Add results endpoint to download a static html file

.github/workflows/format.yaml

@@ -0,0 +1,30 @@
+name: Check formatting
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [main]
+
+jobs:
+  black:
+    name: Black
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Install pipx
+        run: sudo apt update && sudo apt install pipx && pipx ensurepath
+
+      - name: Install Black
+        run: pipx install --global black
+
+      - name: Check formatting
+        run: black --check --diff --include='.*\.py' ./service

.github/workflows/unittest.yml

@@ -4,10 +4,10 @@ name: Run Unittests
 
 # Controls when the action will run.
 on:
-  push:
-    paths: [ main ]
-  pull_request:
-    branches: [ main ]
+  # push:
+  #   paths: [ main ]
+  # pull_request:
+  #   branches: [ main ]
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:

.vscode/launch.json

@@ -13,7 +13,7 @@
             "justMyCode": true,
             "args": [
                 "--project-dir",
-                "../../projects/erp",
+                "../../../structure-comparer-projects/erp",
                 "--html",
                 "--json"
             ],

service/README.md

@@ -16,6 +16,17 @@ From `service/` build and start the image with
 docker compose up
 ```
 
+## CLI mode (WIP)
+The CLI mode is currently a work in progress. However, the following functionality is already available:
+
+### Generating a file containing a mapping 
+(Currently only HTML is supported, but JSON support is coming soon)
+```bash
+python -m structure_comparer output --project-dir {project directory} --format html --mapping_id {mapping id}
+```
+Both --format and --mapping_id are optional. 
+The default format is HTML. If --mapping_id is omitted, the tool will generate files for all the mappings contained in the project.
+
 ### Developers
 
 The project uses _Poetry_ for the project set-up but can also be installed with plain `pip`.

service/src/mapper.py

@@ -1,48 +1,56 @@
 import json
 
+
 def load_json_file(file_path):
     """
     Lädt JSON-Daten aus einer Datei.
     """
-    with open(file_path, 'r') as file:
+    with open(file_path, "r") as file:
         return json.load(file)
 
+
 def map_medication_code_coding(kbv_medication, epa_medication):
     """
     Mappt das Medication.code.coding-Element von einem KBV-Profil zum ePA-Profil.
     """
-    if 'code' in kbv_medication and 'coding' in kbv_medication['code']:
-        epa_medication['code'] = {'coding': []}
-        for coding in kbv_medication['code']['coding']:
-            epa_medication['code']['coding'].append({
-                'system': coding.get('system', ''),
-                'code': coding.get('code', ''),
-                'display': coding.get('display', '')
-            })
+    if "code" in kbv_medication and "coding" in kbv_medication["code"]:
+        epa_medication["code"] = {"coding": []}
+        for coding in kbv_medication["code"]["coding"]:
+            epa_medication["code"]["coding"].append(
+                {
+                    "system": coding.get("system", ""),
+                    "code": coding.get("code", ""),
+                    "display": coding.get("display", ""),
+                }
+            )
+
 
 def map_medication_amount(kbv_medication, epa_medication):
     """
     Mappt das Medication.amount-Element von einem KBV-Profil zum ePA-Profil.
     """
-    if 'amount' in kbv_medication:
-        epa_medication['amount'] = {
-            'numerator': {
-                'value': kbv_medication['amount'].get('numerator', {}).get('value', ''),
-                'unit': kbv_medication['amount'].get('numerator', {}).get('unit', ''),
-                'system': 'http://unitsofmeasure.org',
-                'code': kbv_medication['amount'].get('numerator', {}).get('code', '')
+    if "amount" in kbv_medication:
+        epa_medication["amount"] = {
+            "numerator": {
+                "value": kbv_medication["amount"].get("numerator", {}).get("value", ""),
+                "unit": kbv_medication["amount"].get("numerator", {}).get("unit", ""),
+                "system": "http://unitsofmeasure.org",
+                "code": kbv_medication["amount"].get("numerator", {}).get("code", ""),
+            },
+            "denominator": {
+                "value": kbv_medication["amount"]
+                .get("denominator", {})
+                .get("value", ""),
+                "unit": kbv_medication["amount"].get("denominator", {}).get("unit", ""),
+                "system": "http://unitsofmeasure.org",
+                "code": kbv_medication["amount"].get("denominator", {}).get("code", ""),
             },
-            'denominator': {
-                'value': kbv_medication['amount'].get('denominator', {}).get('value', ''),
-                'unit': kbv_medication['amount'].get('denominator', {}).get('unit', ''),
-                'system': 'http://unitsofmeasure.org',
-                'code': kbv_medication['amount'].get('denominator', {}).get('code', '')
-            }
         }
 
+
 def main():
-    kbv_file_path = 'data/Instances/KBV_PR_ERP_Medication.json'
-    epa_file_path = 'data/Instances/example-epa-medication-2.json'
+    kbv_file_path = "data/Instances/KBV_PR_ERP_Medication.json"
+    epa_file_path = "data/Instances/example-epa-medication-2.json"
 
     # Lade KBV- und ePA-Medikationsdaten
     kbv_medication = load_json_file(kbv_file_path)
@@ -55,5 +63,6 @@ def main():
     # Ergebnis ausgeben
     print("Mapped ePA Medication:", json.dumps(epa_medication, indent=4))
 
+
 if __name__ == "__main__":
     main()

service/src/structure_comparer/__main__.py

@@ -1,14 +1,39 @@
 import argparse
+from pathlib import Path
 
 from .serve import serve
+from .output import output
 
 parser = argparse.ArgumentParser(description="Compare profiles and generate mapping")
 
-subparsers = parser.add_subparsers(dest="cmd")
+subparsers = parser.add_subparsers(dest="cmd", required=True)
 
 parser_serve = subparsers.add_parser("serve", help="start the server")
 
-args = parser.parse_args()
+parser_output = subparsers.add_parser("output", help="generate output files")
+parser_output.add_argument(
+    "--project-dir",
+    type=Path,
+    required=True,
+    help="The project directory containing the profiles and config",
+)
+parser_output.add_argument(
+    "--format",
+    choices=["json", "html"],
+    default="html",
+    help="The output format (default: html)",
+)
+parser_output.add_argument(
+    "--mapping_id",
+    type=str,
+    default=None,
+    help="The ID of the mapping to generate output for (default: all mappings)",
+)
 
+args = parser.parse_args()
 if args.cmd == "serve":
     serve()
+elif args.cmd == "output":
+    output(args.project_dir, args.format, args.mapping_id)
+else:
+    parser.print_help()

service/src/structure_comparer/data/profile.py

@@ -165,7 +165,7 @@ def ref_types(self) -> list[str]:
             [
                 p
                 for t in self.__data.type
-                if t.code == "Reference"
+                if t.code == "Reference" and t.targetProfile is not None
                 for p in t.targetProfile
             ]
             if self.__data.type is not None

service/src/structure_comparer/files/template.html.j2

@@ -2,32 +2,34 @@
 <html>
 
 <head>
-    <title>Mapping: {% for profile in source_profiles %}{{ profile['key'] }}{% if not loop.last %}, {% endif %}{% endfor %} in {{ target_profile['key'] }}</title>
-    <link rel='stylesheet' type='text/css' href='./{{ css_file }}'>
+    <title>Mapping: {% for profile in source_profiles %}{{ profile['key'] }}{% if not loop.last %}, {% endif %}{% endfor %} in {{ target_profile['key'] }}</title>       
     <link rel='stylesheet' type='text/css' href='https://cdn.datatables.net/1.11.3/css/jquery.dataTables.min.css'>
     <link rel='stylesheet' href='https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/all.min.css'>
+    <style>
+        {{ inline_css | safe }}
+    </style> 
     <script type='text/javascript' src='https://code.jquery.com/jquery-3.6.0.min.js'></script>
     <script type='text/javascript' src='https://cdn.datatables.net/1.11.3/js/jquery.dataTables.min.js'></script>
 </head>
 
 <body>
-    <h2>Mapping: {% for profile in source_profiles %}{{ profile['key'] }}{% if not loop.last %}, {% endif %}{% endfor %} in {{ target_profile['key'] }}</h2>
+    <h2>Mapping: {% for profile in source_profiles %}{{ profile['name'] ~ "|" ~ profile['version'] }}{% if not loop.last %}, {% endif %}{% endfor %} in {{ target_profile['name'] ~ "|" ~ target_profile['version'] }}</h2>
 
     <div style="display: flex; justify-content: space-between;">
         <div style="flex: 1;">
             {% if source_profiles|length > 1 %}
             <p>Source Profiles:</p>
             <ul>
                 {% for profile in source_profiles %}
-                <li><a href="{{ profile['url'] }}" target="_blank">{{ profile['key'] }}</a></li>
+                <li><a href="{{ profile['url'] }}" target="_blank">{{ profile['name'] ~ "|" ~ profile['version'] }}</a></li>
                 {% endfor %}
             </ul>
             {% else %}
             <p>Source Profile: 
-            <a href="{{ source_profiles[0]['url'] }}" target="_blank">{{ source_profiles[0]['key'] }}</a></p>
+            <a href="{{ source_profiles[0]['url'] }}" target="_blank">{{ source_profiles[0]['name'] ~ "|" ~ source_profiles[0]['version'] }}</a></p>
             {% endif %}
 
-            <p>Target Profile: <a href="{{ target_profile['url'] }}" target="_blank">{{ target_profile['key'] }}</a></p>
+            <p>Target Profile: <a href="{{ target_profile['url'] }}" target="_blank">{{ target_profile['name'] ~ "|" ~ target_profile['version'] }}</a></p>
             <p>Version: {{version}}, Status: {{status}}</p>
             <p>Last updated on: {{last_updated}}</p>
         </div>
@@ -60,9 +62,9 @@
             </tr>
             <tr>
                 {% for profile in source_profiles %}
-                <th style="text-align: center;">{{ profile['key'] }}</th>
+                <th style="text-align: center;">{{ profile['name'] ~ "|" ~ profile['version'] }}</th>
                 {% endfor %}
-                <th style="text-align: center;">{{ target_profile['key'] }}</th>
+                <th style="text-align: center;">{{ target_profile['name'] ~ "|" ~ target_profile['version'] }}</th>
             </tr>
         </thead>
         <tbody>
@@ -73,8 +75,8 @@
                 </td>
                 {% for profile in source_profiles + [target_profile] %}
                 <td style="text-align: center;">
-                    {% if entry.profiles[profile['key']].present %}
-                        {{ entry.profiles[profile['key']].min_cardinality }}..{{ entry.profiles[profile['key']].max_cardinality | format_cardinality }}
+                    {% if entry.profiles[profile['key']] %}
+                        {{ entry.profiles[profile['key']].min }}..{{ entry.profiles[profile['key']].max | format_cardinality }}
                     {% endif %}
                 </td>
                 {% endfor %}

service/src/structure_comparer/handler/mapping.py

@@ -1,4 +1,4 @@
-from typing import List
+from typing import List, Optional
 
 from ..action import Action
 from ..data.mapping import MappingField
@@ -20,6 +20,7 @@
 from ..model.mapping import MappingFieldMinimal as MappingFieldMinimalModel
 from ..model.mapping import MappingFieldsOutput as MappingFieldsOutputModel
 from .project import ProjectsHandler
+from ..results_html import create_results_html
 
 
 class MappingHandler:
@@ -55,6 +56,27 @@ def get_field(
 
         return field.to_model()
 
+    def get_html(
+        self,
+        project_key: str,
+        mapping_id: str,
+        show_remarks: bool,
+        show_warnings: bool,
+        html_output_dir: Optional[str] = None,
+    ) -> str:
+        mapping = self.get(project_key, mapping_id)
+        mappingDict = {mapping.name: mapping}
+
+        if html_output_dir is None:
+            html_output_dir = self.project_handler._get(
+                project_key
+            ).config.html_output_dir
+
+        return create_results_html(
+            mappingDict, html_output_dir, show_remarks, show_warnings
+        )
+        # return mapping
+
     def set_field(
         self,
         project_key: str,

service/src/structure_comparer/handler/project.py

@@ -17,7 +17,7 @@
 class ProjectsHandler:
     def __init__(self, projects_dir: Path):
         self.projs_dir = projects_dir
-        self.__projs: Dict[str, Project]
+        self.__projs: Dict[str, Project] = {}
 
     @property
     def keys(self) -> List[str]:
@@ -35,13 +35,21 @@ def load(self) -> None:
                     logger.error(e.errors())
                     raise e
 
+        if not self.__projs:
+            path = self.projs_dir
+            if path.is_dir() and (path / "config.json").exists():
+                try:
+                    self.__projs[path.name] = Project(path)
+                except ValidationError as e:
+                    logger.error(e.errors())
+                    raise e
+
     def get_list(self) -> ProjectListModel:
         projects = [p.to_overview_model() for p in self.__projs.values()]
         return ProjectListModel(projects=projects)
 
     def _get(self, project_key: str) -> Project:
         proj = self.__projs.get(project_key)
-
         if proj is None:
             raise ProjectNotFound()