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https://github.com/Sudo-JHare/IggyAPI.git
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patch
update pathing for SD splitting, for odd names in json files. iterate through all json files and read the contents for SD not just based on name.
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parent
655b186197
commit
881669e5e9
173
main.py
173
main.py
@ -589,6 +589,153 @@ async def list_profiles(ig_id: str, version: Optional[str] = None):
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logger.info(f"Found {len(profiles)} profiles in IG {ig_name} (version: {version})")
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return profiles
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#------------------------------------------------------------------OLD
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# @app.get("/igs/{ig_id}/profiles/{profile_id}", response_model=StructureDefinition)
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# async def get_profile(ig_id: str, profile_id: str, version: Optional[str] = None, include_narrative: bool = True):
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# """
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# Retrieve a specific StructureDefinition from an Implementation Guide (IG).
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# This endpoint fetches a specific FHIR StructureDefinition (profile) from the given IG.
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# It supports optional version specification and an option to strip the narrative content.
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# Args:
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# ig_id (str): The ID of the Implementation Guide (e.g., 'hl7.fhir.au.core' or 'hl7.fhir.au.core#1.1.0-preview').
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# If the version is included in the ig_id (after '#'), it takes precedence unless overridden by the version parameter.
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# profile_id (str): The ID or name of the profile to retrieve (e.g., 'AUCorePatient').
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# version (str, optional): The version of the IG (e.g., '1.1.0-preview'). If not provided and ig_id contains a version,
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# the version from ig_id is used; otherwise, the latest version is used.
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# include_narrative (bool, optional): Whether to include the narrative (`text` element) in the StructureDefinition.
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# Defaults to True. Set to False to strip the narrative, removing human-readable content.
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# Returns:
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# StructureDefinition: A dictionary containing the requested StructureDefinition resource.
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# The response includes the `resource` field with the StructureDefinition JSON.
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# If `include_narrative=False`, the `text` element will be set to null.
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# Raises:
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# HTTPException:
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# - 400: If the IG name, version, or profile ID is invalid.
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# - 404: If the IG, version, or profile is not found.
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# - 500: If an error occurs during package retrieval or profile extraction.
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# Example:
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# - GET /igs/hl7.fhir.au.core/profiles/AUCorePatient?version=1.1.0-preview
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# Returns the AUCorePatient profile with narrative included.
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# - GET /igs/hl7.fhir.au.core/profiles/AUCorePatient?version=1.1.0-preview&include_narrative=false
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# Returns the AUCorePatient profile with the narrative (`text` element) stripped.
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# """
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# logger.info(f"Retrieving profile {profile_id} for IG: {ig_id}, version: {version}, include_narrative: {include_narrative}")
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# # Parse ig_id for version if it includes a '#'
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# ig_name = ig_id
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# if '#' in ig_id:
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# parts = ig_id.split('#', 1)
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# ig_name = parts[0]
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# if version and parts[1] != version:
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# logger.warning(f"Version specified in ig_id ({parts[1]}) conflicts with version parameter ({version}). Using version parameter.")
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# else:
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# version = parts[1]
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# logger.info(f"Parsed ig_id: name={ig_name}, version={version}")
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# # Validate ig_name
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# if not ig_name or not re.match(r'^[a-zA-Z0-9\.\-_]+$', ig_name):
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# logger.error(f"Invalid IG name: {ig_name}")
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# raise HTTPException(status_code=400, detail="Invalid IG name. Use format like 'hl7.fhir.au.core'.")
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# # Validate version if provided
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# if version and not re.match(r'^[a-zA-Z0-9\.\-_]+$', version):
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# logger.error(f"Invalid version: {version}")
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# raise HTTPException(status_code=400, detail="Invalid version format. Use format like '1.1.0-preview'.")
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# # Validate profile_id
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# if not profile_id or not re.match(r'^[a-zA-Z0-9\.\-_]+$', profile_id):
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# logger.error(f"Invalid profile ID: {profile_id}")
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# raise HTTPException(status_code=400, detail="Invalid profile ID format.")
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# # Check if profiles are cached
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# cache_key = f"{ig_name}#{version if version else 'latest'}"
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# if cache_key in app_config["PROFILE_CACHE"]:
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# logger.info(f"Using cached profiles for IG {ig_name} (version: {version if version else 'latest'})")
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# profiles = app_config["PROFILE_CACHE"][cache_key]
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# for profile in profiles:
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# if profile.name == profile_id or profile.url.endswith(profile_id):
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# break
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# else:
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# logger.error(f"Profile {profile_id} not found in cached profiles for IG {ig_name} (version: {version if version else 'latest'})")
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# raise HTTPException(status_code=404, detail=f"Profile '{profile_id}' not found in IG '{ig_name}' (version: {version if version else 'latest'}).")
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# else:
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# profiles = await list_profiles(ig_id, version)
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# # Fetch package metadata
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# packages = app_config["MANUAL_PACKAGE_CACHE"]
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# if not packages:
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# logger.error("Package cache is empty. Please refresh the cache using /refresh-cache.")
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# raise HTTPException(status_code=500, detail="Package cache is empty. Please refresh the cache.")
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# package = None
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# for pkg in packages:
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# if pkg['package_name'].lower() == ig_name.lower():
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# package = pkg
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# break
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# if not package:
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# logger.error(f"IG {ig_name} not found in cached packages.")
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# raise HTTPException(status_code=404, detail=f"IG '{ig_name}' not found.")
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# # Determine the version to fetch
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# if version:
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# target_version = None
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# for ver_entry in package['all_versions']:
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# if ver_entry['version'] == version:
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# target_version = ver_entry['version']
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# break
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# if not target_version:
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# logger.error(f"Version {version} not found for IG {ig_name}.")
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# raise HTTPException(status_code=404, detail=f"Version '{version}' not found for IG '{ig_name}'.")
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# else:
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# target_version = package['latest_version']
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# version = target_version
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# logger.info(f"No version specified, using latest version: {target_version}")
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# # Download the package
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# tgz_path, error = download_package(ig_name, version, package)
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# if not tgz_path:
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# logger.error(f"Failed to download package for IG {ig_name} (version: {version}): {error}")
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# if "404" in error:
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# raise HTTPException(status_code=404, detail=f"Package for IG '{ig_name}' (version: {version}) not found.")
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# raise HTTPException(status_code=500, detail=f"Failed to fetch package: {error}")
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# # Extract the specific profile from the .tgz file
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# profile_resource = None
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# try:
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# with tarfile.open(tgz_path, mode="r:gz") as tar:
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# for member in tar.getmembers():
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# if member.name.endswith('.json') and 'StructureDefinition' in member.name:
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# f = tar.extractfile(member)
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# if f:
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# resource = json.load(f)
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# if resource.get("resourceType") == "StructureDefinition":
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# resource_name = resource.get("name", "")
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# resource_url = resource.get("url", "")
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# if resource_name == profile_id or resource_url.endswith(profile_id):
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# profile_resource = resource
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# break
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# if not profile_resource:
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# logger.error(f"Profile {profile_id} not found in package for IG {ig_name} (version: {version})")
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# raise HTTPException(status_code=404, detail=f"Profile '{profile_id}' not found in IG '{ig_name}' (version: {version}).")
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# except Exception as e:
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# logger.error(f"Failed to extract profile {profile_id} from package for IG {ig_name} (version: {version}): {str(e)}")
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# raise HTTPException(status_code=500, detail=f"Failed to extract profile: {str(e)}")
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# # Strip narrative if requested
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# if not include_narrative:
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# logger.info(f"Stripping narrative from profile {profile_id}")
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# if "text" in profile_resource:
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# profile_resource["text"] = None
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# logger.info(f"Successfully retrieved profile {profile_id} for IG {ig_name} (version: {version})")
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# return StructureDefinition(resource=profile_resource)
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#------------------------------------------------------------------------------end
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@app.get("/igs/{ig_id}/profiles/{profile_id}", response_model=StructureDefinition)
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async def get_profile(ig_id: str, profile_id: str, version: Optional[str] = None, include_narrative: bool = True):
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@ -710,16 +857,26 @@ async def get_profile(ig_id: str, profile_id: str, version: Optional[str] = None
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try:
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with tarfile.open(tgz_path, mode="r:gz") as tar:
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for member in tar.getmembers():
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if member.name.endswith('.json') and 'StructureDefinition' in member.name:
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if member.name.endswith('.json'): # Check all JSON files
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logger.debug(f"Processing file: {member.name}")
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f = tar.extractfile(member)
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if f:
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resource = json.load(f)
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if resource.get("resourceType") == "StructureDefinition":
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resource_name = resource.get("name", "")
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resource_url = resource.get("url", "")
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if resource_name == profile_id or resource_url.endswith(profile_id):
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profile_resource = resource
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break
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try:
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resource = json.load(f)
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# Check if the resource is a StructureDefinition
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if resource.get("resourceType") == "StructureDefinition":
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logger.debug(f"Found StructureDefinition in file: {member.name}")
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resource_name = resource.get("name", "")
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resource_url = resource.get("url", "")
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if resource_name == profile_id or resource_url.endswith(profile_id):
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profile_resource = resource
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break
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else:
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logger.debug(f"File {member.name} is not a StructureDefinition, resourceType: {resource.get('resourceType', 'unknown')}")
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except json.JSONDecodeError as e:
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logger.warning(f"Failed to parse JSON in file {member.name}: {str(e)}")
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except Exception as e:
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logger.warning(f"Error processing file {member.name}: {str(e)}")
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if not profile_resource:
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logger.error(f"Profile {profile_id} not found in package for IG {ig_name} (version: {version})")
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raise HTTPException(status_code=404, detail=f"Profile '{profile_id}' not found in IG '{ig_name}' (version: {version}).")
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