mirror of
https://github.com/Sudo-JHare/FHIRFLARE-IG-Toolkit.git
synced 2025-06-15 21:29:59 +00:00
345 lines
19 KiB
Python
345 lines
19 KiB
Python
# app/modules/fhir_ig_importer/services.py
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import requests
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import os
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import tarfile
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import gzip
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import json
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import io
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import re
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import logging
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from flask import current_app
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from collections import defaultdict
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# Constants
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FHIR_REGISTRY_BASE_URL = "https://packages.fhir.org"
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DOWNLOAD_DIR_NAME = "fhir_packages"
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# --- Helper Functions ---
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def _get_download_dir():
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"""Gets the absolute path to the download directory, creating it if needed."""
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logger = logging.getLogger(__name__)
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instance_path = None # Initialize
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try:
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# --- FIX: Indent code inside try block ---
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instance_path = current_app.instance_path
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logger.debug(f"Using instance path from current_app: {instance_path}")
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except RuntimeError:
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# --- FIX: Indent code inside except block ---
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logger.warning("No app context for instance_path, constructing relative path.")
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instance_path = os.path.abspath(os.path.join(os.path.dirname(__file__), '..', '..', '..', 'instance'))
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logger.debug(f"Constructed instance path: {instance_path}")
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# This part depends on instance_path being set above
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if not instance_path:
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logger.error("Fatal Error: Could not determine instance path.")
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return None
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download_dir = os.path.join(instance_path, DOWNLOAD_DIR_NAME)
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try:
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# --- FIX: Indent code inside try block ---
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os.makedirs(download_dir, exist_ok=True)
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return download_dir
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except OSError as e:
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# --- FIX: Indent code inside except block ---
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logger.error(f"Fatal Error creating dir {download_dir}: {e}", exc_info=True)
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return None
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def sanitize_filename_part(text): # Public version
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"""Basic sanitization for name/version parts of filename."""
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# --- FIX: Indent function body ---
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safe_text = "".join(c if c.isalnum() or c in ['.', '-'] else '_' for c in text)
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safe_text = re.sub(r'_+', '_', safe_text) # Uses re
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safe_text = safe_text.strip('_-.')
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return safe_text if safe_text else "invalid_name"
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def _construct_tgz_filename(name, version):
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"""Constructs the standard filename using the sanitized parts."""
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# --- FIX: Indent function body ---
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return f"{sanitize_filename_part(name)}-{sanitize_filename_part(version)}.tgz"
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def find_and_extract_sd(tgz_path, resource_identifier): # Public version
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"""Helper to find and extract SD json from a given tgz path by ID, Name, or Type."""
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# --- FIX: Ensure consistent indentation ---
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sd_data = None
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found_path = None
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logger = logging.getLogger(__name__)
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if not tgz_path or not os.path.exists(tgz_path):
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logger.error(f"File not found in find_and_extract_sd: {tgz_path}")
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return None, None
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try:
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with tarfile.open(tgz_path, "r:gz") as tar:
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logger.debug(f"Searching for SD matching '{resource_identifier}' in {os.path.basename(tgz_path)}")
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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_id = data.get('id')
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sd_name = data.get('name')
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sd_type = data.get('type')
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# Match if requested identifier matches ID, Name, or Base Type
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if resource_identifier == sd_type or resource_identifier == sd_id or resource_identifier == sd_name:
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sd_data = data
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found_path = member.name
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logger.info(f"Found matching SD for '{resource_identifier}' at path: {found_path}")
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break # Stop searching once found
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except Exception as e:
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# Log issues reading/parsing individual files but continue search
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logger.warning(f"Could not read/parse potential SD {member.name}: {e}")
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finally:
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if fileobj: fileobj.close() # Ensure resource cleanup
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if sd_data is None:
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logger.warning(f"SD matching '{resource_identifier}' not found within archive {os.path.basename(tgz_path)}")
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except tarfile.TarError as e:
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logger.error(f"TarError reading {tgz_path} in find_and_extract_sd: {e}")
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raise tarfile.TarError(f"Error reading package archive: {e}") from e
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except FileNotFoundError as e:
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logger.error(f"FileNotFoundError reading {tgz_path} in find_and_extract_sd: {e}")
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raise
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except Exception as e:
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logger.error(f"Unexpected error in find_and_extract_sd for {tgz_path}: {e}", exc_info=True)
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raise
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return sd_data, found_path
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# --- Core Service Functions ---
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def download_package(name, version):
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""" Downloads a single FHIR package. Returns (save_path, error_message) """
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# --- FIX: Ensure consistent indentation ---
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logger = logging.getLogger(__name__)
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download_dir = _get_download_dir()
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if not download_dir:
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return None, "Could not get/create download directory."
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package_id = f"{name}#{version}"
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package_url = f"{FHIR_REGISTRY_BASE_URL}/{name}/{version}"
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filename = _construct_tgz_filename(name, version) # Uses public sanitize via helper
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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"Exists: {filename}")
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return save_path, None
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logger.info(f"Downloading: {package_id} -> {filename}")
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try:
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with requests.get(package_url, stream=True, timeout=90) 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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logger.debug(f"Opened {save_path} for writing.")
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for chunk in r.iter_content(chunk_size=8192):
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if chunk:
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f.write(chunk)
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logger.info(f"Success: Downloaded {filename}")
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return save_path, None
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except requests.exceptions.RequestException as e:
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err_msg = f"Download error for {package_id}: {e}"; logger.error(err_msg); return None, err_msg
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except OSError as e:
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err_msg = f"File save error for {filename}: {e}"; logger.error(err_msg); return None, err_msg
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except Exception as e:
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err_msg = f"Unexpected download error for {package_id}: {e}"; logger.error(err_msg, exc_info=True); return None, err_msg
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def extract_dependencies(tgz_path):
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""" Extracts dependencies dict from package.json. Returns (dep_dict or None on error, error_message) """
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# --- FIX: Ensure consistent indentation ---
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logger = logging.getLogger(__name__)
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package_json_path = "package/package.json"
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dependencies = {}
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error_message = None
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if not tgz_path or not os.path.exists(tgz_path):
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return None, f"File not found at {tgz_path}"
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try:
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with tarfile.open(tgz_path, "r:gz") as tar:
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package_json_member = tar.getmember(package_json_path)
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package_json_fileobj = tar.extractfile(package_json_member)
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if package_json_fileobj:
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try:
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package_data = json.loads(package_json_fileobj.read().decode('utf-8-sig'))
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dependencies = package_data.get('dependencies', {})
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finally:
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package_json_fileobj.close()
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else:
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raise FileNotFoundError(f"Could not extract {package_json_path}")
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except KeyError:
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error_message = f"'{package_json_path}' not found in {os.path.basename(tgz_path)}.";
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logger.warning(error_message) # OK if missing
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except (json.JSONDecodeError, UnicodeDecodeError) as e:
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error_message = f"Parse error in {package_json_path}: {e}"; logger.error(error_message); dependencies = None # Parsing failed
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except (tarfile.TarError, FileNotFoundError) as e:
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error_message = f"Archive error {os.path.basename(tgz_path)}: {e}"; logger.error(error_message); dependencies = None # Archive read failed
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except Exception as e:
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error_message = f"Unexpected error extracting deps: {e}"; logger.error(error_message, exc_info=True); dependencies = None
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return dependencies, error_message
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# --- Recursive Import Orchestrator ---
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def import_package_and_dependencies(initial_name, initial_version):
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"""Orchestrates recursive download and dependency extraction."""
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# --- FIX: Ensure consistent indentation ---
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logger = logging.getLogger(__name__)
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logger.info(f"Starting recursive import for {initial_name}#{initial_version}")
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results = {'requested': (initial_name, initial_version), 'processed': set(), 'downloaded': {}, 'all_dependencies': {}, 'errors': [] }
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pending_queue = [(initial_name, initial_version)]
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processed_lookup = set()
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while pending_queue:
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name, version = pending_queue.pop(0)
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package_id_tuple = (name, version)
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if package_id_tuple in processed_lookup:
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continue
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logger.info(f"Processing: {name}#{version}")
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processed_lookup.add(package_id_tuple)
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save_path, dl_error = download_package(name, version)
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if dl_error:
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error_msg = f"Download failed for {name}#{version}: {dl_error}"
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results['errors'].append(error_msg)
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if package_id_tuple == results['requested']:
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logger.error("Aborting import: Initial package download failed.")
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break
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else:
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continue
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else: # Download OK
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results['downloaded'][package_id_tuple] = save_path
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# --- Correctly indented block ---
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dependencies, dep_error = extract_dependencies(save_path)
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if dep_error:
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results['errors'].append(f"Dependency extraction failed for {name}#{version}: {dep_error}")
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elif dependencies is not None:
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results['all_dependencies'][package_id_tuple] = dependencies
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results['processed'].add(package_id_tuple)
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logger.debug(f"Dependencies for {name}#{version}: {list(dependencies.keys())}")
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for dep_name, dep_version in dependencies.items():
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if isinstance(dep_name, str) and isinstance(dep_version, str) and dep_name and dep_version:
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dep_tuple = (dep_name, dep_version)
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if dep_tuple not in processed_lookup:
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if dep_tuple not in pending_queue:
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pending_queue.append(dep_tuple)
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logger.debug(f"Added to queue: {dep_name}#{dep_version}")
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else:
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logger.warning(f"Skipping invalid dependency '{dep_name}': '{dep_version}' in {name}#{version}")
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# --- End Correctly indented block ---
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proc_count=len(results['processed']); dl_count=len(results['downloaded']); err_count=len(results['errors'])
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logger.info(f"Import finished. Processed: {proc_count}, Downloaded/Verified: {dl_count}, Errors: {err_count}")
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return results
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# --- Package File Content Processor (V6.2 - Fixed MS path handling) ---
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def process_package_file(tgz_path):
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""" Extracts types, profile status, MS elements, and examples from a downloaded .tgz package (Single Pass). """
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logger = logging.getLogger(__name__)
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logger.info(f"Processing package file details (V6.2 Logic): {tgz_path}")
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results = {'resource_types_info': [], 'must_support_elements': {}, 'examples': {}, 'errors': [] }
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resource_info = defaultdict(lambda: {'name': None, 'type': None, 'is_profile': False, 'ms_flag': False, 'ms_paths': set(), 'examples': set()})
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if not tgz_path or not os.path.exists(tgz_path):
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results['errors'].append(f"Package file not found: {tgz_path}"); return results
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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() or not member.name.startswith('package/') or not member.name.lower().endswith(('.json', '.xml', '.html')): continue
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member_name_lower = member.name.lower(); base_filename_lower = os.path.basename(member_name_lower); fileobj = None
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if base_filename_lower in ['package.json', '.index.json', 'validation-summary.json', 'validation-oo.json']: continue
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is_example = member.name.startswith('package/example/') or 'example' in base_filename_lower
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is_json = member_name_lower.endswith('.json')
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try: # Process individual member
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if is_json:
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fileobj = tar.extractfile(member);
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if not fileobj: continue
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content_bytes = fileobj.read(); content_string = content_bytes.decode('utf-8-sig'); data = json.loads(content_string)
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if not isinstance(data, dict) or 'resourceType' not in data: continue
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resource_type = data['resourceType']; entry_key = resource_type; is_sd = False
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if resource_type == 'StructureDefinition':
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is_sd = True; profile_id = data.get('id') or data.get('name'); sd_type = data.get('type'); sd_base = data.get('baseDefinition'); is_profile_sd = bool(sd_base);
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if not profile_id or not sd_type: logger.warning(f"SD missing ID or Type: {member.name}"); continue
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entry_key = profile_id
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entry = resource_info[entry_key]; entry.setdefault('type', resource_type) # Ensure type exists
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if is_sd:
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entry['name'] = entry_key; entry['type'] = sd_type; entry['is_profile'] = is_profile_sd;
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if not entry.get('sd_processed'):
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has_ms = False; ms_paths_for_sd = set()
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for element_list in [data.get('snapshot', {}).get('element', []), data.get('differential', {}).get('element', [])]:
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for element in element_list:
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if isinstance(element, dict) and element.get('mustSupport') is True:
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# --- FIX: Check path safely ---
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element_path = element.get('path')
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if element_path: # Only add if path exists
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ms_paths_for_sd.add(element_path)
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has_ms = True # Mark MS found if we added a path
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else:
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logger.warning(f"Found mustSupport=true without path in element of {entry_key}")
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# --- End FIX ---
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if ms_paths_for_sd: entry['ms_paths'] = ms_paths_for_sd # Store the set of paths
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if has_ms: entry['ms_flag'] = True; logger.debug(f" Found MS elements in {entry_key}") # Use boolean flag
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entry['sd_processed'] = True # Mark MS check done
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elif is_example: # JSON Example
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key_to_use = None; profile_meta = data.get('meta', {}).get('profile', [])
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if profile_meta and isinstance(profile_meta, list):
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for profile_url in profile_meta: profile_id_from_meta = profile_url.split('/')[-1];
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if profile_id_from_meta in resource_info: key_to_use = profile_id_from_meta; break
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if not key_to_use: key_to_use = resource_type
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if key_to_use not in resource_info: resource_info[key_to_use].update({'name': key_to_use, 'type': resource_type})
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resource_info[key_to_use]['examples'].add(member.name)
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elif is_example: # XML/HTML examples
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# ... (XML/HTML example association logic) ...
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guessed_type = base_filename_lower.split('-')[0].capitalize(); guessed_profile_id = base_filename_lower.split('-')[0]; key_to_use = None
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if guessed_profile_id in resource_info: key_to_use = guessed_profile_id
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elif guessed_type in resource_info: key_to_use = guessed_type
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if key_to_use: resource_info[key_to_use]['examples'].add(member.name)
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else: logger.warning(f"Could not associate non-JSON example {member.name}")
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except Exception as e: logger.warning(f"Could not process member {member.name}: {e}", exc_info=False)
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finally:
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if fileobj: fileobj.close()
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# -- End Member Loop --
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# --- Final formatting moved INSIDE the main try block ---
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final_list = []; final_ms_elements = {}; final_examples = {}
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logger.debug(f"Formatting results from resource_info keys: {list(resource_info.keys())}")
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for key, info in resource_info.items():
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display_name = info.get('name') or key; base_type = info.get('type')
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if display_name or base_type:
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logger.debug(f" Formatting item '{display_name}': type='{base_type}', profile='{info.get('is_profile', False)}', ms_flag='{info.get('ms_flag', False)}'")
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final_list.append({'name': display_name, 'type': base_type, 'is_profile': info.get('is_profile', False), 'must_support': info.get('ms_flag', False)}) # Ensure 'must_support' key uses 'ms_flag'
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if info['ms_paths']: final_ms_elements[display_name] = sorted(list(info['ms_paths']))
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if info['examples']: final_examples[display_name] = sorted(list(info['examples']))
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else: logger.warning(f"Skipping formatting for key: {key}")
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results['resource_types_info'] = sorted(final_list, key=lambda x: (not x.get('is_profile', False), x.get('name', '')))
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results['must_support_elements'] = final_ms_elements
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results['examples'] = final_examples
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# --- End formatting moved inside ---
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except Exception as e:
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err_msg = f"Error processing package file {tgz_path}: {e}"; logger.error(err_msg, exc_info=True); results['errors'].append(err_msg)
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# Logging counts
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final_types_count = len(results['resource_types_info']); ms_count = sum(1 for r in results['resource_types_info'] if r['must_support']); total_ms_paths = sum(len(v) for v in results['must_support_elements'].values()); total_examples = sum(len(v) for v in results['examples'].values())
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logger.info(f"V6.2 Extraction: {final_types_count} items ({ms_count} MS; {total_ms_paths} MS paths; {total_examples} examples) from {os.path.basename(tgz_path)}")
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return results |