Fix register_package not registering dependency packages & add finer public API control over package processing (#327)

Author: luisfabib

fhircraft/fhir/packages/client.py

@@ -263,8 +263,8 @@ def _process_package_tar(
         Args:
             tar_file: Opened tar file containing the package
         """
-        results_count = 0
         errors = []
+        results = []
 
         # First, look for package.json to find dependencies
         if install_dependencies:
@@ -287,12 +287,13 @@ def _process_package_tar(
                             if f"{dependency}@{version}" in self.history:
                                 continue
                             try:
-                                self.load_resources_from_package(
+                                dependency_results = self.load_resources_from_package(
                                     target_resource,
                                     dependency,
                                     version,
                                     fail_if_exists=False,
                                 )
+                                results.extend(dependency_results)
                             except Exception as e:
                                 errors.append(
                                     f"Failed to download and load dependency {dependency}: {e}"
@@ -301,7 +302,6 @@ def _process_package_tar(
                     errors.append(
                         f"Error processing package.json looking for dependencies: {e}"
                     )
-        results = []
         for member in tar_file.getmembers():
             if not member.isfile():
                 continue
@@ -324,7 +324,6 @@ def _process_package_tar(
                         # Check if it's a StructureDefinition resource
                         if json_data.get("resourceType") == target_resource:
                             results.append(json_data)
-                            results_count += 1
 
                 except Exception as e:
                     errors.append(f"Error processing {member.name}: {e}")

fhircraft/fhir/resources/definitions/registry.py

@@ -9,6 +9,7 @@
 from dataclasses import asdict, dataclass, field
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Tuple, Union
+import warnings
 
 import requests
 from pydantic import BaseModel
@@ -293,13 +294,30 @@ def download_url(url: str) -> Dict[str, Any]:
         response.raise_for_status()
         return response.json()
 
-    def download_package(self, package_name: str, version: str) -> None:
+    def download_package(
+        self,
+        package_name: str,
+        version: str,
+        skip_invalid: bool = False,
+        include_dependencies: bool = True,
+    ) -> None:
         """Download a package from the registry and add its structure definitions to the registry."""
         for sd in self._package_client.load_resources_from_package(
-            "StructureDefinition", package_name, version
+            "StructureDefinition",
+            package_name,
+            version,
+            install_dependencies=include_dependencies,
         ):
-            structure_definition = self._validate_structure_definition(sd)
-            self.add(structure_definition)
+            try:
+                structure_definition = self._validate_structure_definition(sd)
+                self.add(structure_definition)
+            except ValueError as e:
+                if not skip_invalid:
+                    raise e
+                else:
+                    warnings.warn(
+                        f"Skipping invalid structure definition {sd.get('url', 'unknown')} in package {package_name} version {version}:\n{e}"
+                    )
 
     def set_registry_base_url(self, base_url: str) -> None:
         """Change the package registry base URL."""

fhircraft/fhir/resources/factory/core.py

@@ -108,15 +108,25 @@ def build(
 
         return self._build(structure_definition, mixins=mixins, mode=mode)
 
-    def register_package(self, package_name: str, version: str) -> None:
+    def register_package(
+        self,
+        package_name: str,
+        version: str,
+        skip_invalid: bool = False,
+        include_dependencies: bool = True,
+    ) -> None:
         """
         Download and register all StructureDefinitions from a FHIR npm package.
 
         Args:
             package_name: Package identifier (e.g. ``"hl7.fhir.us.mcode"``).
             version: Package version string (e.g. ``"1.0.0"``).
+            skip_invalid: Whether to skip invalid StructureDefinitions.
+            include_dependencies: Whether to include dependencies when downloading the package.
         """
-        self.definition_registry.download_package(package_name, version)
+        self.definition_registry.download_package(
+            package_name, version, skip_invalid, include_dependencies
+        )
 
     def register(
         self,