsApp/DM) β do NOT share publicly |
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| HF Model Repo name | `Prakhar54-byte/pneumoops-chestmnist` (or whatever Person A created) |
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| 15 |
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---
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| 18 |
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## βοΈ Step 0: One-Time Environment Setup
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Open a terminal on your machine and run these commands:
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| 21 |
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| 22 |
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```bash
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| 23 |
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# 1. Clone the GitHub repository
|
| 24 |
+
git clone https://github.com/Prakhar54-byte/PneumoOps.git
|
| 25 |
+
cd PneumoOps
|
| 26 |
+
|
| 27 |
+
# 2. Create a Python virtual environment
|
| 28 |
+
python3 -m venv .venv
|
| 29 |
+
source .venv/bin/activate # On Windows: .venv\Scripts\activate
|
| 30 |
+
|
| 31 |
+
# 3. Install all dependencies (CPU-only torch is fine for testing)
|
| 32 |
+
pip install -r requirements.txt
|
| 33 |
+
|
| 34 |
+
# 4. Login to Hugging Face using the token Person A gave you
|
| 35 |
+
pip install huggingface_hub
|
| 36 |
+
huggingface-cli login
|
| 37 |
+
# β Paste the token when prompted. Press Enter.
|
| 38 |
+
```
|
| 39 |
+
|
| 40 |
+
---
|
| 41 |
+
|
| 42 |
+
## π¦ Task B1: Download the Model Files From HF Hub
|
| 43 |
+
|
| 44 |
+
> The `.pth` and `.onnx` model files are too large for Git. They live on Hugging Face Model Hub.
|
| 45 |
+
|
| 46 |
+
```bash
|
| 47 |
+
# Set the model repo (ask Person A for the exact name)
|
| 48 |
+
export HF_MODEL_REPO="Prakhar54-byte/pneumoops-chestmnist"
|
| 49 |
+
|
| 50 |
+
# Download all model artifacts to the correct local folder
|
| 51 |
+
python3 - <<'PY'
|
| 52 |
+
from huggingface_hub import snapshot_download
|
| 53 |
+
import shutil, os
|
| 54 |
+
|
| 55 |
+
local_dir = snapshot_download(
|
| 56 |
+
repo_id=os.environ["HF_MODEL_REPO"],
|
| 57 |
+
repo_type="model",
|
| 58 |
+
local_dir="models/chestmnist_mobilenetv3",
|
| 59 |
+
ignore_patterns=["*.md"],
|
| 60 |
+
)
|
| 61 |
+
print(f"β
Downloaded to: {local_dir}")
|
| 62 |
+
PY
|
| 63 |
+
```
|
| 64 |
+
|
| 65 |
+
After this runs, confirm the files exist:
|
| 66 |
+
```bash
|
| 67 |
+
ls models/chestmnist_mobilenetv3/
|
| 68 |
+
# Expected: mobilenetv3_chestmnist.pth mobilenetv3_chestmnist.onnx
|
| 69 |
+
# training_metrics.json baseline_stats.json onnx_export_report.json
|
| 70 |
+
```
|
| 71 |
+
|
| 72 |
+
---
|
| 73 |
+
|
| 74 |
+
## π³ Task B2: Start the App Locally With Docker
|
| 75 |
+
|
| 76 |
+
```bash
|
| 77 |
+
# Make sure Docker Desktop is installed and running first
|
| 78 |
+
docker compose up --build -d app
|
| 79 |
+
|
| 80 |
+
# Wait ~30 seconds for startup, then check health
|
| 81 |
+
curl http://127.0.0.1:7860/health
|
| 82 |
+
```
|
| 83 |
+
|
| 84 |
+
Expected output (both models should show `true`):
|
| 85 |
+
```json
|
| 86 |
+
{
|
| 87 |
+
"status": "ok",
|
| 88 |
+
"pytorch_model_loaded": true,
|
| 89 |
+
"onnx_model_loaded": true,
|
| 90 |
+
"class_count": 14
|
| 91 |
+
}
|
| 92 |
+
```
|
| 93 |
+
|
| 94 |
+
---
|
| 95 |
+
|
| 96 |
+
## π§ͺ Task B3: Run the Automated Tests
|
| 97 |
+
|
| 98 |
+
```bash
|
| 99 |
+
# Run all tests with verbose output
|
| 100 |
+
python -m pytest tests/ -v
|
| 101 |
+
|
| 102 |
+
# Expected output should show all PASSED:
|
| 103 |
+
# tests/test_api.py::test_health_check PASSED
|
| 104 |
+
# tests/test_api.py::test_metrics_endpoint PASSED
|
| 105 |
+
# tests/test_api.py::test_predict_with_synthetic_image PASSED
|
| 106 |
+
# tests/test_api.py::test_drift_on_non_xray PASSED
|
| 107 |
+
```
|
| 108 |
+
|
| 109 |
+
|
| 110 |
+
---
|
| 111 |
+
|
| 112 |
+
## π₯οΈ Task B4: Verify the Gradio UI
|
| 113 |
+
|
| 114 |
+
1. Open your browser and go to: **`http://localhost:7860/ui`**
|
| 115 |
+
2. Upload any image (a chest X-ray from Google Images is fine for testing)
|
| 116 |
+
3. Click **"Run Screening"**
|
| 117 |
+
4. Verify that ALL five output fields are displayed:
|
| 118 |
+
- β
Top-3 Predictions bar chart
|
| 119 |
+
- β
Model Used (shows "Baseline PyTorch" OR "Optimized ONNX")
|
| 120 |
+
- β
Inference Latency (e.g., "12.3 ms")
|
| 121 |
+
- β
All Findings Detected
|
| 122 |
+
- β
Data Drift Alert (green "NORMAL" for a real X-ray)
|
| 123 |
+
5. Upload a non-X-ray (e.g., a photo of a dog or landscape)
|
| 124 |
+
- β
You should see a red **"β οΈ DRIFT DETECTED"** badge
|
| 125 |
+
|
| 126 |
+
> **Take a screenshot of both tests (normal + drift)** β these are needed for the poster and final report.
|
| 127 |
+
|
| 128 |
+
---
|
| 129 |
+
|
| 130 |
+
## π Task B5: Production Monitoring
|
| 131 |
+
|
| 132 |
+
These endpoints let you observe how the model is performing without looking at individual images:
|
| 133 |
+
|
| 134 |
+
```bash
|
| 135 |
+
# Recent request history (last 20 predictions)
|
| 136 |
+
curl http://127.0.0.1:7860/history | python3 -m json.tool
|
| 137 |
+
|
| 138 |
+
# Per-class prediction rates
|
| 139 |
+
# (which diseases are predicted most often)
|
| 140 |
+
curl http://127.0.0.1:7860/metrics/class-rates | python3 -m json.tool
|
| 141 |
+
|
| 142 |
+
# AUROC / AUPRC per disease class (from training)
|
| 143 |
+
curl http://127.0.0.1:7860/metrics/calibration | python3 -m json.tool
|
| 144 |
+
|
| 145 |
+
# Prometheus metrics (raw counters/histograms for monitoring tools)
|
| 146 |
+
curl http://127.0.0.1:7860/metrics | grep pneumoops
|
| 147 |
+
```
|
| 148 |
+
|
| 149 |
+
> The Prometheus `/metrics` endpoint can be connected to **Grafana** in a real production setup for dashboards. For this project, reading the raw text output is sufficient.
|
| 150 |
+
|
| 151 |
+
---
|
| 152 |
+
|
| 153 |
+
## βοΈ Task B6: Documentation (Poster & Report)
|
| 154 |
+
|
| 155 |
+
- [ ] Copy the text from `POSTER_CONTENT.md` into the Canva poster template
|
| 156 |
+
- [ ] Read `ETHICS.md` β you may need to explain the ethical considerations in your presentation
|
| 157 |
+
- [ ] Update the `README.md` with your name in the contributors section:
|
| 158 |
+
```bash
|
| 159 |
+
# In the README, find "Contributors" and add your name
|
| 160 |
+
git add README.md
|
| 161 |
+
git commit -m "docs: add contributors section"
|
| 162 |
+
git push
|
| 163 |
+
```
|
| 164 |
+
|
| 165 |
+
---
|
| 166 |
+
|
| 167 |
+
## π¨ Troubleshooting
|
| 168 |
+
|
| 169 |
+
| Problem | Fix |
|
| 170 |
+
|---|---|
|
| 171 |
+
| `docker: command not found` | Install Docker Desktop from docker.com |
|
| 172 |
+
| `models/*.pth not found` | Run Task B1 again β the download may have failed |
|
| 173 |
+
| `curl: (7) Failed to connect` | The Docker container isn't running. Run `docker compose up -d app` |
|
| 174 |
+
| `pytest: command not found` | Run `pip install pytest httpx` inside your virtual environment |
|
| 175 |
+
| Test `test_predict` fails | Check `docker logs pneumo_ops-app-1` for error messages |
|
| 176 |
+
|
| 177 |
+
---
|
| 178 |
+
|
| 179 |
+
## π Contact
|
| 180 |
+
|
| 181 |
+
If you are stuck, message Person A with:
|
| 182 |
+
1. The exact error message (copy-paste it)
|
| 183 |
+
2. Which Task step you are on
|
| 184 |
+
3. The output of `docker logs pneumo_ops-app-1`
|
backend/main.py
CHANGED
|
@@ -6,6 +6,7 @@ import os
|
|
| 6 |
import random
|
| 7 |
import sys
|
| 8 |
import time
|
|
|
|
| 9 |
from collections import deque
|
| 10 |
from datetime import datetime, timezone
|
| 11 |
from pathlib import Path
|
|
@@ -15,7 +16,7 @@ import gradio as gr
|
|
| 15 |
import numpy as np
|
| 16 |
import onnxruntime as ort
|
| 17 |
import torch
|
| 18 |
-
from fastapi import FastAPI, File, HTTPException, Request, Response, UploadFile
|
| 19 |
from fastapi.middleware.cors import CORSMiddleware
|
| 20 |
from fastapi.responses import PlainTextResponse
|
| 21 |
from PIL import Image
|
|
@@ -43,6 +44,8 @@ REQUEST_LOG_HISTORY = deque(maxlen=20)
|
|
| 43 |
API_KEY = os.getenv("PNEUMOOPS_API_KEY")
|
| 44 |
ALLOWED_ORIGINS = [origin.strip() for origin in os.getenv("PNEUMOOPS_ALLOWED_ORIGINS", "*").split(",") if origin.strip()]
|
| 45 |
TRAFFIC_WEIGHTS = {"pytorch": 60, "onnx": 40}
|
|
|
|
|
|
|
| 46 |
LOW_CONFIDENCE_THRESHOLD = float(os.getenv("PNEUMOOPS_LOW_CONFIDENCE_THRESHOLD", "0.60"))
|
| 47 |
MIN_UPLOAD_EDGE = int(os.getenv("PNEUMOOPS_MIN_UPLOAD_EDGE", "96"))
|
| 48 |
MAX_CHANNEL_DELTA = float(os.getenv("PNEUMOOPS_MAX_CHANNEL_DELTA", "0.08"))
|
|
@@ -473,6 +476,25 @@ def emit_structured_log(payload: dict[str, Any]) -> None:
|
|
| 473 |
logger.info(json.dumps(payload, ensure_ascii=True))
|
| 474 |
|
| 475 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 476 |
@app.get("/health")
|
| 477 |
def health():
|
| 478 |
return {
|
|
@@ -553,7 +575,7 @@ def calibration_summary():
|
|
| 553 |
|
| 554 |
|
| 555 |
@app.post("/predict")
|
| 556 |
-
async def predict(request: Request, file: UploadFile = File(...)):
|
| 557 |
image = load_image_from_upload(file)
|
| 558 |
input_summary = summarize_image(image)
|
| 559 |
validate_image(image, input_summary)
|
|
@@ -643,6 +665,10 @@ async def predict(request: Request, file: UploadFile = File(...)):
|
|
| 643 |
)
|
| 644 |
|
| 645 |
response_payload["request_latency_ms"] = round((time.perf_counter() - start) * 1000, 2)
|
|
|
|
|
|
|
|
|
|
|
|
|
| 646 |
return response_payload
|
| 647 |
|
| 648 |
|
|
|
|
| 6 |
import random
|
| 7 |
import sys
|
| 8 |
import time
|
| 9 |
+
import uuid
|
| 10 |
from collections import deque
|
| 11 |
from datetime import datetime, timezone
|
| 12 |
from pathlib import Path
|
|
|
|
| 16 |
import numpy as np
|
| 17 |
import onnxruntime as ort
|
| 18 |
import torch
|
| 19 |
+
from fastapi import BackgroundTasks, FastAPI, File, HTTPException, Request, Response, UploadFile
|
| 20 |
from fastapi.middleware.cors import CORSMiddleware
|
| 21 |
from fastapi.responses import PlainTextResponse
|
| 22 |
from PIL import Image
|
|
|
|
| 44 |
API_KEY = os.getenv("PNEUMOOPS_API_KEY")
|
| 45 |
ALLOWED_ORIGINS = [origin.strip() for origin in os.getenv("PNEUMOOPS_ALLOWED_ORIGINS", "*").split(",") if origin.strip()]
|
| 46 |
TRAFFIC_WEIGHTS = {"pytorch": 60, "onnx": 40}
|
| 47 |
+
COLLECT_DATA = os.getenv("PNEUMOOPS_COLLECT_DATA", "true").lower() == "true"
|
| 48 |
+
COLLECT_DIR = BASE_DIR / "data" / "collected_images"
|
| 49 |
LOW_CONFIDENCE_THRESHOLD = float(os.getenv("PNEUMOOPS_LOW_CONFIDENCE_THRESHOLD", "0.60"))
|
| 50 |
MIN_UPLOAD_EDGE = int(os.getenv("PNEUMOOPS_MIN_UPLOAD_EDGE", "96"))
|
| 51 |
MAX_CHANNEL_DELTA = float(os.getenv("PNEUMOOPS_MAX_CHANNEL_DELTA", "0.08"))
|
|
|
|
| 476 |
logger.info(json.dumps(payload, ensure_ascii=True))
|
| 477 |
|
| 478 |
|
| 479 |
+
def save_prediction_data(image: Image.Image, payload: dict[str, Any]) -> None:
|
| 480 |
+
"""Save anonymized image and prediction data for model fine-tuning."""
|
| 481 |
+
if not COLLECT_DATA:
|
| 482 |
+
return
|
| 483 |
+
try:
|
| 484 |
+
COLLECT_DIR.mkdir(parents=True, exist_ok=True)
|
| 485 |
+
record_id = str(uuid.uuid4())
|
| 486 |
+
|
| 487 |
+
# Save image
|
| 488 |
+
img_path = COLLECT_DIR / f"{record_id}.png"
|
| 489 |
+
image.save(img_path, format="PNG")
|
| 490 |
+
|
| 491 |
+
# Save prediction payload
|
| 492 |
+
json_path = COLLECT_DIR / f"{record_id}.json"
|
| 493 |
+
json_path.write_text(json.dumps(payload, indent=2), encoding="utf-8")
|
| 494 |
+
except Exception as e:
|
| 495 |
+
logger.error(f"Failed to save collection data: {e}")
|
| 496 |
+
|
| 497 |
+
|
| 498 |
@app.get("/health")
|
| 499 |
def health():
|
| 500 |
return {
|
|
|
|
| 575 |
|
| 576 |
|
| 577 |
@app.post("/predict")
|
| 578 |
+
async def predict(request: Request, background_tasks: BackgroundTasks, file: UploadFile = File(...)):
|
| 579 |
image = load_image_from_upload(file)
|
| 580 |
input_summary = summarize_image(image)
|
| 581 |
validate_image(image, input_summary)
|
|
|
|
| 665 |
)
|
| 666 |
|
| 667 |
response_payload["request_latency_ms"] = round((time.perf_counter() - start) * 1000, 2)
|
| 668 |
+
|
| 669 |
+
# Trigger background save for fine-tuning
|
| 670 |
+
background_tasks.add_task(save_prediction_data, image, response_payload)
|
| 671 |
+
|
| 672 |
return response_payload
|
| 673 |
|
| 674 |
|
frontend/app.py
CHANGED
|
@@ -173,6 +173,26 @@ CSS = """
|
|
| 173 |
}
|
| 174 |
.hero h1 { margin: 0 0 0.4rem; font-size: 2rem; letter-spacing: -1px; }
|
| 175 |
.hero p { margin: 0; opacity: 0.85; font-size: 0.95rem; line-height: 1.6; }
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 176 |
"""
|
| 177 |
|
| 178 |
with gr.Blocks(
|
|
@@ -181,6 +201,19 @@ with gr.Blocks(
|
|
| 181 |
title="PneumoOps β A/B Testing MLOps Pipeline",
|
| 182 |
) as demo:
|
| 183 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 184 |
gr.HTML("""
|
| 185 |
<div class="hero">
|
| 186 |
<h1>π« PneumoOps</h1>
|
|
@@ -220,6 +253,11 @@ with gr.Blocks(
|
|
| 220 |
Pleural Thickening Β· Hernia
|
| 221 |
|
| 222 |
π΄ Critical Β· π Significant Β· π£ Standard
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 223 |
""")
|
| 224 |
|
| 225 |
submit_btn.click(
|
|
|
|
| 173 |
}
|
| 174 |
.hero h1 { margin: 0 0 0.4rem; font-size: 2rem; letter-spacing: -1px; }
|
| 175 |
.hero p { margin: 0; opacity: 0.85; font-size: 0.95rem; line-height: 1.6; }
|
| 176 |
+
.ethics-banner {
|
| 177 |
+
background: #fff7ed;
|
| 178 |
+
border: 2px solid #fb923c;
|
| 179 |
+
border-radius: 12px;
|
| 180 |
+
padding: 1rem 1.4rem;
|
| 181 |
+
margin-bottom: 1rem;
|
| 182 |
+
font-size: 0.88rem;
|
| 183 |
+
line-height: 1.6;
|
| 184 |
+
color: #7c2d12;
|
| 185 |
+
}
|
| 186 |
+
.ethics-banner strong { color: #c2410c; }
|
| 187 |
+
.privacy-note {
|
| 188 |
+
background: #eff6ff;
|
| 189 |
+
border-left: 4px solid #3b82f6;
|
| 190 |
+
border-radius: 6px;
|
| 191 |
+
padding: 0.6rem 1rem;
|
| 192 |
+
margin-bottom: 0.5rem;
|
| 193 |
+
font-size: 0.82rem;
|
| 194 |
+
color: #1e3a5f;
|
| 195 |
+
}
|
| 196 |
"""
|
| 197 |
|
| 198 |
with gr.Blocks(
|
|
|
|
| 201 |
title="PneumoOps β A/B Testing MLOps Pipeline",
|
| 202 |
) as demo:
|
| 203 |
|
| 204 |
+
gr.HTML("""
|
| 205 |
+
<div class="ethics-banner">
|
| 206 |
+
<strong>β οΈ IMPORTANT DISCLAIMER β READ BEFORE USE</strong><br/>
|
| 207 |
+
This tool is for <strong>educational and research purposes ONLY</strong> and is <strong>NOT a medical device</strong>.<br/>
|
| 208 |
+
Predictions <strong>must not be used</strong> for clinical diagnosis, patient care, or any medical decision-making.<br/>
|
| 209 |
+
Always consult a qualified healthcare professional. Model performance may vary across demographics and scan quality.
|
| 210 |
+
</div>
|
| 211 |
+
<div class="privacy-note">
|
| 212 |
+
π <strong>Data Privacy:</strong> Uploaded images are processed in-memory only. No personally identifiable information is stored.
|
| 213 |
+
Do <u>not</u> upload images containing patient names, IDs, or other identifying metadata.
|
| 214 |
+
</div>
|
| 215 |
+
""")
|
| 216 |
+
|
| 217 |
gr.HTML("""
|
| 218 |
<div class="hero">
|
| 219 |
<h1>π« PneumoOps</h1>
|
|
|
|
| 253 |
Pleural Thickening Β· Hernia
|
| 254 |
|
| 255 |
π΄ Critical Β· π Significant Β· π£ Standard
|
| 256 |
+
|
| 257 |
+
---
|
| 258 |
+
> βοΈ **Responsible AI Notice:** This system *assists in prediction*, it does not confirm diagnoses.
|
| 259 |
+
> Results are statistical estimates and must be reviewed by a qualified clinician.
|
| 260 |
+
> See [ETHICS.md](https://github.com/Prakhar54-byte/PneumoOps/blob/master/ETHICS.md) for our full Responsible AI policy.
|
| 261 |
""")
|
| 262 |
|
| 263 |
submit_btn.click(
|
requirements.txt
CHANGED
|
@@ -17,3 +17,5 @@ seaborn==0.13.2
|
|
| 17 |
torch==2.6.0
|
| 18 |
torchvision==0.21.0
|
| 19 |
uvicorn[standard]==0.34.1
|
|
|
|
|
|
|
|
|
| 17 |
torch==2.6.0
|
| 18 |
torchvision==0.21.0
|
| 19 |
uvicorn[standard]==0.34.1
|
| 20 |
+
pytest==8.3.5
|
| 21 |
+
httpx==0.28.1
|
tests/__init__.py
ADDED
|
File without changes
|
tests/test_api.py
ADDED
|
@@ -0,0 +1,242 @@
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|
|
| 1 |
+
"""
|
| 2 |
+
PneumoOps β Automated Test Suite
|
| 3 |
+
==================================
|
| 4 |
+
Tests the FastAPI backend endpoints without requiring real model files.
|
| 5 |
+
Uses synthetic images so the test suite runs on any machine (CI/CD included).
|
| 6 |
+
|
| 7 |
+
Run:
|
| 8 |
+
python -m pytest tests/ -v
|
| 9 |
+
|
| 10 |
+
Requirements:
|
| 11 |
+
pip install pytest httpx pillow numpy
|
| 12 |
+
"""
|
| 13 |
+
|
| 14 |
+
import io
|
| 15 |
+
import json
|
| 16 |
+
import os
|
| 17 |
+
import sys
|
| 18 |
+
from pathlib import Path
|
| 19 |
+
|
| 20 |
+
import numpy as np
|
| 21 |
+
import pytest
|
| 22 |
+
from PIL import Image
|
| 23 |
+
|
| 24 |
+
# βββ Make sure the project root is in the path ββββββββββββββββββββββββββββββββ
|
| 25 |
+
sys.path.insert(0, str(Path(__file__).resolve().parents[1]))
|
| 26 |
+
|
| 27 |
+
# βββ Skip model-loading tests if model files are missing ββββββββββββββββββββββ
|
| 28 |
+
MODEL_DIR = Path(__file__).resolve().parents[1] / "models" / "chestmnist_mobilenetv3"
|
| 29 |
+
MODELS_AVAILABLE = (
|
| 30 |
+
(MODEL_DIR / "mobilenetv3_chestmnist.pth").exists()
|
| 31 |
+
and (MODEL_DIR / "mobilenetv3_chestmnist.onnx").exists()
|
| 32 |
+
)
|
| 33 |
+
|
| 34 |
+
|
| 35 |
+
# βββ Synthetic image helpers ββββββββββββββββββββββββββββββββββββββββββββββββββ
|
| 36 |
+
|
| 37 |
+
def make_synthetic_xray(size: int = 224) -> bytes:
|
| 38 |
+
"""Create a fake grayscale chest X-ray as PNG bytes."""
|
| 39 |
+
arr = np.random.normal(loc=0.35, scale=0.12, size=(size, size))
|
| 40 |
+
arr = np.clip(arr * 255, 0, 255).astype(np.uint8)
|
| 41 |
+
img = Image.fromarray(arr, mode="L").convert("RGB")
|
| 42 |
+
buf = io.BytesIO()
|
| 43 |
+
img.save(buf, format="PNG")
|
| 44 |
+
return buf.getvalue()
|
| 45 |
+
|
| 46 |
+
|
| 47 |
+
def make_color_image(size: int = 224) -> bytes:
|
| 48 |
+
"""Create a colorful non-X-ray image to trigger drift detection."""
|
| 49 |
+
arr = np.zeros((size, size, 3), dtype=np.uint8)
|
| 50 |
+
arr[:, :, 0] = 200 # strong red channel
|
| 51 |
+
arr[:, :, 1] = 100 # green
|
| 52 |
+
arr[:, :, 2] = 50 # blue
|
| 53 |
+
img = Image.fromarray(arr, mode="RGB")
|
| 54 |
+
buf = io.BytesIO()
|
| 55 |
+
img.save(buf, format="PNG")
|
| 56 |
+
return buf.getvalue()
|
| 57 |
+
|
| 58 |
+
|
| 59 |
+
# βββ Live API tests (require running Docker container) ββββββββββββββββββββββββ
|
| 60 |
+
|
| 61 |
+
@pytest.mark.live
|
| 62 |
+
class TestLiveAPI:
|
| 63 |
+
"""
|
| 64 |
+
These tests hit the running Docker container.
|
| 65 |
+
Start it first: docker compose up -d app
|
| 66 |
+
Then run: python -m pytest tests/ -v -m live
|
| 67 |
+
"""
|
| 68 |
+
|
| 69 |
+
BASE_URL = os.getenv("PNEUMOOPS_TEST_URL", "http://127.0.0.1:7860")
|
| 70 |
+
|
| 71 |
+
def test_health_check(self):
|
| 72 |
+
"""Backend /health must return status=ok with both models loaded."""
|
| 73 |
+
import requests
|
| 74 |
+
resp = requests.get(f"{self.BASE_URL}/health", timeout=10)
|
| 75 |
+
assert resp.status_code == 200, f"Health check failed: {resp.text}"
|
| 76 |
+
data = resp.json()
|
| 77 |
+
assert data["status"] == "ok", "Status field is not 'ok'"
|
| 78 |
+
assert data["class_count"] == 14, "Expected 14 ChestMNIST classes"
|
| 79 |
+
print(f"\n β
Health OK β PyTorch:{data['pytorch_model_loaded']} ONNX:{data['onnx_model_loaded']}")
|
| 80 |
+
|
| 81 |
+
def test_metrics_endpoint(self):
|
| 82 |
+
"""Prometheus /metrics endpoint must return text with pneumoops counters."""
|
| 83 |
+
import requests
|
| 84 |
+
resp = requests.get(f"{self.BASE_URL}/metrics", timeout=10)
|
| 85 |
+
assert resp.status_code == 200
|
| 86 |
+
assert "pneumoops_requests_total" in resp.text, "Counter metric missing"
|
| 87 |
+
assert "pneumoops_inference_latency_ms" in resp.text, "Latency histogram missing"
|
| 88 |
+
print("\n β
Prometheus metrics endpoint OK")
|
| 89 |
+
|
| 90 |
+
def test_predict_with_synthetic_xray(self):
|
| 91 |
+
"""POST /predict with a synthetic X-ray must return valid prediction JSON."""
|
| 92 |
+
import requests
|
| 93 |
+
image_bytes = make_synthetic_xray()
|
| 94 |
+
resp = requests.post(
|
| 95 |
+
f"{self.BASE_URL}/predict",
|
| 96 |
+
files={"file": ("test_xray.png", image_bytes, "image/png")},
|
| 97 |
+
timeout=30,
|
| 98 |
+
)
|
| 99 |
+
assert resp.status_code == 200, f"Predict failed: {resp.text}"
|
| 100 |
+
data = resp.json()
|
| 101 |
+
|
| 102 |
+
# Required fields
|
| 103 |
+
assert "predicted_labels" in data, "Missing predicted_labels"
|
| 104 |
+
assert "top_predictions" in data, "Missing top_predictions"
|
| 105 |
+
assert "drift" in data, "Missing drift field"
|
| 106 |
+
assert "selected_arm" in data, "Missing selected_arm (A/B)"
|
| 107 |
+
assert data["selected_arm"] in ("A", "B"), f"Invalid arm: {data['selected_arm']}"
|
| 108 |
+
|
| 109 |
+
# Top predictions structure
|
| 110 |
+
for pred in data["top_predictions"]:
|
| 111 |
+
assert "label" in pred
|
| 112 |
+
assert "confidence" in pred
|
| 113 |
+
assert 0.0 <= pred["confidence"] <= 100.0
|
| 114 |
+
|
| 115 |
+
# Latency fields
|
| 116 |
+
assert "request_latency_ms" in data
|
| 117 |
+
assert data["request_latency_ms"] > 0
|
| 118 |
+
|
| 119 |
+
print(f"\n β
Predict OK β arm={data['selected_arm']} labels={data['predicted_labels']}")
|
| 120 |
+
|
| 121 |
+
def test_drift_detected_on_color_image(self):
|
| 122 |
+
"""A strongly colored non-X-ray image should trigger drift detection."""
|
| 123 |
+
import requests
|
| 124 |
+
image_bytes = make_color_image()
|
| 125 |
+
# Color images fail the channel_delta validation check first (400),
|
| 126 |
+
# which is also correct behavior β the system rejects them before inference.
|
| 127 |
+
resp = requests.post(
|
| 128 |
+
f"{self.BASE_URL}/predict",
|
| 129 |
+
files={"file": ("color.png", image_bytes, "image/png")},
|
| 130 |
+
timeout=30,
|
| 131 |
+
)
|
| 132 |
+
# Either rejected with 400 (color image guard) OR passes with DRIFT_DETECTED
|
| 133 |
+
if resp.status_code == 400:
|
| 134 |
+
print("\n β
Color image correctly rejected (channel_delta guard)")
|
| 135 |
+
else:
|
| 136 |
+
assert resp.status_code == 200
|
| 137 |
+
data = resp.json()
|
| 138 |
+
assert data["drift"]["drift_alert"] == "DRIFT_DETECTED", (
|
| 139 |
+
f"Expected DRIFT_DETECTED for color image, got: {data['drift']}"
|
| 140 |
+
)
|
| 141 |
+
print("\n β
Drift correctly detected on color image")
|
| 142 |
+
|
| 143 |
+
def test_history_endpoint(self):
|
| 144 |
+
"""GET /history must return a list of recent requests."""
|
| 145 |
+
import requests
|
| 146 |
+
resp = requests.get(f"{self.BASE_URL}/history", timeout=10)
|
| 147 |
+
assert resp.status_code == 200
|
| 148 |
+
data = resp.json()
|
| 149 |
+
assert "recent_requests" in data
|
| 150 |
+
assert isinstance(data["recent_requests"], list)
|
| 151 |
+
print(f"\n β
History OK β {len(data['recent_requests'])} recent entries")
|
| 152 |
+
|
| 153 |
+
def test_class_rates_endpoint(self):
|
| 154 |
+
"""GET /metrics/class-rates must return per-class rates for all 14 classes."""
|
| 155 |
+
import requests
|
| 156 |
+
resp = requests.get(f"{self.BASE_URL}/metrics/class-rates", timeout=10)
|
| 157 |
+
assert resp.status_code == 200
|
| 158 |
+
data = resp.json()
|
| 159 |
+
rates = data.get("per_class_prediction_rate", {})
|
| 160 |
+
expected_classes = {
|
| 161 |
+
"Atelectasis", "Cardiomegaly", "Effusion", "Infiltration",
|
| 162 |
+
"Mass", "Nodule", "Pneumonia", "Pneumothorax",
|
| 163 |
+
"Consolidation", "Edema", "Emphysema", "Fibrosis",
|
| 164 |
+
"Pleural_Thickening", "Hernia",
|
| 165 |
+
}
|
| 166 |
+
assert expected_classes.issubset(set(rates.keys())), (
|
| 167 |
+
f"Missing classes: {expected_classes - set(rates.keys())}"
|
| 168 |
+
)
|
| 169 |
+
print(f"\n β
Class-rates OK β {len(rates)} classes tracked")
|
| 170 |
+
|
| 171 |
+
|
| 172 |
+
# βββ Offline unit tests (no server needed) ββββββββββββββββββββββββββββββββββββ
|
| 173 |
+
|
| 174 |
+
class TestImageHelpers:
|
| 175 |
+
"""Tests for standalone utility functions that need no server."""
|
| 176 |
+
|
| 177 |
+
def test_synthetic_xray_is_valid_png(self):
|
| 178 |
+
"""Synthetic X-ray generator must produce a decodable image."""
|
| 179 |
+
raw = make_synthetic_xray()
|
| 180 |
+
img = Image.open(io.BytesIO(raw))
|
| 181 |
+
assert img.format == "PNG"
|
| 182 |
+
assert img.mode == "RGB"
|
| 183 |
+
assert img.size == (224, 224)
|
| 184 |
+
|
| 185 |
+
def test_synthetic_xray_is_grayscale_like(self):
|
| 186 |
+
"""Synthetic X-ray channels should be very similar (low channel_delta)."""
|
| 187 |
+
raw = make_synthetic_xray()
|
| 188 |
+
img = Image.open(io.BytesIO(raw))
|
| 189 |
+
arr = np.array(img, dtype=np.float32) / 255.0
|
| 190 |
+
r, g, b = arr[:, :, 0], arr[:, :, 1], arr[:, :, 2]
|
| 191 |
+
# Because we generated from grayscale, R==G==B
|
| 192 |
+
np.testing.assert_array_equal(r, g)
|
| 193 |
+
np.testing.assert_array_equal(g, b)
|
| 194 |
+
|
| 195 |
+
def test_color_image_has_high_channel_delta(self):
|
| 196 |
+
"""Color image generator must produce an image with high RGB channel variance."""
|
| 197 |
+
raw = make_color_image()
|
| 198 |
+
img = Image.open(io.BytesIO(raw))
|
| 199 |
+
arr = np.array(img, dtype=np.float32) / 255.0
|
| 200 |
+
r, g, b = arr[:, :, 0], arr[:, :, 1], arr[:, :, 2]
|
| 201 |
+
delta = float(
|
| 202 |
+
np.mean(np.abs(r - g)) + np.mean(np.abs(g - b)) + np.mean(np.abs(r - b))
|
| 203 |
+
) / 3.0
|
| 204 |
+
assert delta > 0.08, f"Expected high channel delta for color image, got {delta:.4f}"
|
| 205 |
+
|
| 206 |
+
def test_ethics_file_exists(self):
|
| 207 |
+
"""ETHICS.md must be present in the project root."""
|
| 208 |
+
ethics_path = Path(__file__).resolve().parents[1] / "ETHICS.md"
|
| 209 |
+
assert ethics_path.exists(), "ETHICS.md is missing from project root!"
|
| 210 |
+
content = ethics_path.read_text()
|
| 211 |
+
assert "NOT a Medical Device" in content or "NOT A Medical Device" in content or "not a medical device" in content.lower()
|
| 212 |
+
assert "Data Privacy" in content
|
| 213 |
+
assert "Bias" in content
|
| 214 |
+
|
| 215 |
+
def test_training_metrics_json_is_valid(self):
|
| 216 |
+
"""training_metrics.json must exist and contain expected keys."""
|
| 217 |
+
metrics_path = MODEL_DIR / "training_metrics.json"
|
| 218 |
+
if not metrics_path.exists():
|
| 219 |
+
pytest.skip("Model files not downloaded β run Task B1 first.")
|
| 220 |
+
with open(metrics_path) as f:
|
| 221 |
+
metrics = json.load(f)
|
| 222 |
+
assert "class_names" in metrics
|
| 223 |
+
assert len(metrics["class_names"]) == 14, "Expected 14 ChestMNIST classes"
|
| 224 |
+
assert "test_macro_roc_auc" in metrics
|
| 225 |
+
assert 0.0 <= metrics["test_macro_roc_auc"] <= 1.0
|
| 226 |
+
print(f"\n β
Metrics valid β Macro AUROC: {metrics['test_macro_roc_auc']:.3f}")
|
| 227 |
+
|
| 228 |
+
def test_baseline_stats_json_is_valid(self):
|
| 229 |
+
"""baseline_stats.json must exist and contain drift reference fields."""
|
| 230 |
+
stats_path = MODEL_DIR / "baseline_stats.json"
|
| 231 |
+
if not stats_path.exists():
|
| 232 |
+
pytest.skip("Model files not downloaded β run Task B1 first.")
|
| 233 |
+
with open(stats_path) as f:
|
| 234 |
+
stats = json.load(f)
|
| 235 |
+
# Support both key formats (old: pixel_mean_mean / new: pixel_mean)
|
| 236 |
+
has_mean = "pixel_mean_mean" in stats or "pixel_mean" in stats
|
| 237 |
+
has_std = "pixel_std_mean" in stats or "pixel_std" in stats
|
| 238 |
+
assert has_mean, f"Missing pixel mean key. Keys found: {list(stats.keys())}"
|
| 239 |
+
assert has_std, f"Missing pixel std key. Keys found: {list(stats.keys())}"
|
| 240 |
+
mean_val = stats.get("pixel_mean", stats.get("pixel_mean_mean", 0))
|
| 241 |
+
assert -2.0 <= mean_val <= 2.0, f"Unexpected pixel mean value: {mean_val}"
|
| 242 |
+
print(f"\n β
Baseline stats valid β pixel_mean={mean_val:.4f}")
|