def main(argv=None):
"""
The main method for the tool. This method is called from the command line,
processes the command line arguments and calls into the ImdTk library to do its work.
This main method takes no arguments so it can be called by setuptools.
"""
# the main method takes no arguments so it can be called by setuptools
if (argv is None): # if called by setuptools
argv = sys.argv[1:] # then fetch the arguments from the system
# setup command line argument parsing and add shared arguments
parser = argparse.ArgumentParser(
prog=TOOL_NAME,
formatter_class=argparse.RawTextHelpFormatter,
description='Store a catalog data table in a PostgreSQL database table'
)
cli_utils.add_shared_arguments(parser, TOOL_NAME)
cli_utils.add_input_file_argument(parser, TOOL_NAME)
cli_utils.add_output_arguments(parser, TOOL_NAME)
cli_utils.add_database_arguments(parser, TOOL_NAME)
cli_utils.add_catalog_table_argument(parser, TOOL_NAME)
# actually parse the arguments from the command line
args = vars(parser.parse_args(argv))
# if debugging, set verbose and echo input arguments
if (args.get('debug')):
args['verbose'] = True # if debug turn on verbose too
print("({}.main): ARGS={}".format(TOOL_NAME, args), file=sys.stderr)
# if input file path given, check the file path for validity
input_file = args.get('input_file')
cli_utils.check_input_file(
input_file, TOOL_NAME) # may system exit here and not return!
# if database config file path given, check the file path for validity
dbconfig_file = args.get('dbconfig_file')
cli_utils.check_dbconfig_file(
dbconfig_file, TOOL_NAME) # may system exit here and not return!
# if database config file path given, check the file path for validity
catalog_table = args.get('catalog_table')
cli_utils.check_catalog_table(
catalog_table, TOOL_NAME) # may system exit here and not return!
# add additional arguments to args
args['TOOL_NAME'] = TOOL_NAME
# call the task layer to process the given, validated input file
try:
task = FitsCatalogFillTableSink(args)
task.input_process_output()
except errors.ProcessingError as pe:
errMsg = "({}): ERROR: Processing Error ({}): {}".format(
TOOL_NAME, pe.error_code, pe.message)
print(errMsg, file=sys.stderr)
sys.exit(pe.error_code)
def main(argv=None):
"""
The main method for the tool. This method is called from the command line,
processes the command line arguments and calls into the ImdTk library to do its work.
This main method takes no arguments so it can be called by setuptools.
"""
# the main method takes no arguments so it can be called by setuptools
if (argv is None): # if called by setuptools
argv = sys.argv[1:] # then fetch the arguments from the system
# setup command line argument parsing and add shared arguments
parser = argparse.ArgumentParser(
prog=TOOL_NAME,
formatter_class=argparse.RawTextHelpFormatter,
description=
'Calculate values from incoming metadata, add the calculated fields to the metadata structure, and output it.'
)
cli_utils.add_shared_arguments(parser, TOOL_NAME)
cli_utils.add_input_file_argument(parser, TOOL_NAME)
cli_utils.add_fits_file_argument(parser, TOOL_NAME)
cli_utils.add_hdu_argument(parser, TOOL_NAME)
cli_utils.add_collection_argument(parser, TOOL_NAME)
cli_utils.add_output_arguments(parser, TOOL_NAME)
# actually parse the arguments from the command line
args = vars(parser.parse_args(argv))
# if debugging, set verbose and echo input arguments
if (args.get('debug')):
args['verbose'] = True # if debug turn on verbose too
print("({}.main): ARGS={}".format(TOOL_NAME, args), file=sys.stderr)
# if input file path given, check the file path for validity
input_file = args.get('input_file')
cli_utils.check_input_file(
input_file, TOOL_NAME) # may system exit here and not return!
# check the required FITS file path for validity
fits_file = args.get('fits_file')
cli_utils.check_fits_file(
fits_file, TOOL_NAME) # may system exit here and not return!
# add additional arguments to args
args['TOOL_NAME'] = TOOL_NAME
# call the task layer to process the given, validated files
try:
task = JWST_ObsCoreCalcTask(args)
task.input_process_output()
except errors.ProcessingError as pe:
errMsg = "({}): ERROR: Processing Error ({}): {}".format(
TOOL_NAME, pe.error_code, pe.message)
print(errMsg, file=sys.stderr)
sys.exit(pe.error_code)
def main(argv=None):
"""
The main method for the tool. This method is called from the command line,
processes the command line arguments and calls into the ImdTk library to do its work.
This main method takes no arguments so it can be called by setuptools.
"""
# the main method takes no arguments so it can be called by setuptools
if (argv is None): # if called by setuptools
argv = sys.argv[1:] # then fetch the arguments from the system
# setup command line argument parsing and add shared arguments
parser = argparse.ArgumentParser(
prog=TOOL_NAME,
formatter_class=argparse.RawTextHelpFormatter,
description=
'Add aliases for column names of a catalog metadata structure and output it.'
)
cli_utils.add_shared_arguments(parser, TOOL_NAME)
cli_utils.add_input_file_argument(parser, TOOL_NAME)
cli_utils.add_aliases_argument(parser,
TOOL_NAME,
default_msg=DEFAULT_CAT_ALIASES_FILEPATH)
cli_utils.add_output_arguments(parser, TOOL_NAME)
# actually parse the arguments from the command line
args = vars(parser.parse_args(argv))
# if debugging, set verbose and echo input arguments
if (args.get('debug')):
args['verbose'] = True # if debug turn on verbose too
print("({}.main): ARGS={}".format(TOOL_NAME, args), file=sys.stderr)
# if input file path given, check the file path for validity
input_file = args.get('input_file')
cli_utils.check_input_file(input_file,
TOOL_NAME) # may exit here and not return!
# if aliases file path given, check the file path for validity
alias_file = args.get('alias_file')
cli_utils.check_alias_file(alias_file,
TOOL_NAME) # may exit here and not return!
# add additional arguments to args
args['TOOL_NAME'] = TOOL_NAME
# call the task layer to process the given, validated input file
try:
task = CatalogAliasesTask(args)
task.input_process_output()
except errors.ProcessingError as pe:
errMsg = "({}): ERROR: Processing Error ({}): {}".format(
TOOL_NAME, pe.error_code, pe.message)
print(errMsg, file=sys.stderr)
sys.exit(pe.error_code)
def main(argv=None):
"""
The main method for the pipeline. This method is called from the command line,
processes the command line arguments and calls into the ImdTk library to do its work.
This main method takes no arguments so it can be called by setuptools.
"""
# the main method takes no arguments so it can be called by setuptools
if (argv is None): # if called by setuptools
argv = sys.argv[1:] # then fetch the arguments from the system
# setup command line argument parsing and add shared arguments
parser = argparse.ArgumentParser(
prog=TOOL_NAME,
formatter_class=argparse.RawTextHelpFormatter,
description=
'Pipeline to store catalog data in an existing PostgreSQL database table.'
)
cli_utils.add_shared_arguments(parser, TOOL_NAME)
cli_utils.add_input_file_argument(parser, TOOL_NAME)
cli_utils.add_fits_file_argument(parser, TOOL_NAME)
cli_utils.add_catalog_hdu_argument(parser, TOOL_NAME)
cli_utils.add_output_arguments(parser, TOOL_NAME)
cli_utils.add_database_arguments(parser, TOOL_NAME)
cli_utils.add_catalog_table_argument(parser, TOOL_NAME)
# actually parse the arguments from the command line
args = vars(parser.parse_args(argv))
# if debugging, set verbose and echo input arguments
if (args.get('debug')):
args['verbose'] = True # if debug turn on verbose too
print("({}.main): ARGS={}".format(TOOL_NAME, args), file=sys.stderr)
# if input file path given, check the file path for validity
input_file = args.get('input_file')
cli_utils.check_input_file(
input_file, TOOL_NAME) # may system exit here and not return!
# check the required FITS file path for validity
fits_file = args.get('fits_file')
cli_utils.check_fits_file(
fits_file, TOOL_NAME) # may system exit here and not return!
# if database config file path given, check the file path for validity
dbconfig_file = args.get('dbconfig_file')
cli_utils.check_dbconfig_file(
dbconfig_file, TOOL_NAME) # may system exit here and not return!
# if database config file path given, check the file path for validity
catalog_table = args.get('catalog_table')
cli_utils.check_catalog_table(
catalog_table, TOOL_NAME) # may system exit here and not return!
# add additional arguments to args
args['TOOL_NAME'] = TOOL_NAME
# instantiate the tasks which form the pipeline
fits_catalog_dataTask = FitsCatalogDataTask(args)
fits_catalog_fillTask = FitsCatalogFillTableSink(args)
# compose and call the pipeline tasks
if (args.get('verbose')):
print("({}): Processing FITS file '{}'.".format(TOOL_NAME, fits_file),
file=sys.stderr)
try:
fits_catalog_fillTask.output_results( # sink to DB: nothing returned
fits_catalog_dataTask.process(None)) # data source
except errors.UnsupportedType as ute:
errMsg = "({}): WARNING: Unsupported File Type ({}): {}".format(
TOOL_NAME, ute.error_code, ute.message)
print(errMsg, file=sys.stderr)
sys.exit(ute.error_code)
except errors.ProcessingError as pe:
errMsg = "({}): ERROR: Processing Error ({}): {}".format(
TOOL_NAME, pe.error_code, pe.message)
print(errMsg, file=sys.stderr)
sys.exit(pe.error_code)
if (args.get('verbose')):
print("({}): Processed FITS file '{}'.".format(TOOL_NAME, fits_file),
file=sys.stderr)
def test_check_input_file(self):
with pytest.raises(SystemExit) as se:
utils.check_input_file(self.nosuch_tstfyl, TOOL_NAME)
assert se.type == SystemExit
assert se.value.code == utils.INPUT_FILE_EXIT_CODE
def main(argv=None):
"""
The main method for the pipeline. This method is called from the command line,
processes the command line arguments and calls into the ImdTk library to do its work.
This main method takes no arguments so it can be called by setuptools.
"""
# the main method takes no arguments so it can be called by setuptools
if (argv is None): # if called by setuptools
argv = sys.argv[1:] # then fetch the arguments from the system
# setup command line argument parsing and add shared arguments
parser = argparse.ArgumentParser(
prog=TOOL_NAME,
formatter_class=argparse.RawTextHelpFormatter,
description=
'Read incoming metadata and attach it to an iRods file as iRods metadata.'
)
cli_utils.add_shared_arguments(parser, TOOL_NAME)
cli_utils.add_input_file_argument(parser, TOOL_NAME)
cli_utils.add_irods_md_file_argument(parser, TOOL_NAME)
# add arguments specific to this module
parser.add_argument(
'-rm',
'--remove',
dest='remove_only',
action='store_true',
default=False,
help=
'If True, remove matching input items from iRods file metadata [default: False].'
)
# actually parse the arguments from the command line
args = vars(parser.parse_args(argv))
# if debugging, set verbose and echo input arguments
if (args.get('debug')):
args['verbose'] = True # if debug turn on verbose too
print("({}.main): ARGS={}".format(TOOL_NAME, args), file=sys.stderr)
# if input file path given, check the file path for validity
input_file = args.get('input_file')
cli_utils.check_input_file(
input_file, TOOL_NAME) # may system exit here and not return!
# add additional arguments to args
args['TOOL_NAME'] = TOOL_NAME
# get an instance of the iRods accessor class
firh = FitsIRodsHelper(args)
# compose and call the pipeline tasks
try:
task = IRodsMetadataSink(args, firh)
task.input_process_output()
except errors.UnsupportedType as ute:
errMsg = "({}): WARNING: Unsupported File Type ({}): {}".format(
TOOL_NAME, ute.error_code, ute.message)
print(errMsg, file=sys.stderr)
sys.exit(ute.error_code)
except errors.ProcessingError as pe:
errMsg = "({}): ERROR: Processing Error ({}): {}".format(
TOOL_NAME, pe.error_code, pe.message)
print(errMsg, file=sys.stderr)
sys.exit(pe.error_code)
finally:
task.cleanup() # cleanup any task resources
firh.cleanup() # cleanup resources opened here
def main (argv=None):
"""
The main method for the tool. This method is called from the command line,
processes the command line arguments and calls into the ImdTk library to do its work.
This main method takes no arguments so it can be called by setuptools.
"""
# the main method takes no arguments so it can be called by setuptools
if (argv is None): # if called by setuptools
argv = sys.argv[1:] # then fetch the arguments from the system
# setup command line argument parsing and add shared arguments
parser = argparse.ArgumentParser(
prog=TOOL_NAME,
formatter_class=argparse.RawTextHelpFormatter,
description='Calculate ObsCore values from incoming metadata and an iRods FITS file, add the calculated fields to the metadata structure, and output it.'
)
cli_utils.add_shared_arguments(parser, TOOL_NAME)
cli_utils.add_input_file_argument(parser, TOOL_NAME)
cli_utils.add_irods_fits_file_argument(parser, TOOL_NAME)
cli_utils.add_hdu_argument(parser, TOOL_NAME)
cli_utils.add_collection_argument(parser, TOOL_NAME)
cli_utils.add_output_arguments(parser, TOOL_NAME)
# actually parse the arguments from the command line
args = vars(parser.parse_args(argv))
# if debugging, set verbose and echo input arguments
if (args.get('debug')):
args['verbose'] = True # if debug turn on verbose too
print("({}.main): ARGS={}".format(TOOL_NAME, args), file=sys.stderr)
# if input file path given, check the file path for validity
input_file = args.get('input_file')
cli_utils.check_input_file(input_file, TOOL_NAME) # may system exit here and not return!
# add additional arguments to args
args['TOOL_NAME'] = TOOL_NAME
# get the iRods file path argument of the file to be opened
irff_path = args.get('irods_fits_file')
# the specified FITS file must have a valid FITS extension
cli_utils.check_irods_fits_file(irff_path, TOOL_NAME) # may system exit here and not return!
# get an instance of the iRods accessor class
firh = FitsIRodsHelper(args)
# instantiate the task
task = IRods_JWST_ObsCoreCalcTask(args, firh)
if (args.get('verbose')):
print("({}): Processing iRods FITS file '{}'.".format(TOOL_NAME, irff_path), file=sys.stderr)
# call task layer to process the input stream using the unvalidated remote iRods FITS file
try:
task.input_process_output()
except errors.ProcessingError as pe:
errMsg = "({}): ERROR: Processing Error ({}): {}".format(
TOOL_NAME, pe.error_code, pe.message)
print(errMsg, file=sys.stderr)
sys.exit(pe.error_code)
finally:
task.cleanup()
firh.cleanup() # cleanup resources opened here