mirror of
https://github.com/Sudo-JHare/FHIRFLARE-IG-Toolkit.git
synced 2025-06-14 12:10:03 +00:00
Patched
Patched for New IG processing, to handle non standard structures, names, and versions formats in IG's
This commit is contained in:
parent
b6f9d2697e
commit
6412e537a8
140
app.py
140
app.py
@ -42,6 +42,7 @@ from services import (
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from forms import IgImportForm, ValidationForm, FSHConverterForm, TestDataUploadForm, RetrieveSplitDataForm
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from wtforms import SubmitField
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from package import package_bp
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from copy import deepcopy
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import tempfile
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from logging.handlers import RotatingFileHandler
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@ -913,6 +914,101 @@ def get_example():
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logger.error(f"Unexpected error getting example '{filename}' from {tgz_filename}: {e}", exc_info=True)
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return jsonify({"error": f"Unexpected error: {str(e)}"}), 500
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#----------------------------------------------------------------------new
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def collect_all_structure_definitions(tgz_path):
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"""Collect all StructureDefinitions from a .tgz package."""
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structure_definitions = {}
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try:
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with tarfile.open(tgz_path, "r:gz") as tar:
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for member in tar:
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if not (member.isfile() and member.name.startswith('package/') and member.name.lower().endswith('.json')):
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continue
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if os.path.basename(member.name).lower() in ['package.json', '.index.json', 'validation-summary.json', 'validation-oo.json']:
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continue
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fileobj = None
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try:
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fileobj = tar.extractfile(member)
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if fileobj:
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content_bytes = fileobj.read()
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content_string = content_bytes.decode('utf-8-sig')
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data = json.loads(content_string)
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if isinstance(data, dict) and data.get('resourceType') == 'StructureDefinition':
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sd_url = data.get('url')
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if sd_url:
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structure_definitions[sd_url] = data
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except Exception as e:
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logger.warning(f"Could not read/parse potential SD {member.name}, skipping: {e}")
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finally:
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if fileobj:
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fileobj.close()
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except Exception as e:
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logger.error(f"Unexpected error collecting StructureDefinitions from {tgz_path}: {e}", exc_info=True)
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return structure_definitions
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def generate_snapshot(structure_def, core_package_path, local_package_path):
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"""Generate a snapshot by merging the differential with the base StructureDefinition."""
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if 'snapshot' in structure_def:
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return structure_def
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# Fetch all StructureDefinitions from the local package for reference resolution
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local_sds = collect_all_structure_definitions(local_package_path)
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# Get the base StructureDefinition from the core package
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base_url = structure_def.get('baseDefinition')
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if not base_url:
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logger.error("No baseDefinition found in StructureDefinition.")
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return structure_def
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resource_type = structure_def.get('type')
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base_sd_data, _ = services.find_and_extract_sd(core_package_path, resource_type, profile_url=base_url)
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if not base_sd_data or 'snapshot' not in base_sd_data:
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logger.error(f"Could not fetch or find snapshot in base StructureDefinition: {base_url}")
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return structure_def
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# Copy the base snapshot elements
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snapshot_elements = deepcopy(base_sd_data['snapshot']['element'])
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differential_elements = structure_def.get('differential', {}).get('element', [])
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# Map snapshot elements by path and id for easier lookup
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snapshot_by_path = {el['path']: el for el in snapshot_elements}
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snapshot_by_id = {el['id']: el for el in snapshot_elements if 'id' in el}
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# Process differential elements
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for diff_el in differential_elements:
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diff_path = diff_el.get('path')
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diff_id = diff_el.get('id')
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# Resolve extensions or referenced types
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if 'type' in diff_el:
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for type_info in diff_el['type']:
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if 'profile' in type_info:
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for profile_url in type_info['profile']:
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if profile_url in local_sds:
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# Add elements from the referenced StructureDefinition
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ref_sd = local_sds[profile_url]
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ref_elements = ref_sd.get('snapshot', {}).get('element', []) or ref_sd.get('differential', {}).get('element', [])
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for ref_el in ref_elements:
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# Adjust paths to fit within the current structure
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ref_path = ref_el.get('path')
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if ref_path.startswith(ref_sd.get('type')):
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new_path = diff_path + ref_path[len(ref_sd.get('type')):]
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new_el = deepcopy(ref_el)
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new_el['path'] = new_path
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new_el['id'] = diff_id + ref_path[len(ref_sd.get('type')):]
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snapshot_elements.append(new_el)
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# Find matching element in snapshot
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target_el = snapshot_by_id.get(diff_id) or snapshot_by_path.get(diff_path)
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if target_el:
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# Update existing element with differential constraints
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target_el.update(diff_el)
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else:
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# Add new element (e.g., extensions or new slices)
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snapshot_elements.append(diff_el)
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structure_def['snapshot'] = {'element': snapshot_elements}
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return structure_def
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@app.route('/get-structure')
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def get_structure():
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package_name = request.args.get('package_name')
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@ -954,7 +1050,6 @@ def get_structure():
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if sd_data is None:
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logger.info(f"SD for '{resource_type}' not found or failed to load from {source_package_id}. Attempting fallback to {services.CANONICAL_PACKAGE_ID}.")
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if not core_package_exists:
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logger.error(f"Core package {services.CANONICAL_PACKAGE_ID} not found locally at {core_tgz_path}.")
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error_message = f"SD for '{resource_type}' not found in primary package, and core package is missing." if primary_package_exists else f"Primary package {package_name}#{version} and core package are missing."
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return jsonify({"error": error_message}), 500 if primary_package_exists else 404
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try:
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@ -970,23 +1065,43 @@ def get_structure():
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if not sd_data:
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logger.error(f"SD for '{resource_type}' could not be found in primary or fallback packages.")
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return jsonify({"error": f"StructureDefinition for '{resource_type}' not found."}), 404
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# Generate snapshot if missing
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if 'snapshot' not in sd_data:
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logger.info(f"Snapshot missing for {resource_type}. Generating snapshot...")
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sd_data = generate_snapshot(sd_data, core_tgz_path, tgz_path)
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if raw:
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return Response(json.dumps(sd_data, indent=None, separators=(',', ':')), mimetype='application/json')
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# Prepare elements based on the view
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snapshot_elements = sd_data.get('snapshot', {}).get('element', [])
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differential_elements = sd_data.get('differential', {}).get('element', [])
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differential_ids = {el.get('id') for el in differential_elements if el.get('id')}
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logger.debug(f"Found {len(differential_ids)} unique IDs in differential.")
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# Select elements based on the view
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enriched_elements = []
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if snapshot_elements:
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logger.debug(f"Processing {len(snapshot_elements)} snapshot elements to add isInDifferential flag.")
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for element in snapshot_elements:
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element_id = element.get('id')
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element['isInDifferential'] = bool(element_id and element_id in differential_ids)
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enriched_elements.append(element)
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enriched_elements = [services.remove_narrative(el, include_narrative=include_narrative) for el in enriched_elements]
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else:
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logger.warning(f"No snapshot found for {resource_type} in {source_package_id}. Returning empty element list.")
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enriched_elements = []
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if view == 'snapshot':
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if snapshot_elements:
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logger.debug(f"Processing {len(snapshot_elements)} snapshot elements for Snapshot view.")
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for element in snapshot_elements:
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element_id = element.get('id')
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element['isInDifferential'] = bool(element_id and element_id in differential_ids)
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enriched_elements.append(element)
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else:
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logger.warning(f"No snapshot elements found for {resource_type} in {source_package_id} for Snapshot view.")
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else: # Differential, Must Support, Key Elements views use differential elements as a base
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if differential_elements:
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logger.debug(f"Processing {len(differential_elements)} differential elements for {view} view.")
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for element in differential_elements:
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element['isInDifferential'] = True
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enriched_elements.append(element)
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else:
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logger.warning(f"No differential elements found for {resource_type} in {source_package_id} for {view} view.")
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enriched_elements = [services.remove_narrative(el, include_narrative=include_narrative) for el in enriched_elements]
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must_support_paths = []
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processed_ig_record = ProcessedIg.query.filter_by(package_name=package_name, version=version).first()
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if processed_ig_record and processed_ig_record.must_support_elements:
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@ -1002,6 +1117,7 @@ def get_structure():
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logger.debug(f"No specific MS paths found for keys '{resource_type}' or '{base_resource_type_for_sp}' in DB.")
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else:
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logger.debug(f"No processed IG record or no must_support_elements found in DB for {package_name}#{version}")
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if base_resource_type_for_sp and primary_package_exists:
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try:
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logger.info(f"Fetching SearchParameters for base type '{base_resource_type_for_sp}' from primary package {tgz_path}")
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@ -1060,6 +1176,8 @@ def get_structure():
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'source_package': source_package_id
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}
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return Response(json.dumps(response_data, indent=None, separators=(',', ':')), mimetype='application/json')
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#------------------------------------------------------------------------
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@app.route('/get-package-metadata')
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def get_package_metadata():
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223
services.py
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services.py
@ -735,26 +735,76 @@ def basic_fhir_xml_to_dict(xml_string):
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logger.error(f"Unexpected error during basic_fhir_xml_to_dict: {e}", exc_info=True)
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return None
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# def parse_package_filename(filename):
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# """Parses a standard FHIR package filename into name and version."""
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# if not filename or not filename.endswith('.tgz'):
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# logger.debug(f"Filename '{filename}' does not end with .tgz")
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# return None, None
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# base_name = filename[:-4]
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# last_hyphen_index = base_name.rfind('-')
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# while last_hyphen_index != -1:
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# potential_name = base_name[:last_hyphen_index]
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# potential_version = base_name[last_hyphen_index + 1:]
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# if potential_version and (potential_version[0].isdigit() or any(potential_version.startswith(kw) for kw in ['v', 'dev', 'draft', 'preview', 'release', 'alpha', 'beta'])):
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# name = potential_name.replace('_', '.')
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# version = potential_version
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# logger.debug(f"Parsed '{filename}' -> name='{name}', version='{version}'")
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# return name, version
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# else:
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# last_hyphen_index = base_name.rfind('-', 0, last_hyphen_index)
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# logger.warning(f"Could not parse version from '{filename}'. Treating '{base_name}' as name.")
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# name = base_name.replace('_', '.')
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# version = ""
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# return name, version
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def parse_package_filename(filename):
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"""Parses a standard FHIR package filename into name and version."""
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"""
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Parses a standard FHIR package filename into name and version.
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Handles various version formats including semantic versions, pre-releases, snapshots, and complex suffixes.
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"""
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if not filename or not filename.endswith('.tgz'):
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logger.debug(f"Filename '{filename}' does not end with .tgz")
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return None, None
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base_name = filename[:-4]
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last_hyphen_index = base_name.rfind('-')
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while last_hyphen_index != -1:
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potential_name = base_name[:last_hyphen_index]
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potential_version = base_name[last_hyphen_index + 1:]
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if potential_version and (potential_version[0].isdigit() or any(potential_version.startswith(kw) for kw in ['v', 'dev', 'draft', 'preview', 'release', 'alpha', 'beta'])):
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name = potential_name.replace('_', '.')
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version = potential_version
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logger.debug(f"Parsed '{filename}' -> name='{name}', version='{version}'")
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return name, version
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else:
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last_hyphen_index = base_name.rfind('-', 0, last_hyphen_index)
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logger.warning(f"Could not parse version from '{filename}'. Treating '{base_name}' as name.")
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name = base_name.replace('_', '.')
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version = ""
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base_name = filename[:-4] # Remove '.tgz'
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# Define a comprehensive pattern for FHIR package versions as a single string
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# Matches versions like:
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# - 1.0.0, 4.0.2
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# - 1.1.0-preview, 0.1.0-draft, 1.0.0-ballot-3
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# - 1.0.0-alpha.1, 1.0.0-RC2, 0.9.0-alpha1.0.8
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# - 1.1.0-snapshot-3, 0.0.1-snapshot
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# - 2.3.5-buildnumbersuffix2
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version_pattern = r'(\d+\.\d+\.\d+)(?:-(?:preview|ballot|draft|snapshot|alpha|beta|RC\d*|buildnumbersuffix\d*|alpha\d+\.\d+\.\d+|snapshot-\d+|ballot-\d+|alpha\.\d+))?$'
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# Find the last occurrence of the version pattern in the base_name
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match = None
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for i in range(len(base_name), 0, -1):
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substring = base_name[:i]
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if re.search(version_pattern, substring):
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match = re.search(version_pattern, base_name[:i])
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if match:
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break
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if not match:
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logger.warning(f"Could not parse version from '{filename}'. Treating '{base_name}' as name.")
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name = base_name.replace('_', '.')
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version = ""
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return name, version
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# Extract the matched version
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version_start_idx = match.start(1) # Start of the version (e.g., start of "1.1.0" in "1.1.0-preview")
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name = base_name[:version_start_idx].rstrip('-').replace('_', '.') # Everything before the version
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version = base_name[version_start_idx:] # The full version string
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# Validate the name and version
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if not name or not version:
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logger.warning(f"Invalid parse for '{filename}': name='{name}', version='{version}'. Using fallback.")
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name = base_name.replace('_', '.')
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version = ""
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return name, version
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logger.debug(f"Parsed '{filename}' -> name='{name}', version='{version}'")
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return name, version
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def remove_narrative(resource, include_narrative=False):
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@ -1953,30 +2003,129 @@ def _load_definition(details, download_dir):
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logger.error(f"Failed to load definition {details['filename']} from {tgz_path}: {e}")
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return None
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def download_package(name, version):
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"""Downloads a single FHIR package."""
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# def download_package(name, version):
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# """Downloads a single FHIR package."""
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# download_dir = _get_download_dir()
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# if not download_dir: return None, "Download dir error"
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# filename = construct_tgz_filename(name, version)
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# if not filename: return None, "Filename construction error"
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# save_path = os.path.join(download_dir, filename)
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# if os.path.exists(save_path):
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# logger.info(f"Package already exists: {save_path}")
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# return save_path, None
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# package_url = f"{FHIR_REGISTRY_BASE_URL}/{name}/{version}"
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# try:
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# with requests.get(package_url, stream=True, timeout=60) as r:
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# r.raise_for_status()
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# with open(save_path, 'wb') as f:
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# for chunk in r.iter_content(chunk_size=8192): f.write(chunk)
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# logger.info(f"Downloaded {filename}")
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# return save_path, None
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# except requests.exceptions.RequestException as e:
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# logger.error(f"Download failed for {name}#{version}: {e}")
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# return None, f"Download error: {e}"
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# except IOError as e:
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# logger.error(f"File write error for {save_path}: {e}")
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# return None, f"File write error: {e}"
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def download_package(name, version, dependency_mode='none'):
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"""Downloads a FHIR package by name and version to the configured directory."""
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download_dir = _get_download_dir()
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if not download_dir: return None, "Download dir error"
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filename = construct_tgz_filename(name, version)
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if not filename: return None, "Filename construction error"
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save_path = os.path.join(download_dir, filename)
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if os.path.exists(save_path):
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logger.info(f"Package already exists: {save_path}")
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return save_path, None
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package_url = f"{FHIR_REGISTRY_BASE_URL}/{name}/{version}"
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if not download_dir:
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return None, ["Could not determine download directory"]
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tgz_filename = construct_tgz_filename(name, version)
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if not tgz_filename:
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return None, [f"Could not construct filename for {name}#{version}"]
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download_path = os.path.join(download_dir, tgz_filename)
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errors = []
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# Check if already downloaded
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if os.path.exists(download_path):
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logger.info(f"Package {name}#{version} already downloaded at {download_path}")
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return download_path, []
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# Primary download URL
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primary_url = f"{FHIR_REGISTRY_BASE_URL}/{name}/{version}"
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logger.info(f"Attempting download of {name}#{version} from {primary_url}")
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try:
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with requests.get(package_url, stream=True, timeout=60) as r:
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r.raise_for_status()
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with open(save_path, 'wb') as f:
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for chunk in r.iter_content(chunk_size=8192): f.write(chunk)
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logger.info(f"Downloaded {filename}")
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return save_path, None
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response = requests.get(primary_url, timeout=30)
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response.raise_for_status()
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with open(download_path, 'wb') as f:
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f.write(response.content)
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logger.info(f"Successfully downloaded {name}#{version} to {download_path}")
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save_package_metadata(name, version, dependency_mode, [])
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return download_path, []
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except requests.exceptions.HTTPError as e:
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if e.response.status_code == 404:
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logger.warning(f"Primary download failed (404) for {name}#{version} at {primary_url}. Attempting fallback URL.")
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else:
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error_msg = f"Download error for {name}#{version}: {str(e)}"
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logger.error(error_msg, exc_info=True)
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errors.append(error_msg)
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return None, errors
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except requests.exceptions.RequestException as e:
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logger.error(f"Download failed for {name}#{version}: {e}")
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return None, f"Download error: {e}"
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except IOError as e:
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logger.error(f"File write error for {save_path}: {e}")
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return None, f"File write error: {e}"
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error_msg = f"Download error for {name}#{version}: {str(e)}"
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logger.error(error_msg, exc_info=True)
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errors.append(error_msg)
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return None, errors
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except Exception as e:
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error_msg = f"Unexpected error downloading {name}#{version}: {str(e)}"
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logger.error(error_msg, exc_info=True)
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errors.append(error_msg)
|
||||
return None, errors
|
||||
|
||||
# Fallback: Try the package's URL from the normalized package data
|
||||
if errors and "404" in errors[0]:
|
||||
logger.info(f"Looking up alternative download URL for {name}#{version}")
|
||||
try:
|
||||
# Access the in-memory cache from the Flask app config
|
||||
normalized_packages = current_app.config.get('MANUAL_PACKAGE_CACHE', [])
|
||||
package_data = next((pkg for pkg in normalized_packages if pkg.get('name') == name), None)
|
||||
if not package_data:
|
||||
error_msg = f"Package {name} not found in cache for fallback download."
|
||||
logger.error(error_msg)
|
||||
errors.append(error_msg)
|
||||
return None, errors
|
||||
|
||||
package_url = package_data.get('url')
|
||||
if not package_url:
|
||||
error_msg = f"No alternative URL found for {name}#{version}."
|
||||
logger.error(error_msg)
|
||||
errors.append(error_msg)
|
||||
return None, errors
|
||||
|
||||
# Construct a download URL using the package's URL
|
||||
# Assuming the URL is a base (e.g., https://packages.simplifier.net/fhir.ieb.core)
|
||||
# and we append the version to form the download URL
|
||||
# This may need adjustment based on the actual format of 'url'
|
||||
fallback_url = f"{package_url.rstrip('/')}/{version}.tgz"
|
||||
logger.info(f"Attempting fallback download of {name}#{version} from {fallback_url}")
|
||||
|
||||
response = requests.get(fallback_url, timeout=30)
|
||||
response.raise_for_status()
|
||||
with open(download_path, 'wb') as f:
|
||||
f.write(response.content)
|
||||
logger.info(f"Successfully downloaded {name}#{version} using fallback URL to {download_path}")
|
||||
save_package_metadata(name, version, dependency_mode, [])
|
||||
return download_path, []
|
||||
except requests.exceptions.HTTPError as e:
|
||||
error_msg = f"Fallback download error for {name}#{version} at {fallback_url}: {str(e)}"
|
||||
logger.error(error_msg, exc_info=True)
|
||||
errors.append(error_msg)
|
||||
return None, errors
|
||||
except requests.exceptions.RequestException as e:
|
||||
error_msg = f"Fallback download network error for {name}#{version}: {str(e)}"
|
||||
logger.error(error_msg, exc_info=True)
|
||||
errors.append(error_msg)
|
||||
return None, errors
|
||||
except Exception as e:
|
||||
error_msg = f"Unexpected error during fallback download of {name}#{version}: {str(e)}"
|
||||
logger.error(error_msg, exc_info=True)
|
||||
errors.append(error_msg)
|
||||
return None, errors
|
||||
|
||||
return None, errors
|
||||
|
||||
def extract_dependencies(tgz_path):
|
||||
"""Extracts dependencies from package.json."""
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
</p>
|
||||
<!-----------------------------------------------------------------remove the buttons-----------------------------------------------------
|
||||
<div class="d-grid gap-2 d-sm-flex justify-content-sm-center">
|
||||
<a href="{{ url_for('import_ig') }}" class="btn btn-primary btn-lg px-4 gap-3">Import IGs</a>
|
||||
<a href="{{ url_for('search-and-import') }}" class="btn btn-primary btn-lg px-4 gap-3">Import IGs</a>
|
||||
<a href="{{ url_for('view_igs') }}" class="btn btn-outline-secondary btn-lg px-4 disabled">Manage FHIR Packages</a>
|
||||
<a href="{{ url_for('push_igs') }}" class="btn btn-outline-secondary btn-lg px-4">Upload IG's</a>
|
||||
</div>
|
||||
@ -34,7 +34,7 @@
|
||||
<div class="d-flex justify-content-between align-items-center mb-4">
|
||||
<h2><i class="bi bi-journal-arrow-down me-2"></i>Manage FHIR Packages</h2>
|
||||
<div>
|
||||
<a href="{{ url_for('import_ig') }}" class="btn btn-success"><i class="bi bi-download me-1"></i> Import More IGs</a>
|
||||
<a href="{{ url_for('search-and-import') }}" class="btn btn-success"><i class="bi bi-download me-1"></i> Import More IGs</a>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user