Patient case summary #90
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WalkthroughThis update introduces three new files to the Patient Case Summary Workflow project. The project documentation is now provided in a README that explains the application’s purpose, technologies, and setup instructions. A new Streamlit-based application (app.py) enables users to upload patient JSON files for asynchronous processing. Additionally, a comprehensive module (patient_case_summary.py) has been added which defines data models, implements functions to parse patient data from a FHIR bundle, creates condition bundles, and integrates clinical guideline matching via asynchronous workflows. Changes
Sequence Diagram(s)sequenceDiagram
participant U as User
participant S as Streamlit UI
participant P as process_patient
participant W as Workflow Module
U->>S: Upload JSON file
S->>P: Pass file path
P->>W: Invoke parsing of patient data
W->>W: Create condition bundles & match guidelines (async)
W-->>P: Return case summary
P->>S: Display patient summary
sequenceDiagram
participant GRW as GuidelineRecommendationWorkflow
participant PSP as parse_synthea_patient
participant CCB as create_condition_bundles
participant GCS as generate_case_summary
GRW->>PSP: Extract patient data from FHIR bundle
GRW->>CCB: Assemble condition bundles (awaited)
GRW->>GCS: Generate final case summary with guidelines
GCS-->>GRW: Output structured case summary
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Actionable comments posted: 6
🧹 Nitpick comments (3)
patient_case_summary/README.md (1)
30-30: Wrap URL within Markdown syntax.Markdown lint tool (MD034) flags the bare URL. Consider formatting it as a link for better readability, for example:
- Link to X thread: https://x.com/marziabil/status/1900598708682846514 + [Link to X thread](https://x.com/marziabil/status/1900598708682846514)🧰 Tools
🪛 markdownlint-cli2 (0.17.2)
30-30: Bare URL used
null(MD034, no-bare-urls)
patient_case_summary/patient_case_summary.py (2)
408-412: Remove unused imports and variables.Imports such as
SimpleDirectoryReader,Document,FunctionCallingAgentWorker,ChatMessage, andMessageRoleare unused based on the static analysis hints; alsoclear_outputis never used. Removing them improves readability and avoids confusion.- from llama_index.core import SimpleDirectoryReader - from llama_index.core.schema import Document - from llama_index.core.agent import FunctionCallingAgentWorker - from llama_index.core.llms import ChatMessage, MessageRole - from IPython.display import clear_outputAlso applies to: 764-764
🧰 Tools
🪛 Ruff (0.8.2)
408-408:
llama_index.core.SimpleDirectoryReaderimported but unusedRemove unused import:
llama_index.core.SimpleDirectoryReader(F401)
409-409:
llama_index.core.schema.Documentimported but unusedRemove unused import:
llama_index.core.schema.Document(F401)
410-410:
llama_index.core.agent.FunctionCallingAgentWorkerimported but unusedRemove unused import:
llama_index.core.agent.FunctionCallingAgentWorker(F401)
411-411: Redefinition of unused
ChatPromptTemplatefrom line 236Remove definition:
ChatPromptTemplate(F811)
412-412:
llama_index.core.llms.ChatMessageimported but unusedRemove unused import
(F401)
412-412:
llama_index.core.llms.MessageRoleimported but unusedRemove unused import
(F401)
574-574: Use context managers to handle file I/O.Open files with
withstatements to ensure proper resource management. For example:- patient_info_dict = json.load(open(str(patient_info_path), "r")) + with open(patient_info_path, "r") as f: + patient_info_dict = json.load(f)Also applies to: 604-604
🧰 Tools
🪛 Ruff (0.8.2)
574-574: Use a context manager for opening files
(SIM115)
📜 Review details
Configuration used: CodeRabbit UI
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📒 Files selected for processing (3)
patient_case_summary/README.md(1 hunks)patient_case_summary/app.py(1 hunks)patient_case_summary/patient_case_summary.py(1 hunks)
🧰 Additional context used
🪛 markdownlint-cli2 (0.17.2)
patient_case_summary/README.md
30-30: Bare URL used
null
(MD034, no-bare-urls)
🪛 Ruff (0.8.2)
patient_case_summary/patient_case_summary.py
19-19: Undefined name get_ipython
(F821)
156-156: Undefined name datetime
(F821)
156-156: Undefined name datetime
(F821)
260-260: Undefined name ConditionEncounters
(F821)
282-282: await statement outside of a function
(F704)
408-408: llama_index.core.SimpleDirectoryReader imported but unused
Remove unused import: llama_index.core.SimpleDirectoryReader
(F401)
409-409: llama_index.core.schema.Document imported but unused
Remove unused import: llama_index.core.schema.Document
(F401)
410-410: llama_index.core.agent.FunctionCallingAgentWorker imported but unused
Remove unused import: llama_index.core.agent.FunctionCallingAgentWorker
(F401)
411-411: Redefinition of unused ChatPromptTemplate from line 236
Remove definition: ChatPromptTemplate
(F811)
412-412: llama_index.core.llms.ChatMessage imported but unused
Remove unused import
(F401)
412-412: llama_index.core.llms.MessageRole imported but unused
Remove unused import
(F401)
574-574: Use a context manager for opening files
(SIM115)
604-604: Use a context manager for opening files
(SIM115)
736-736: Redefinition of unused OpenAI from line 234
Remove definition: OpenAI
(F811)
764-764: IPython.display.clear_output imported but unused
Remove unused import: IPython.display.clear_output
(F401)
774-774: await statement outside of a function
(F704)
🔇 Additional comments (3)
patient_case_summary/README.md (1)
1-29: README looks clear and thorough.Your introduction, project overview, and technology stack explanation are concise and helpful to any new developer exploring the project.
patient_case_summary/app.py (1)
27-29: Validate the asyncio usage pattern.Creating a new event loop and using
asyncio.run_coroutine_threadsafemight cause compatibility issues or concurrency pitfalls in certain environments. Verify the approach aligns with Streamlit’s best practices, which generally require a standard synchronous flow or well-integrated async approach within Streamlit's event loop.patient_case_summary/patient_case_summary.py (1)
282-282:awaitstatements outside an async function.Using
awaitat the top level can result in syntax errors in standard Python scripts (works only in notebooks/interactive shells). To run this asynchronously in normal Python, wrap calls in an async function and invoke viaasyncio.run(...)or a similar approach.Also applies to: 774-774
🧰 Tools
🪛 Ruff (0.8.2)
282-282:
awaitstatement outside of a function(F704)
| from patient_case_summary import parse_synthea_patient, create_condition_bundles, generate_case_summary | ||
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| # Set up LlamaCloud API key | ||
| os.environ["LLAMA_CLOUD_API_KEY"] = "your-llx-api-key" |
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🛠️ Refactor suggestion
Avoid hardcoding secrets in the source code.
Storing an API key directly in the code can pose security risks. It's best practice to load secrets from environment variables or a secure vault (e.g., .env file) and avoid committing them to version control.
- os.environ["LLAMA_CLOUD_API_KEY"] = "your-llx-api-key"
+ if "LLAMA_CLOUD_API_KEY" not in os.environ:
+ st.warning("LLAMA_CLOUD_API_KEY is not set. Some features may not work properly.")📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| os.environ["LLAMA_CLOUD_API_KEY"] = "your-llx-api-key" | |
| if "LLAMA_CLOUD_API_KEY" not in os.environ: | |
| st.warning("LLAMA_CLOUD_API_KEY is not set. Some features may not work properly.") |
| # In[ ]: | ||
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| get_ipython().system('pip install llama-index llama-index-indices-managed-llama-cloud llama-cloud llama-parse') |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Remove or conditionally define Jupyter-specific code.
get_ipython() is a Jupyter utility and may cause errors in non-notebook environments. To keep this file environment-agnostic, consider removing or wrapping this code in a check that ensures it’s running in a Jupyter environment.
🧰 Tools
🪛 Ruff (0.8.2)
19-19: Undefined name get_ipython
(F821)
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| async def create_condition_bundles( | ||
| patient_data: PatientInfo, llm: Optional[LLM] = None | ||
| ) -> ConditionEncounters: |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Undefined return type.
-> ConditionEncounters: is referenced, but there is no ConditionEncounters definition anywhere in the code. Either remove or define this type.
🧰 Tools
🪛 Ruff (0.8.2)
260-260: Undefined name ConditionEncounters
(F821)
| from llama_index.core import SimpleDirectoryReader | ||
| from llama_index.core.schema import Document | ||
| from llama_index.core.agent import FunctionCallingAgentWorker | ||
| from llama_index.core.prompts import ChatPromptTemplate |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Redefinition of ChatPromptTemplate/OpenAI.
ChatPromptTemplate and OpenAI were already defined earlier. Consider removing or aliasing the re-import to avoid confusion or collisions.
Also applies to: 736-736
🧰 Tools
🪛 Ruff (0.8.2)
411-411: Redefinition of unused ChatPromptTemplate from line 236
Remove definition: ChatPromptTemplate
(F811)
| def parse_synthea_patient(file_path: str, filter_active: bool = True) -> PatientInfo: | ||
| # Load the Synthea-generated FHIR Bundle | ||
| with open(file_path, "r") as f: | ||
| bundle = json.load(f) | ||
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There was a problem hiding this comment.
Import the 'json' module before usage.
json.load(f) is called, but there's no import json. Add the necessary import:
+ import json📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| def parse_synthea_patient(file_path: str, filter_active: bool = True) -> PatientInfo: | |
| # Load the Synthea-generated FHIR Bundle | |
| with open(file_path, "r") as f: | |
| bundle = json.load(f) | |
| import json | |
| def parse_synthea_patient(file_path: str, filter_active: bool = True) -> PatientInfo: | |
| # Load the Synthea-generated FHIR Bundle | |
| with open(file_path, "r") as f: | |
| bundle = json.load(f) |
| def get_encounter_date(enc): | ||
| period = enc.get("period", {}) | ||
| start = period.get("start") | ||
| return datetime.fromisoformat(start) if start else datetime.min |
There was a problem hiding this comment.
Import datetime before usage.
You are calling datetime.fromisoformat(start) but have not imported the datetime module. Add the missing import statement for datetime:
+ from datetime import datetime📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| return datetime.fromisoformat(start) if start else datetime.min | |
| from datetime import datetime | |
| return datetime.fromisoformat(start) if start else datetime.min |
🧰 Tools
🪛 Ruff (0.8.2)
156-156: Undefined name datetime
(F821)
156-156: Undefined name datetime
(F821)
Link to X thread added in the Readme
Summary by CodeRabbit
Documentation
New Features