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initial commit
Browse files- .env +0 -0
- .gitignore +54 -0
- app.py +191 -0
- send_email.py +65 -0
.env
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.gitignore
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# These are some examples of commonly ignored file patterns.
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# You should customize this list as applicable to your project.
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# Learn more about .gitignore:
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# https://www.atlassian.com/git/tutorials/saving-changes/gitignore
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# Node artifact files
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node_modules/
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dist/
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# Compiled Java class files
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*.class
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# Compiled Python bytecode
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*.py[cod]
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# Log files
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*.log
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# Package files
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*.jar
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# Maven
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target/
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# JetBrains IDE
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.idea/
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# Unit test reports
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TEST*.xml
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# Generated by MacOS
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.DS_Store
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# Generated by Windows
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Thumbs.db
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# Applications
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*.app
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*.exe
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*.war
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# Large media files
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*.mp4
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*.tiff
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*.avi
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*.flv
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*.mov
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*.wmv
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# env
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.env
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app.py
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import gradio as gr
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import requests
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import json
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from send_email import send_email
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import os
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from dotenv import load_dotenv
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def request_email_form(req_email, req_reason, req_message):
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# Check if all required fields are filled and the conditions are met
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if not req_email or not req_reason or not req_message:
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return "**Please fill in all required fields.**"
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if "@" not in req_email or "." not in req_email:
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return "**Please enter a valid email.**"
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send_email(req_reason, req_email, req_message)
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return "**Your email has been submitted successfully! We will get back to you shortly!**"
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def request_meddra_encode_form(req_reported_term, req_version, req_terms_checkbox):
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# Check if all required fields are filled and the conditions are met
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if not req_reported_term:
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return "**Please enter a medical term.**"
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if not req_version:
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return "**Please select a valid ICD version.**"
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if not req_terms_checkbox:
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return "**You need to agree to Safeterm terms of use.**"
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load_dotenv()
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req_apikey = os.getenv("SAFETERM_API_KEY")
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encode_output = encode_caller(req_apikey, req_reported_term, req_version)
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return encode_output
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def encode_caller(apikey, reported_terms, icd_version):
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url = os.getenv("SAFETERM_ENCODE_URL")
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reported_terms_list = [reported_terms.strip()] # Ensure it's a list of strings
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payload = json.dumps({
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"reported_terms": reported_terms_list,
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"version": int(icd_version),
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"medical_dictionary": "icd-11"
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})
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headers = {
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'Content-Type': 'application/json',
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'Authorization': f'Bearer {apikey}'
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}
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response = requests.post(url, headers=headers, data=payload)
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data = response.json()
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if "detail" in data:
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return data["detail"]
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results = []
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for term_data in data.get('responses', []):
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reported_term = term_data.get('reported_term', 'Term missing')
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encoded_term_data = term_data.get('encoded_term')
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llt_term = ''
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pt_term = ''
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llt_id = ''
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pt_id = ''
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alt_pt_term = []
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result = f"Reported Term:\t {reported_term}\n-------------------------\n"
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if isinstance(encoded_term_data, dict) and encoded_term_data:
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report = encoded_term_data.get('report', ' ')
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icd_id = encoded_term_data.get('icd_code', 'no_result')
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icd_term = encoded_term_data.get('icd_term', 'no_result')
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icd_parent_id = encoded_term_data.get('icd_parent_code', 'no_result')
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icd_parent_term = encoded_term_data.get('icd_parent_term', 'no_result')
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alt_icd_terms = encoded_term_data.get('alternative_icd_terms', [])
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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"
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if alt_icd_terms:
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result += "\nAlternative ICD Parent Terms:\n"
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for term in alt_icd_terms:
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result += f"\t\t\t\t\t\t\t{term}\n"
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result += f"{report}\n-------------------------\n"
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result += f"Status: {term_data['status']}"
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# if detected_language: # Check if detected_language is not null and add to result
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# result += f"\nDetected Language: {detected_language}"
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results.append(result)
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# Add the API messages at the end.
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api_message = data.get("messages", "No API message available")
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api_message = "OK" if api_message is None else api_message
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results.append(f"API Message: {api_message}")
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return "\n".join(results)
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# Create Gradio interface with improved styling
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with gr.Blocks() as demo:
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gr.Markdown("### Safeterm: Translate Medical Narratives into Standardized Dictionaries")
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desc_text = gr.HTML("""
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<div style="line-height: 1.6; padding: 10px;">
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<p>Navigate through the tabs to discover the various features of Safeterm:</p>
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<ul>
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<li>Multilanguage encoding of medical verbatims in MedDRA</li>
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<li>Extract medical information from narrative by type</li>
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<li>Verify existing MedDRA encodings and upgrade terms to latest version</li>
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</ul>
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</div>
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""")
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with gr.Row():
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with gr.Tab("ICD Encoder"):
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# Multi-column layout for MedDRA Encoder tab
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with gr.Row():
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# Column 1: Inputs
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with gr.Column():
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intro_text = gr.HTML("""
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Encode a medical verbatim into ICD. <br>
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A ICD parent term is reported along with a few optional alternatives. <br>
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After encoding, the matching term can be verified using the verify tab. <br>
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""")
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encode_reported_terms = gr.Dropdown(
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["While walking across the street the patient was hit by a motor vehicle",
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"Pijn in derde vinger",
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"Mientras cruzaba la calle, el paciente fue golpeado por un vehículo motorizado.",
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"a bigg Migrein W1th 0Ra", "lower left limb varices", "basse pression sanguine"],
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label="Medical term",
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info="Enter your medical term here or choose from presets.",
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allow_custom_value=True
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)
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version_list = ["2023"]
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# Set the only version as the default value for the dropdown.
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encode_version = gr.Dropdown(choices=version_list, label="MedDRA Version", value=version_list[0])
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terms_text = gr.HTML("""
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I agree to the Safeterm <a href=https://www.proddis.com/pdf/Proddis_Terms_of_Use.pdf>Terms of Use</a>.
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I consent to the storage of my personal data for training and communication purposes.
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""")
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terms_checkbox = gr.Checkbox(label="I agree.")
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submit_button = gr.Button("Encode into ICD")
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# Column 2: Output and Terms of use
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with gr.Column():
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api_response_encode = gr.Textbox(label="Safeterm Output")
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submit_button.click(request_meddra_encode_form,
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inputs=[encode_reported_terms, encode_version, terms_checkbox],
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outputs=api_response_encode)
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with gr.Tab("Contact us"):
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# Multi-column layout for Contact us tab
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with gr.Row():
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with gr.Column():
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gr.Markdown("### Safeterm Features:")
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gr.Markdown(
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"- ICD encode provides ICD-10 and ICD-11 encoding support for epidemiological tracking, health management"
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"and legacy projects.")
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gr.Markdown(
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"- It simplifies tasks with its API-driven approach. It is easy to integrate within existing "
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"e-clinical systems.")
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gr.Markdown(
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"- Subscription plans are adaptable to your needs, with a monthly fee and limited cost per "
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"encoding.")
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gr.Markdown("- Our team is available if you have any question.")
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gr.Markdown("- Interested? Contact us for inquiries!")
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with gr.Column():
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gr.Markdown("### Contact us:")
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email = gr.Textbox(label="Email", placeholder="Enter your professional email address...")
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request_list = ["API Key", "Commercial inquiry", "Encoding support", "Partnership", "Others"]
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reason = gr.Dropdown(choices=request_list, label="Request", value=request_list[0])
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message = gr.Textbox(label="Message", placeholder="Enter your message...")
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feedback_textbox = gr.Markdown(label="Feedback")
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api_key_button = gr.Button("Submit your message")
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api_key_button.click(request_email_form,
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inputs=[email, reason, message],
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outputs=feedback_textbox)
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with gr.Row():
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gr.Markdown("Safeterm v 0224 (c) Proddis - 2024. Contact us at info@proddis.com")
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demo.launch()
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send_email.py
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import os
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from dotenv import load_dotenv
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import msal
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import requests
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def send_email(reason, email, message) -> None:
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body = f"""
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Safeterm_demo v1123 (Huggingface)
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Subject: {reason}
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Message: {message}
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Contact Information: {email}
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"""
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load_dotenv()
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client_id = os.getenv("CLIENT_ID")
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client_secret = os.getenv("CLIENT_SECRET")
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tenant_id = os.getenv("TENANT_ID")
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authority = f"https://login.microsoftonline.com/{tenant_id}"
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sender = os.getenv("MAIL_SENDER")
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receiver = os.getenv("MAIL_RECIPIENT")
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cc_receiver = os.getenv("CC_RECIPIENT")
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app = msal.ConfidentialClientApplication(
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client_id=client_id,
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client_credential=client_secret,
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authority=authority)
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scopes = ["https://graph.microsoft.com/.default"]
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result = app.acquire_token_silent(scopes, account=None)
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if not result:
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print("No suitable token exists in cache. Let's get a new one from Azure Active Directory.")
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result = app.acquire_token_for_client(scopes=scopes)
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if "access_token" in result:
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endpoint = f'https://graph.microsoft.com/v1.0/users/{sender}/sendMail'
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email_msg = {
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'Message': {
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'Subject': reason,
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'Body': {
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'ContentType': 'Text',
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'Content': body
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},
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'ToRecipients': [{'EmailAddress': {'Address': receiver}}],
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'CcRecipients': [{'EmailAddress': {'Address': cc_receiver}}] # Added CcRecipients here
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},
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'SaveToSentItems': 'true'
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}
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r = requests.post(endpoint, headers={'Authorization': 'Bearer ' + result['access_token']}, json=email_msg)
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if r.ok:
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print('Sent email successfully')
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else:
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print(r.json())
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else:
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print(result.get("error"))
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print(result.get("error_description"))
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print(result.get("correlation_id"))
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