Merge pull request #42 from SvenSommer/feature/config-object

Feature/config object

.devcontainer/devcontainer.json

@@ -5,12 +5,15 @@
         "ghcr.io/devcontainers-contrib/features/black:2": {},
         "node": "18"
     },
-    "forwardPorts": [4200],
+    "forwardPorts": [
+        4200
+    ],
     "postCreateCommand": "pip3 install --user -r requirements.txt && npm install -g @angular/cli@16",
     "customizations": {
         "vscode": {
             "extensions": [
                 "ms-python.black-formatter",
+                "ms-python.flake8",
                 "ms-python.debugpy",
                 "ms-python.python",
                 "samuelcolvin.jinjahtml",

service/src/main.py

@@ -9,6 +9,7 @@
     create_results_html,
     gen_mapping_dict,
 )
+from structure_comparer.config import Config
 
 
 def write_mapping_json(structured_mapping: dict, output_file: Path):
@@ -26,7 +27,8 @@ def get_args():
         type=Path,
         help="The project directory containing the profiles and config",
     )
-    parser.add_argument("--html", action="store_true", help="Generate html files")
+    parser.add_argument("--html", action="store_true",
+                        help="Generate html files")
     parser.add_argument(
         "--json",
         action="store_true",
@@ -39,25 +41,23 @@ def get_args():
 if __name__ == "__main__":
     args = get_args()
 
-    config = json.loads((args.project_dir / "config.json").read_text())
+    config = Config.from_json(args.project_dir / "config.json")
 
     # Read the manual entries
-    manual_entries_file = config.get("manual_entries_file", "manual_entries.yaml")
+    manual_entries_file = config.manual_entries_file
     MANUAL_ENTRIES.read(args.project_dir / manual_entries_file)
 
-    profiles_to_compare = config["profiles_to_compare"]
-    data_dir = args.project_dir / config.get("data_dir", "data")
-    structured_mapping = compare_profiles(profiles_to_compare, data_dir)
+    data_dir = args.project_dir / config.data_dir
+    structured_mapping = compare_profiles(config.profiles_to_compare, data_dir)
 
     if args.html:
         # Create the result html files
-        show_remarks = config.get("show_remarks", True)
-        html_output_dir = args.project_dir / config.get("html_output_dir", "html")
+        show_remarks = config.show_remarks
+        html_output_dir = args.project_dir / \
+            config.html_output_dir
         create_results_html(structured_mapping, html_output_dir, show_remarks)
 
     if args.json:
         # Generate the mapping dict and write to file
-        mapping_output_file = args.project_dir / config.get(
-            "mapping_output_file", "mapping.json"
-        )
+        mapping_output_file = args.project_dir / config.mapping_output_file
         write_mapping_json(structured_mapping, mapping_output_file)

service/src/server.py

@@ -216,7 +216,7 @@ def get_mapping(id: str):
                   type: string
                 classification:
                   type: string
-                classifications_allowed
+                classifications_allowed:
                   type: array
                   items:
                     string

service/src/structure_comparer/compare.py

@@ -1,9 +1,9 @@
 import logging
 from collections import OrderedDict
 from pathlib import Path
-from profile import Profile
 from typing import Dict, List
 
+from .config import CompareConfig
 from .classification import Classification
 from .consts import REMARKS
 from .data.comparison import Comparison, ComparisonField, ProfileField
@@ -35,7 +35,7 @@
 logger = logging.getLogger()
 
 
-def compare_profiles(profiles_to_compare: List, datapath: Path):
+def compare_profiles(profiles_to_compare: List[CompareConfig], datapath: Path):
     """
     Compares the presence of properties in KBV and ePA profiles.
     """
@@ -46,7 +46,7 @@ def compare_profiles(profiles_to_compare: List, datapath: Path):
     return structured_results
 
 
-def load_profiles(profiles_to_compare: List, datapath: Path) -> Dict[str, ProfileMap]:
+def load_profiles(profiles_to_compare: List[CompareConfig], datapath: Path) -> Dict[str, ProfileMap]:
     """
     Loads the FHIR structure definitions from the local JSON files.
     """
@@ -60,7 +60,8 @@ def load_profiles(profiles_to_compare: List, datapath: Path) -> Dict[str, Profil
 def _compare_profiles(profile_maps: Dict[str, ProfileMap]) -> Dict[str, Comparison]:
     mapping = {}
     for map in profile_maps.values():
-        sources_key = tuple((entry.name, entry.version) for entry in map.sources)
+        sources_key = tuple((entry.name, entry.version)
+                            for entry in map.sources)
         target_key = (map.target.name, map.target.version)
         key = str((sources_key, target_key))
         mapping[key] = compare_profile(map)
@@ -95,7 +96,8 @@ def generate_comparison(profile_map: ProfileMap) -> Comparison:
                 not (field_entry := comparison.fields.get(field.name))
                 or field_entry.extension != field.extension
             ):
-                comparison.fields[field.name] = ComparisonField(field.name, field.id)
+                comparison.fields[field.name] = ComparisonField(
+                    field.name, field.id)
                 comparison.fields[field.name].extension = field.extension
 
             profile_key = source_profile.profile_key
@@ -180,7 +182,8 @@ def _classify_remark_field(
         )
 
         # If there is a remark in the manual entry, use it else use the default remark
-        remark = manual_entry.get(MANUAL_ENTRIES_REMARK, REMARKS[classification])
+        remark = manual_entry.get(
+            MANUAL_ENTRIES_REMARK, REMARKS[classification])
 
         # If the classification needs extra information, generate the remark with the extra information
         if classification in EXTRA_CLASSIFICATIONS:
@@ -201,7 +204,7 @@ def _classify_remark_field(
         if classification in EXTRA_CLASSIFICATIONS:
 
             # Cut away the common part with the parent and add the remainder to the parent's extra
-            extra = parent_update.extra + field.name[len(parent) :]
+            extra = parent_update.extra + field.name[len(parent):]
             remark = REMARKS[classification].format(extra)
 
         # Else use the parent's remark

service/src/structure_comparer/config.py

@@ -0,0 +1,99 @@
+from datetime import datetime, timedelta, timezone
+import json
+from pathlib import Path
+from typing import Dict, List
+
+
+class Config:
+    def __init__(self) -> None:
+        self.manual_entries_file: str = None
+        self.data_dir: str = None
+        self.html_output_dir: str = None
+        self.mapping_output_file: str = None
+        self.profiles_to_compare: List[CompareConfig] = None
+        self.show_remarks: bool = None
+
+    @staticmethod
+    def from_json(file: str | Path) -> "Config":
+        file = Path(file)
+        dict_ = json.loads(file.read_text())
+        return Config.from_dict(dict_)
+
+    @staticmethod
+    def from_dict(dict_: Dict) -> "Config":
+        config = Config()
+        config.manual_entries_file = dict_.get(
+            "manual_entries_file", "manual_entries.yaml"
+        )
+        config.data_dir = dict_.get("data_dir", "data")
+        config.html_output_dir = dict_.get("html_output_dir", "docs")
+        config.mapping_output_file = dict_.get(
+            "mapping_output_file", "mapping.json")
+        config.profiles_to_compare = [
+            CompareConfig.from_dict(compare)
+            for compare in dict_.get("profiles_to_compare")
+        ]
+        config.show_remarks = dict_.get("show_remarks", True)
+        return config
+
+
+class CompareConfig:
+    def __init__(self) -> None:
+        self.id = None
+        self.version: str = None
+        self.status: str = None
+        self.mappings: MappingConfig = None
+        self.last_updated: str = None
+        self.status: str = None
+
+    @staticmethod
+    def from_dict(dict_: Dict) -> "CompareConfig":
+        config = CompareConfig()
+        config.id = dict_["id"]
+        config.version = dict_.get("version")
+
+        if config.version is None:
+            raise KeyError(
+                "The 'version' key is not set in the configuration of the mapping. Please set the version and try again."
+            )
+
+        config.status = dict_.get("status", "draft")
+        config.mappings = MappingConfig.from_dict(dict_.get("mappings"))
+        config.last_updated = dict_.get("last_updated") or (
+            datetime.now(timezone.utc) + timedelta(hours=2)
+        ).strftime("%Y-%m-%d %H:%M:%S")
+        return config
+
+
+class MappingConfig:
+    def __init__(self) -> None:
+        self.source_profiles: List[ProfileConfig] = None
+        self.target_profile: ProfileConfig = None
+
+    @staticmethod
+    def from_dict(dict_: Dict) -> "MappingConfig":
+        config = MappingConfig()
+        config.source_profiles = [
+            ProfileConfig.from_dict(profile) for profile in dict_.get("sourceprofiles")
+        ]
+        config.target_profile = ProfileConfig.from_dict(
+            dict_.get("targetprofile"))
+        return config
+
+
+class ProfileConfig:
+    def __init__(self) -> None:
+        self.file: str = None
+        self.version: str = None
+        self.simplifier_url: str = None
+        self.file_download_url: str = None
+
+    @staticmethod
+    def from_dict(dict_: Dict) -> "ProfileConfig":
+        config = ProfileConfig()
+        config.file = dict_["file"]
+        config.version = dict_.get("version")
+        config.simplifier_url = dict_.get("simplifier_url")
+        config.file_download_url = dict_.get("file_download_url")
+
+        return config

service/src/structure_comparer/data/profile.py

@@ -1,10 +1,11 @@
-import datetime
 import json
 from collections import OrderedDict
 from pathlib import Path
 from typing import Dict, List
 from uuid import uuid4
 
+from structure_comparer.config import CompareConfig, ProfileConfig
+
 IGNORE_ENDS = ["id", "extension", "modifierExtension"]
 IGNORE_SLICES = [
     "slice(url)",
@@ -27,25 +28,19 @@ def __init__(self) -> None:
         self.status: str = None
 
     @staticmethod
-    def from_json(profile_mapping: Dict, datapath: Path) -> "ProfileMap":
-        sources = profile_mapping["mappings"]["sourceprofiles"]
-        target = profile_mapping["mappings"]["targetprofile"]
+    def from_json(compare_config: CompareConfig, datapath: Path) -> "ProfileMap":
+        sources = compare_config.mappings.source_profiles
+        target = compare_config.mappings.target_profile
 
         profiles_map = ProfileMap()
-        profiles_map.id = profile_mapping["id"]
+        profiles_map.id = compare_config.id
         profiles_map.sources = [
             Profile.from_dict(source, datapath) for source in sources
         ]
         profiles_map.target = Profile.from_dict(target, datapath)
-        profiles_map.version = profile_mapping.get("version")
-        if not profiles_map.version:
-            raise ValueError(
-                "The 'version' key is not set in the configuration of the mapping. Please set the version and try again."
-            )
-        profiles_map.last_updated = profile_mapping.get("last_updated") or (
-            datetime.datetime.now(datetime.timezone.utc) + datetime.timedelta(hours=2)
-        ).strftime("%Y-%m-%d %H:%M:%S")
-        profiles_map.status = profile_mapping.get("status", "draft")
+        profiles_map.version = compare_config.version
+        profiles_map.last_updated = compare_config.last_updated
+        profiles_map.status = compare_config.status
 
         return profiles_map
 
@@ -79,20 +74,21 @@ def __repr__(self) -> str:
         return str(self)
 
     @staticmethod
-    def from_dict(data: Dict, datapath: Path) -> "Profile":
-        file_path = datapath / data["file"]
+    def from_dict(config: ProfileConfig, datapath: Path) -> "Profile":
+        file_path = datapath / config.file
         if not file_path.exists():
             raise FileNotFoundError(
-                f"The file {file_path} does not exist. Please check the file path and try again."
+                f"The file {
+                    file_path} does not exist. Please check the file path and try again."
             )
 
         content = json.loads(file_path.read_text())
 
         profile = Profile(
             name=content["name"],
-            version=data.get("version"),
-            simplifier_url=data.get("simplifier_url"),
-            file_download_url=data.get("file_download_url"),
+            version=config.version,
+            simplifier_url=config.simplifier_url,
+            file_download_url=config.file_download_url,
         )
 
         extracted_elements = _extract_elements(content["snapshot"]["element"])

service/src/structure_comparer/serve.py

@@ -1,4 +1,3 @@
-import json
 from pathlib import Path
 
 from flask import jsonify
@@ -13,16 +12,19 @@
     MANUAL_ENTRIES_CLASSIFICATION,
     MANUAL_ENTRIES_EXTRA,
 )
+from .config import Config
 
 
 def init_project(project_dir: Path):
-    project_obj = lambda: None
+    def project_obj():
+        return None
+
     project_obj.dir = project_dir
-    project_obj.config = json.loads((project_dir / "config.json").read_text())
-    project_obj.data_dir = project_dir / project_obj.config.get("data_dir", "data")
+    project_obj.config = Config.from_json(project_dir / "config.json")
+    project_obj.data_dir = project_dir / project_obj.config.data_dir
 
     # Get profiles to compare
-    project_obj.profiles_to_compare_list = project_obj.config["profiles_to_compare"]
+    project_obj.profiles_to_compare_list = project_obj.config.profiles_to_compare
 
     # Load profiles
     load_profiles(project_obj)
@@ -34,22 +36,26 @@ def init_project(project_dir: Path):
 
 
 def read_manual_entries(project):
-    manual_entries_file = project.dir / project.config.get(
-        "manual_entries_file", "manual_entries.json"
-    )
+    manual_entries_file = project.dir / project.config.manual_entries_file
+
+    if not manual_entries_file.exists():
+        manual_entries_file.touch()
+
     MANUAL_ENTRIES.read(manual_entries_file)
 
 
 def load_profiles(project):
-    profile_maps = _load_profiles(project.profiles_to_compare_list, project.data_dir)
+    profile_maps = _load_profiles(
+        project.profiles_to_compare_list, project.data_dir)
     project.comparisons = {
         entry.id: generate_comparison(entry) for entry in profile_maps.values()
     }
 
 
 def get_classifications_int():
     classifications = [
-        {"value": c.value, "remark": REMARKS[c], "instruction": INSTRUCTIONS[c]}
+        {"value": c.value, "remark": REMARKS[c],
+            "instruction": INSTRUCTIONS[c]}
         for c in Classification
     ]
     return jsonify({"classifications": classifications})
@@ -137,7 +143,8 @@ def post_mapping_classification_int(
     # Check if action is allowed for this field
     if action not in field.classifications_allowed:
         raise ValueError(
-            f"action '{action.value}' not allowed for this field, allowed: {', '.join([field.value for field in field.classifications_allowed])}"
+            f"action '{action.value}' not allowed for this field, allowed: {
+                ', '.join([field.value for field in field.classifications_allowed])}"
         )
 
     # Build the entry that should be created/updated