initial commit

.gitignore

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+# These are some examples of commonly ignored file patterns.
+# You should customize this list as applicable to your project.
+# Learn more about .gitignore:
+#     https://www.atlassian.com/git/tutorials/saving-changes/gitignore
+
+# Node artifact files
+node_modules/
+dist/
+
+# Compiled Java class files
+*.class
+
+# Compiled Python bytecode
+*.py[cod]
+
+# Log files
+*.log
+
+# Package files
+*.jar
+
+# Maven
+target/
+
+# JetBrains IDE
+.idea/
+
+# Unit test reports
+TEST*.xml
+
+# Generated by MacOS
+.DS_Store
+
+# Generated by Windows
+Thumbs.db
+
+# Applications
+*.app
+*.exe
+*.war
+
+# Large media files
+*.mp4
+*.tiff
+*.avi
+*.flv
+*.mov
+*.wmv
+
+# env
+.env
+
+
+

app.py

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+import gradio as gr
+import requests
+import json
+from send_email import send_email
+import os
+from dotenv import load_dotenv
+
+
+def request_email_form(req_email, req_reason, req_message):
+    # Check if all required fields are filled and the conditions are met
+    if not req_email or not req_reason or not req_message:
+        return "**Please fill in all required fields.**"
+    if "@" not in req_email or "." not in req_email:
+        return "**Please enter a valid email.**"
+
+    send_email(req_reason, req_email, req_message)
+
+    return "**Your email has been submitted successfully! We will get back to you shortly!**"
+
+
+def request_meddra_encode_form(req_reported_term, req_version, req_terms_checkbox):
+    # Check if all required fields are filled and the conditions are met
+    if not req_reported_term:
+        return "**Please enter a medical term.**"
+    if not req_version:
+        return "**Please select a valid ICD version.**"
+    if not req_terms_checkbox:
+        return "**You need to agree to Safeterm terms of use.**"
+    load_dotenv()
+
+    req_apikey = os.getenv("SAFETERM_API_KEY")
+
+    encode_output = encode_caller(req_apikey, req_reported_term, req_version)
+    return encode_output
+
+
+def encode_caller(apikey, reported_terms, icd_version):
+    url = os.getenv("SAFETERM_ENCODE_URL")
+    reported_terms_list = [reported_terms.strip()]  # Ensure it's a list of strings
+
+    payload = json.dumps({
+        "reported_terms": reported_terms_list,
+        "version": int(icd_version),
+        "medical_dictionary": "icd-11"
+    })
+
+    headers = {
+        'Content-Type': 'application/json',
+        'Authorization': f'Bearer {apikey}'
+    }
+
+    response = requests.post(url, headers=headers, data=payload)
+    data = response.json()
+
+    if "detail" in data:
+        return data["detail"]
+
+    results = []
+
+    for term_data in data.get('responses', []):
+        reported_term = term_data.get('reported_term', 'Term missing')
+        encoded_term_data = term_data.get('encoded_term')
+
+        llt_term = ''
+        pt_term = ''
+        llt_id = ''
+        pt_id = ''
+        alt_pt_term = []
+        result = f"Reported Term:\t {reported_term}\n-------------------------\n"
+
+        if isinstance(encoded_term_data, dict) and encoded_term_data:
+            report = encoded_term_data.get('report', ' ')
+            icd_id = encoded_term_data.get('icd_code', 'no_result')
+            icd_term = encoded_term_data.get('icd_term', 'no_result')
+            icd_parent_id = encoded_term_data.get('icd_parent_code', 'no_result')
+            icd_parent_term = encoded_term_data.get('icd_parent_term', 'no_result')
+            alt_icd_terms = encoded_term_data.get('alternative_icd_terms', [])
+
+            result += f"ICD code:\t\t\t\t {icd_term} [{icd_id}]\nIcd term:\t\t\t\t\t {icd_parent_term} [{icd_parent_id}]\n"
+
+            if alt_icd_terms:
+                result += "\nAlternative ICD Parent Terms:\n"
+                for term in alt_icd_terms:
+                    result += f"\t\t\t\t\t\t\t{term}\n"
+
+            result += f"{report}\n-------------------------\n"
+
+        result += f"Status: {term_data['status']}"
+        # if detected_language:  # Check if detected_language is not null and add to result
+        #     result += f"\nDetected Language: {detected_language}"
+        results.append(result)
+
+    # Add the API messages at the end.
+    api_message = data.get("messages", "No API message available")
+    api_message = "OK" if api_message is None else api_message
+    results.append(f"API Message: {api_message}")
+
+    return "\n".join(results)
+
+
+# Create Gradio interface with improved styling
+with gr.Blocks() as demo:
+    gr.Markdown("### Safeterm: Translate Medical Narratives into Standardized Dictionaries")
+    desc_text = gr.HTML("""
+        <div style="line-height: 1.6; padding: 10px;">
+            <p>Navigate through the tabs to discover the various features of Safeterm:</p>
+            <ul>
+                <li>Multilanguage encoding of medical verbatims in MedDRA</li>
+                <li>Extract medical information from narrative by type</li>
+                <li>Verify existing MedDRA encodings and upgrade terms to latest version</li>
+            </ul>
+        </div>
+    """)
+
+    with gr.Row():
+        with gr.Tab("ICD Encoder"):
+            # Multi-column layout for MedDRA Encoder tab
+            with gr.Row():
+                # Column 1: Inputs
+                with gr.Column():
+                    intro_text = gr.HTML("""
+                                            Encode a medical verbatim into ICD. <br>
+                                            A ICD parent term is reported along with a few optional alternatives. <br>
+                                            After encoding, the matching term can be verified using the verify tab. <br>
+                                         """)
+                    encode_reported_terms = gr.Dropdown(
+                        ["While walking across the street the patient was hit by a motor vehicle",
+                         "Pijn in derde vinger",
+                         "Mientras cruzaba la calle, el paciente fue golpeado por un vehículo motorizado.",
+                         "a bigg Migrein W1th 0Ra", "lower left limb varices", "basse pression sanguine"],
+                        label="Medical term",
+                        info="Enter your medical term here or choose from presets.",
+                        allow_custom_value=True
+                    )
+
+                    version_list = ["2023"]
+
+                    # Set the only version as the default value for the dropdown.
+                    encode_version = gr.Dropdown(choices=version_list, label="MedDRA Version", value=version_list[0])
+
+                    terms_text = gr.HTML("""
+                         I agree to the Safeterm <a href=https://www.proddis.com/pdf/Proddis_Terms_of_Use.pdf>Terms of Use</a>.
+                         I consent to the storage of my personal data for training and communication purposes.
+                     """)
+                    terms_checkbox = gr.Checkbox(label="I agree.")
+
+                    submit_button = gr.Button("Encode into ICD")
+
+                # Column 2: Output and Terms of use
+                with gr.Column():
+                    api_response_encode = gr.Textbox(label="Safeterm Output")
+
+                    submit_button.click(request_meddra_encode_form,
+                                        inputs=[encode_reported_terms, encode_version, terms_checkbox],
+                                        outputs=api_response_encode)
+
+        with gr.Tab("Contact us"):
+            # Multi-column layout for Contact us tab
+            with gr.Row():
+                with gr.Column():
+                    gr.Markdown("### Safeterm Features:")
+                    gr.Markdown(
+                        "- ICD encode provides ICD-10 and ICD-11 encoding support for epidemiological tracking, health management"
+                        "and legacy projects.")
+                    gr.Markdown(
+                        "- It simplifies tasks with its API-driven approach. It is easy to integrate within existing "
+                        "e-clinical systems.")
+                    gr.Markdown(
+                        "- Subscription plans are adaptable to your needs, with a monthly fee and limited cost per "
+                        "encoding.")
+                    gr.Markdown("- Our team is available if you have any question.")
+                    gr.Markdown("- Interested? Contact us for inquiries!")
+
+                with gr.Column():
+                    gr.Markdown("### Contact us:")
+                    email = gr.Textbox(label="Email", placeholder="Enter your professional email address...")
+                    request_list = ["API Key", "Commercial inquiry", "Encoding support", "Partnership", "Others"]
+                    reason = gr.Dropdown(choices=request_list, label="Request", value=request_list[0])
+                    message = gr.Textbox(label="Message", placeholder="Enter your message...")
+
+                    feedback_textbox = gr.Markdown(label="Feedback")
+
+                    api_key_button = gr.Button("Submit your message")
+                    api_key_button.click(request_email_form,
+                                         inputs=[email, reason, message],
+                                         outputs=feedback_textbox)
+
+    with gr.Row():
+        gr.Markdown("Safeterm v 0224 (c) Proddis - 2024. Contact us at [email protected]")
+
+demo.launch()

send_email.py

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+import os
+from dotenv import load_dotenv
+import msal
+import requests
+
+
+def send_email(reason, email, message) -> None:
+    body = f"""
+        Safeterm_demo v1123 (Huggingface)
+
+        Subject: {reason}
+
+        Message: {message}
+
+        Contact Information: {email}
+        """
+
+    load_dotenv()
+
+    client_id = os.getenv("CLIENT_ID")
+    client_secret = os.getenv("CLIENT_SECRET")
+    tenant_id = os.getenv("TENANT_ID")
+    authority = f"https://login.microsoftonline.com/{tenant_id}"
+    sender = os.getenv("MAIL_SENDER")
+    receiver = os.getenv("MAIL_RECIPIENT")
+    cc_receiver = os.getenv("CC_RECIPIENT")
+
+    app = msal.ConfidentialClientApplication(
+        client_id=client_id,
+        client_credential=client_secret,
+        authority=authority)
+
+    scopes = ["https://graph.microsoft.com/.default"]
+
+    result = app.acquire_token_silent(scopes, account=None)
+
+    if not result:
+        print("No suitable token exists in cache. Let's get a new one from Azure Active Directory.")
+        result = app.acquire_token_for_client(scopes=scopes)
+
+    if "access_token" in result:
+        endpoint = f'https://graph.microsoft.com/v1.0/users/{sender}/sendMail'
+        email_msg = {
+            'Message': {
+                'Subject': reason,
+                'Body': {
+                    'ContentType': 'Text',
+                    'Content': body
+                },
+                'ToRecipients': [{'EmailAddress': {'Address': receiver}}],
+                'CcRecipients': [{'EmailAddress': {'Address': cc_receiver}}]  # Added CcRecipients here
+            },
+            'SaveToSentItems': 'true'
+        }
+
+        r = requests.post(endpoint, headers={'Authorization': 'Bearer ' + result['access_token']}, json=email_msg)
+
+        if r.ok:
+            print('Sent email successfully')
+        else:
+            print(r.json())
+    else:
+        print(result.get("error"))
+        print(result.get("error_description"))
+        print(result.get("correlation_id"))