def cli_parser():
"""
:type parser: argparse.ArgumentParser
:rtype: argparse.ArgumentParser
"""
parser = bin_utils.basic_cli_parser(bin_utils.doc_as_description(__doc__))
parser.add_argument('--after-time', metavar='TIMESTAMP',
help='Optional timestamp to constrain that we look '
'for entries added after the given time stamp. '
'This should be formatted according to Solr\'s '
'timestamp format (e.g. '
'"2016-01-01T00:00:00.000Z"). Sub-seconds are '
'optional. Timestamps should be in UTC (Zulu). '
'The constraint is inclusive.')
parser.add_argument('--before-time', metavar='TIMESTAMP',
help='Optional timestamp to constrin that we look for '
'entries added before the given time stamp. See '
'the description of `--after-time` for format '
'info.')
g_required = parser.add_argument_group("Required options")
g_required.add_argument('-p', '--paths-file',
help='Path to the file to output collected file '
'paths to (local filesystem path).')
return parser
def cli_parser():
parser = bin_utils.basic_cli_parser(__doc__)
# Application options
group_application = parser.add_argument_group("Application Selection")
group_application.add_argument(
'-l',
'--list',
default=False,
action="store_true",
help="List currently available applications "
"for running. More description is "
"included if SMQTK verbosity is "
"increased (-v | --debug-smqtk)")
group_application.add_argument('-a',
'--application',
default=None,
help="Label of the web application to run.")
# Server options
group_server = parser.add_argument_group("Server options")
group_server.add_argument('-r',
'--reload',
action='store_true',
default=False,
help='Turn on server reloading.')
group_server.add_argument('-t',
'--threaded',
action='store_true',
default=False,
help="Turn on server multi-threading.")
group_server.add_argument('--host',
default=None,
help="Run host address specification override. "
"This will override all other configuration "
"method specifications.")
group_server.add_argument(
'--port',
default=None,
help="Run port specification override. This will "
"override all other configuration method "
"specifications.")
group_server.add_argument("--use-basic-auth",
action="store_true",
default=False,
help="Use global basic authentication as "
"configured.")
# Other options
group_other = parser.add_argument_group("Other options")
group_other.add_argument('--debug-server',
action='store_true',
default=False,
help='Turn on server debugging messages ONLY')
group_other.add_argument('--debug-smqtk',
action='store_true',
default=False,
help='Turn on SMQTK debugging messages ONLY')
return parser
def cli_parser():
"""
:type parser: argparse.ArgumentParser
:rtype: argparse.ArgumentParser
"""
parser = bin_utils.basic_cli_parser(bin_utils.doc_as_description(__doc__))
parser.add_argument('--after-time',
metavar='TIMESTAMP',
help='Optional timestamp to constrain that we look '
'for entries added after the given time stamp. '
'This should be formatted according to Solr\'s '
'timestamp format (e.g. '
'"2016-01-01T00:00:00.000Z"). Sub-seconds are '
'optional. Timestamps should be in UTC (Zulu). '
'The constraint is inclusive.')
parser.add_argument('--before-time',
metavar='TIMESTAMP',
help='Optional timestamp to constrin that we look for '
'entries added before the given time stamp. See '
'the description of `--after-time` for format '
'info.')
g_required = parser.add_argument_group("Required options")
g_required.add_argument('-p',
'--paths-file',
help='Path to the file to output collected file '
'paths to (local filesystem path).')
return parser
def get_cli_parser():
parser = basic_cli_parser(__doc__)
g_classifier = parser.add_argument_group("Classification")
g_classifier.add_argument('--overwrite',
action='store_true',
default=False,
help='When generating a configuration file, '
'overwrite an existing file.')
g_classifier.add_argument('-l',
'--label',
type=str,
default=None,
help='The class to filter by. This is based on '
'the classifier configuration/model used. '
'If this is not provided, we will list the '
'available labels in the provided '
'classifier configuration.')
# Positional
parser.add_argument("file_globs",
nargs='*',
metavar='GLOB',
help='Series of shell globs specifying the files to '
'classify.')
return parser
def cli_parser():
parser = basic_cli_parser(__doc__, configuration_group=False)
parser.add_argument("hash2uuids_fp", type=str)
parser.add_argument("bit_len", type=int)
parser.add_argument("leaf_size", type=int)
parser.add_argument("rand_seed", type=int)
parser.add_argument("balltree_model_fp", type=str)
return parser
def cli_parser():
p = basic_cli_parser(__doc__)
g_output = p.add_argument_group("output")
g_output.add_argument('-o', '--output-map',
metavar="PATH",
help="Path to output the clustering class mapping "
"to. Saved as a pickle file with -1 format.")
return p
def cli_parser():
p = basic_cli_parser(__doc__)
g_output = p.add_argument_group("output")
g_output.add_argument('-o', '--output-map',
metavar="PATH",
help="Path to output the clustering class mapping "
"to. Saved as a pickle file with -1 format.")
return p
def cli_parser():
parser = bin_utils.basic_cli_parser(__doc__)
g_io = parser.add_argument_group("Input Output Files")
g_io.add_argument('--uuids-list', metavar='PATH',
help='Path to the input file listing UUIDs to process.')
g_io.add_argument('--csv-header', metavar='PATH',
help='Path to the file to output column header labels.')
g_io.add_argument('--csv-data', metavar='PATH',
help='Path to the file to output the CSV data to.')
return parser
def cli_parser():
parser = bin_utils.basic_cli_parser(__doc__)
g_io = parser.add_argument_group("I/O")
g_io.add_argument("--uuids-list",
default=None, metavar="PATH",
help='Optional path to a file listing UUIDs of '
'descriptors to computed hash codes for. If '
'not provided we compute hash codes for all '
'descriptors in the configured descriptor index.')
return parser
def get_cli_parser():
parser = basic_cli_parser(__doc__, configuration_group=False)
parser.add_argument('-i', '--invert',
default=False, action='store_true',
help='Invert results, showing only invalid images.')
g_required = parser.add_argument_group("Required Arguments")
g_required.add_argument('-f', '--file-list',
type=str, default=None, metavar='PATH',
help='Path to a file that lists data file paths.')
return parser
def cli_parser():
parser = bin_utils.basic_cli_parser(__doc__)
g_io = parser.add_argument_group("IO Options")
g_io.add_argument('-f', metavar='PATH',
help='Path to the csv file mapping descriptor UUIDs to '
'their class label. String labels are transformed '
'into integers for libSVM. Integers start at 1 '
'and are applied in the order that labels are '
'seen in this input file.')
g_io.add_argument('-o', metavar='PATH',
help='Path to the output file to write libSVM labeled '
'descriptors to.')
return parser
def get_cli_parser():
parser = basic_cli_parser(__doc__)
parser.add_argument('-u', '--uuid-list',
default=None, metavar='PATH',
help='Path to list of UUIDs to calculate nearest '
'neighbors for. If empty, all UUIDs present '
'in the descriptor index will be used.')
parser.add_argument('-n', '--num',
default=10, metavar='INT', type=int,
help='Number of maximum nearest neighbors to return '
'for each UUID, defaults to retrieving 10 nearest '
'neighbors. Set to 0 to retrieve all nearest '
'neighbors.')
return parser
def cli_parser():
parser = bin_utils.basic_cli_parser(__doc__)
g_io = parser.add_argument_group("IO Options")
g_io.add_argument('-f',
metavar='PATH',
help='Path to the csv file mapping descriptor UUIDs to '
'their class label. String labels are transformed '
'into integers for libSVM. Integers start at 1 '
'and are applied in the order that labels are '
'seen in this input file.')
g_io.add_argument('-o',
metavar='PATH',
help='Path to the output file to write libSVM labeled '
'descriptors to.')
return parser
def cli_parser():
parser = bin_utils.basic_cli_parser(__doc__)
# Application options
group_application = parser.add_argument_group("Application Selection")
group_application.add_argument('-l', '--list',
default=False, action="store_true",
help="List currently available applications "
"for running. More description is "
"included if SMQTK verbosity is "
"increased (-v | --debug-smqtk)")
group_application.add_argument('-a', '--application', default=None,
help="Label of the web application to run.")
# Server options
group_server = parser.add_argument_group("Server options")
group_server.add_argument('-r', '--reload',
action='store_true', default=False,
help='Turn on server reloading.')
group_server.add_argument('-t', '--threaded',
action='store_true', default=False,
help="Turn on server multi-threading.")
group_server.add_argument('--host',
default=None,
help="Run host address specification override. "
"This will override all other configuration "
"method specifications.")
group_server.add_argument('--port',
default=None,
help="Run port specification override. This will "
"override all other configuration method "
"specifications.")
group_server.add_argument("--use-basic-auth",
action="store_true", default=False,
help="Use global basic authentication as "
"configured.")
# Other options
group_other = parser.add_argument_group("Other options")
group_other.add_argument('--debug-server',
action='store_true', default=False,
help='Turn on server debugging messages ONLY')
group_other.add_argument('--debug-smqtk',
action='store_true', default=False,
help='Turn on SMQTK debugging messages ONLY')
return parser
def cli_parser():
parser = basic_cli_parser(__doc__)
parser.add_argument('-b',
'--batch-size',
type=int,
default=0,
metavar='INT',
help="Number of files to batch together into a single "
"compute async call. This defines the "
"granularity of the checkpoint file in regards "
"to computation completed. If given 0, we do not "
"batch and will perform a single "
"``compute_async`` call on the configured "
"generator. Default batch size is 0.")
parser.add_argument('--check-image',
default=False,
action='store_true',
help="If se should check image pixel loading before "
"queueing an input image for processing. If we "
"cannot load the image pixels via "
"``PIL.Image.open``, the input image is not "
"queued for processing")
# Non-config required arguments
g_required = parser.add_argument_group("Required Arguments")
g_required.add_argument('-f',
'--file-list',
type=str,
default=None,
metavar='PATH',
help="Path to a file that lists data file paths. "
"Paths in this file may be relative, but "
"will at some point be coerced into absolute "
"paths based on the current working "
"directory.")
g_required.add_argument('-p',
'--completed-files',
default=None,
metavar='PATH',
help='Path to a file into which we add CSV '
'format lines detailing filepaths that have '
'been computed from the file-list provided, '
'as the UUID for that data (currently the '
'SHA1 checksum of the data).')
return parser
def cli_parser():
parser = bin_utils.basic_cli_parser(__doc__)
parser.add_argument('--overwrite',
action='store_true', default=False,
help="Force descriptor computation even if an "
"existing descriptor vector was "
"discovered based on the given content "
"descriptor type and data combination.")
parser.add_argument('-o', '--output-filepath',
help='Optional path to a file to output '
'feature vector to. Otherwise the feature '
'vector is printed to standard out. '
'Output is saved in numpy binary format '
'(.npy suffix recommended).')
parser.add_argument("input_file",
nargs="?",
help="Data file to compute descriptor on")
return parser
def cli_parser():
"""
:rtype: argparse.ArgumentParser
"""
parser = basic_cli_parser(doc_as_description(__doc__))
parser.add_argument('-s',
'--report-size',
action='store_true',
default=False,
help="Report the number of elements that would be "
"scanned by the ElasticSearch query generated "
"and then exit.")
parser.add_argument('--crawled-after',
default=None,
help="Optional timestamp constraint to only get "
"content that was crawled after the given time. "
"Time should be in UTC."
"Timestamp format like: '2016-01-01T12:00:00Z'")
parser.add_argument('--inserted-after',
default=None,
help="Optional timestamp constraint to only get "
"content that was inserted into the "
"ElasticSearch instance/index after the given "
"time. Time should be in UTC."
"Timestamp format like: '2016-01-01T12:00:00Z'")
g_output = parser.add_argument_group("Output")
g_output.add_argument('-d',
'--output-dir',
metavar='PATH',
help='Output image directory path.')
g_output.add_argument('-l',
'--file-list',
metavar='PATH',
help='Path to an output CSV file where downloaded '
'files are recorded along with their '
'associated CDR identifier as SHA1 checksum.')
return parser
def get_cli_parser():
parser = basic_cli_parser(__doc__)
g_classifier = parser.add_argument_group("Classification")
g_classifier.add_argument('--overwrite',
action='store_true', default=False,
help='When generating a configuration file, '
'overwrite an existing file.')
g_classifier.add_argument('-l', '--label',
type=str, default=None,
help='The class to filter by. This is based on '
'the classifier configuration/model used. '
'If this is not provided, we will list the '
'available labels in the provided '
'classifier configuration.')
# Positional
parser.add_argument("file_globs",
nargs='*',
metavar='GLOB',
help='Series of shell globs specifying the files to '
'classify.')
return parser
def cli_parser():
parser = bin_utils.basic_cli_parser(__doc__)
g_girder = parser.add_argument_group('Girder References')
g_girder.add_argument('-F',
'--folder',
nargs='*',
default=[],
metavar='FOLDER_ID',
help='Specify specific folder IDs')
g_girder.add_argument('--folder-list',
metavar='PATH',
help='Path to a new-line separated file of folder '
'IDs')
g_girder.add_argument('-i',
'--item',
nargs='*',
default=[],
metavar='ITEM_ID',
help='Specify specific item IDs')
g_girder.add_argument('--item-list',
metavar='PATH',
help='Path to a new-line separated file of item IDs')
g_girder.add_argument('-f',
'--file',
nargs='*',
default=[],
metavar='FILE_ID',
help='Specify specific file IDs')
g_girder.add_argument('--file-list',
metavar='PATH',
help='Path to a new-line separated file of file IDs')
return parser
def cli_parser():
"""
:rtype: argparse.ArgumentParser
"""
parser = basic_cli_parser(doc_as_description(__doc__))
parser.add_argument('-s', '--report-size',
action='store_true', default=False,
help="Report the number of elements that would be "
"scanned by the ElasticSearch query generated "
"and then exit.")
parser.add_argument('--crawled-after',
default=None,
help="Optional timestamp constraint to only get "
"content that was crawled after the given time. "
"Time should be in UTC."
"Timestamp format like: '2016-01-01T12:00:00Z'")
parser.add_argument('--inserted-after',
default=None,
help="Optional timestamp constraint to only get "
"content that was inserted into the "
"ElasticSearch instance/index after the given "
"time. Time should be in UTC."
"Timestamp format like: '2016-01-01T12:00:00Z'")
g_output = parser.add_argument_group("Output")
g_output.add_argument('-d', '--output-dir',
metavar='PATH',
help='Output image directory path.')
g_output.add_argument('-l', '--file-list',
metavar='PATH',
help='Path to an output CSV file where downloaded '
'files are recorded along with their '
'associated CDR identifier as SHA1 checksum.')
return parser
def cli_parser():
parser = bin_utils.basic_cli_parser(__doc__)
g_girder = parser.add_argument_group('Girder References')
g_girder.add_argument('-F', '--folder',
nargs='*', default=[], metavar='FOLDER_ID',
help='Specify specific folder IDs')
g_girder.add_argument('--folder-list', metavar='PATH',
help='Path to a new-line separated file of folder '
'IDs')
g_girder.add_argument('-i', '--item',
nargs='*', default=[], metavar='ITEM_ID',
help='Specify specific item IDs')
g_girder.add_argument('--item-list', metavar='PATH',
help='Path to a new-line separated file of item IDs')
g_girder.add_argument('-f', '--file',
nargs='*', default=[], metavar='FILE_ID',
help='Specify specific file IDs')
g_girder.add_argument('--file-list', metavar='PATH',
help='Path to a new-line separated file of file IDs')
return parser
def cli_parser():
return bin_utils.basic_cli_parser(__doc__)
def get_cli_parser():
parser = basic_cli_parser(__doc__)
parser.add_argument('-i',
'--iqr-state',
help="Path to the ZIP file saved from an IQR session.")
return parser
def cli_parser():
parser = bin_utils.basic_cli_parser(__doc__)
parser.add_argument("input_files", metavar='GLOB', nargs='*')
return parser
def cli_parser():
return bin_utils.basic_cli_parser(__doc__)
def cli_parser():
parser = bin_utils.basic_cli_parser(__doc__)
parser.add_argument("input_files", metavar='GLOB', nargs='*')
return parser
def get_cli_parser():
parser = basic_cli_parser(__doc__)
parser.add_argument('-i', '--iqr-state',
help="Path to the ZIP file saved from an IQR session.")
return parser
