From e995145a49448cc652abfc639f3a558fff8e04df Mon Sep 17 00:00:00 2001 From: ElektrikSpark Date: Thu, 9 May 2024 08:42:14 +0000 Subject: [PATCH] first pass on FastAPI --- .vscode/extensions.json | 3 +- .vscode/wellchart-new.code-workspace | 33 + apps/api/.gitignore | 176 ++ apps/api/.python-version | 1 + apps/api/.vscode/launch.json | 13 + apps/api/.vscode/settings.json | 5 + apps/api/README.md | 8 + apps/api/package.json | 8 + apps/api/poetry.lock | 1833 +++++++++++++++++ apps/api/poetry.toml | 3 + apps/api/pyproject.toml | 26 + apps/api/requirements.txt | 20 + apps/api/run.py | 4 + apps/api/src/__init__.py | 1 + apps/api/src/api/__init__.py | 0 apps/api/src/api/api_v1/__init__.py | 0 apps/api/src/api/api_v1/api.py | 18 + apps/api/src/api/api_v1/auth/__init__.py | 0 apps/api/src/api/api_v1/auth/verify.py | 45 + apps/api/src/api/api_v1/clients/__init__.py | 0 apps/api/src/api/api_v1/clients/anthropic.py | 143 ++ .../api/src/api/api_v1/processing/__init__.py | 0 apps/api/src/api/api_v1/processing/text.py | 130 ++ apps/api/src/api/api_v1/routers/__init__.py | 0 apps/api/src/api/api_v1/routers/health.py | 22 + apps/api/src/api/api_v1/routers/upload.py | 54 + apps/api/src/api/api_v1/utils.py | 7 + apps/api/src/config.py | 25 + apps/api/src/main.py | 51 + apps/api/tests/__init__.py | 0 apps/api/tests/test_api.py | 5 + apps/api/vercel.json | 18 + apps/nextjs/.vscode/launch.json | 17 + apps/nextjs/package.json | 1 + pnpm-lock.yaml | 310 ++- 35 files changed, 2975 insertions(+), 5 deletions(-) create mode 100644 .vscode/wellchart-new.code-workspace create mode 100644 apps/api/.gitignore create mode 100644 apps/api/.python-version create mode 100644 apps/api/.vscode/launch.json create mode 100644 apps/api/.vscode/settings.json create mode 100644 apps/api/README.md create mode 100644 apps/api/package.json create mode 100644 apps/api/poetry.lock create mode 100644 apps/api/poetry.toml create mode 100644 apps/api/pyproject.toml create mode 100644 apps/api/requirements.txt create mode 100644 apps/api/run.py create mode 100644 apps/api/src/__init__.py create mode 100644 apps/api/src/api/__init__.py create mode 100644 apps/api/src/api/api_v1/__init__.py create mode 100644 apps/api/src/api/api_v1/api.py create mode 100644 apps/api/src/api/api_v1/auth/__init__.py create mode 100644 apps/api/src/api/api_v1/auth/verify.py create mode 100644 apps/api/src/api/api_v1/clients/__init__.py create mode 100644 apps/api/src/api/api_v1/clients/anthropic.py create mode 100644 apps/api/src/api/api_v1/processing/__init__.py create mode 100644 apps/api/src/api/api_v1/processing/text.py create mode 100644 apps/api/src/api/api_v1/routers/__init__.py create mode 100644 apps/api/src/api/api_v1/routers/health.py create mode 100644 apps/api/src/api/api_v1/routers/upload.py create mode 100644 apps/api/src/api/api_v1/utils.py create mode 100644 apps/api/src/config.py create mode 100644 apps/api/src/main.py create mode 100644 apps/api/tests/__init__.py create mode 100644 apps/api/tests/test_api.py create mode 100644 apps/api/vercel.json create mode 100644 apps/nextjs/.vscode/launch.json diff --git a/.vscode/extensions.json b/.vscode/extensions.json index 4e58391..7813393 100644 --- a/.vscode/extensions.json +++ b/.vscode/extensions.json @@ -4,6 +4,7 @@ "dbaeumer.vscode-eslint", "esbenp.prettier-vscode", "expo.vscode-expo-tools", - "yoavbls.pretty-ts-errors" + "yoavbls.pretty-ts-errors", + "tamasfe.even-better-toml" ] } diff --git a/.vscode/wellchart-new.code-workspace b/.vscode/wellchart-new.code-workspace new file mode 100644 index 0000000..bb78034 --- /dev/null +++ b/.vscode/wellchart-new.code-workspace @@ -0,0 +1,33 @@ +{ + "folders": [ + { + "name": "Web", + "path": "../apps/nextjs", + }, + { + "name": "FastAPI", + "path": "../apps/api", + }, + { + "name": "Root", + "path": "../", + }, + ], + "extensions": { + "recommendations": [ + "joshx.workspace-terminals", + "teticio.python-envy", + "charliermarsh.ruff", + ], + }, + "launch": { + "version": "0.2.0", + "configurations": [], + "compounds": [ + { + "name": "Launch Web and FastAPI", + "configurations": ["Next.js: Chrome", "Python: FastAPI"], + }, + ], + }, +} diff --git a/apps/api/.gitignore b/apps/api/.gitignore new file mode 100644 index 0000000..b4f7962 --- /dev/null +++ b/apps/api/.gitignore @@ -0,0 +1,176 @@ +# Created by https://www.toptal.com/developers/gitignore/api/python +# Edit at https://www.toptal.com/developers/gitignore?templates=python + +### Python ### +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +#poetry.lock + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/#use-with-ide +.pdm.toml + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +#.idea/ + +### Python Patch ### +# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration +# poetry.toml + +# ruff +.ruff_cache/ + +# LSP config files +pyrightconfig.json + +# End of https://www.toptal.com/developers/gitignore/api/python diff --git a/apps/api/.python-version b/apps/api/.python-version new file mode 100644 index 0000000..8531a3b --- /dev/null +++ b/apps/api/.python-version @@ -0,0 +1 @@ +3.12.2 diff --git a/apps/api/.vscode/launch.json b/apps/api/.vscode/launch.json new file mode 100644 index 0000000..0585794 --- /dev/null +++ b/apps/api/.vscode/launch.json @@ -0,0 +1,13 @@ +{ + "version": "0.2.0", + "configurations": [ + { + "name": "Python: FastAPI", + "type": "debugpy", + "request": "launch", + "module": "uvicorn", + "args": ["src.main:app", "--reload"], + "jinja": true + } + ] +} diff --git a/apps/api/.vscode/settings.json b/apps/api/.vscode/settings.json new file mode 100644 index 0000000..d969f96 --- /dev/null +++ b/apps/api/.vscode/settings.json @@ -0,0 +1,5 @@ +{ + "python.testing.pytestArgs": ["tests"], + "python.testing.unittestEnabled": false, + "python.testing.pytestEnabled": true +} diff --git a/apps/api/README.md b/apps/api/README.md new file mode 100644 index 0000000..51da84c --- /dev/null +++ b/apps/api/README.md @@ -0,0 +1,8 @@ +Generate requirements.txt using Poetry package manager: + +``` +poetry export --without-hashes --format=requirements.txt > requirements.txt +``` + +Python monorepo info: +https://medium.com/@ashley.e.shultz/python-mono-repo-with-only-built-in-tooling-7c2d52c2fc66 diff --git a/apps/api/package.json b/apps/api/package.json new file mode 100644 index 0000000..f8a9070 --- /dev/null +++ b/apps/api/package.json @@ -0,0 +1,8 @@ +{ + "name": "api", + "version": "0.1.0", + "scripts": { + "dev": ".venv/bin/python run.py", + "generate:requirements": "poetry export --without-hashes --format=requirements.txt > requirements.txt" + } +} diff --git a/apps/api/poetry.lock b/apps/api/poetry.lock new file mode 100644 index 0000000..7f1ce7a --- /dev/null +++ b/apps/api/poetry.lock @@ -0,0 +1,1833 @@ +# This file is automatically @generated by Poetry 1.8.1 and should not be changed by hand. + +[[package]] +name = "annotated-types" +version = "0.6.0" +description = "Reusable constraint types to use with typing.Annotated" +optional = false +python-versions = ">=3.8" +files = [ + {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"}, + {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"}, +] + +[[package]] +name = "anyio" +version = "4.3.0" +description = "High level compatibility layer for multiple asynchronous event loop implementations" +optional = false +python-versions 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b/apps/api/pyproject.toml new file mode 100644 index 0000000..c55852b --- /dev/null +++ b/apps/api/pyproject.toml @@ -0,0 +1,26 @@ +[tool.poetry] +name = "api" +version = "0.1.0" +description = "" +authors = ["trevorpfiz ", "zacharypfiz "] +readme = "README.md" + +[tool.poetry.dependencies] +python = "^3.12" +python-dotenv = "^1.0.1" +fastapi = "^0.111.0" +uvicorn = "^0.27.1" +pydantic-settings = "^2.2.1" +pymupdf = "^1.24.2" +pandas = "^2.2.2" +python-jose = {extras = ["cryptography"], version = "^3.3.0"} +requests = "^2.31.0" + +[tool.poetry.group.dev.dependencies] +ruff = "^0.4.3" +pytest = "^8.0.1" +pylint-pydantic = "^0.3.2" + +[build-system] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" diff --git a/apps/api/requirements.txt b/apps/api/requirements.txt new file mode 100644 index 0000000..b0cfd45 --- /dev/null +++ b/apps/api/requirements.txt @@ -0,0 +1,20 @@ +Updating dependencies +Resolving dependencies... + +Writing lock file +annotated-types==0.6.0 ; python_version >= "3.9" and python_version < "4.0" +anyio==4.3.0 ; python_version >= "3.9" and python_version < "4.0" +click==8.1.7 ; python_version >= "3.9" and python_version < "4.0" +colorama==0.4.6 ; python_version >= "3.9" and python_version < "4.0" and platform_system == "Windows" +exceptiongroup==1.2.1 ; python_version >= "3.9" and python_version < "3.11" +fastapi==0.109.2 ; python_version >= "3.9" and python_version < "4.0" +h11==0.14.0 ; python_version >= "3.9" and python_version < "4.0" +idna==3.7 ; python_version >= "3.9" and python_version < "4.0" +pydantic-core==2.18.2 ; python_version >= "3.9" and python_version < "4.0" +pydantic-settings==2.2.1 ; python_version >= "3.9" and python_version < "4.0" +pydantic==2.7.1 ; python_version >= "3.9" and python_version < "4.0" +python-dotenv==1.0.1 ; python_version >= "3.9" and python_version < "4.0" +sniffio==1.3.1 ; python_version >= "3.9" and python_version < "4.0" +starlette==0.36.3 ; python_version >= 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b/apps/api/src/api/api_v1/api.py @@ -0,0 +1,18 @@ +from fastapi import APIRouter + +from src.api.api_v1.routers import health, upload + + +api_router = APIRouter() +api_router.include_router( + health.router, + prefix="/health", + tags=["health"], + responses={404: {"description": "Not found"}}, +) +api_router.include_router( + upload.router, + prefix="/upload", + tags=["upload"], + responses={404: {"description": "Not found"}}, +) diff --git a/apps/api/src/api/api_v1/auth/__init__.py b/apps/api/src/api/api_v1/auth/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/apps/api/src/api/api_v1/auth/verify.py b/apps/api/src/api/api_v1/auth/verify.py new file mode 100644 index 0000000..d4977eb --- /dev/null +++ b/apps/api/src/api/api_v1/auth/verify.py @@ -0,0 +1,45 @@ +from datetime import datetime, timezone + +from fastapi import HTTPException, Security +from fastapi.security import HTTPAuthorizationCredentials, HTTPBearer +from jose import JWTError, jwt + +from src.config import settings + +ALGORITHM = "HS256" +security = HTTPBearer() + + +def decode_jwt(token: str) -> dict: + """Decode a JWT token and verify its expiration.""" + try: + payload = jwt.decode(token, settings.JWT_SECRET, algorithms=[ALGORITHM]) + exp = payload.get("exp") + + # Verify that the token has not expired + if exp and datetime.fromtimestamp(exp, tz=timezone.utc) < datetime.now( + tz=timezone.utc + ): + return None + + return payload + except JWTError: + return None + + +def verify_token(credentials: HTTPAuthorizationCredentials = Security(security)): + """Verify the incoming token using the `decode_jwt` function.""" + token = credentials.credentials + credentials_exception = HTTPException( + status_code=401, + detail="Could not validate credentials", + headers={"WWW-Authenticate": "Bearer"}, + ) + + # Decode the JWT token + payload = decode_jwt(token) + if not payload or "sub" not in payload: + raise credentials_exception + + # Return the user's subject or identifier for further checks + return payload["sub"] diff --git a/apps/api/src/api/api_v1/clients/__init__.py b/apps/api/src/api/api_v1/clients/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/apps/api/src/api/api_v1/clients/anthropic.py b/apps/api/src/api/api_v1/clients/anthropic.py new file mode 100644 index 0000000..f8ad150 --- /dev/null +++ b/apps/api/src/api/api_v1/clients/anthropic.py @@ -0,0 +1,143 @@ +import time + +import requests + +from src.api.api_v1.utils import parse_rfc3339 +from src.config import settings + + +def call_anthropic_api(batches, headers=None): + headers = headers or { + "x-api-key": settings.ANTHROPIC_API_KEY, + "anthropic-version": "2023-06-01", + "content-type": "application/json", + } + + url = "https://api.anthropic.com/v1/messages" + previous_summary = "" + responses = [] + + if len(batches) > 30: + return "Batch size exceeds 30." + + for i, batch in enumerate(batches): + user_message = ( + f"Previous summary: {previous_summary} New information: {batch}" + if previous_summary + else batch + ) + + data = { + "model": "claude-3-haiku-20240307", + "max_tokens": 4096, + "temperature": 0, + "system": prompt, + "messages": [{"role": "user", "content": user_message}], + } + + response = requests.post(url, headers=headers, json=data) + + if response.ok: + response_data = response.json() + previous_summary = response_data["content"][0]["text"] + responses.append(response_data) + print(f"Message{i}: {previous_summary}") + + if i < len(batches) - 1: + reset_time = parse_rfc3339( + response.headers.get("anthropic-ratelimit-tokens-reset") + ) + sleep_time = reset_time - time.time() if reset_time else 60 + if sleep_time > 0: + time.sleep(sleep_time) + + else: + print( + f"API call failed with status {response.status_code}: {response.text}" + ) + return f"API call failed for batch {i+1}." + + return previous_summary + + +# Feed each batch iteratively into the LLM model +template = """ +Header +Patient Identifier: [Name, DOB, MRN] +Date of Report: [Date] +Prepared for: [Provider Name, Specialty] + +1. Chief Complaints +Reasons for Upcoming and Recent Encounters: [Brief summary] + +2. Recent Encounters and Interventions +Date: [Date] +Provider: [Name, Specialty] +Summary: [Reason for visit, key findings, interventions, outcomes] +Follow-Up Needs: [Monitoring or additional care required] + +3. Medications +Current Medications: [Drug name, dosage, frequency, purpose] +Medication Changes: [Newly added or discontinued, reasons] +Compliance and Issues: [Non-adherence flags, side effects] + +4. Allergies +Substance: [Allergen] +Reaction: [Clinical reaction] +Severity: [Mild/Moderate/Severe] + +5. Labs and Imaging Summary +Recent Findings: [Abnormal results and trends] +Pending Results: [Tests with results pending] +Interpretations: [Provider interpretations where applicable] + +6. Vitals Trends +Recent Readings: [Trends and abnormal values] + +7. Functional and Cognitive Status +ADLs and IADLs: [Independence level, assistance required] +Mobility and Fall Risk: [Mobility aids used, fall risk assessment] +Cognitive Function: [Screening results, cognitive impairments] +Behavioral and Psychological Symptoms: [Mood disorders, behavioral issues] +Nutritional Status: [Assessment, weight monitoring] +Sensory Impairments: [Hearing, vision, communication needs] +Social Support System: [Caregiver support, social engagement] + +8. Medical History Summary +Chronic Conditions: [List with onset start and end dates and current status] +Past Hospitalizations/Surgeries: [Dates, reasons, outcomes] +Significant Past Interventions: [Medications, therapies, outcomes] +Family History: [Relevant genetic or familial diseases] +Social History: [Smoking, alcohol use, drug use, living situation] + +9. Assessment and Plan +Assessment: [Consolidated view from recent encounters] +Plan: [Management plans, pending tests/procedures] + +10. Advanced Directives +Type: [DNR, living will, healthcare proxy] +Specifications: [Detailed directives] + +11. Insurance/Financial Considerations +Coverage Details: [Insurance type, limitations] +Financial Concerns: [Concerns affecting care choices] + +12. Referrals and Correspondence +Referral Date: [Date] +From: [Provider Name, Specialty, Institution] +Reason for Referral/Correspondence: [Concise summary] +Key Information Provided: [Summary of relevant patient history, diagnostic findings, treatments tried, and questions or goals from the referring provider] +Recommendations and Requests: [Specific recommendations or diagnostic/treatment requests from the referring provider] + +Footer +Prepared By: WellChart, Version +Confidentiality Notice: [Standard disclaimer] +""" + +prompt = f""" +Context: Using only the detailed text resource information from an EMR provided without hallucinating and leaving fields blank if you don't have the required information, generate a precharting report that adheres to the following structured format, including all relevant medical and clinical information under each heading and subheading as detailed below: +{template} +Ensure the generated precharting report is organized, concise, and clearly separates each section and subheading as outlined. Make it as clear and concise as possible without losing relevant information and list start and end dates whenever you have that information. When listing things alphabetically, list a first and z last. When listing things by date, include the start date and end date where applicable to create a timeline, and list the most recent event first. The report should accurately reflect the patient's condition, plan of care, and timeline based only on the current date and information provided. +You may not be given all of the patient's information at once, so update the unfinished report as you get more information. +Generate the precharting report based on the structured format and detailed instructions provided above. +""" diff --git a/apps/api/src/api/api_v1/processing/__init__.py b/apps/api/src/api/api_v1/processing/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/apps/api/src/api/api_v1/processing/text.py b/apps/api/src/api/api_v1/processing/text.py new file mode 100644 index 0000000..911165b --- /dev/null +++ b/apps/api/src/api/api_v1/processing/text.py @@ -0,0 +1,130 @@ +import os + +import fitz # PyMuPDF +import pandas as pd + + +def process_pdf(file_path): + """Extract text and form field data from a PDF using PyMuPDF.""" + # Open the PDF file + document = fitz.open(file_path) + text = "" + + # Iterate through each page of the PDF + for page in document: + # Extract text from the page and append to the text variable + text += page.get_text() + + # Close the document + document.close() + + return text + + +def process_csv(file_path): + """Convert CSV data to a formatted string in a descriptive text format.""" + df = pd.read_csv(file_path) + descriptive_text = [] + + # Iterate over each row in the DataFrame + for index, row in df.iterrows(): + # Build a descriptive string for each row + row_description = [] + for field, value in row.items(): + if pd.notna(value): # Only include fields with non-missing values + # Format the field name by capitalizing each word and replace underscores with spaces + formatted_field = " ".join( + word.capitalize() for word in field.replace("_", " ").split() + ) + # Append the formatted description to the row description list + row_description.append(f"{formatted_field}: {value}") + # Join all descriptions in the row into a single string with periods separating them + descriptive_text.append(". ".join(row_description) + ".") + + # Join all row descriptions into one large string separated by newlines + return "\n".join(descriptive_text) + + +def consolidate_texts(base_folder_path): + """Consolidate texts from CSVs and PDFs, ignoring specific files.""" + pdf_texts = [] + csv_texts = [] + documents_path = os.path.join( + base_folder_path, "documents" + ) # Path to the documents subfolder + + # Process files in the main directory + for file_name in os.listdir(base_folder_path): + if file_name == "Insurance.csv": + print("Skipping Insurance.csv file") + continue # Skip the Insurance.csv file + full_path = os.path.join(base_folder_path, file_name) + if file_name.endswith(".pdf"): + pdf_texts.append(process_pdf(full_path)) + elif file_name.endswith(".csv"): + csv_texts.append(process_csv(full_path)) + + # Process PDF files in the 'documents' subfolder + if os.path.exists(documents_path): + for file_name in os.listdir(documents_path): + if file_name.endswith(".pdf"): + full_path = os.path.join(documents_path, file_name) + pdf_texts.append(process_pdf(full_path)) + + # Join the PDF and CSV texts into a single string + pdf_texts = "\n".join(pdf_texts) + csv_texts = "\n".join(csv_texts) + + return pdf_texts, csv_texts + + +def combine_texts(pdf_content, csv_content): + """ + Combine texts from consolidated PDFs and CSVs. + + Args: + pdf_content (str): Text content from consolidated PDFs. + csv_content (str): Text content from consolidated CSVs. + + Returns: + str: Combined text content. + """ + try: + # Combine both contents, adding a newline if needed between the two contents + combined_content = pdf_content + "\n\n" + csv_content + + return combined_content + + except Exception as e: + print("An error occurred while combining texts:", e) + raise e # Raising the exception to be handled by the caller + + +def group_text_into_batches(file_stream, target_batch_size): + """ + Processes text stream and groups it into batches, ensuring each batch does not exceed the target batch size in bytes. + Each batch is a continuous blob of text. + """ + batches = [] + current_batch = "" + current_batch_size = 0 + + for line in file_stream: + line = line.strip() + if not line: + continue # Skip empty lines + resource_size = len(line.encode("utf-8")) + + if current_batch_size + resource_size + len("\n") <= target_batch_size: + current_batch += ("" if current_batch == "" else "\n") + line + current_batch_size += resource_size + len("\n") + else: + if current_batch: + batches.append(current_batch) + current_batch = line + current_batch_size = resource_size + + if current_batch: + batches.append(current_batch) + + return batches diff --git a/apps/api/src/api/api_v1/routers/__init__.py b/apps/api/src/api/api_v1/routers/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/apps/api/src/api/api_v1/routers/health.py b/apps/api/src/api/api_v1/routers/health.py new file mode 100644 index 0000000..857393b --- /dev/null +++ b/apps/api/src/api/api_v1/routers/health.py @@ -0,0 +1,22 @@ +from fastapi import APIRouter, Depends, HTTPException +from fastapi.responses import JSONResponse + +from src.api.api_v1.auth.verify import verify_token + +router = APIRouter() + + +@router.get("/health", status_code=200) +async def health_check(user: str = Depends(verify_token)): + """Secured health check endpoint.""" + if not user: + raise HTTPException(status_code=401, detail="Unauthorized") + + return JSONResponse( + status_code=200, + content={ + "message": "Service is running smoothly", + "batches_processed": 0, + "prechart": "hi", + }, + ) diff --git a/apps/api/src/api/api_v1/routers/upload.py b/apps/api/src/api/api_v1/routers/upload.py new file mode 100644 index 0000000..87c7a3c --- /dev/null +++ b/apps/api/src/api/api_v1/routers/upload.py @@ -0,0 +1,54 @@ +import os +import tempfile +import zipfile + +from fastapi import APIRouter, Depends, File, HTTPException, UploadFile +from fastapi.responses import JSONResponse + +from src.api.api_v1.auth.verify import verify_token +from src.api.api_v1.clients.anthropic import call_anthropic_api +from src.api.api_v1.processing.text import ( + combine_texts, + consolidate_texts, + group_text_into_batches, +) +from src.config import settings + +router = APIRouter() + + +@router.post("/upload", status_code=200) +async def upload_zip(file: UploadFile = File(...), user: str = Depends(verify_token)): + """Secure endpoint to upload and process zip files, ensuring valid JWTs.""" + try: + with tempfile.TemporaryDirectory() as temp_dir: + zip_path = os.path.join(temp_dir, file.filename) + with open(zip_path, "wb") as f: + contents = await file.read() + f.write(contents) + + with zipfile.ZipFile(zip_path, "r") as zip_ref: + zip_ref.extractall(temp_dir) + + pdf_texts, csv_texts = consolidate_texts(temp_dir) + combined_text = combine_texts(pdf_texts, csv_texts) + batches = group_text_into_batches( + combined_text.splitlines(keepends=True), target_batch_size=86000 + ) + + headers = { + "x-api-key": settings.ANTHROPIC_API_KEY, + "anthropic-version": "2023-06-01", + "content-type": "application/json", + } + prechart = call_anthropic_api(batches, headers) + + return JSONResponse( + content={ + "message": f"File processed and API called successfully by user {user}", + "batches_processed": len(batches), + "prechart": prechart, + } + ) + except Exception as e: + raise HTTPException(status_code=500, detail=f"An error occurred: {str(e)}") diff --git a/apps/api/src/api/api_v1/utils.py b/apps/api/src/api/api_v1/utils.py new file mode 100644 index 0000000..8c643a7 --- /dev/null +++ b/apps/api/src/api/api_v1/utils.py @@ -0,0 +1,7 @@ +from datetime import datetime, timezone + + +# Function to parse RFC 3339 datetime and convert to epoch time +def parse_rfc3339(time_str): + dt = datetime.fromisoformat(time_str.replace("Z", "+00:00")) + return dt.replace(tzinfo=timezone.utc).timestamp() diff --git a/apps/api/src/config.py b/apps/api/src/config.py new file mode 100644 index 0000000..b5cf390 --- /dev/null +++ b/apps/api/src/config.py @@ -0,0 +1,25 @@ +import os + +from dotenv import load_dotenv +from pydantic_settings import BaseSettings, SettingsConfigDict + +load_dotenv() + + +# Otherwise, the root path will be the local host. ROOT_PATH is an env var configured in Vercel deployment. +# The value for production is equal to the root path of the deployment URL in Vercel. +ROOT_PATH = os.getenv("ROOT_PATH", "http://127.0.0.1:8000") + + +class Settings(BaseSettings): + PROJECT_NAME: str = "FastAPI App" + PROJECT_DESCRIPTION: str = "A simple FastAPI app" + JWT_SECRET: str = os.getenv("JWT_SECRET") + ANTHROPIC_API_KEY: str = os.getenv("ANTHROPIC_API_KEY") + OPENAI_API_KEY: str = os.getenv("OPENAI_API_KEY") + model_config = SettingsConfigDict(env_file=".env") + API_VERSION: str = "/api/v1" + ROOT: str = ROOT_PATH + + +settings = Settings() diff --git a/apps/api/src/main.py b/apps/api/src/main.py new file mode 100644 index 0000000..9f556d3 --- /dev/null +++ b/apps/api/src/main.py @@ -0,0 +1,51 @@ +from fastapi import APIRouter, FastAPI +from fastapi.middleware.cors import CORSMiddleware +from fastapi.routing import APIRoute + +from src.api.api_v1.api import api_router +from src.config import settings + +info_router = APIRouter() + + +@info_router.get("/", status_code=200, include_in_schema=False) +async def info(): + return [{"Status": "API Running"}] + + +def custom_generate_unique_id(route: APIRoute): + """Generates a custom ID when using the TypeScript Generator Client + + Args: + route (APIRoute): The route to be customised + + Returns: + str: tag-route_name, e.g. items-CreateItem + """ + return f"{route.tags[0]}-{route.name}" + + +def get_application(): + _app = FastAPI( + title=settings.PROJECT_NAME, + description=settings.PROJECT_DESCRIPTION, + generate_unique_id_function=custom_generate_unique_id, + root_path=settings.ROOT, + root_path_in_servers=True, + ) + + _app.add_middleware( + CORSMiddleware, + allow_origins=["*"], + allow_credentials=True, + allow_methods=["*"], + allow_headers=["*"], + ) + + _app.include_router(api_router, prefix=settings.API_VERSION) + _app.include_router(info_router, tags=[""]) + + return _app + + +app = get_application() diff --git a/apps/api/tests/__init__.py b/apps/api/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/apps/api/tests/test_api.py b/apps/api/tests/test_api.py new file mode 100644 index 0000000..d855243 --- /dev/null +++ b/apps/api/tests/test_api.py @@ -0,0 +1,5 @@ +from src import __version__ + + +def test_version(): + assert __version__ == '0.1.0' diff --git a/apps/api/vercel.json b/apps/api/vercel.json new file mode 100644 index 0000000..75e99f2 --- /dev/null +++ b/apps/api/vercel.json @@ -0,0 +1,18 @@ +{ + "version": 2, + "builds": [ + { + "src": "/src/main.py", + "use": "@vercel/python" + } + ], + "routes": [ + { + "src": "/(.*)", + "dest": "src/main.py" + } + ], + "env": { + "APP_MODULE": "src.main:app" + } +} diff --git a/apps/nextjs/.vscode/launch.json b/apps/nextjs/.vscode/launch.json new file mode 100644 index 0000000..3804a07 --- /dev/null +++ b/apps/nextjs/.vscode/launch.json @@ -0,0 +1,17 @@ +{ + "version": "0.2.0", + "configurations": [ + { + "name": "Next.js: Chrome", + "type": "node-terminal", + "request": "launch", + "command": "pnpm run dev", + "serverReadyAction": { + "pattern": "- Local:.+(https?://.+)", + "uriFormat": "%s", + "action": "debugWithChrome", + "webRoot": "${workspaceFolder}" + } + } + ] +} diff --git a/apps/nextjs/package.json b/apps/nextjs/package.json index ac10dcf..51f1f2c 100644 --- a/apps/nextjs/package.json +++ b/apps/nextjs/package.json @@ -36,6 +36,7 @@ "zod": "^3.23.6" }, "devDependencies": { + "@hey-api/openapi-ts": "^0.43.2", "@types/node": "^20.12.10", "@types/react": "^18.3.1", "@types/react-dom": "^18.3.0", diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index a261a04..b0c187a 100644 --- a/pnpm-lock.yaml +++ b/pnpm-lock.yaml @@ -87,6 +87,9 @@ importers: specifier: ^3.23.6 version: 3.23.7 devDependencies: + '@hey-api/openapi-ts': + specifier: ^0.43.2 + version: 0.43.2(typescript@5.4.5) '@types/node': specifier: ^20.12.10 version: 20.12.10 @@ -336,7 +339,7 @@ importers: version: 7.34.1(eslint@9.2.0) eslint-plugin-react-hooks: 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