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Merge pull request #342 from kedhammar/AKe-dev
Organize modules and add EPP wrapper
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| Original file line number | Diff line number | Diff line change |
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@@ -8,3 +8,4 @@ build/ | |
| *.swp | ||
| __pycache__ | ||
| node_modules | ||
| dist | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,104 @@ | ||
| #!/usr/bin/env python | ||
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| import logging | ||
| import os | ||
| import sys | ||
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| from genologics.config import BASEURI, PASSWORD, USERNAME | ||
| from genologics.entities import Process | ||
| from genologics.lims import Lims | ||
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| from scilifelab_epps.epp import upload_file | ||
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| def epp_decorator(script_path: str, timestamp: str): | ||
| """This top-level decorator is meant to be used on EPP scripts' main functions. | ||
| It receives the script path (__file__) and timestamp (yymmdd_hhmmss) as arguments to | ||
| pass on to it's children which wrap the main function to handle logging and graceful failure. | ||
| """ | ||
| script_name: str = os.path.basename(script_path).split(".")[0] | ||
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| def _epp_decorator(script_main): | ||
| def epp_wrapper(args): | ||
| """General wrapper for EPP scripts.""" | ||
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| # Set up LIMS | ||
| lims = Lims(BASEURI, USERNAME, PASSWORD) | ||
| lims.check_version() | ||
| process = Process(lims, id=args.pid) | ||
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| # Name log file | ||
| log_filename: str = ( | ||
| "_".join( | ||
| [ | ||
| script_name, | ||
| process.id, | ||
| timestamp, | ||
| process.technician.name.replace(" ", ""), | ||
| ] | ||
| ) | ||
| + ".log" | ||
| ) | ||
|
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||
| # Set up logging | ||
| logging.basicConfig( | ||
| filename=log_filename, | ||
| filemode="w", | ||
| format="%(levelname)s: %(message)s", | ||
| level=logging.INFO, | ||
| ) | ||
|
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| # Start logging | ||
| logging.info(f"Script '{script_name}' started at {timestamp}.") | ||
| logging.info( | ||
| f"Launched in step '{process.type.name}' ({process.id}) by {process.technician.name}." | ||
| ) | ||
| args_str = "\n\t".join( | ||
| [f"'{arg}': {getattr(args, arg)}" for arg in vars(args)] | ||
| ) | ||
| logging.info(f"Script called with arguments: \n\t{args_str}") | ||
|
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| # Run | ||
| try: | ||
| script_main(args) | ||
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| # On script error | ||
| except Exception as e: | ||
| # Post error to LIMS GUI | ||
| logging.error(str(e), exc_info=True) | ||
| logging.shutdown() | ||
| upload_file( | ||
| file_path=log_filename, | ||
| file_slot=args.log, | ||
| process=process, | ||
| lims=lims, | ||
| ) | ||
| os.remove(log_filename) | ||
| sys.stderr.write(str(e)) | ||
| sys.exit(2) | ||
|
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||
| # On script success | ||
| else: | ||
| logging.info("Script completed successfully.") | ||
| logging.shutdown() | ||
| upload_file( | ||
| file_path=log_filename, | ||
| file_slot=args.log, | ||
| process=process, | ||
| lims=lims, | ||
| ) | ||
| # Check log for errors and warnings | ||
| log_content = open(log_filename).read() | ||
| os.remove(log_filename) | ||
| if "ERROR:" in log_content or "WARNING:" in log_content: | ||
| sys.stderr.write( | ||
| "Script finished successfully, but log contains errors or warnings, please have a look." | ||
| ) | ||
| sys.exit(2) | ||
| else: | ||
| sys.exit(0) | ||
|
|
||
| return epp_wrapper | ||
|
|
||
| return _epp_decorator |
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