Pdf gen button

.github/workflows/deploy-to-cloud-run.yml

@@ -41,3 +41,10 @@ jobs:
           --platform managed \
           --region us-central1 \
           --allow-unauthenticated
+
+    - name: Notify Slack on failure
+      if: failure()
+      run: |
+        curl -X POST -H 'Content-type: application/json' \
+        --data '{"text": "Deployment failed for branch ${{ github.ref }}. Here are the details:\n\n Branch: ${{ github.ref }}\n Commit: ${{ github.sha }}\n Author: ${{ github.actor }}\n"}' \
+        ${{ secrets.SLACK_WEBHOOK_URL }}

.python-version

@@ -0,0 +1 @@
+3.10.2

UI/README.md

@@ -0,0 +1,26 @@
+## Pipeline Overview
+
+The CI/CD pipeline automates the deployment of the Streamlit application to Google Cloud Platform (GCP). Here's an overview of the steps:
+
+1. **Trigger on Push**:
+   - The pipeline is triggered when changes are pushed to the `UI/` directory in the `feature/UI-deploy`, `dev`, or `main` branches.
+
+2. **Authenticate with Google Cloud**:
+   - The pipeline uses a service account key stored in GitHub Secrets to authenticate with GCP.
+
+3. **Build and Push Docker Image**:
+   - The pipeline builds a Docker image for the Streamlit application using the `Dockerfile` in the `UI/` directory.
+   - The Docker image is tagged and pushed to **Google Artifact Registry** under the repository `us-docker.pkg.dev/medscript-437117/gcr.io/streamlit-app`.
+
+4. **Deploy to Cloud Run**:
+   - The Docker image is deployed to **Cloud Run**, which provides a managed, scalable environment to host the Streamlit app.
+   - The application is exposed to the internet and configured to allow unauthenticated access.
+
+This pipeline ensures that any updates to the `UI/` directory in the specified branches are automatically deployed to the production environment.
+
+### Slack Alert Notification Integration
+
+We’ve integrated Slack alert notifications into the deployment pipeline to keep developers informed about deployment failures. If a deployment fails, an alert is sent to a specified Slack channel with details including the branch, commit and author. Slack notifications are triggered through a webhook and provide real-time information about the deployment status. Screenshot of sample notification is below:
+<img width="1280" alt="Screenshot 2024-12-03 at 6 37 47 PM" src="https://github.com/user-attachments/assets/ca66cb1f-8871-4695-89b6-52db59ccdbe9">
+
+

UI/generate_patient_report_pdf.py

@@ -0,0 +1,99 @@
+import json
+from fpdf import FPDF
+
+class PatientReportPDF(FPDF):
+    def header(self):
+        # Add a title
+        self.set_font('Times', 'B', 16)
+        self.cell(0, 10, 'Patient report', border=False, ln=1, align='C')
+        self.set_line_width(0.5)
+        self.line(10, self.get_y(), 200, self.get_y()) 
+        self.ln(5)
+
+    def footer(self):
+        # Add a footer with page number
+        self.set_y(-15)
+        self.set_font('Times', 'I', 10)
+        self.cell(0, 10, f'{self.page_no()}', align='C')
+
+    def draw_patient_id(self, value):
+        # Write the patient ID
+        self.set_font("Times", "I", 12)
+        self.cell(0, 10, f"Patient ID: {value}", 0, 1)
+        self.ln(5)
+
+    def draw_patient_record(self, value):
+        # Write the patient record
+        self.set_font("Times", "B", 12)
+        self.cell(0, 10, "Patient Record", 0, 1)
+        self.ln(2)
+
+        self.set_font("Times", "", 10)
+        for record_key, record_value in value.items():
+            self.multi_cell(0, 8, u"{0}: {1}".format(record_key, record_value))
+        self.ln(5)
+
+    def draw_possible_diagnosis(self, value):
+        # Write possible diagnosis
+        self.set_font("Times", "B", 11)
+        self.cell(0, 8, "Possible Diagnosis:", 0, 1)
+
+        # Write primary diagnosis
+        self.set_font("Times", "B", 10)
+        self.cell(0, 8, "Primary Diagnosis:", 0, 1)
+        self.set_font("Times", "", 10)
+        self.multi_cell(0, 8, "- {0}".format(value['Primary Diagnosis']))
+
+        # Write Differential Diagnosis
+        self.set_font("Times", "B", 11)
+        self.cell(0,8,"Differential Diagnosis", 0, 1)
+        self.set_font("Times", "", 10)
+
+        # Loop through the list and write to pdf
+        for index, item in enumerate(value['Differential Diagnoses']):
+            self.cell(5)
+            self.multi_cell(0, 10, f"{index}. {item}")
+
+    def draw_diagnosis_report(self, value):
+        # Write diagnosis report
+        self.set_font("Times", "B", 12)
+        self.cell(0, 10, "Diagnosis Report", 0, 1)
+        self.ln(2)
+
+        self.set_font("Times", "", 10)
+        for report_key, report_value in value.items():
+            # Write the possible diagnosis
+            if report_key == 'Possible Diagnoses':
+                self.draw_possible_diagnosis(report_value)
+
+            # Write all other elements in the possible diagnosis
+            else:
+                self.set_font("Times", "B", 10)
+                self.cell(0, 8, report_key, 0, 1)
+                self.set_font("Times", "", 10)
+
+                self.multi_cell(0, 8, f"{report_value}".encode().decode('unicode-escape'))
+            self.ln(3)
+
+def create_pdf():
+    # Create an instance of the PDF class
+    pdf = PatientReportPDF()
+    pdf.add_page()
+
+    # Set font and add some content
+    # pdf.set_font('Times', '', 12)
+    # pdf.multi_cell(0, 10, "This is a sample PDF generated using Python and the FPDF library. "
+    #                       "You can add multiple lines of text, and the text will automatically wrap.")
+
+    with open('../models/test_records_with_med42.json') as file:
+        data = json.load(file)[1]
+
+        pdf.draw_patient_id(data['patientId'])
+
+        pdf.draw_patient_record(data['patientRecord'])
+
+        pdf.draw_diagnosis_report(data['diagnosisReport'])
+
+        print(f"Report created succesfully.")
+
+    return pdf.output(dest="S").encode("latin1")

UI/patient_form.py

@@ -1,4 +1,5 @@
 import streamlit as st
+from generate_patient_report_pdf import create_pdf
 
 st.title("Welcome to MedScript")
 # Streamlit application
@@ -60,7 +61,17 @@
 
 # Button to view diagnostic report
 if st.button("View Diagnostic Report"):
-    st.write("Diagnostic report is not yet available. Please contact your healthcare provider.")
+    try:
+        pdf = create_pdf()
+        st.download_button(
+            label="Download PDF",
+            data=pdf,
+            file_name="diagnostic_report.pdf",
+            mime="application/pdf"
+        )
+    except Exception as e:
+        print(f"An error occured: {e}")
+    # st.write("Diagnostic report is not yet available. Please contact your healthcare provider.")
 
 st.subheader("Diagnosis")
 primary_diagnosis = st.text_area("Primary Diagnosis", placeholder="Enter the primary diagnosis...", height=150)

UI/requirements.txt

@@ -1 +1,2 @@
+fpdf=1.7.2
 streamlit==1.24.0

requirements.txt

@@ -73,6 +73,7 @@ filelock==3.16.1
 Flask==2.2.5
 flatten-dict==0.4.2
 flufl.lock==8.1.0
+fpdf==1.7.2
 fonttools==4.54.1
 frozenlist==1.5.0
 fsspec==2024.9.0