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update_uuid.py
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update_uuid.py
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"""
This script updates the UUIDs of concepts in an OCL source.
"""
import argparse
import uuid
import json
import csv
from datetime import datetime
import requests
# Parse command-line arguments
parser = argparse.ArgumentParser(description="OCL Concept External ID Updater")
parser.add_argument("--dry-run", action="store_true", help="Enable dry run mode")
args = parser.parse_args()
# Load configuration from config.json
with open('config.json', encoding='utf-8') as config_file:
config = json.load(config_file)
OCL_API_URL = config['OCL_API_URL']
SOURCE_ID = config['SOURCE_ID']
COLLECTION_ID = config['COLLECTION_ID']
OCL_TOKEN = config['OCL_TOKEN']
ORG_ID = config['ORG_ID']
# Dry run option
DRY_RUN = args.dry_run
# Counters for updated and skipped concepts
COUNTERS = {
'UPDATED_EMPTY': 0,
'UPDATED_MSF': 0,
'UPDATED_INVALID': 0,
'SKIPPED': 0
}
# Headers for the API request
HEADERS = {
"Authorization": f"Token {OCL_TOKEN}",
"Content-Type": "application/json"
}
# Prepare CSV file for dry run mode
CSV_FILENAME = 'updated_concepts_dry_run.csv' if DRY_RUN else 'updated_concepts.csv'
with open(CSV_FILENAME, mode='w', newline='', encoding='utf-8') as csv_file:
fieldnames = [
'Timestamp', 'Status', 'Valid External ID', 'Concept ID', 'Name', 'URL',
'Current External ID', 'New External ID', 'Original Response', 'Update Payload'
]
writer = csv.DictWriter(csv_file, fieldnames=fieldnames)
writer.writeheader()
def generate_new_uuid():
"""Generate a new UUID (16 characters)."""
return str(uuid.uuid4())[:36]
def is_valid_36_char_uuid(ext_id):
"""Check if the external ID is a valid 36-character UUID."""
if ext_id is None or ext_id == '':
COUNTERS['UPDATED_EMPTY'] += 1
return False
if ext_id.startswith("MSF-"):
COUNTERS['UPDATED_MSF'] += 1
return False
if len(ext_id) != 36:
COUNTERS['UPDATED_INVALID'] += 1
return False
COUNTERS['SKIPPED'] += 1
return True
def update_concept_external_id(url, id_param, name, ext_id, original_resp):
"""Update the external ID of a concept."""
valid_uuid = is_valid_36_char_uuid(ext_id)
changed_uuid = False
concept_names = concept_details.get('names', [])
if not DRY_RUN and not valid_uuid:
new_external_id = generate_new_uuid()
data = {
"id": id_param,
"external_id": new_external_id,
"names": concept_names
}
print(f"Updating concept {id_param} with url {url}")
resp = requests.patch(url, headers=HEADERS, data=json.dumps(data), timeout=30)
resp.raise_for_status()
changed_uuid = True
valid_uuid = True
timestamp = datetime.now().isoformat()
writer.writerow({
'Timestamp': timestamp,
'Status': 'New ID' if not DRY_RUN and changed_uuid else 'No Change',
'Valid External ID': 'Yes' if valid_uuid else 'No',
'Concept ID': id_param,
'Name': name,
'URL': url,
'Current External ID': ext_id,
'New External ID': new_external_id if not DRY_RUN and changed_uuid else '{}',
'Original Response': original_resp,
'Update Payload': json.dumps(data) if not DRY_RUN and changed_uuid else '{}'
})
def fetch_all_concepts(url):
"Fetch all concepts from the API and return them as a list."
all_concepts = []
total_concepts = 0
page = 1
while True:
data = requests.get(f"{url}&page={page}", timeout=30)
if data.status_code == 200:
data = data.json()
total_concepts += len(data)
# If no more data is available, break the loop
if not data:
break
# Add data to all_concepts list
all_concepts.extend(data)
page += 1
# Print progress
print(f"Page {page} fetched. Total concepts: {total_concepts}")
else:
print(f"Error fetching page {page}: {data.status_code}")
break
return all_concepts
# Get the list of concepts in the source
LIMIT = "?q=&limit=0"
if not SOURCE_ID:
concepts_url = f"{OCL_API_URL}/orgs/{ORG_ID}/collections/{COLLECTION_ID}/concepts/{LIMIT}"
else:
concepts_url = f"{OCL_API_URL}/orgs/{ORG_ID}/sources/{SOURCE_ID}/concepts/{LIMIT}"
# Print the total number of concepts to be processed
concepts = fetch_all_concepts(concepts_url)
TOTAL_CONCEPTS = len(concepts)
PROCESSED_CONCEPTS_COUNT = 0
# Iterate over the concepts and update external IDs based on the conditions
for concept in concepts:
concept_url = f"{OCL_API_URL}{concept['url']}"
print(concept_url)
concept_id = concept['id']
external_id = concept.get('external_id', '')
response = requests.get(concept_url, headers=HEADERS, timeout=30)
response.raise_for_status()
concept_details = response.json()
concept_name = concept['display_name']
update_concept_external_id(
concept_url, concept_id, concept_name, external_id, concept_details
)
# Update progress
PROCESSED_CONCEPTS_COUNT += 1
progress_percentage = (PROCESSED_CONCEPTS_COUNT / TOTAL_CONCEPTS) * 100
print(
f"Progress: {PROCESSED_CONCEPTS_COUNT}/{TOTAL_CONCEPTS} concepts verified "
f"({progress_percentage:.2f}%) - Last concept: {concept_name} (ExtID: {external_id})"
)
# Print the results
if DRY_RUN:
print("DRY RUN MODE: No changes will be made to the OCL source.")
print(f"TOTAL CONCEPTS ARE {TOTAL_CONCEPTS} AND PROCESSED CONCEPTS ARE {PROCESSED_CONCEPTS_COUNT}")
print(f"Number of concepts updated because they were empty: {COUNTERS['UPDATED_EMPTY']}")
print(f"Number of concepts updated because they started with 'MSF-': {COUNTERS['UPDATED_MSF']}")
print(f"Number of concepts updated because ID was <36 characters: {COUNTERS['UPDATED_INVALID']}")
print(f"Number of concepts skipped: {COUNTERS['SKIPPED']}")