patchy mcpatchy

patch here patch there patch everywhere

main.py

@@ -10,6 +10,7 @@ import tarfile
 import json
 from datetime import datetime, timedelta
 import asyncio
+import os
 
 # Import from core
 from core import (
@@ -381,7 +382,106 @@ async def search_igs(query: str = '', search_type: str = 'semantic'):
     finally:
         db.close()
         logger.info("Closed database session after search")
+#-----------------------------------------------------------------------------OLD
+# @app.get("/igs/{ig_id}/profiles", response_model=List[ProfileMetadata])
+# async def list_profiles(ig_id: str, version: Optional[str] = None):
+#     """List StructureDefinition profiles in the specified IG, optionally for a specific version."""
+#     logger.info(f"Listing profiles for IG: {ig_id}, version: {version}")
 
+#     # Parse ig_id for version if it includes a '#'
+#     ig_name = ig_id
+#     if '#' in ig_id:
+#         parts = ig_id.split('#', 1)
+#         ig_name = parts[0]
+#         if version and parts[1] != version:
+#             logger.warning(f"Version specified in ig_id ({parts[1]}) conflicts with version parameter ({version}). Using version parameter.")
+#         else:
+#             version = parts[1]
+#         logger.info(f"Parsed ig_id: name={ig_name}, version={version}")
+
+#     # Validate ig_name
+#     if not ig_name or not re.match(r'^[a-zA-Z0-9\.\-_]+$', ig_name):
+#         logger.error(f"Invalid IG name: {ig_name}")
+#         raise HTTPException(status_code=400, detail="Invalid IG name. Use format like 'hl7.fhir.au.core'.")
+
+#     # Validate version if provided
+#     if version and not re.match(r'^[a-zA-Z0-9\.\-_]+$', version):
+#         logger.error(f"Invalid version: {version}")
+#         raise HTTPException(status_code=400, detail="Invalid version format. Use format like '1.1.0-preview'.")
+
+#     # Check if profiles are cached
+#     cache_key = f"{ig_name}#{version if version else 'latest'}"
+#     if cache_key in app_config["PROFILE_CACHE"]:
+#         logger.info(f"Returning cached profiles for IG {ig_name} (version: {version if version else 'latest'})")
+#         return app_config["PROFILE_CACHE"][cache_key]
+
+#     # Fetch package metadata from cache
+#     packages = app_config["MANUAL_PACKAGE_CACHE"]
+#     if not packages:
+#         logger.error("Package cache is empty. Please refresh the cache using /refresh-cache.")
+#         raise HTTPException(status_code=500, detail="Package cache is empty. Please refresh the cache.")
+
+#     # Find the package
+#     package = None
+#     for pkg in packages:
+#         if pkg['package_name'].lower() == ig_name.lower():
+#             package = pkg
+#             break
+
+#     if not package:
+#         logger.error(f"IG {ig_name} not found in cached packages.")
+#         raise HTTPException(status_code=404, detail=f"IG '{ig_name}' not found.")
+
+#     # Determine the version to fetch
+#     if version:
+#         target_version = None
+#         for ver_entry in package['all_versions']:
+#             if ver_entry['version'] == version:
+#                 target_version = ver_entry['version']
+#                 break
+#         if not target_version:
+#             logger.error(f"Version {version} not found for IG {ig_name}.")
+#             raise HTTPException(status_code=404, detail=f"Version '{version}' not found for IG '{ig_name}'.")
+#     else:
+#         target_version = package['latest_version']
+#         version = target_version
+#         logger.info(f"No version specified, using latest version: {target_version}")
+
+#     # Download the package
+#     tgz_path, error = download_package(ig_name, version, package)
+#     if not tgz_path:
+#         logger.error(f"Failed to download package for IG {ig_name} (version: {version}): {error}")
+#         if "404" in error:
+#             raise HTTPException(status_code=404, detail=f"Package for IG '{ig_name}' (version: {version}) not found.")
+#         raise HTTPException(status_code=500, detail=f"Failed to fetch package: {error}")
+
+#     # Extract profiles from the .tgz file
+#     profiles = []
+#     try:
+#         with tarfile.open(tgz_path, mode="r:gz") as tar:
+#             for member in tar.getmembers():
+#                 if member.name.endswith('.json') and 'StructureDefinition' in member.name:
+#                     f = tar.extractfile(member)
+#                     if f:
+#                         resource = json.load(f)
+#                         if resource.get("resourceType") == "StructureDefinition":
+#                             profiles.append(ProfileMetadata(
+#                                 name=resource.get("name", ""),
+#                                 description=resource.get("description"),
+#                                 version=resource.get("version"),
+#                                 url=resource.get("url", "")
+#                             ))
+#     except Exception as e:
+#         logger.error(f"Failed to extract profiles from package for IG {ig_name} (version: {version}): {str(e)}")
+#         raise HTTPException(status_code=500, detail=f"Failed to extract profiles: {str(e)}")
+
+#     # Cache the profiles
+#     app_config["PROFILE_CACHE"][cache_key] = profiles
+#     logger.info(f"Cached {len(profiles)} profiles for IG {ig_name} (version: {version})")
+
+#     logger.info(f"Found {len(profiles)} profiles in IG {ig_name} (version: {version})")
+#     return profiles
+#----------------------------------------------------------------------------end
 @app.get("/igs/{ig_id}/profiles", response_model=List[ProfileMetadata])
 async def list_profiles(ig_id: str, version: Optional[str] = None):
     """List StructureDefinition profiles in the specified IG, optionally for a specific version."""
@@ -459,17 +559,27 @@ async def list_profiles(ig_id: str, version: Optional[str] = None):
     try:
         with tarfile.open(tgz_path, mode="r:gz") as tar:
             for member in tar.getmembers():
-                if member.name.endswith('.json') and 'StructureDefinition' in member.name:
+                if member.name.endswith('.json'):  # Check all JSON files
+                    logger.debug(f"Processing file: {member.name}")
                     f = tar.extractfile(member)
                     if f:
-                        resource = json.load(f)
+                        try:
-                        if resource.get("resourceType") == "StructureDefinition":
+                            resource = json.load(f)
-                            profiles.append(ProfileMetadata(
+                            # Check if the resource is a StructureDefinition
-                                name=resource.get("name", ""),
+                            if resource.get("resourceType") == "StructureDefinition":
-                                description=resource.get("description"),
+                                logger.debug(f"Found StructureDefinition in file: {member.name}")
-                                version=resource.get("version"),
+                                profiles.append(ProfileMetadata(
-                                url=resource.get("url", "")
+                                    name=resource.get("name", ""),
-                            ))
+                                    description=resource.get("description"),
+                                    version=resource.get("version"),
+                                    url=resource.get("url", "")
+                                ))
+                            else:
+                                logger.debug(f"File {member.name} is not a StructureDefinition, resourceType: {resource.get('resourceType', 'unknown')}")
+                        except json.JSONDecodeError as e:
+                            logger.warning(f"Failed to parse JSON in file {member.name}: {str(e)}")
+                        except Exception as e:
+                            logger.warning(f"Error processing file {member.name}: {str(e)}")
     except Exception as e:
         logger.error(f"Failed to extract profiles from package for IG {ig_name} (version: {version}): {str(e)}")
         raise HTTPException(status_code=500, detail=f"Failed to extract profiles: {str(e)}")
@@ -480,6 +590,153 @@ async def list_profiles(ig_id: str, version: Optional[str] = None):
 
     logger.info(f"Found {len(profiles)} profiles in IG {ig_name} (version: {version})")
     return profiles
+#------------------------------------------------------------------OLD
+# @app.get("/igs/{ig_id}/profiles/{profile_id}", response_model=StructureDefinition)
+# async def get_profile(ig_id: str, profile_id: str, version: Optional[str] = None, include_narrative: bool = True):
+#     """
+#     Retrieve a specific StructureDefinition from an Implementation Guide (IG).
+
+#     This endpoint fetches a specific FHIR StructureDefinition (profile) from the given IG.
+#     It supports optional version specification and an option to strip the narrative content.
+
+#     Args:
+#         ig_id (str): The ID of the Implementation Guide (e.g., 'hl7.fhir.au.core' or 'hl7.fhir.au.core#1.1.0-preview').
+#                      If the version is included in the ig_id (after '#'), it takes precedence unless overridden by the version parameter.
+#         profile_id (str): The ID or name of the profile to retrieve (e.g., 'AUCorePatient').
+#         version (str, optional): The version of the IG (e.g., '1.1.0-preview'). If not provided and ig_id contains a version,
+#                                  the version from ig_id is used; otherwise, the latest version is used.
+#         include_narrative (bool, optional): Whether to include the narrative (`text` element) in the StructureDefinition.
+#                                             Defaults to True. Set to False to strip the narrative, removing human-readable content.
+
+#     Returns:
+#         StructureDefinition: A dictionary containing the requested StructureDefinition resource.
+#                              The response includes the `resource` field with the StructureDefinition JSON.
+#                              If `include_narrative=False`, the `text` element will be set to null.
+
+#     Raises:
+#         HTTPException: 
+#             - 400: If the IG name, version, or profile ID is invalid.
+#             - 404: If the IG, version, or profile is not found.
+#             - 500: If an error occurs during package retrieval or profile extraction.
+
+#     Example:
+#         - GET /igs/hl7.fhir.au.core/profiles/AUCorePatient?version=1.1.0-preview
+#           Returns the AUCorePatient profile with narrative included.
+#         - GET /igs/hl7.fhir.au.core/profiles/AUCorePatient?version=1.1.0-preview&include_narrative=false
+#           Returns the AUCorePatient profile with the narrative (`text` element) stripped.
+#     """
+#     logger.info(f"Retrieving profile {profile_id} for IG: {ig_id}, version: {version}, include_narrative: {include_narrative}")
+
+#     # Parse ig_id for version if it includes a '#'
+#     ig_name = ig_id
+#     if '#' in ig_id:
+#         parts = ig_id.split('#', 1)
+#         ig_name = parts[0]
+#         if version and parts[1] != version:
+#             logger.warning(f"Version specified in ig_id ({parts[1]}) conflicts with version parameter ({version}). Using version parameter.")
+#         else:
+#             version = parts[1]
+#         logger.info(f"Parsed ig_id: name={ig_name}, version={version}")
+
+#     # Validate ig_name
+#     if not ig_name or not re.match(r'^[a-zA-Z0-9\.\-_]+$', ig_name):
+#         logger.error(f"Invalid IG name: {ig_name}")
+#         raise HTTPException(status_code=400, detail="Invalid IG name. Use format like 'hl7.fhir.au.core'.")
+
+#     # Validate version if provided
+#     if version and not re.match(r'^[a-zA-Z0-9\.\-_]+$', version):
+#         logger.error(f"Invalid version: {version}")
+#         raise HTTPException(status_code=400, detail="Invalid version format. Use format like '1.1.0-preview'.")
+
+#     # Validate profile_id
+#     if not profile_id or not re.match(r'^[a-zA-Z0-9\.\-_]+$', profile_id):
+#         logger.error(f"Invalid profile ID: {profile_id}")
+#         raise HTTPException(status_code=400, detail="Invalid profile ID format.")
+
+#     # Check if profiles are cached
+#     cache_key = f"{ig_name}#{version if version else 'latest'}"
+#     if cache_key in app_config["PROFILE_CACHE"]:
+#         logger.info(f"Using cached profiles for IG {ig_name} (version: {version if version else 'latest'})")
+#         profiles = app_config["PROFILE_CACHE"][cache_key]
+#         for profile in profiles:
+#             if profile.name == profile_id or profile.url.endswith(profile_id):
+#                 break
+#         else:
+#             logger.error(f"Profile {profile_id} not found in cached profiles for IG {ig_name} (version: {version if version else 'latest'})")
+#             raise HTTPException(status_code=404, detail=f"Profile '{profile_id}' not found in IG '{ig_name}' (version: {version if version else 'latest'}).")
+#     else:
+#         profiles = await list_profiles(ig_id, version)
+
+#     # Fetch package metadata
+#     packages = app_config["MANUAL_PACKAGE_CACHE"]
+#     if not packages:
+#         logger.error("Package cache is empty. Please refresh the cache using /refresh-cache.")
+#         raise HTTPException(status_code=500, detail="Package cache is empty. Please refresh the cache.")
+
+#     package = None
+#     for pkg in packages:
+#         if pkg['package_name'].lower() == ig_name.lower():
+#             package = pkg
+#             break
+
+#     if not package:
+#         logger.error(f"IG {ig_name} not found in cached packages.")
+#         raise HTTPException(status_code=404, detail=f"IG '{ig_name}' not found.")
+
+#     # Determine the version to fetch
+#     if version:
+#         target_version = None
+#         for ver_entry in package['all_versions']:
+#             if ver_entry['version'] == version:
+#                 target_version = ver_entry['version']
+#                 break
+#         if not target_version:
+#             logger.error(f"Version {version} not found for IG {ig_name}.")
+#             raise HTTPException(status_code=404, detail=f"Version '{version}' not found for IG '{ig_name}'.")
+#     else:
+#         target_version = package['latest_version']
+#         version = target_version
+#         logger.info(f"No version specified, using latest version: {target_version}")
+
+#     # Download the package
+#     tgz_path, error = download_package(ig_name, version, package)
+#     if not tgz_path:
+#         logger.error(f"Failed to download package for IG {ig_name} (version: {version}): {error}")
+#         if "404" in error:
+#             raise HTTPException(status_code=404, detail=f"Package for IG '{ig_name}' (version: {version}) not found.")
+#         raise HTTPException(status_code=500, detail=f"Failed to fetch package: {error}")
+
+#     # Extract the specific profile from the .tgz file
+#     profile_resource = None
+#     try:
+#         with tarfile.open(tgz_path, mode="r:gz") as tar:
+#             for member in tar.getmembers():
+#                 if member.name.endswith('.json') and 'StructureDefinition' in member.name:
+#                     f = tar.extractfile(member)
+#                     if f:
+#                         resource = json.load(f)
+#                         if resource.get("resourceType") == "StructureDefinition":
+#                             resource_name = resource.get("name", "")
+#                             resource_url = resource.get("url", "")
+#                             if resource_name == profile_id or resource_url.endswith(profile_id):
+#                                 profile_resource = resource
+#                                 break
+#         if not profile_resource:
+#             logger.error(f"Profile {profile_id} not found in package for IG {ig_name} (version: {version})")
+#             raise HTTPException(status_code=404, detail=f"Profile '{profile_id}' not found in IG '{ig_name}' (version: {version}).")
+#     except Exception as e:
+#         logger.error(f"Failed to extract profile {profile_id} from package for IG {ig_name} (version: {version}): {str(e)}")
+#         raise HTTPException(status_code=500, detail=f"Failed to extract profile: {str(e)}")
+
+#     # Strip narrative if requested
+#     if not include_narrative:
+#         logger.info(f"Stripping narrative from profile {profile_id}")
+#         if "text" in profile_resource:
+#             profile_resource["text"] = None
+
+#     logger.info(f"Successfully retrieved profile {profile_id} for IG {ig_name} (version: {version})")
+#     return StructureDefinition(resource=profile_resource)
+#------------------------------------------------------------------------------end
 
 @app.get("/igs/{ig_id}/profiles/{profile_id}", response_model=StructureDefinition)
 async def get_profile(ig_id: str, profile_id: str, version: Optional[str] = None, include_narrative: bool = True):
@@ -492,7 +749,7 @@ async def get_profile(ig_id: str, profile_id: str, version: Optional[str] = None
     Args:
         ig_id (str): The ID of the Implementation Guide (e.g., 'hl7.fhir.au.core' or 'hl7.fhir.au.core#1.1.0-preview').
                      If the version is included in the ig_id (after '#'), it takes precedence unless overridden by the version parameter.
-        profile_id (str): The ID or name of the profile to retrieve (e.g., 'AUCorePatient').
+        profile_id (str): The ID or name of the profile to retrieve (e.g., 'AUCorePatient' or 'DAV_PR_ERP_Abrechnungszeilen').
         version (str, optional): The version of the IG (e.g., '1.1.0-preview'). If not provided and ig_id contains a version,
                                  the version from ig_id is used; otherwise, the latest version is used.
         include_narrative (bool, optional): Whether to include the narrative (`text` element) in the StructureDefinition.
@@ -546,15 +803,24 @@ async def get_profile(ig_id: str, profile_id: str, version: Optional[str] = None
     # Check if profiles are cached
     cache_key = f"{ig_name}#{version if version else 'latest'}"
     if cache_key in app_config["PROFILE_CACHE"]:
-        logger.info(f"Using cached profiles for IG {ig_name} (version: {version if version else 'latest'})")
+        logger.info(f"Cache hit for IG {ig_name} (version: {version if version else 'latest'})")
         profiles = app_config["PROFILE_CACHE"][cache_key]
+        logger.debug(f"Cached profiles: {[profile.name for profile in profiles]}")
+        profile_found = False
+        # Normalize profile_id for matching (remove hyphens, underscores, and convert to lowercase)
+        normalized_profile_id = profile_id.lower().replace('-', '').replace('_', '')
         for profile in profiles:
-            if profile.name == profile_id or profile.url.endswith(profile_id):
+            normalized_name = profile.name.lower().replace('-', '').replace('_', '') if profile.name else ''
+            normalized_url_end = profile.url.lower().split('/')[-1].replace('-', '').replace('_', '') if profile.url else ''
+            if normalized_name == normalized_profile_id or normalized_url_end == normalized_profile_id:
+                logger.info(f"Found profile {profile_id} in cached profiles: name={profile.name}, url={profile.url}")
+                profile_found = True
                 break
-        else:
+        if not profile_found:
             logger.error(f"Profile {profile_id} not found in cached profiles for IG {ig_name} (version: {version if version else 'latest'})")
             raise HTTPException(status_code=404, detail=f"Profile '{profile_id}' not found in IG '{ig_name}' (version: {version if version else 'latest'}).")
     else:
+        logger.info(f"Cache miss for IG {ig_name} (version: {version if version else 'latest'}), calling list_profiles")
         profiles = await list_profiles(ig_id, version)
 
     # Fetch package metadata
@@ -588,7 +854,15 @@ async def get_profile(ig_id: str, profile_id: str, version: Optional[str] = None
         version = target_version
         logger.info(f"No version specified, using latest version: {target_version}")
 
+    # Check directory state before calling download_package
+    instance_dir = "instance"
+    if os.path.exists(instance_dir):
+        logger.info(f"Directory {instance_dir} exists before calling download_package in get_profile")
+    else:
+        logger.warning(f"Directory {instance_dir} does NOT exist before calling download_package in get_profile")
+
     # Download the package
+    logger.info(f"Calling download_package for IG {ig_name} (version: {version}) in get_profile")
     tgz_path, error = download_package(ig_name, version, package)
     if not tgz_path:
         logger.error(f"Failed to download package for IG {ig_name} (version: {version}): {error}")
@@ -600,17 +874,34 @@ async def get_profile(ig_id: str, profile_id: str, version: Optional[str] = None
     profile_resource = None
     try:
         with tarfile.open(tgz_path, mode="r:gz") as tar:
+            # Normalize profile_id for matching (remove hyphens, underscores, and convert to lowercase)
+            normalized_profile_id = profile_id.lower().replace('-', '').replace('_', '')
             for member in tar.getmembers():
-                if member.name.endswith('.json') and 'StructureDefinition' in member.name:
+                if member.name.endswith('.json'):  # Check all JSON files
+                    logger.debug(f"Processing file: {member.name}")
                     f = tar.extractfile(member)
                     if f:
-                        resource = json.load(f)
+                        try:
-                        if resource.get("resourceType") == "StructureDefinition":
+                            resource = json.load(f)
-                            resource_name = resource.get("name", "")
+                            # Check if the resource is a StructureDefinition
-                            resource_url = resource.get("url", "")
+                            if resource.get("resourceType") == "StructureDefinition":
-                            if resource_name == profile_id or resource_url.endswith(profile_id):
+                                resource_name = resource.get("name", "")
-                                profile_resource = resource
+                                resource_url = resource.get("url", "")
-                                break
+                                # Normalize name and URL for matching
+                                normalized_name = resource_name.lower().replace('-', '').replace('_', '') if resource_name else ''
+                                normalized_url_end = resource_url.lower().split('/')[-1].replace('-', '').replace('_', '') if resource_url else ''
+                                logger.debug(f"Found StructureDefinition in file: {member.name}, name={resource_name}, url={resource_url}, normalized_name={normalized_name}, normalized_url_end={normalized_url_end}")
+                                # Match profile_id against name or the last segment of the URL
+                                if normalized_name == normalized_profile_id or normalized_url_end == normalized_profile_id:
+                                    logger.info(f"Matched profile {profile_id} in file {member.name}: name={resource_name}, url={resource_url}")
+                                    profile_resource = resource
+                                    break
+                            else:
+                                logger.debug(f"File {member.name} is not a StructureDefinition, resourceType: {resource.get('resourceType', 'unknown')}")
+                        except json.JSONDecodeError as e:
+                            logger.warning(f"Failed to parse JSON in file {member.name}: {str(e)}")
+                        except Exception as e:
+                            logger.warning(f"Error processing file {member.name}: {str(e)}")
         if not profile_resource:
             logger.error(f"Profile {profile_id} not found in package for IG {ig_name} (version: {version})")
             raise HTTPException(status_code=404, detail=f"Profile '{profile_id}' not found in IG '{ig_name}' (version: {version}).")
@@ -626,7 +917,6 @@ async def get_profile(ig_id: str, profile_id: str, version: Optional[str] = None
 
     logger.info(f"Successfully retrieved profile {profile_id} for IG {ig_name} (version: {version})")
     return StructureDefinition(resource=profile_resource)
-
 @app.get("/status", response_model=RefreshStatus)
 async def get_refresh_status():
     """Get the status of the last cache refresh."""