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 test_add_fits_file_argument(self):
parser = argparse.ArgumentParser(
formatter_class=argparse.RawTextHelpFormatter)
utils.add_fits_file_argument(parser, TOOL_NAME)
with pytest.raises(SystemExit) as se:
args = vars(parser.parse_args([])) # fits-file is required
assert se.type == SystemExit
args = vars(parser.parse_args(['-ff', 'astro.fits']))
print(args)
assert 'fits_file' in args
assert 'which_hdu' not in args
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 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 extract FITS image metadata and store it into a PostreSQL/JSON hybrid database.'
)
cli_utils.add_shared_arguments(parser, TOOL_NAME)
cli_utils.add_fits_file_argument(parser, TOOL_NAME)
cli_utils.add_hdu_argument(parser, TOOL_NAME)
cli_utils.add_ignore_list_argument(parser, TOOL_NAME)
cli_utils.add_aliases_argument(parser, TOOL_NAME)
cli_utils.add_fields_info_argument(parser, TOOL_NAME)
cli_utils.add_collection_argument(parser, TOOL_NAME)
cli_utils.add_report_format_argument(parser, TOOL_NAME)
cli_utils.add_output_arguments(parser, TOOL_NAME)
cli_utils.add_database_arguments(parser,
TOOL_NAME,
table_msg=DEFAULT_HYBRID_TABLE_NAME)
cli_utils.add_table_name_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)
# 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
# instantiate the tasks which form the pipeline
fits_image_mdTask = FitsImageMetadataTask(args)
image_aliasesTask = ImageAliasesTask(args)
fields_infoTask = FieldsInfoTask(args)
jwst_oc_calcTask = JWST_ObsCoreCalcTask(args)
miss_reportTask = MissingFieldsTask(args)
jwst_pghybrid_sinkTask = JWST_HybridPostgreSQLSink(args)
# compose and call the pipeline tasks
if (args.get('verbose')):
print("({}): Processing FITS file '{}'.".format(TOOL_NAME, fits_file),
file=sys.stderr)
try:
jwst_pghybrid_sinkTask.output_results( # sink: nothing returned
miss_reportTask.process( # report: passes data through
jwst_oc_calcTask.process(
fields_infoTask.process(
image_aliasesTask.process(
fits_image_mdTask.process(
None)))))) # metadata 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 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=
'Extract a catalog data table from a FITS file and output it as JSON.')
cli_utils.add_shared_arguments(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)
# 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)
# 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 FITS file
if (args.get('verbose')):
print("({}): Processing FITS file '{}'.".format(TOOL_NAME, fits_file),
file=sys.stderr)
try:
task = FitsCatalogDataTask(args)
task.process_and_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)
if (args.get('verbose')):
print("({}): Processed FITS file '{}'.".format(TOOL_NAME, fits_file),
file=sys.stderr)