repository_name stringlengths 5 67 | func_path_in_repository stringlengths 4 234 | func_name stringlengths 0 314 | whole_func_string stringlengths 52 3.87M | language stringclasses 6
values | func_code_string stringlengths 52 3.87M | func_code_tokens listlengths 15 672k | func_documentation_string stringlengths 1 47.2k | func_documentation_tokens listlengths 1 3.92k | split_name stringclasses 1
value | func_code_url stringlengths 85 339 |
|---|---|---|---|---|---|---|---|---|---|---|
greenbone/ospd | ospd/ospd.py | OSPDaemon.get_vts_xml | def get_vts_xml(self, vt_id=None, filtered_vts=None):
""" Gets collection of vulnerability test information in XML format.
If vt_id is specified, the collection will contain only this vt, if
found.
If no vt_id is specified, the collection will contain all vts or those
passed in f... | python | def get_vts_xml(self, vt_id=None, filtered_vts=None):
""" Gets collection of vulnerability test information in XML format.
If vt_id is specified, the collection will contain only this vt, if
found.
If no vt_id is specified, the collection will contain all vts or those
passed in f... | [
"def",
"get_vts_xml",
"(",
"self",
",",
"vt_id",
"=",
"None",
",",
"filtered_vts",
"=",
"None",
")",
":",
"vts_xml",
"=",
"Element",
"(",
"'vts'",
")",
"if",
"vt_id",
":",
"vts_xml",
".",
"append",
"(",
"self",
".",
"get_vt_xml",
"(",
"vt_id",
")",
"... | Gets collection of vulnerability test information in XML format.
If vt_id is specified, the collection will contain only this vt, if
found.
If no vt_id is specified, the collection will contain all vts or those
passed in filtered_vts.
Arguments:
vt_id (vt_id, optiona... | [
"Gets",
"collection",
"of",
"vulnerability",
"test",
"information",
"in",
"XML",
"format",
".",
"If",
"vt_id",
"is",
"specified",
"the",
"collection",
"will",
"contain",
"only",
"this",
"vt",
"if",
"found",
".",
"If",
"no",
"vt_id",
"is",
"specified",
"the",... | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/ospd.py#L1415-L1442 |
greenbone/ospd | ospd/ospd.py | OSPDaemon.handle_get_scanner_details | def handle_get_scanner_details(self):
""" Handles <get_scanner_details> command.
@return: Response string for <get_scanner_details> command.
"""
desc_xml = Element('description')
desc_xml.text = self.get_scanner_description()
details = [
desc_xml,
... | python | def handle_get_scanner_details(self):
""" Handles <get_scanner_details> command.
@return: Response string for <get_scanner_details> command.
"""
desc_xml = Element('description')
desc_xml.text = self.get_scanner_description()
details = [
desc_xml,
... | [
"def",
"handle_get_scanner_details",
"(",
"self",
")",
":",
"desc_xml",
"=",
"Element",
"(",
"'description'",
")",
"desc_xml",
".",
"text",
"=",
"self",
".",
"get_scanner_description",
"(",
")",
"details",
"=",
"[",
"desc_xml",
",",
"self",
".",
"get_scanner_p... | Handles <get_scanner_details> command.
@return: Response string for <get_scanner_details> command. | [
"Handles",
"<get_scanner_details",
">",
"command",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/ospd.py#L1444-L1455 |
greenbone/ospd | ospd/ospd.py | OSPDaemon.handle_get_version_command | def handle_get_version_command(self):
""" Handles <get_version> command.
@return: Response string for <get_version> command.
"""
protocol = Element('protocol')
for name, value in [('name', 'OSP'), ('version', self.get_protocol_version())]:
elem = SubElement(protocol,... | python | def handle_get_version_command(self):
""" Handles <get_version> command.
@return: Response string for <get_version> command.
"""
protocol = Element('protocol')
for name, value in [('name', 'OSP'), ('version', self.get_protocol_version())]:
elem = SubElement(protocol,... | [
"def",
"handle_get_version_command",
"(",
"self",
")",
":",
"protocol",
"=",
"Element",
"(",
"'protocol'",
")",
"for",
"name",
",",
"value",
"in",
"[",
"(",
"'name'",
",",
"'OSP'",
")",
",",
"(",
"'version'",
",",
"self",
".",
"get_protocol_version",
"(",
... | Handles <get_version> command.
@return: Response string for <get_version> command. | [
"Handles",
"<get_version",
">",
"command",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/ospd.py#L1457-L1485 |
greenbone/ospd | ospd/ospd.py | OSPDaemon.handle_command | def handle_command(self, command):
""" Handles an osp command in a string.
@return: OSP Response to command.
"""
try:
tree = secET.fromstring(command)
except secET.ParseError:
logger.debug("Erroneous client input: %s", command)
raise OSPDError... | python | def handle_command(self, command):
""" Handles an osp command in a string.
@return: OSP Response to command.
"""
try:
tree = secET.fromstring(command)
except secET.ParseError:
logger.debug("Erroneous client input: %s", command)
raise OSPDError... | [
"def",
"handle_command",
"(",
"self",
",",
"command",
")",
":",
"try",
":",
"tree",
"=",
"secET",
".",
"fromstring",
"(",
"command",
")",
"except",
"secET",
".",
"ParseError",
":",
"logger",
".",
"debug",
"(",
"\"Erroneous client input: %s\"",
",",
"command"... | Handles an osp command in a string.
@return: OSP Response to command. | [
"Handles",
"an",
"osp",
"command",
"in",
"a",
"string",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/ospd.py#L1487-L1518 |
greenbone/ospd | ospd/ospd.py | OSPDaemon.run | def run(self, address, port, unix_path):
""" Starts the Daemon, handling commands until interrupted.
@return False if error. Runs indefinitely otherwise.
"""
assert address or unix_path
if unix_path:
sock = bind_unix_socket(unix_path)
else:
sock =... | python | def run(self, address, port, unix_path):
""" Starts the Daemon, handling commands until interrupted.
@return False if error. Runs indefinitely otherwise.
"""
assert address or unix_path
if unix_path:
sock = bind_unix_socket(unix_path)
else:
sock =... | [
"def",
"run",
"(",
"self",
",",
"address",
",",
"port",
",",
"unix_path",
")",
":",
"assert",
"address",
"or",
"unix_path",
"if",
"unix_path",
":",
"sock",
"=",
"bind_unix_socket",
"(",
"unix_path",
")",
"else",
":",
"sock",
"=",
"bind_socket",
"(",
"add... | Starts the Daemon, handling commands until interrupted.
@return False if error. Runs indefinitely otherwise. | [
"Starts",
"the",
"Daemon",
"handling",
"commands",
"until",
"interrupted",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/ospd.py#L1524-L1560 |
greenbone/ospd | ospd/ospd.py | OSPDaemon.create_scan | def create_scan(self, scan_id, targets, options, vts):
""" Creates a new scan.
@target: Target to scan.
@options: Miscellaneous scan options.
@return: New scan's ID.
"""
if self.scan_exists(scan_id):
logger.info("Scan %s exists. Resuming scan.", scan_id)
... | python | def create_scan(self, scan_id, targets, options, vts):
""" Creates a new scan.
@target: Target to scan.
@options: Miscellaneous scan options.
@return: New scan's ID.
"""
if self.scan_exists(scan_id):
logger.info("Scan %s exists. Resuming scan.", scan_id)
... | [
"def",
"create_scan",
"(",
"self",
",",
"scan_id",
",",
"targets",
",",
"options",
",",
"vts",
")",
":",
"if",
"self",
".",
"scan_exists",
"(",
"scan_id",
")",
":",
"logger",
".",
"info",
"(",
"\"Scan %s exists. Resuming scan.\"",
",",
"scan_id",
")",
"ret... | Creates a new scan.
@target: Target to scan.
@options: Miscellaneous scan options.
@return: New scan's ID. | [
"Creates",
"a",
"new",
"scan",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/ospd.py#L1566-L1577 |
greenbone/ospd | ospd/ospd.py | OSPDaemon.set_scan_option | def set_scan_option(self, scan_id, name, value):
""" Sets a scan's option to a provided value. """
return self.scan_collection.set_option(scan_id, name, value) | python | def set_scan_option(self, scan_id, name, value):
""" Sets a scan's option to a provided value. """
return self.scan_collection.set_option(scan_id, name, value) | [
"def",
"set_scan_option",
"(",
"self",
",",
"scan_id",
",",
"name",
",",
"value",
")",
":",
"return",
"self",
".",
"scan_collection",
".",
"set_option",
"(",
"scan_id",
",",
"name",
",",
"value",
")"
] | Sets a scan's option to a provided value. | [
"Sets",
"a",
"scan",
"s",
"option",
"to",
"a",
"provided",
"value",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/ospd.py#L1583-L1585 |
greenbone/ospd | ospd/ospd.py | OSPDaemon.check_scan_process | def check_scan_process(self, scan_id):
""" Check the scan's process, and terminate the scan if not alive. """
scan_process = self.scan_processes[scan_id]
progress = self.get_scan_progress(scan_id)
if progress < 100 and not scan_process.is_alive():
self.set_scan_status(scan_id... | python | def check_scan_process(self, scan_id):
""" Check the scan's process, and terminate the scan if not alive. """
scan_process = self.scan_processes[scan_id]
progress = self.get_scan_progress(scan_id)
if progress < 100 and not scan_process.is_alive():
self.set_scan_status(scan_id... | [
"def",
"check_scan_process",
"(",
"self",
",",
"scan_id",
")",
":",
"scan_process",
"=",
"self",
".",
"scan_processes",
"[",
"scan_id",
"]",
"progress",
"=",
"self",
".",
"get_scan_progress",
"(",
"scan_id",
")",
"if",
"progress",
"<",
"100",
"and",
"not",
... | Check the scan's process, and terminate the scan if not alive. | [
"Check",
"the",
"scan",
"s",
"process",
"and",
"terminate",
"the",
"scan",
"if",
"not",
"alive",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/ospd.py#L1587-L1597 |
greenbone/ospd | ospd/ospd.py | OSPDaemon.add_scan_log | def add_scan_log(self, scan_id, host='', name='', value='', port='',
test_id='', qod=''):
""" Adds a log result to scan_id scan. """
self.scan_collection.add_result(scan_id, ResultType.LOG, host, name,
value, port, test_id, 0.0, qod) | python | def add_scan_log(self, scan_id, host='', name='', value='', port='',
test_id='', qod=''):
""" Adds a log result to scan_id scan. """
self.scan_collection.add_result(scan_id, ResultType.LOG, host, name,
value, port, test_id, 0.0, qod) | [
"def",
"add_scan_log",
"(",
"self",
",",
"scan_id",
",",
"host",
"=",
"''",
",",
"name",
"=",
"''",
",",
"value",
"=",
"''",
",",
"port",
"=",
"''",
",",
"test_id",
"=",
"''",
",",
"qod",
"=",
"''",
")",
":",
"self",
".",
"scan_collection",
".",
... | Adds a log result to scan_id scan. | [
"Adds",
"a",
"log",
"result",
"to",
"scan_id",
"scan",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/ospd.py#L1632-L1636 |
greenbone/ospd | ospd/ospd.py | OSPDaemon.add_scan_error | def add_scan_error(self, scan_id, host='', name='', value='', port=''):
""" Adds an error result to scan_id scan. """
self.scan_collection.add_result(scan_id, ResultType.ERROR, host, name,
value, port) | python | def add_scan_error(self, scan_id, host='', name='', value='', port=''):
""" Adds an error result to scan_id scan. """
self.scan_collection.add_result(scan_id, ResultType.ERROR, host, name,
value, port) | [
"def",
"add_scan_error",
"(",
"self",
",",
"scan_id",
",",
"host",
"=",
"''",
",",
"name",
"=",
"''",
",",
"value",
"=",
"''",
",",
"port",
"=",
"''",
")",
":",
"self",
".",
"scan_collection",
".",
"add_result",
"(",
"scan_id",
",",
"ResultType",
"."... | Adds an error result to scan_id scan. | [
"Adds",
"an",
"error",
"result",
"to",
"scan_id",
"scan",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/ospd.py#L1638-L1641 |
greenbone/ospd | ospd/ospd.py | OSPDaemon.add_scan_host_detail | def add_scan_host_detail(self, scan_id, host='', name='', value=''):
""" Adds a host detail result to scan_id scan. """
self.scan_collection.add_result(scan_id, ResultType.HOST_DETAIL, host,
name, value) | python | def add_scan_host_detail(self, scan_id, host='', name='', value=''):
""" Adds a host detail result to scan_id scan. """
self.scan_collection.add_result(scan_id, ResultType.HOST_DETAIL, host,
name, value) | [
"def",
"add_scan_host_detail",
"(",
"self",
",",
"scan_id",
",",
"host",
"=",
"''",
",",
"name",
"=",
"''",
",",
"value",
"=",
"''",
")",
":",
"self",
".",
"scan_collection",
".",
"add_result",
"(",
"scan_id",
",",
"ResultType",
".",
"HOST_DETAIL",
",",
... | Adds a host detail result to scan_id scan. | [
"Adds",
"a",
"host",
"detail",
"result",
"to",
"scan_id",
"scan",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/ospd.py#L1643-L1646 |
greenbone/ospd | ospd/ospd.py | OSPDaemon.add_scan_alarm | def add_scan_alarm(self, scan_id, host='', name='', value='', port='',
test_id='', severity='', qod=''):
""" Adds an alarm result to scan_id scan. """
self.scan_collection.add_result(scan_id, ResultType.ALARM, host, name,
value, port, test_i... | python | def add_scan_alarm(self, scan_id, host='', name='', value='', port='',
test_id='', severity='', qod=''):
""" Adds an alarm result to scan_id scan. """
self.scan_collection.add_result(scan_id, ResultType.ALARM, host, name,
value, port, test_i... | [
"def",
"add_scan_alarm",
"(",
"self",
",",
"scan_id",
",",
"host",
"=",
"''",
",",
"name",
"=",
"''",
",",
"value",
"=",
"''",
",",
"port",
"=",
"''",
",",
"test_id",
"=",
"''",
",",
"severity",
"=",
"''",
",",
"qod",
"=",
"''",
")",
":",
"self... | Adds an alarm result to scan_id scan. | [
"Adds",
"an",
"alarm",
"result",
"to",
"scan_id",
"scan",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/ospd.py#L1648-L1652 |
greenbone/ospd | ospd/vtfilter.py | VtsFilter.parse_filters | def parse_filters(self, vt_filter):
""" Parse a string containing one or more filters
and return a list of filters
Arguments:
vt_filter (string): String containing filters separated with
semicolon.
Return:
List with filters. Each filters is a list... | python | def parse_filters(self, vt_filter):
""" Parse a string containing one or more filters
and return a list of filters
Arguments:
vt_filter (string): String containing filters separated with
semicolon.
Return:
List with filters. Each filters is a list... | [
"def",
"parse_filters",
"(",
"self",
",",
"vt_filter",
")",
":",
"filter_list",
"=",
"vt_filter",
".",
"split",
"(",
"';'",
")",
"filters",
"=",
"list",
"(",
")",
"for",
"single_filter",
"in",
"filter_list",
":",
"filter_aux",
"=",
"re",
".",
"split",
"(... | Parse a string containing one or more filters
and return a list of filters
Arguments:
vt_filter (string): String containing filters separated with
semicolon.
Return:
List with filters. Each filters is a list with 3 elements
e.g. [arg, operator... | [
"Parse",
"a",
"string",
"containing",
"one",
"or",
"more",
"filters",
"and",
"return",
"a",
"list",
"of",
"filters"
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/vtfilter.py#L41-L67 |
greenbone/ospd | ospd/vtfilter.py | VtsFilter.format_filter_value | def format_filter_value(self, element, value):
""" Calls the specific function to format value,
depending on the given element.
Arguments:
element (string): The element of the VT to be formatted.
value (dictionary): The element value.
Returns:
Return... | python | def format_filter_value(self, element, value):
""" Calls the specific function to format value,
depending on the given element.
Arguments:
element (string): The element of the VT to be formatted.
value (dictionary): The element value.
Returns:
Return... | [
"def",
"format_filter_value",
"(",
"self",
",",
"element",
",",
"value",
")",
":",
"format_func",
"=",
"self",
".",
"allowed_filter",
".",
"get",
"(",
"element",
")",
"return",
"format_func",
"(",
"value",
")"
] | Calls the specific function to format value,
depending on the given element.
Arguments:
element (string): The element of the VT to be formatted.
value (dictionary): The element value.
Returns:
Returns a formatted value. | [
"Calls",
"the",
"specific",
"function",
"to",
"format",
"value",
"depending",
"on",
"the",
"given",
"element",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/vtfilter.py#L81-L94 |
greenbone/ospd | ospd/vtfilter.py | VtsFilter.get_filtered_vts_list | def get_filtered_vts_list(self, vts, vt_filter):
""" Gets a collection of vulnerability test from the vts dictionary,
which match the filter.
Arguments:
vt_filter (string): Filter to apply to the vts collection.
vts (dictionary): The complete vts collection.
Ret... | python | def get_filtered_vts_list(self, vts, vt_filter):
""" Gets a collection of vulnerability test from the vts dictionary,
which match the filter.
Arguments:
vt_filter (string): Filter to apply to the vts collection.
vts (dictionary): The complete vts collection.
Ret... | [
"def",
"get_filtered_vts_list",
"(",
"self",
",",
"vts",
",",
"vt_filter",
")",
":",
"if",
"not",
"vt_filter",
":",
"raise",
"RequiredArgument",
"(",
"'vt_filter: A valid filter is required.'",
")",
"filters",
"=",
"self",
".",
"parse_filters",
"(",
"vt_filter",
"... | Gets a collection of vulnerability test from the vts dictionary,
which match the filter.
Arguments:
vt_filter (string): Filter to apply to the vts collection.
vts (dictionary): The complete vts collection.
Returns:
Dictionary with filtered vulnerability test... | [
"Gets",
"a",
"collection",
"of",
"vulnerability",
"test",
"from",
"the",
"vts",
"dictionary",
"which",
"match",
"the",
"filter",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/vtfilter.py#L96-L127 |
greenbone/ospd | ospd/cvss.py | CVSS.cvss_base_v2_value | def cvss_base_v2_value(cls, cvss_base_vector):
""" Calculate the cvss base score from a cvss base vector
for cvss version 2.
Arguments:
cvss_base_vector (str) Cvss base vector v2.
Return the calculated score
"""
if not cvss_base_vector:
return Non... | python | def cvss_base_v2_value(cls, cvss_base_vector):
""" Calculate the cvss base score from a cvss base vector
for cvss version 2.
Arguments:
cvss_base_vector (str) Cvss base vector v2.
Return the calculated score
"""
if not cvss_base_vector:
return Non... | [
"def",
"cvss_base_v2_value",
"(",
"cls",
",",
"cvss_base_vector",
")",
":",
"if",
"not",
"cvss_base_vector",
":",
"return",
"None",
"_av",
",",
"_ac",
",",
"_au",
",",
"_c",
",",
"_i",
",",
"_a",
"=",
"cls",
".",
"_parse_cvss_base_vector",
"(",
"cvss_base_... | Calculate the cvss base score from a cvss base vector
for cvss version 2.
Arguments:
cvss_base_vector (str) Cvss base vector v2.
Return the calculated score | [
"Calculate",
"the",
"cvss",
"base",
"score",
"from",
"a",
"cvss",
"base",
"vector",
"for",
"cvss",
"version",
"2",
".",
"Arguments",
":",
"cvss_base_vector",
"(",
"str",
")",
"Cvss",
"base",
"vector",
"v2",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/cvss.py#L65-L91 |
greenbone/ospd | ospd/cvss.py | CVSS.cvss_base_v3_value | def cvss_base_v3_value(cls, cvss_base_vector):
""" Calculate the cvss base score from a cvss base vector
for cvss version 3.
Arguments:
cvss_base_vector (str) Cvss base vector v3.
Return the calculated score, None on fail.
"""
if not cvss_base_vector:
... | python | def cvss_base_v3_value(cls, cvss_base_vector):
""" Calculate the cvss base score from a cvss base vector
for cvss version 3.
Arguments:
cvss_base_vector (str) Cvss base vector v3.
Return the calculated score, None on fail.
"""
if not cvss_base_vector:
... | [
"def",
"cvss_base_v3_value",
"(",
"cls",
",",
"cvss_base_vector",
")",
":",
"if",
"not",
"cvss_base_vector",
":",
"return",
"None",
"_ver",
",",
"_av",
",",
"_ac",
",",
"_pr",
",",
"_ui",
",",
"_s",
",",
"_c",
",",
"_i",
",",
"_a",
"=",
"cls",
".",
... | Calculate the cvss base score from a cvss base vector
for cvss version 3.
Arguments:
cvss_base_vector (str) Cvss base vector v3.
Return the calculated score, None on fail. | [
"Calculate",
"the",
"cvss",
"base",
"score",
"from",
"a",
"cvss",
"base",
"vector",
"for",
"cvss",
"version",
"3",
".",
"Arguments",
":",
"cvss_base_vector",
"(",
"str",
")",
"Cvss",
"base",
"vector",
"v3",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/cvss.py#L94-L139 |
greenbone/ospd | ospd/misc.py | inet_pton | def inet_pton(address_family, ip_string):
""" A platform independent version of inet_pton """
global __inet_pton
if __inet_pton is None:
if hasattr(socket, 'inet_pton'):
__inet_pton = socket.inet_pton
else:
from ospd import win_socket
__inet_pton = win_soc... | python | def inet_pton(address_family, ip_string):
""" A platform independent version of inet_pton """
global __inet_pton
if __inet_pton is None:
if hasattr(socket, 'inet_pton'):
__inet_pton = socket.inet_pton
else:
from ospd import win_socket
__inet_pton = win_soc... | [
"def",
"inet_pton",
"(",
"address_family",
",",
"ip_string",
")",
":",
"global",
"__inet_pton",
"if",
"__inet_pton",
"is",
"None",
":",
"if",
"hasattr",
"(",
"socket",
",",
"'inet_pton'",
")",
":",
"__inet_pton",
"=",
"socket",
".",
"inet_pton",
"else",
":",... | A platform independent version of inet_pton | [
"A",
"platform",
"independent",
"version",
"of",
"inet_pton"
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L365-L375 |
greenbone/ospd | ospd/misc.py | inet_ntop | def inet_ntop(address_family, packed_ip):
""" A platform independent version of inet_ntop """
global __inet_ntop
if __inet_ntop is None:
if hasattr(socket, 'inet_ntop'):
__inet_ntop = socket.inet_ntop
else:
from ospd import win_socket
__inet_ntop = win_soc... | python | def inet_ntop(address_family, packed_ip):
""" A platform independent version of inet_ntop """
global __inet_ntop
if __inet_ntop is None:
if hasattr(socket, 'inet_ntop'):
__inet_ntop = socket.inet_ntop
else:
from ospd import win_socket
__inet_ntop = win_soc... | [
"def",
"inet_ntop",
"(",
"address_family",
",",
"packed_ip",
")",
":",
"global",
"__inet_ntop",
"if",
"__inet_ntop",
"is",
"None",
":",
"if",
"hasattr",
"(",
"socket",
",",
"'inet_ntop'",
")",
":",
"__inet_ntop",
"=",
"socket",
".",
"inet_ntop",
"else",
":",... | A platform independent version of inet_ntop | [
"A",
"platform",
"independent",
"version",
"of",
"inet_ntop"
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L381-L391 |
greenbone/ospd | ospd/misc.py | ipv4_range_to_list | def ipv4_range_to_list(start_packed, end_packed):
""" Return a list of IPv4 entries from start_packed to end_packed. """
new_list = list()
start = struct.unpack('!L', start_packed)[0]
end = struct.unpack('!L', end_packed)[0]
for value in range(start, end + 1):
new_ip = socket.inet_ntoa(stru... | python | def ipv4_range_to_list(start_packed, end_packed):
""" Return a list of IPv4 entries from start_packed to end_packed. """
new_list = list()
start = struct.unpack('!L', start_packed)[0]
end = struct.unpack('!L', end_packed)[0]
for value in range(start, end + 1):
new_ip = socket.inet_ntoa(stru... | [
"def",
"ipv4_range_to_list",
"(",
"start_packed",
",",
"end_packed",
")",
":",
"new_list",
"=",
"list",
"(",
")",
"start",
"=",
"struct",
".",
"unpack",
"(",
"'!L'",
",",
"start_packed",
")",
"[",
"0",
"]",
"end",
"=",
"struct",
".",
"unpack",
"(",
"'!... | Return a list of IPv4 entries from start_packed to end_packed. | [
"Return",
"a",
"list",
"of",
"IPv4",
"entries",
"from",
"start_packed",
"to",
"end_packed",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L414-L423 |
greenbone/ospd | ospd/misc.py | target_to_ipv4_short | def target_to_ipv4_short(target):
""" Attempt to return a IPv4 short range list from a target string. """
splitted = target.split('-')
if len(splitted) != 2:
return None
try:
start_packed = inet_pton(socket.AF_INET, splitted[0])
end_value = int(splitted[1])
except (socket.er... | python | def target_to_ipv4_short(target):
""" Attempt to return a IPv4 short range list from a target string. """
splitted = target.split('-')
if len(splitted) != 2:
return None
try:
start_packed = inet_pton(socket.AF_INET, splitted[0])
end_value = int(splitted[1])
except (socket.er... | [
"def",
"target_to_ipv4_short",
"(",
"target",
")",
":",
"splitted",
"=",
"target",
".",
"split",
"(",
"'-'",
")",
"if",
"len",
"(",
"splitted",
")",
"!=",
"2",
":",
"return",
"None",
"try",
":",
"start_packed",
"=",
"inet_pton",
"(",
"socket",
".",
"AF... | Attempt to return a IPv4 short range list from a target string. | [
"Attempt",
"to",
"return",
"a",
"IPv4",
"short",
"range",
"list",
"from",
"a",
"target",
"string",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L426-L441 |
greenbone/ospd | ospd/misc.py | target_to_ipv4_cidr | def target_to_ipv4_cidr(target):
""" Attempt to return a IPv4 CIDR list from a target string. """
splitted = target.split('/')
if len(splitted) != 2:
return None
try:
start_packed = inet_pton(socket.AF_INET, splitted[0])
block = int(splitted[1])
except (socket.error, ValueEr... | python | def target_to_ipv4_cidr(target):
""" Attempt to return a IPv4 CIDR list from a target string. """
splitted = target.split('/')
if len(splitted) != 2:
return None
try:
start_packed = inet_pton(socket.AF_INET, splitted[0])
block = int(splitted[1])
except (socket.error, ValueEr... | [
"def",
"target_to_ipv4_cidr",
"(",
"target",
")",
":",
"splitted",
"=",
"target",
".",
"split",
"(",
"'/'",
")",
"if",
"len",
"(",
"splitted",
")",
"!=",
"2",
":",
"return",
"None",
"try",
":",
"start_packed",
"=",
"inet_pton",
"(",
"socket",
".",
"AF_... | Attempt to return a IPv4 CIDR list from a target string. | [
"Attempt",
"to",
"return",
"a",
"IPv4",
"CIDR",
"list",
"from",
"a",
"target",
"string",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L444-L462 |
greenbone/ospd | ospd/misc.py | target_to_ipv6_cidr | def target_to_ipv6_cidr(target):
""" Attempt to return a IPv6 CIDR list from a target string. """
splitted = target.split('/')
if len(splitted) != 2:
return None
try:
start_packed = inet_pton(socket.AF_INET6, splitted[0])
block = int(splitted[1])
except (socket.error, ValueE... | python | def target_to_ipv6_cidr(target):
""" Attempt to return a IPv6 CIDR list from a target string. """
splitted = target.split('/')
if len(splitted) != 2:
return None
try:
start_packed = inet_pton(socket.AF_INET6, splitted[0])
block = int(splitted[1])
except (socket.error, ValueE... | [
"def",
"target_to_ipv6_cidr",
"(",
"target",
")",
":",
"splitted",
"=",
"target",
".",
"split",
"(",
"'/'",
")",
"if",
"len",
"(",
"splitted",
")",
"!=",
"2",
":",
"return",
"None",
"try",
":",
"start_packed",
"=",
"inet_pton",
"(",
"socket",
".",
"AF_... | Attempt to return a IPv6 CIDR list from a target string. | [
"Attempt",
"to",
"return",
"a",
"IPv6",
"CIDR",
"list",
"from",
"a",
"target",
"string",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L465-L487 |
greenbone/ospd | ospd/misc.py | target_to_ipv4_long | def target_to_ipv4_long(target):
""" Attempt to return a IPv4 long-range list from a target string. """
splitted = target.split('-')
if len(splitted) != 2:
return None
try:
start_packed = inet_pton(socket.AF_INET, splitted[0])
end_packed = inet_pton(socket.AF_INET, splitted[1])
... | python | def target_to_ipv4_long(target):
""" Attempt to return a IPv4 long-range list from a target string. """
splitted = target.split('-')
if len(splitted) != 2:
return None
try:
start_packed = inet_pton(socket.AF_INET, splitted[0])
end_packed = inet_pton(socket.AF_INET, splitted[1])
... | [
"def",
"target_to_ipv4_long",
"(",
"target",
")",
":",
"splitted",
"=",
"target",
".",
"split",
"(",
"'-'",
")",
"if",
"len",
"(",
"splitted",
")",
"!=",
"2",
":",
"return",
"None",
"try",
":",
"start_packed",
"=",
"inet_pton",
"(",
"socket",
".",
"AF_... | Attempt to return a IPv4 long-range list from a target string. | [
"Attempt",
"to",
"return",
"a",
"IPv4",
"long",
"-",
"range",
"list",
"from",
"a",
"target",
"string",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L490-L503 |
greenbone/ospd | ospd/misc.py | ipv6_range_to_list | def ipv6_range_to_list(start_packed, end_packed):
""" Return a list of IPv6 entries from start_packed to end_packed. """
new_list = list()
start = int(binascii.hexlify(start_packed), 16)
end = int(binascii.hexlify(end_packed), 16)
for value in range(start, end + 1):
high = value >> 64
... | python | def ipv6_range_to_list(start_packed, end_packed):
""" Return a list of IPv6 entries from start_packed to end_packed. """
new_list = list()
start = int(binascii.hexlify(start_packed), 16)
end = int(binascii.hexlify(end_packed), 16)
for value in range(start, end + 1):
high = value >> 64
... | [
"def",
"ipv6_range_to_list",
"(",
"start_packed",
",",
"end_packed",
")",
":",
"new_list",
"=",
"list",
"(",
")",
"start",
"=",
"int",
"(",
"binascii",
".",
"hexlify",
"(",
"start_packed",
")",
",",
"16",
")",
"end",
"=",
"int",
"(",
"binascii",
".",
"... | Return a list of IPv6 entries from start_packed to end_packed. | [
"Return",
"a",
"list",
"of",
"IPv6",
"entries",
"from",
"start_packed",
"to",
"end_packed",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L506-L518 |
greenbone/ospd | ospd/misc.py | target_to_ipv6_short | def target_to_ipv6_short(target):
""" Attempt to return a IPv6 short-range list from a target string. """
splitted = target.split('-')
if len(splitted) != 2:
return None
try:
start_packed = inet_pton(socket.AF_INET6, splitted[0])
end_value = int(splitted[1], 16)
except (sock... | python | def target_to_ipv6_short(target):
""" Attempt to return a IPv6 short-range list from a target string. """
splitted = target.split('-')
if len(splitted) != 2:
return None
try:
start_packed = inet_pton(socket.AF_INET6, splitted[0])
end_value = int(splitted[1], 16)
except (sock... | [
"def",
"target_to_ipv6_short",
"(",
"target",
")",
":",
"splitted",
"=",
"target",
".",
"split",
"(",
"'-'",
")",
"if",
"len",
"(",
"splitted",
")",
"!=",
"2",
":",
"return",
"None",
"try",
":",
"start_packed",
"=",
"inet_pton",
"(",
"socket",
".",
"AF... | Attempt to return a IPv6 short-range list from a target string. | [
"Attempt",
"to",
"return",
"a",
"IPv6",
"short",
"-",
"range",
"list",
"from",
"a",
"target",
"string",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L521-L536 |
greenbone/ospd | ospd/misc.py | target_to_ipv6_long | def target_to_ipv6_long(target):
""" Attempt to return a IPv6 long-range list from a target string. """
splitted = target.split('-')
if len(splitted) != 2:
return None
try:
start_packed = inet_pton(socket.AF_INET6, splitted[0])
end_packed = inet_pton(socket.AF_INET6, splitted[1]... | python | def target_to_ipv6_long(target):
""" Attempt to return a IPv6 long-range list from a target string. """
splitted = target.split('-')
if len(splitted) != 2:
return None
try:
start_packed = inet_pton(socket.AF_INET6, splitted[0])
end_packed = inet_pton(socket.AF_INET6, splitted[1]... | [
"def",
"target_to_ipv6_long",
"(",
"target",
")",
":",
"splitted",
"=",
"target",
".",
"split",
"(",
"'-'",
")",
"if",
"len",
"(",
"splitted",
")",
"!=",
"2",
":",
"return",
"None",
"try",
":",
"start_packed",
"=",
"inet_pton",
"(",
"socket",
".",
"AF_... | Attempt to return a IPv6 long-range list from a target string. | [
"Attempt",
"to",
"return",
"a",
"IPv6",
"long",
"-",
"range",
"list",
"from",
"a",
"target",
"string",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L539-L552 |
greenbone/ospd | ospd/misc.py | target_to_hostname | def target_to_hostname(target):
""" Attempt to return a single hostname list from a target string. """
if len(target) == 0 or len(target) > 255:
return None
if not re.match(r'^[\w.-]+$', target):
return None
return [target] | python | def target_to_hostname(target):
""" Attempt to return a single hostname list from a target string. """
if len(target) == 0 or len(target) > 255:
return None
if not re.match(r'^[\w.-]+$', target):
return None
return [target] | [
"def",
"target_to_hostname",
"(",
"target",
")",
":",
"if",
"len",
"(",
"target",
")",
"==",
"0",
"or",
"len",
"(",
"target",
")",
">",
"255",
":",
"return",
"None",
"if",
"not",
"re",
".",
"match",
"(",
"r'^[\\w.-]+$'",
",",
"target",
")",
":",
"r... | Attempt to return a single hostname list from a target string. | [
"Attempt",
"to",
"return",
"a",
"single",
"hostname",
"list",
"from",
"a",
"target",
"string",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L555-L562 |
greenbone/ospd | ospd/misc.py | target_to_list | def target_to_list(target):
""" Attempt to return a list of single hosts from a target string. """
# Is it an IPv4 address ?
new_list = target_to_ipv4(target)
# Is it an IPv6 address ?
if not new_list:
new_list = target_to_ipv6(target)
# Is it an IPv4 CIDR ?
if not new_list:
... | python | def target_to_list(target):
""" Attempt to return a list of single hosts from a target string. """
# Is it an IPv4 address ?
new_list = target_to_ipv4(target)
# Is it an IPv6 address ?
if not new_list:
new_list = target_to_ipv6(target)
# Is it an IPv4 CIDR ?
if not new_list:
... | [
"def",
"target_to_list",
"(",
"target",
")",
":",
"# Is it an IPv4 address ?",
"new_list",
"=",
"target_to_ipv4",
"(",
"target",
")",
"# Is it an IPv6 address ?",
"if",
"not",
"new_list",
":",
"new_list",
"=",
"target_to_ipv6",
"(",
"target",
")",
"# Is it an IPv4 CID... | Attempt to return a list of single hosts from a target string. | [
"Attempt",
"to",
"return",
"a",
"list",
"of",
"single",
"hosts",
"from",
"a",
"target",
"string",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L565-L594 |
greenbone/ospd | ospd/misc.py | target_str_to_list | def target_str_to_list(target_str):
""" Parses a targets string into a list of individual targets. """
new_list = list()
for target in target_str.split(','):
target = target.strip()
target_list = target_to_list(target)
if target_list:
new_list.extend(target_list)
... | python | def target_str_to_list(target_str):
""" Parses a targets string into a list of individual targets. """
new_list = list()
for target in target_str.split(','):
target = target.strip()
target_list = target_to_list(target)
if target_list:
new_list.extend(target_list)
... | [
"def",
"target_str_to_list",
"(",
"target_str",
")",
":",
"new_list",
"=",
"list",
"(",
")",
"for",
"target",
"in",
"target_str",
".",
"split",
"(",
"','",
")",
":",
"target",
"=",
"target",
".",
"strip",
"(",
")",
"target_list",
"=",
"target_to_list",
"... | Parses a targets string into a list of individual targets. | [
"Parses",
"a",
"targets",
"string",
"into",
"a",
"list",
"of",
"individual",
"targets",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L597-L608 |
greenbone/ospd | ospd/misc.py | port_range_expand | def port_range_expand(portrange):
"""
Receive a port range and expands it in individual ports.
@input Port range.
e.g. "4-8"
@return List of integers.
e.g. [4, 5, 6, 7, 8]
"""
if not portrange or '-' not in portrange:
LOGGER.info("Invalid port range format")
return None... | python | def port_range_expand(portrange):
"""
Receive a port range and expands it in individual ports.
@input Port range.
e.g. "4-8"
@return List of integers.
e.g. [4, 5, 6, 7, 8]
"""
if not portrange or '-' not in portrange:
LOGGER.info("Invalid port range format")
return None... | [
"def",
"port_range_expand",
"(",
"portrange",
")",
":",
"if",
"not",
"portrange",
"or",
"'-'",
"not",
"in",
"portrange",
":",
"LOGGER",
".",
"info",
"(",
"\"Invalid port range format\"",
")",
"return",
"None",
"port_list",
"=",
"list",
"(",
")",
"for",
"sing... | Receive a port range and expands it in individual ports.
@input Port range.
e.g. "4-8"
@return List of integers.
e.g. [4, 5, 6, 7, 8] | [
"Receive",
"a",
"port",
"range",
"and",
"expands",
"it",
"in",
"individual",
"ports",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L621-L638 |
greenbone/ospd | ospd/misc.py | port_str_arrange | def port_str_arrange(ports):
""" Gives a str in the format (always tcp listed first).
T:<tcp ports/portrange comma separated>U:<udp ports comma separated>
"""
b_tcp = ports.find("T")
b_udp = ports.find("U")
if (b_udp != -1 and b_tcp != -1) and b_udp < b_tcp:
return ports[b_tcp:] + ports[... | python | def port_str_arrange(ports):
""" Gives a str in the format (always tcp listed first).
T:<tcp ports/portrange comma separated>U:<udp ports comma separated>
"""
b_tcp = ports.find("T")
b_udp = ports.find("U")
if (b_udp != -1 and b_tcp != -1) and b_udp < b_tcp:
return ports[b_tcp:] + ports[... | [
"def",
"port_str_arrange",
"(",
"ports",
")",
":",
"b_tcp",
"=",
"ports",
".",
"find",
"(",
"\"T\"",
")",
"b_udp",
"=",
"ports",
".",
"find",
"(",
"\"U\"",
")",
"if",
"(",
"b_udp",
"!=",
"-",
"1",
"and",
"b_tcp",
"!=",
"-",
"1",
")",
"and",
"b_ud... | Gives a str in the format (always tcp listed first).
T:<tcp ports/portrange comma separated>U:<udp ports comma separated> | [
"Gives",
"a",
"str",
"in",
"the",
"format",
"(",
"always",
"tcp",
"listed",
"first",
")",
".",
"T",
":",
"<tcp",
"ports",
"/",
"portrange",
"comma",
"separated",
">",
"U",
":",
"<udp",
"ports",
"comma",
"separated",
">"
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L641-L650 |
greenbone/ospd | ospd/misc.py | ports_str_check_failed | def ports_str_check_failed(port_str):
"""
Check if the port string is well formed.
Return True if fail, False other case.
"""
pattern = r'[^TU:0-9, \-]'
if (
re.search(pattern, port_str)
or port_str.count('T') > 1
or port_str.count('U') > 1
or port_str.count(':')... | python | def ports_str_check_failed(port_str):
"""
Check if the port string is well formed.
Return True if fail, False other case.
"""
pattern = r'[^TU:0-9, \-]'
if (
re.search(pattern, port_str)
or port_str.count('T') > 1
or port_str.count('U') > 1
or port_str.count(':')... | [
"def",
"ports_str_check_failed",
"(",
"port_str",
")",
":",
"pattern",
"=",
"r'[^TU:0-9, \\-]'",
"if",
"(",
"re",
".",
"search",
"(",
"pattern",
",",
"port_str",
")",
"or",
"port_str",
".",
"count",
"(",
"'T'",
")",
">",
"1",
"or",
"port_str",
".",
"coun... | Check if the port string is well formed.
Return True if fail, False other case. | [
"Check",
"if",
"the",
"port",
"string",
"is",
"well",
"formed",
".",
"Return",
"True",
"if",
"fail",
"False",
"other",
"case",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L653-L667 |
greenbone/ospd | ospd/misc.py | ports_as_list | def ports_as_list(port_str):
"""
Parses a ports string into two list of individual tcp and udp ports.
@input string containing a port list
e.g. T:1,2,3,5-8 U:22,80,600-1024
@return two list of sorted integers, for tcp and udp ports respectively.
"""
if not port_str:
LOGGER.info("In... | python | def ports_as_list(port_str):
"""
Parses a ports string into two list of individual tcp and udp ports.
@input string containing a port list
e.g. T:1,2,3,5-8 U:22,80,600-1024
@return two list of sorted integers, for tcp and udp ports respectively.
"""
if not port_str:
LOGGER.info("In... | [
"def",
"ports_as_list",
"(",
"port_str",
")",
":",
"if",
"not",
"port_str",
":",
"LOGGER",
".",
"info",
"(",
"\"Invalid port value\"",
")",
"return",
"[",
"None",
",",
"None",
"]",
"if",
"ports_str_check_failed",
"(",
"port_str",
")",
":",
"LOGGER",
".",
"... | Parses a ports string into two list of individual tcp and udp ports.
@input string containing a port list
e.g. T:1,2,3,5-8 U:22,80,600-1024
@return two list of sorted integers, for tcp and udp ports respectively. | [
"Parses",
"a",
"ports",
"string",
"into",
"two",
"list",
"of",
"individual",
"tcp",
"and",
"udp",
"ports",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L670-L729 |
greenbone/ospd | ospd/misc.py | port_list_compress | def port_list_compress(port_list):
""" Compress a port list and return a string. """
if not port_list or len(port_list) == 0:
LOGGER.info("Invalid or empty port list.")
return ''
port_list = sorted(set(port_list))
compressed_list = []
for key, group in itertools.groupby(enumerate(p... | python | def port_list_compress(port_list):
""" Compress a port list and return a string. """
if not port_list or len(port_list) == 0:
LOGGER.info("Invalid or empty port list.")
return ''
port_list = sorted(set(port_list))
compressed_list = []
for key, group in itertools.groupby(enumerate(p... | [
"def",
"port_list_compress",
"(",
"port_list",
")",
":",
"if",
"not",
"port_list",
"or",
"len",
"(",
"port_list",
")",
"==",
"0",
":",
"LOGGER",
".",
"info",
"(",
"\"Invalid or empty port list.\"",
")",
"return",
"''",
"port_list",
"=",
"sorted",
"(",
"set",... | Compress a port list and return a string. | [
"Compress",
"a",
"port",
"list",
"and",
"return",
"a",
"string",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L742-L759 |
greenbone/ospd | ospd/misc.py | valid_uuid | def valid_uuid(value):
""" Check if value is a valid UUID. """
try:
uuid.UUID(value, version=4)
return True
except (TypeError, ValueError, AttributeError):
return False | python | def valid_uuid(value):
""" Check if value is a valid UUID. """
try:
uuid.UUID(value, version=4)
return True
except (TypeError, ValueError, AttributeError):
return False | [
"def",
"valid_uuid",
"(",
"value",
")",
":",
"try",
":",
"uuid",
".",
"UUID",
"(",
"value",
",",
"version",
"=",
"4",
")",
"return",
"True",
"except",
"(",
"TypeError",
",",
"ValueError",
",",
"AttributeError",
")",
":",
"return",
"False"
] | Check if value is a valid UUID. | [
"Check",
"if",
"value",
"is",
"a",
"valid",
"UUID",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L762-L769 |
greenbone/ospd | ospd/misc.py | create_args_parser | def create_args_parser(description):
""" Create a command-line arguments parser for OSPD. """
parser = argparse.ArgumentParser(description=description)
def network_port(string):
""" Check if provided string is a valid network port. """
value = int(string)
if not 0 < value <= 65535... | python | def create_args_parser(description):
""" Create a command-line arguments parser for OSPD. """
parser = argparse.ArgumentParser(description=description)
def network_port(string):
""" Check if provided string is a valid network port. """
value = int(string)
if not 0 < value <= 65535... | [
"def",
"create_args_parser",
"(",
"description",
")",
":",
"parser",
"=",
"argparse",
".",
"ArgumentParser",
"(",
"description",
"=",
"description",
")",
"def",
"network_port",
"(",
"string",
")",
":",
"\"\"\" Check if provided string is a valid network port. \"\"\"",
"... | Create a command-line arguments parser for OSPD. | [
"Create",
"a",
"command",
"-",
"line",
"arguments",
"parser",
"for",
"OSPD",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L772-L846 |
greenbone/ospd | ospd/misc.py | go_to_background | def go_to_background():
""" Daemonize the running process. """
try:
if os.fork():
sys.exit()
except OSError as errmsg:
LOGGER.error('Fork failed: {0}'.format(errmsg))
sys.exit('Fork failed') | python | def go_to_background():
""" Daemonize the running process. """
try:
if os.fork():
sys.exit()
except OSError as errmsg:
LOGGER.error('Fork failed: {0}'.format(errmsg))
sys.exit('Fork failed') | [
"def",
"go_to_background",
"(",
")",
":",
"try",
":",
"if",
"os",
".",
"fork",
"(",
")",
":",
"sys",
".",
"exit",
"(",
")",
"except",
"OSError",
"as",
"errmsg",
":",
"LOGGER",
".",
"error",
"(",
"'Fork failed: {0}'",
".",
"format",
"(",
"errmsg",
")"... | Daemonize the running process. | [
"Daemonize",
"the",
"running",
"process",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L849-L856 |
greenbone/ospd | ospd/misc.py | get_common_args | def get_common_args(parser, args=None):
""" Return list of OSPD common command-line arguments from parser, after
validating provided values or setting default ones.
"""
options = parser.parse_args(args)
# TCP Port to listen on.
port = options.port
# Network address to bind listener to
... | python | def get_common_args(parser, args=None):
""" Return list of OSPD common command-line arguments from parser, after
validating provided values or setting default ones.
"""
options = parser.parse_args(args)
# TCP Port to listen on.
port = options.port
# Network address to bind listener to
... | [
"def",
"get_common_args",
"(",
"parser",
",",
"args",
"=",
"None",
")",
":",
"options",
"=",
"parser",
".",
"parse_args",
"(",
"args",
")",
"# TCP Port to listen on.",
"port",
"=",
"options",
".",
"port",
"# Network address to bind listener to",
"address",
"=",
... | Return list of OSPD common command-line arguments from parser, after
validating provided values or setting default ones. | [
"Return",
"list",
"of",
"OSPD",
"common",
"command",
"-",
"line",
"arguments",
"from",
"parser",
"after",
"validating",
"provided",
"values",
"or",
"setting",
"default",
"ones",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L859-L899 |
greenbone/ospd | ospd/misc.py | print_version | def print_version(wrapper):
""" Prints the server version and license information."""
scanner_name = wrapper.get_scanner_name()
server_version = wrapper.get_server_version()
print("OSP Server for {0} version {1}".format(scanner_name, server_version))
protocol_version = wrapper.get_protocol_version(... | python | def print_version(wrapper):
""" Prints the server version and license information."""
scanner_name = wrapper.get_scanner_name()
server_version = wrapper.get_server_version()
print("OSP Server for {0} version {1}".format(scanner_name, server_version))
protocol_version = wrapper.get_protocol_version(... | [
"def",
"print_version",
"(",
"wrapper",
")",
":",
"scanner_name",
"=",
"wrapper",
".",
"get_scanner_name",
"(",
")",
"server_version",
"=",
"wrapper",
".",
"get_server_version",
"(",
")",
"print",
"(",
"\"OSP Server for {0} version {1}\"",
".",
"format",
"(",
"sca... | Prints the server version and license information. | [
"Prints",
"the",
"server",
"version",
"and",
"license",
"information",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L902-L917 |
greenbone/ospd | ospd/misc.py | main | def main(name, klass):
""" OSPD Main function. """
# Common args parser.
parser = create_args_parser(name)
# Common args
cargs = get_common_args(parser)
logging.getLogger().setLevel(cargs['log_level'])
wrapper = klass(certfile=cargs['certfile'], keyfile=cargs['keyfile'],
... | python | def main(name, klass):
""" OSPD Main function. """
# Common args parser.
parser = create_args_parser(name)
# Common args
cargs = get_common_args(parser)
logging.getLogger().setLevel(cargs['log_level'])
wrapper = klass(certfile=cargs['certfile'], keyfile=cargs['keyfile'],
... | [
"def",
"main",
"(",
"name",
",",
"klass",
")",
":",
"# Common args parser.",
"parser",
"=",
"create_args_parser",
"(",
"name",
")",
"# Common args",
"cargs",
"=",
"get_common_args",
"(",
"parser",
")",
"logging",
".",
"getLogger",
"(",
")",
".",
"setLevel",
... | OSPD Main function. | [
"OSPD",
"Main",
"function",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L920-L962 |
greenbone/ospd | ospd/misc.py | ScanCollection.add_result | def add_result(self, scan_id, result_type, host='', name='', value='',
port='', test_id='', severity='', qod=''):
""" Add a result to a scan in the table. """
assert scan_id
assert len(name) or len(value)
result = dict()
result['type'] = result_type
re... | python | def add_result(self, scan_id, result_type, host='', name='', value='',
port='', test_id='', severity='', qod=''):
""" Add a result to a scan in the table. """
assert scan_id
assert len(name) or len(value)
result = dict()
result['type'] = result_type
re... | [
"def",
"add_result",
"(",
"self",
",",
"scan_id",
",",
"result_type",
",",
"host",
"=",
"''",
",",
"name",
"=",
"''",
",",
"value",
"=",
"''",
",",
"port",
"=",
"''",
",",
"test_id",
"=",
"''",
",",
"severity",
"=",
"''",
",",
"qod",
"=",
"''",
... | Add a result to a scan in the table. | [
"Add",
"a",
"result",
"to",
"a",
"scan",
"in",
"the",
"table",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L87-L105 |
greenbone/ospd | ospd/misc.py | ScanCollection.set_progress | def set_progress(self, scan_id, progress):
""" Sets scan_id scan's progress. """
if progress > 0 and progress <= 100:
self.scans_table[scan_id]['progress'] = progress
if progress == 100:
self.scans_table[scan_id]['end_time'] = int(time.time()) | python | def set_progress(self, scan_id, progress):
""" Sets scan_id scan's progress. """
if progress > 0 and progress <= 100:
self.scans_table[scan_id]['progress'] = progress
if progress == 100:
self.scans_table[scan_id]['end_time'] = int(time.time()) | [
"def",
"set_progress",
"(",
"self",
",",
"scan_id",
",",
"progress",
")",
":",
"if",
"progress",
">",
"0",
"and",
"progress",
"<=",
"100",
":",
"self",
".",
"scans_table",
"[",
"scan_id",
"]",
"[",
"'progress'",
"]",
"=",
"progress",
"if",
"progress",
... | Sets scan_id scan's progress. | [
"Sets",
"scan_id",
"scan",
"s",
"progress",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L107-L113 |
greenbone/ospd | ospd/misc.py | ScanCollection.set_target_progress | def set_target_progress(self, scan_id, target, host, progress):
""" Sets scan_id scan's progress. """
if progress > 0 and progress <= 100:
targets = self.scans_table[scan_id]['target_progress']
targets[target][host] = progress
# Set scan_info's target_progress to pro... | python | def set_target_progress(self, scan_id, target, host, progress):
""" Sets scan_id scan's progress. """
if progress > 0 and progress <= 100:
targets = self.scans_table[scan_id]['target_progress']
targets[target][host] = progress
# Set scan_info's target_progress to pro... | [
"def",
"set_target_progress",
"(",
"self",
",",
"scan_id",
",",
"target",
",",
"host",
",",
"progress",
")",
":",
"if",
"progress",
">",
"0",
"and",
"progress",
"<=",
"100",
":",
"targets",
"=",
"self",
".",
"scans_table",
"[",
"scan_id",
"]",
"[",
"'t... | Sets scan_id scan's progress. | [
"Sets",
"scan_id",
"scan",
"s",
"progress",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L115-L122 |
greenbone/ospd | ospd/misc.py | ScanCollection.set_host_finished | def set_host_finished(self, scan_id, target, host):
""" Add the host in a list of finished hosts """
finished_hosts = self.scans_table[scan_id]['finished_hosts']
finished_hosts[target].extend(host)
self.scans_table[scan_id]['finished_hosts'] = finished_hosts | python | def set_host_finished(self, scan_id, target, host):
""" Add the host in a list of finished hosts """
finished_hosts = self.scans_table[scan_id]['finished_hosts']
finished_hosts[target].extend(host)
self.scans_table[scan_id]['finished_hosts'] = finished_hosts | [
"def",
"set_host_finished",
"(",
"self",
",",
"scan_id",
",",
"target",
",",
"host",
")",
":",
"finished_hosts",
"=",
"self",
".",
"scans_table",
"[",
"scan_id",
"]",
"[",
"'finished_hosts'",
"]",
"finished_hosts",
"[",
"target",
"]",
".",
"extend",
"(",
"... | Add the host in a list of finished hosts | [
"Add",
"the",
"host",
"in",
"a",
"list",
"of",
"finished",
"hosts"
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L124-L128 |
greenbone/ospd | ospd/misc.py | ScanCollection.get_hosts_unfinished | def get_hosts_unfinished(self, scan_id):
""" Get a list of finished hosts."""
unfinished_hosts = list()
for target in self.scans_table[scan_id]['finished_hosts']:
unfinished_hosts.extend(target_str_to_list(target))
for target in self.scans_table[scan_id]['finished_hosts']:
... | python | def get_hosts_unfinished(self, scan_id):
""" Get a list of finished hosts."""
unfinished_hosts = list()
for target in self.scans_table[scan_id]['finished_hosts']:
unfinished_hosts.extend(target_str_to_list(target))
for target in self.scans_table[scan_id]['finished_hosts']:
... | [
"def",
"get_hosts_unfinished",
"(",
"self",
",",
"scan_id",
")",
":",
"unfinished_hosts",
"=",
"list",
"(",
")",
"for",
"target",
"in",
"self",
".",
"scans_table",
"[",
"scan_id",
"]",
"[",
"'finished_hosts'",
"]",
":",
"unfinished_hosts",
".",
"extend",
"("... | Get a list of finished hosts. | [
"Get",
"a",
"list",
"of",
"finished",
"hosts",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L130-L140 |
greenbone/ospd | ospd/misc.py | ScanCollection.results_iterator | def results_iterator(self, scan_id, pop_res):
""" Returns an iterator over scan_id scan's results. If pop_res is True,
it removed the fetched results from the list.
"""
if pop_res:
result_aux = self.scans_table[scan_id]['results']
self.scans_table[scan_id]['result... | python | def results_iterator(self, scan_id, pop_res):
""" Returns an iterator over scan_id scan's results. If pop_res is True,
it removed the fetched results from the list.
"""
if pop_res:
result_aux = self.scans_table[scan_id]['results']
self.scans_table[scan_id]['result... | [
"def",
"results_iterator",
"(",
"self",
",",
"scan_id",
",",
"pop_res",
")",
":",
"if",
"pop_res",
":",
"result_aux",
"=",
"self",
".",
"scans_table",
"[",
"scan_id",
"]",
"[",
"'results'",
"]",
"self",
".",
"scans_table",
"[",
"scan_id",
"]",
"[",
"'res... | Returns an iterator over scan_id scan's results. If pop_res is True,
it removed the fetched results from the list. | [
"Returns",
"an",
"iterator",
"over",
"scan_id",
"scan",
"s",
"results",
".",
"If",
"pop_res",
"is",
"True",
"it",
"removed",
"the",
"fetched",
"results",
"from",
"the",
"list",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L142-L151 |
greenbone/ospd | ospd/misc.py | ScanCollection.del_results_for_stopped_hosts | def del_results_for_stopped_hosts(self, scan_id):
""" Remove results from the result table for those host
"""
unfinished_hosts = self.get_hosts_unfinished(scan_id)
for result in self.results_iterator(scan_id, False):
if result['host'] in unfinished_hosts:
self... | python | def del_results_for_stopped_hosts(self, scan_id):
""" Remove results from the result table for those host
"""
unfinished_hosts = self.get_hosts_unfinished(scan_id)
for result in self.results_iterator(scan_id, False):
if result['host'] in unfinished_hosts:
self... | [
"def",
"del_results_for_stopped_hosts",
"(",
"self",
",",
"scan_id",
")",
":",
"unfinished_hosts",
"=",
"self",
".",
"get_hosts_unfinished",
"(",
"scan_id",
")",
"for",
"result",
"in",
"self",
".",
"results_iterator",
"(",
"scan_id",
",",
"False",
")",
":",
"i... | Remove results from the result table for those host | [
"Remove",
"results",
"from",
"the",
"result",
"table",
"for",
"those",
"host"
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L162-L168 |
greenbone/ospd | ospd/misc.py | ScanCollection.resume_scan | def resume_scan(self, scan_id, options):
""" Reset the scan status in the scan_table to INIT.
Also, overwrite the options, because a resume task cmd
can add some new option. E.g. exclude hosts list.
Parameters:
scan_id (uuid): Scan ID to identify the scan process to be resume... | python | def resume_scan(self, scan_id, options):
""" Reset the scan status in the scan_table to INIT.
Also, overwrite the options, because a resume task cmd
can add some new option. E.g. exclude hosts list.
Parameters:
scan_id (uuid): Scan ID to identify the scan process to be resume... | [
"def",
"resume_scan",
"(",
"self",
",",
"scan_id",
",",
"options",
")",
":",
"self",
".",
"scans_table",
"[",
"scan_id",
"]",
"[",
"'status'",
"]",
"=",
"ScanStatus",
".",
"INIT",
"if",
"options",
":",
"self",
".",
"scans_table",
"[",
"scan_id",
"]",
"... | Reset the scan status in the scan_table to INIT.
Also, overwrite the options, because a resume task cmd
can add some new option. E.g. exclude hosts list.
Parameters:
scan_id (uuid): Scan ID to identify the scan process to be resumed.
options (dict): Options for the scan t... | [
"Reset",
"the",
"scan",
"status",
"in",
"the",
"scan_table",
"to",
"INIT",
".",
"Also",
"overwrite",
"the",
"options",
"because",
"a",
"resume",
"task",
"cmd",
"can",
"add",
"some",
"new",
"option",
".",
"E",
".",
"g",
".",
"exclude",
"hosts",
"list",
... | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L170-L189 |
greenbone/ospd | ospd/misc.py | ScanCollection.create_scan | def create_scan(self, scan_id='', targets='', options=None, vts=''):
""" Creates a new scan with provided scan information. """
if self.data_manager is None:
self.data_manager = multiprocessing.Manager()
# Check if it is possible to resume task. To avoid to resume, the
# sc... | python | def create_scan(self, scan_id='', targets='', options=None, vts=''):
""" Creates a new scan with provided scan information. """
if self.data_manager is None:
self.data_manager = multiprocessing.Manager()
# Check if it is possible to resume task. To avoid to resume, the
# sc... | [
"def",
"create_scan",
"(",
"self",
",",
"scan_id",
"=",
"''",
",",
"targets",
"=",
"''",
",",
"options",
"=",
"None",
",",
"vts",
"=",
"''",
")",
":",
"if",
"self",
".",
"data_manager",
"is",
"None",
":",
"self",
".",
"data_manager",
"=",
"multiproce... | Creates a new scan with provided scan information. | [
"Creates",
"a",
"new",
"scan",
"with",
"provided",
"scan",
"information",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L191-L222 |
greenbone/ospd | ospd/misc.py | ScanCollection.set_option | def set_option(self, scan_id, name, value):
""" Set a scan_id scan's name option to value. """
self.scans_table[scan_id]['options'][name] = value | python | def set_option(self, scan_id, name, value):
""" Set a scan_id scan's name option to value. """
self.scans_table[scan_id]['options'][name] = value | [
"def",
"set_option",
"(",
"self",
",",
"scan_id",
",",
"name",
",",
"value",
")",
":",
"self",
".",
"scans_table",
"[",
"scan_id",
"]",
"[",
"'options'",
"]",
"[",
"name",
"]",
"=",
"value"
] | Set a scan_id scan's name option to value. | [
"Set",
"a",
"scan_id",
"scan",
"s",
"name",
"option",
"to",
"value",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L238-L241 |
greenbone/ospd | ospd/misc.py | ScanCollection.get_target_progress | def get_target_progress(self, scan_id, target):
""" Get a target's current progress value.
The value is calculated with the progress of each single host
in the target."""
total_hosts = len(target_str_to_list(target))
host_progresses = self.scans_table[scan_id]['target_progress']... | python | def get_target_progress(self, scan_id, target):
""" Get a target's current progress value.
The value is calculated with the progress of each single host
in the target."""
total_hosts = len(target_str_to_list(target))
host_progresses = self.scans_table[scan_id]['target_progress']... | [
"def",
"get_target_progress",
"(",
"self",
",",
"scan_id",
",",
"target",
")",
":",
"total_hosts",
"=",
"len",
"(",
"target_str_to_list",
"(",
"target",
")",
")",
"host_progresses",
"=",
"self",
".",
"scans_table",
"[",
"scan_id",
"]",
"[",
"'target_progress'"... | Get a target's current progress value.
The value is calculated with the progress of each single host
in the target. | [
"Get",
"a",
"target",
"s",
"current",
"progress",
"value",
".",
"The",
"value",
"is",
"calculated",
"with",
"the",
"progress",
"of",
"each",
"single",
"host",
"in",
"the",
"target",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L248-L260 |
greenbone/ospd | ospd/misc.py | ScanCollection.get_target_list | def get_target_list(self, scan_id):
""" Get a scan's target list. """
target_list = []
for target, _, _ in self.scans_table[scan_id]['targets']:
target_list.append(target)
return target_list | python | def get_target_list(self, scan_id):
""" Get a scan's target list. """
target_list = []
for target, _, _ in self.scans_table[scan_id]['targets']:
target_list.append(target)
return target_list | [
"def",
"get_target_list",
"(",
"self",
",",
"scan_id",
")",
":",
"target_list",
"=",
"[",
"]",
"for",
"target",
",",
"_",
",",
"_",
"in",
"self",
".",
"scans_table",
"[",
"scan_id",
"]",
"[",
"'targets'",
"]",
":",
"target_list",
".",
"append",
"(",
... | Get a scan's target list. | [
"Get",
"a",
"scan",
"s",
"target",
"list",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L272-L278 |
greenbone/ospd | ospd/misc.py | ScanCollection.get_ports | def get_ports(self, scan_id, target):
""" Get a scan's ports list. If a target is specified
it will return the corresponding port for it. If not,
it returns the port item of the first nested list in
the target's list.
"""
if target:
for item in self.scans_tabl... | python | def get_ports(self, scan_id, target):
""" Get a scan's ports list. If a target is specified
it will return the corresponding port for it. If not,
it returns the port item of the first nested list in
the target's list.
"""
if target:
for item in self.scans_tabl... | [
"def",
"get_ports",
"(",
"self",
",",
"scan_id",
",",
"target",
")",
":",
"if",
"target",
":",
"for",
"item",
"in",
"self",
".",
"scans_table",
"[",
"scan_id",
"]",
"[",
"'targets'",
"]",
":",
"if",
"target",
"==",
"item",
"[",
"0",
"]",
":",
"retu... | Get a scan's ports list. If a target is specified
it will return the corresponding port for it. If not,
it returns the port item of the first nested list in
the target's list. | [
"Get",
"a",
"scan",
"s",
"ports",
"list",
".",
"If",
"a",
"target",
"is",
"specified",
"it",
"will",
"return",
"the",
"corresponding",
"port",
"for",
"it",
".",
"If",
"not",
"it",
"returns",
"the",
"port",
"item",
"of",
"the",
"first",
"nested",
"list"... | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L280-L291 |
greenbone/ospd | ospd/misc.py | ScanCollection.get_credentials | def get_credentials(self, scan_id, target):
""" Get a scan's credential list. It return dictionary with
the corresponding credential for a given target.
"""
if target:
for item in self.scans_table[scan_id]['targets']:
if target == item[0]:
... | python | def get_credentials(self, scan_id, target):
""" Get a scan's credential list. It return dictionary with
the corresponding credential for a given target.
"""
if target:
for item in self.scans_table[scan_id]['targets']:
if target == item[0]:
... | [
"def",
"get_credentials",
"(",
"self",
",",
"scan_id",
",",
"target",
")",
":",
"if",
"target",
":",
"for",
"item",
"in",
"self",
".",
"scans_table",
"[",
"scan_id",
"]",
"[",
"'targets'",
"]",
":",
"if",
"target",
"==",
"item",
"[",
"0",
"]",
":",
... | Get a scan's credential list. It return dictionary with
the corresponding credential for a given target. | [
"Get",
"a",
"scan",
"s",
"credential",
"list",
".",
"It",
"return",
"dictionary",
"with",
"the",
"corresponding",
"credential",
"for",
"a",
"given",
"target",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L293-L300 |
greenbone/ospd | ospd/misc.py | ScanCollection.delete_scan | def delete_scan(self, scan_id):
""" Delete a scan if fully finished. """
if self.get_status(scan_id) == ScanStatus.RUNNING:
return False
self.scans_table.pop(scan_id)
if len(self.scans_table) == 0:
del self.data_manager
self.data_manager = None
... | python | def delete_scan(self, scan_id):
""" Delete a scan if fully finished. """
if self.get_status(scan_id) == ScanStatus.RUNNING:
return False
self.scans_table.pop(scan_id)
if len(self.scans_table) == 0:
del self.data_manager
self.data_manager = None
... | [
"def",
"delete_scan",
"(",
"self",
",",
"scan_id",
")",
":",
"if",
"self",
".",
"get_status",
"(",
"scan_id",
")",
"==",
"ScanStatus",
".",
"RUNNING",
":",
"return",
"False",
"self",
".",
"scans_table",
".",
"pop",
"(",
"scan_id",
")",
"if",
"len",
"("... | Delete a scan if fully finished. | [
"Delete",
"a",
"scan",
"if",
"fully",
"finished",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L312-L321 |
greenbone/ospd | ospd/misc.py | ResultType.get_str | def get_str(cls, result_type):
""" Return string name of a result type. """
if result_type == cls.ALARM:
return "Alarm"
elif result_type == cls.LOG:
return "Log Message"
elif result_type == cls.ERROR:
return "Error Message"
elif result_type == ... | python | def get_str(cls, result_type):
""" Return string name of a result type. """
if result_type == cls.ALARM:
return "Alarm"
elif result_type == cls.LOG:
return "Log Message"
elif result_type == cls.ERROR:
return "Error Message"
elif result_type == ... | [
"def",
"get_str",
"(",
"cls",
",",
"result_type",
")",
":",
"if",
"result_type",
"==",
"cls",
".",
"ALARM",
":",
"return",
"\"Alarm\"",
"elif",
"result_type",
"==",
"cls",
".",
"LOG",
":",
"return",
"\"Log Message\"",
"elif",
"result_type",
"==",
"cls",
".... | Return string name of a result type. | [
"Return",
"string",
"name",
"of",
"a",
"result",
"type",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L334-L345 |
greenbone/ospd | ospd/misc.py | ResultType.get_type | def get_type(cls, result_name):
""" Return string name of a result type. """
if result_name == "Alarm":
return cls.ALARM
elif result_name == "Log Message":
return cls.LOG
elif result_name == "Error Message":
return cls.ERROR
elif result_name ==... | python | def get_type(cls, result_name):
""" Return string name of a result type. """
if result_name == "Alarm":
return cls.ALARM
elif result_name == "Log Message":
return cls.LOG
elif result_name == "Error Message":
return cls.ERROR
elif result_name ==... | [
"def",
"get_type",
"(",
"cls",
",",
"result_name",
")",
":",
"if",
"result_name",
"==",
"\"Alarm\"",
":",
"return",
"cls",
".",
"ALARM",
"elif",
"result_name",
"==",
"\"Log Message\"",
":",
"return",
"cls",
".",
"LOG",
"elif",
"result_name",
"==",
"\"Error M... | Return string name of a result type. | [
"Return",
"string",
"name",
"of",
"a",
"result",
"type",
"."
] | train | https://github.com/greenbone/ospd/blob/cef773166b15a19c17764721d3fe404fa0e107bf/ospd/misc.py#L348-L359 |
Grokzen/pykwalify | pykwalify/types.py | is_float | def is_float(obj):
"""
Valid types are:
- objects of float type
- Strings that can be converted to float. For example '1e-06'
"""
is_f = isinstance(obj, float)
if not is_f:
try:
float(obj)
is_f = True
except (ValueError, TypeError):
is_f ... | python | def is_float(obj):
"""
Valid types are:
- objects of float type
- Strings that can be converted to float. For example '1e-06'
"""
is_f = isinstance(obj, float)
if not is_f:
try:
float(obj)
is_f = True
except (ValueError, TypeError):
is_f ... | [
"def",
"is_float",
"(",
"obj",
")",
":",
"is_f",
"=",
"isinstance",
"(",
"obj",
",",
"float",
")",
"if",
"not",
"is_f",
":",
"try",
":",
"float",
"(",
"obj",
")",
"is_f",
"=",
"True",
"except",
"(",
"ValueError",
",",
"TypeError",
")",
":",
"is_f",... | Valid types are:
- objects of float type
- Strings that can be converted to float. For example '1e-06' | [
"Valid",
"types",
"are",
":",
"-",
"objects",
"of",
"float",
"type",
"-",
"Strings",
"that",
"can",
"be",
"converted",
"to",
"float",
".",
"For",
"example",
"1e",
"-",
"06"
] | train | https://github.com/Grokzen/pykwalify/blob/02b7e21eafb97926f17b7c33e2ee7b3ea67c3ef7/pykwalify/types.py#L87-L100 |
Grokzen/pykwalify | pykwalify/types.py | is_timestamp | def is_timestamp(obj):
"""
Yaml either have automatically converted it to a datetime object
or it is a string that will be validated later.
"""
return isinstance(obj, datetime.datetime) or is_string(obj) or is_int(obj) or is_float(obj) | python | def is_timestamp(obj):
"""
Yaml either have automatically converted it to a datetime object
or it is a string that will be validated later.
"""
return isinstance(obj, datetime.datetime) or is_string(obj) or is_int(obj) or is_float(obj) | [
"def",
"is_timestamp",
"(",
"obj",
")",
":",
"return",
"isinstance",
"(",
"obj",
",",
"datetime",
".",
"datetime",
")",
"or",
"is_string",
"(",
"obj",
")",
"or",
"is_int",
"(",
"obj",
")",
"or",
"is_float",
"(",
"obj",
")"
] | Yaml either have automatically converted it to a datetime object
or it is a string that will be validated later. | [
"Yaml",
"either",
"have",
"automatically",
"converted",
"it",
"to",
"a",
"datetime",
"object",
"or",
"it",
"is",
"a",
"string",
"that",
"will",
"be",
"validated",
"later",
"."
] | train | https://github.com/Grokzen/pykwalify/blob/02b7e21eafb97926f17b7c33e2ee7b3ea67c3ef7/pykwalify/types.py#L131-L136 |
Grokzen/pykwalify | pykwalify/__init__.py | init_logging | def init_logging(log_level):
"""
Init logging settings with default set to INFO
"""
log_level = log_level_to_string_map[min(log_level, 5)]
msg = "%(levelname)s - %(name)s:%(lineno)s - %(message)s" if log_level in os.environ else "%(levelname)s - %(message)s"
logging_conf = {
"version":... | python | def init_logging(log_level):
"""
Init logging settings with default set to INFO
"""
log_level = log_level_to_string_map[min(log_level, 5)]
msg = "%(levelname)s - %(name)s:%(lineno)s - %(message)s" if log_level in os.environ else "%(levelname)s - %(message)s"
logging_conf = {
"version":... | [
"def",
"init_logging",
"(",
"log_level",
")",
":",
"log_level",
"=",
"log_level_to_string_map",
"[",
"min",
"(",
"log_level",
",",
"5",
")",
"]",
"msg",
"=",
"\"%(levelname)s - %(name)s:%(lineno)s - %(message)s\"",
"if",
"log_level",
"in",
"os",
".",
"environ",
"e... | Init logging settings with default set to INFO | [
"Init",
"logging",
"settings",
"with",
"default",
"set",
"to",
"INFO"
] | train | https://github.com/Grokzen/pykwalify/blob/02b7e21eafb97926f17b7c33e2ee7b3ea67c3ef7/pykwalify/__init__.py#L25-L54 |
Grokzen/pykwalify | pykwalify/rule.py | Rule.keywords | def keywords(self):
"""
Returns a list of all keywords that this rule object has defined.
A keyword is considered defined if the value it returns != None.
"""
defined_keywords = [
('allowempty_map', 'allowempty_map'),
('assertion', 'assertion'),
... | python | def keywords(self):
"""
Returns a list of all keywords that this rule object has defined.
A keyword is considered defined if the value it returns != None.
"""
defined_keywords = [
('allowempty_map', 'allowempty_map'),
('assertion', 'assertion'),
... | [
"def",
"keywords",
"(",
"self",
")",
":",
"defined_keywords",
"=",
"[",
"(",
"'allowempty_map'",
",",
"'allowempty_map'",
")",
",",
"(",
"'assertion'",
",",
"'assertion'",
")",
",",
"(",
"'default'",
",",
"'default'",
")",
",",
"(",
"'class'",
",",
"'class... | Returns a list of all keywords that this rule object has defined.
A keyword is considered defined if the value it returns != None. | [
"Returns",
"a",
"list",
"of",
"all",
"keywords",
"that",
"this",
"rule",
"object",
"has",
"defined",
".",
"A",
"keyword",
"is",
"considered",
"defined",
"if",
"the",
"value",
"it",
"returns",
"!",
"=",
"None",
"."
] | train | https://github.com/Grokzen/pykwalify/blob/02b7e21eafb97926f17b7c33e2ee7b3ea67c3ef7/pykwalify/rule.py#L319-L364 |
Grokzen/pykwalify | pykwalify/rule.py | Rule.check_type_keywords | def check_type_keywords(self, schema, rule, path):
"""
All supported keywords:
- allowempty_map
- assertion
- class
- date
- default
- desc
- enum
- example
- extensions
- func
- ident
- include_n... | python | def check_type_keywords(self, schema, rule, path):
"""
All supported keywords:
- allowempty_map
- assertion
- class
- date
- default
- desc
- enum
- example
- extensions
- func
- ident
- include_n... | [
"def",
"check_type_keywords",
"(",
"self",
",",
"schema",
",",
"rule",
",",
"path",
")",
":",
"if",
"not",
"self",
".",
"strict_rule_validation",
":",
"return",
"global_keywords",
"=",
"[",
"'type'",
",",
"'desc'",
",",
"'example'",
",",
"'extensions'",
",",... | All supported keywords:
- allowempty_map
- assertion
- class
- date
- default
- desc
- enum
- example
- extensions
- func
- ident
- include_name
- map_regex_rule
- mapping
- matching
... | [
"All",
"supported",
"keywords",
":",
"-",
"allowempty_map",
"-",
"assertion",
"-",
"class",
"-",
"date",
"-",
"default",
"-",
"desc",
"-",
"enum",
"-",
"example",
"-",
"extensions",
"-",
"func",
"-",
"ident",
"-",
"include_name",
"-",
"map_regex_rule",
"-"... | train | https://github.com/Grokzen/pykwalify/blob/02b7e21eafb97926f17b7c33e2ee7b3ea67c3ef7/pykwalify/rule.py#L1212-L1282 |
Grokzen/pykwalify | pykwalify/core.py | Core._load_extensions | def _load_extensions(self):
"""
Load all extension files into the namespace pykwalify.ext
"""
log.debug(u"loading all extensions : %s", self.extensions)
self.loaded_extensions = []
for f in self.extensions:
if not os.path.isabs(f):
f = os.pat... | python | def _load_extensions(self):
"""
Load all extension files into the namespace pykwalify.ext
"""
log.debug(u"loading all extensions : %s", self.extensions)
self.loaded_extensions = []
for f in self.extensions:
if not os.path.isabs(f):
f = os.pat... | [
"def",
"_load_extensions",
"(",
"self",
")",
":",
"log",
".",
"debug",
"(",
"u\"loading all extensions : %s\"",
",",
"self",
".",
"extensions",
")",
"self",
".",
"loaded_extensions",
"=",
"[",
"]",
"for",
"f",
"in",
"self",
".",
"extensions",
":",
"if",
"n... | Load all extension files into the namespace pykwalify.ext | [
"Load",
"all",
"extension",
"files",
"into",
"the",
"namespace",
"pykwalify",
".",
"ext"
] | train | https://github.com/Grokzen/pykwalify/blob/02b7e21eafb97926f17b7c33e2ee7b3ea67c3ef7/pykwalify/core.py#L131-L149 |
Grokzen/pykwalify | pykwalify/core.py | Core._handle_func | def _handle_func(self, value, rule, path, done=None):
"""
Helper function that should check if func is specified for this rule and
then handle it for all cases in a generic way.
"""
func = rule.func
# func keyword is not defined so nothing to do
if not func:
... | python | def _handle_func(self, value, rule, path, done=None):
"""
Helper function that should check if func is specified for this rule and
then handle it for all cases in a generic way.
"""
func = rule.func
# func keyword is not defined so nothing to do
if not func:
... | [
"def",
"_handle_func",
"(",
"self",
",",
"value",
",",
"rule",
",",
"path",
",",
"done",
"=",
"None",
")",
":",
"func",
"=",
"rule",
".",
"func",
"# func keyword is not defined so nothing to do",
"if",
"not",
"func",
":",
"return",
"found_method",
"=",
"Fals... | Helper function that should check if func is specified for this rule and
then handle it for all cases in a generic way. | [
"Helper",
"function",
"that",
"should",
"check",
"if",
"func",
"is",
"specified",
"for",
"this",
"rule",
"and",
"then",
"handle",
"it",
"for",
"all",
"cases",
"in",
"a",
"generic",
"way",
"."
] | train | https://github.com/Grokzen/pykwalify/blob/02b7e21eafb97926f17b7c33e2ee7b3ea67c3ef7/pykwalify/core.py#L241-L277 |
Grokzen/pykwalify | pykwalify/core.py | Core._validate_range | def _validate_range(self, max_, min_, max_ex, min_ex, value, path, prefix):
"""
Validate that value is within range values.
"""
if not isinstance(value, int) and not isinstance(value, float):
raise CoreError("Value must be a integer type")
log.debug(
u"Va... | python | def _validate_range(self, max_, min_, max_ex, min_ex, value, path, prefix):
"""
Validate that value is within range values.
"""
if not isinstance(value, int) and not isinstance(value, float):
raise CoreError("Value must be a integer type")
log.debug(
u"Va... | [
"def",
"_validate_range",
"(",
"self",
",",
"max_",
",",
"min_",
",",
"max_ex",
",",
"min_ex",
",",
"value",
",",
"path",
",",
"prefix",
")",
":",
"if",
"not",
"isinstance",
"(",
"value",
",",
"int",
")",
"and",
"not",
"isinstance",
"(",
"value",
","... | Validate that value is within range values. | [
"Validate",
"that",
"value",
"is",
"within",
"range",
"values",
"."
] | train | https://github.com/Grokzen/pykwalify/blob/02b7e21eafb97926f17b7c33e2ee7b3ea67c3ef7/pykwalify/core.py#L919-L966 |
Grokzen/pykwalify | pykwalify/cli.py | parse_cli | def parse_cli():
"""
The outline of this function needs to be like this:
1. parse arguments
2. validate arguments only, dont go into other logic/code
3. run application logic
"""
#
# 1. parse cli arguments
#
__docopt__ = """
usage: pykwalify -d FILE -s FILE ... [-e FILE ...]
... | python | def parse_cli():
"""
The outline of this function needs to be like this:
1. parse arguments
2. validate arguments only, dont go into other logic/code
3. run application logic
"""
#
# 1. parse cli arguments
#
__docopt__ = """
usage: pykwalify -d FILE -s FILE ... [-e FILE ...]
... | [
"def",
"parse_cli",
"(",
")",
":",
"#",
"# 1. parse cli arguments",
"#",
"__docopt__",
"=",
"\"\"\"\nusage: pykwalify -d FILE -s FILE ... [-e FILE ...]\n [--strict-rule-validation] [--fix-ruby-style-regex] [--allow-assertions] [--encoding ENCODING]\n [-v ...] [-q]\n\noptional argumen... | The outline of this function needs to be like this:
1. parse arguments
2. validate arguments only, dont go into other logic/code
3. run application logic | [
"The",
"outline",
"of",
"this",
"function",
"needs",
"to",
"be",
"like",
"this",
":"
] | train | https://github.com/Grokzen/pykwalify/blob/02b7e21eafb97926f17b7c33e2ee7b3ea67c3ef7/pykwalify/cli.py#L14-L65 |
Grokzen/pykwalify | pykwalify/cli.py | run | def run(cli_args):
"""
Split the functionality into 2 methods.
One for parsing the cli and one that runs the application.
"""
from .core import Core
c = Core(
source_file=cli_args["--data-file"],
schema_files=cli_args["--schema-file"],
extensions=cli_args['--extension']... | python | def run(cli_args):
"""
Split the functionality into 2 methods.
One for parsing the cli and one that runs the application.
"""
from .core import Core
c = Core(
source_file=cli_args["--data-file"],
schema_files=cli_args["--schema-file"],
extensions=cli_args['--extension']... | [
"def",
"run",
"(",
"cli_args",
")",
":",
"from",
".",
"core",
"import",
"Core",
"c",
"=",
"Core",
"(",
"source_file",
"=",
"cli_args",
"[",
"\"--data-file\"",
"]",
",",
"schema_files",
"=",
"cli_args",
"[",
"\"--schema-file\"",
"]",
",",
"extensions",
"=",... | Split the functionality into 2 methods.
One for parsing the cli and one that runs the application. | [
"Split",
"the",
"functionality",
"into",
"2",
"methods",
"."
] | train | https://github.com/Grokzen/pykwalify/blob/02b7e21eafb97926f17b7c33e2ee7b3ea67c3ef7/pykwalify/cli.py#L68-L86 |
tisimst/pyDOE | pyDOE/doe_plackett_burman.py | pbdesign | def pbdesign(n):
"""
Generate a Plackett-Burman design
Parameter
---------
n : int
The number of factors to create a matrix for.
Returns
-------
H : 2d-array
An orthogonal design matrix with n columns, one for each factor, and
the number of ... | python | def pbdesign(n):
"""
Generate a Plackett-Burman design
Parameter
---------
n : int
The number of factors to create a matrix for.
Returns
-------
H : 2d-array
An orthogonal design matrix with n columns, one for each factor, and
the number of ... | [
"def",
"pbdesign",
"(",
"n",
")",
":",
"assert",
"n",
">",
"0",
",",
"'Number of factors must be a positive integer'",
"keep",
"=",
"int",
"(",
"n",
")",
"n",
"=",
"4",
"*",
"(",
"int",
"(",
"n",
"/",
"4",
")",
"+",
"1",
")",
"# calculate the correct n... | Generate a Plackett-Burman design
Parameter
---------
n : int
The number of factors to create a matrix for.
Returns
-------
H : 2d-array
An orthogonal design matrix with n columns, one for each factor, and
the number of rows being the next multiple of... | [
"Generate",
"a",
"Plackett",
"-",
"Burman",
"design",
"Parameter",
"---------",
"n",
":",
"int",
"The",
"number",
"of",
"factors",
"to",
"create",
"a",
"matrix",
"for",
".",
"Returns",
"-------",
"H",
":",
"2d",
"-",
"array",
"An",
"orthogonal",
"design",
... | train | https://github.com/tisimst/pyDOE/blob/436143702507a5c8ff87b361223eee8171d6a1d7/pyDOE/doe_plackett_burman.py#L22-L94 |
tisimst/pyDOE | pyDOE/doe_star.py | star | def star(n, alpha='faced', center=(1, 1)):
"""
Create the star points of various design matrices
Parameters
----------
n : int
The number of variables in the design
Optional
--------
alpha : str
Available values are 'faced' (default), 'orthogonal', o... | python | def star(n, alpha='faced', center=(1, 1)):
"""
Create the star points of various design matrices
Parameters
----------
n : int
The number of variables in the design
Optional
--------
alpha : str
Available values are 'faced' (default), 'orthogonal', o... | [
"def",
"star",
"(",
"n",
",",
"alpha",
"=",
"'faced'",
",",
"center",
"=",
"(",
"1",
",",
"1",
")",
")",
":",
"# Star points at the center of each face of the factorial\r",
"if",
"alpha",
"==",
"'faced'",
":",
"a",
"=",
"1",
"elif",
"alpha",
"==",
"'orthog... | Create the star points of various design matrices
Parameters
----------
n : int
The number of variables in the design
Optional
--------
alpha : str
Available values are 'faced' (default), 'orthogonal', or 'rotatable'
center : array
A 1-by-2 array... | [
"Create",
"the",
"star",
"points",
"of",
"various",
"design",
"matrices",
"Parameters",
"----------",
"n",
":",
"int",
"The",
"number",
"of",
"variables",
"in",
"the",
"design",
"Optional",
"--------",
"alpha",
":",
"str",
"Available",
"values",
"are",
"faced"... | train | https://github.com/tisimst/pyDOE/blob/436143702507a5c8ff87b361223eee8171d6a1d7/pyDOE/doe_star.py#L18-L79 |
tisimst/pyDOE | pyDOE/doe_fold.py | fold | def fold(H, columns=None):
"""
Fold a design to reduce confounding effects.
Parameters
----------
H : 2d-array
The design matrix to be folded.
columns : array
Indices of of columns to fold (Default: None). If ``columns=None`` is
used, then all columns will ... | python | def fold(H, columns=None):
"""
Fold a design to reduce confounding effects.
Parameters
----------
H : 2d-array
The design matrix to be folded.
columns : array
Indices of of columns to fold (Default: None). If ``columns=None`` is
used, then all columns will ... | [
"def",
"fold",
"(",
"H",
",",
"columns",
"=",
"None",
")",
":",
"H",
"=",
"np",
".",
"array",
"(",
"H",
")",
"assert",
"len",
"(",
"H",
".",
"shape",
")",
"==",
"2",
",",
"'Input design matrix must be 2d.'",
"if",
"columns",
"is",
"None",
":",
"col... | Fold a design to reduce confounding effects.
Parameters
----------
H : 2d-array
The design matrix to be folded.
columns : array
Indices of of columns to fold (Default: None). If ``columns=None`` is
used, then all columns will be folded.
Returns
------... | [
"Fold",
"a",
"design",
"to",
"reduce",
"confounding",
"effects",
".",
"Parameters",
"----------",
"H",
":",
"2d",
"-",
"array",
"The",
"design",
"matrix",
"to",
"be",
"folded",
".",
"columns",
":",
"array",
"Indices",
"of",
"of",
"columns",
"to",
"fold",
... | train | https://github.com/tisimst/pyDOE/blob/436143702507a5c8ff87b361223eee8171d6a1d7/pyDOE/doe_fold.py#L20-L59 |
tisimst/pyDOE | pyDOE/build_regression_matrix.py | build_regression_matrix | def build_regression_matrix(H, model, build=None):
"""
Build a regression matrix using a DOE matrix and a list of monomials.
Parameters
----------
H : 2d-array
model : str
build : bool-array
Returns
-------
R : 2d-array
"""
ListOfTokens = mod... | python | def build_regression_matrix(H, model, build=None):
"""
Build a regression matrix using a DOE matrix and a list of monomials.
Parameters
----------
H : 2d-array
model : str
build : bool-array
Returns
-------
R : 2d-array
"""
ListOfTokens = mod... | [
"def",
"build_regression_matrix",
"(",
"H",
",",
"model",
",",
"build",
"=",
"None",
")",
":",
"ListOfTokens",
"=",
"model",
".",
"split",
"(",
"' '",
")",
"if",
"H",
".",
"shape",
"[",
"1",
"]",
"==",
"1",
":",
"size_index",
"=",
"len",
"(",
"str"... | Build a regression matrix using a DOE matrix and a list of monomials.
Parameters
----------
H : 2d-array
model : str
build : bool-array
Returns
-------
R : 2d-array | [
"Build",
"a",
"regression",
"matrix",
"using",
"a",
"DOE",
"matrix",
"and",
"a",
"list",
"of",
"monomials",
".",
"Parameters",
"----------",
"H",
":",
"2d",
"-",
"array",
"model",
":",
"str",
"build",
":",
"bool",
"-",
"array",
"Returns",
"-------",
"R",... | train | https://github.com/tisimst/pyDOE/blob/436143702507a5c8ff87b361223eee8171d6a1d7/pyDOE/build_regression_matrix.py#L27-L95 |
daler/gffutils | gffutils/pybedtools_integration.py | to_bedtool | def to_bedtool(iterator):
"""
Convert any iterator into a pybedtools.BedTool object.
Note that the supplied iterator is not consumed by this function. To save
to a temp file or to a known location, use the `.saveas()` method of the
returned BedTool object.
"""
def gen():
for i in it... | python | def to_bedtool(iterator):
"""
Convert any iterator into a pybedtools.BedTool object.
Note that the supplied iterator is not consumed by this function. To save
to a temp file or to a known location, use the `.saveas()` method of the
returned BedTool object.
"""
def gen():
for i in it... | [
"def",
"to_bedtool",
"(",
"iterator",
")",
":",
"def",
"gen",
"(",
")",
":",
"for",
"i",
"in",
"iterator",
":",
"yield",
"helpers",
".",
"asinterval",
"(",
"i",
")",
"return",
"pybedtools",
".",
"BedTool",
"(",
"gen",
"(",
")",
")"
] | Convert any iterator into a pybedtools.BedTool object.
Note that the supplied iterator is not consumed by this function. To save
to a temp file or to a known location, use the `.saveas()` method of the
returned BedTool object. | [
"Convert",
"any",
"iterator",
"into",
"a",
"pybedtools",
".",
"BedTool",
"object",
"."
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/pybedtools_integration.py#L12-L23 |
daler/gffutils | gffutils/pybedtools_integration.py | tsses | def tsses(db, merge_overlapping=False, attrs=None, attrs_sep=":",
merge_kwargs=None, as_bed6=False, bedtools_227_or_later=True):
"""
Create 1-bp transcription start sites for all transcripts in the database
and return as a sorted pybedtools.BedTool object pointing to a temporary
file.
To ... | python | def tsses(db, merge_overlapping=False, attrs=None, attrs_sep=":",
merge_kwargs=None, as_bed6=False, bedtools_227_or_later=True):
"""
Create 1-bp transcription start sites for all transcripts in the database
and return as a sorted pybedtools.BedTool object pointing to a temporary
file.
To ... | [
"def",
"tsses",
"(",
"db",
",",
"merge_overlapping",
"=",
"False",
",",
"attrs",
"=",
"None",
",",
"attrs_sep",
"=",
"\":\"",
",",
"merge_kwargs",
"=",
"None",
",",
"as_bed6",
"=",
"False",
",",
"bedtools_227_or_later",
"=",
"True",
")",
":",
"_override",
... | Create 1-bp transcription start sites for all transcripts in the database
and return as a sorted pybedtools.BedTool object pointing to a temporary
file.
To save the file to a known location, use the `.moveto()` method on the
resulting `pybedtools.BedTool` object.
To extend regions upstream/downstr... | [
"Create",
"1",
"-",
"bp",
"transcription",
"start",
"sites",
"for",
"all",
"transcripts",
"in",
"the",
"database",
"and",
"return",
"as",
"a",
"sorted",
"pybedtools",
".",
"BedTool",
"object",
"pointing",
"to",
"a",
"temporary",
"file",
"."
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/pybedtools_integration.py#L26-L237 |
daler/gffutils | gffutils/gffwriter.py | GFFWriter.write_gene_recs | def write_gene_recs(self, db, gene_id):
"""
NOTE: The goal of this function is to have a canonical ordering when
outputting a gene and all of its records to a file. The order is
intended to be:
gene
# mRNAs sorted by length, with longest mRNA first
mRNA_1
... | python | def write_gene_recs(self, db, gene_id):
"""
NOTE: The goal of this function is to have a canonical ordering when
outputting a gene and all of its records to a file. The order is
intended to be:
gene
# mRNAs sorted by length, with longest mRNA first
mRNA_1
... | [
"def",
"write_gene_recs",
"(",
"self",
",",
"db",
",",
"gene_id",
")",
":",
"gene_rec",
"=",
"db",
"[",
"gene_id",
"]",
"# Output gene record",
"self",
".",
"write_rec",
"(",
"gene_rec",
")",
"# Get each mRNA's lengths",
"mRNA_lens",
"=",
"{",
"}",
"c",
"=",... | NOTE: The goal of this function is to have a canonical ordering when
outputting a gene and all of its records to a file. The order is
intended to be:
gene
# mRNAs sorted by length, with longest mRNA first
mRNA_1
# Exons of mRNA, sorted by start position (ascendi... | [
"NOTE",
":",
"The",
"goal",
"of",
"this",
"function",
"is",
"to",
"have",
"a",
"canonical",
"ordering",
"when",
"outputting",
"a",
"gene",
"and",
"all",
"of",
"its",
"records",
"to",
"a",
"file",
".",
"The",
"order",
"is",
"intended",
"to",
"be",
":"
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/gffwriter.py#L79-L134 |
daler/gffutils | gffutils/gffwriter.py | GFFWriter.write_mRNA_children | def write_mRNA_children(self, db, mRNA_id):
"""
Write out the children records of the mRNA given by the ID
(not including the mRNA record itself) in a canonical
order, where exons are sorted by start position and given
first.
"""
mRNA_children = db.children(mRNA_i... | python | def write_mRNA_children(self, db, mRNA_id):
"""
Write out the children records of the mRNA given by the ID
(not including the mRNA record itself) in a canonical
order, where exons are sorted by start position and given
first.
"""
mRNA_children = db.children(mRNA_i... | [
"def",
"write_mRNA_children",
"(",
"self",
",",
"db",
",",
"mRNA_id",
")",
":",
"mRNA_children",
"=",
"db",
".",
"children",
"(",
"mRNA_id",
",",
"order_by",
"=",
"'start'",
")",
"nonexonic_children",
"=",
"[",
"]",
"for",
"child_rec",
"in",
"mRNA_children",... | Write out the children records of the mRNA given by the ID
(not including the mRNA record itself) in a canonical
order, where exons are sorted by start position and given
first. | [
"Write",
"out",
"the",
"children",
"records",
"of",
"the",
"mRNA",
"given",
"by",
"the",
"ID",
"(",
"not",
"including",
"the",
"mRNA",
"record",
"itself",
")",
"in",
"a",
"canonical",
"order",
"where",
"exons",
"are",
"sorted",
"by",
"start",
"position",
... | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/gffwriter.py#L136-L151 |
daler/gffutils | gffutils/gffwriter.py | GFFWriter.write_exon_children | def write_exon_children(self, db, exon_id):
"""
Write out the children records of the exon given by
the ID (not including the exon record itself).
"""
exon_children = db.children(exon_id, order_by='start')
for exon_child in exon_children:
self.write_rec(exon_c... | python | def write_exon_children(self, db, exon_id):
"""
Write out the children records of the exon given by
the ID (not including the exon record itself).
"""
exon_children = db.children(exon_id, order_by='start')
for exon_child in exon_children:
self.write_rec(exon_c... | [
"def",
"write_exon_children",
"(",
"self",
",",
"db",
",",
"exon_id",
")",
":",
"exon_children",
"=",
"db",
".",
"children",
"(",
"exon_id",
",",
"order_by",
"=",
"'start'",
")",
"for",
"exon_child",
"in",
"exon_children",
":",
"self",
".",
"write_rec",
"(... | Write out the children records of the exon given by
the ID (not including the exon record itself). | [
"Write",
"out",
"the",
"children",
"records",
"of",
"the",
"exon",
"given",
"by",
"the",
"ID",
"(",
"not",
"including",
"the",
"exon",
"record",
"itself",
")",
"."
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/gffwriter.py#L153-L160 |
daler/gffutils | gffutils/gffwriter.py | GFFWriter.close | def close(self):
"""
Close the stream. Assumes stream has 'close' method.
"""
self.out_stream.close()
# If we're asked to write in place, substitute the named
# temporary file for the current file
if self.in_place:
shutil.move(self.temp_file.name, self... | python | def close(self):
"""
Close the stream. Assumes stream has 'close' method.
"""
self.out_stream.close()
# If we're asked to write in place, substitute the named
# temporary file for the current file
if self.in_place:
shutil.move(self.temp_file.name, self... | [
"def",
"close",
"(",
"self",
")",
":",
"self",
".",
"out_stream",
".",
"close",
"(",
")",
"# If we're asked to write in place, substitute the named",
"# temporary file for the current file",
"if",
"self",
".",
"in_place",
":",
"shutil",
".",
"move",
"(",
"self",
"."... | Close the stream. Assumes stream has 'close' method. | [
"Close",
"the",
"stream",
".",
"Assumes",
"stream",
"has",
"close",
"method",
"."
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/gffwriter.py#L162-L170 |
tisimst/pyDOE | pyDOE/var_regression_matrix.py | var_regression_matrix | def var_regression_matrix(H, x, model, sigma=1):
"""
Compute the variance of the 'regression error'.
Parameters
----------
H : 2d-array
The regression matrix
x : 2d-array
The coordinates to calculate the regression error variance at.
model : str
A stri... | python | def var_regression_matrix(H, x, model, sigma=1):
"""
Compute the variance of the 'regression error'.
Parameters
----------
H : 2d-array
The regression matrix
x : 2d-array
The coordinates to calculate the regression error variance at.
model : str
A stri... | [
"def",
"var_regression_matrix",
"(",
"H",
",",
"x",
",",
"model",
",",
"sigma",
"=",
"1",
")",
":",
"x",
"=",
"np",
".",
"atleast_2d",
"(",
"x",
")",
"H",
"=",
"np",
".",
"atleast_2d",
"(",
"H",
")",
"if",
"x",
".",
"shape",
"[",
"0",
"]",
"=... | Compute the variance of the 'regression error'.
Parameters
----------
H : 2d-array
The regression matrix
x : 2d-array
The coordinates to calculate the regression error variance at.
model : str
A string of tokens that define the regression model (e.g.
'... | [
"Compute",
"the",
"variance",
"of",
"the",
"regression",
"error",
".",
"Parameters",
"----------",
"H",
":",
"2d",
"-",
"array",
"The",
"regression",
"matrix",
"x",
":",
"2d",
"-",
"array",
"The",
"coordinates",
"to",
"calculate",
"the",
"regression",
"error... | train | https://github.com/tisimst/pyDOE/blob/436143702507a5c8ff87b361223eee8171d6a1d7/pyDOE/var_regression_matrix.py#L18-L51 |
daler/gffutils | gffutils/biopython_integration.py | to_seqfeature | def to_seqfeature(feature):
"""
Converts a gffutils.Feature object to a Bio.SeqFeature object.
The GFF fields `source`, `score`, `seqid`, and `frame` are stored as
qualifiers. GFF `attributes` are also stored as qualifiers.
Parameters
----------
feature : Feature object, or string
... | python | def to_seqfeature(feature):
"""
Converts a gffutils.Feature object to a Bio.SeqFeature object.
The GFF fields `source`, `score`, `seqid`, and `frame` are stored as
qualifiers. GFF `attributes` are also stored as qualifiers.
Parameters
----------
feature : Feature object, or string
... | [
"def",
"to_seqfeature",
"(",
"feature",
")",
":",
"if",
"isinstance",
"(",
"feature",
",",
"six",
".",
"string_types",
")",
":",
"feature",
"=",
"feature_from_line",
"(",
"feature",
")",
"qualifiers",
"=",
"{",
"'source'",
":",
"[",
"feature",
".",
"source... | Converts a gffutils.Feature object to a Bio.SeqFeature object.
The GFF fields `source`, `score`, `seqid`, and `frame` are stored as
qualifiers. GFF `attributes` are also stored as qualifiers.
Parameters
----------
feature : Feature object, or string
If string, assume it is a GFF or GTF-fo... | [
"Converts",
"a",
"gffutils",
".",
"Feature",
"object",
"to",
"a",
"Bio",
".",
"SeqFeature",
"object",
"."
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/biopython_integration.py#L21-L52 |
daler/gffutils | gffutils/biopython_integration.py | from_seqfeature | def from_seqfeature(s, **kwargs):
"""
Converts a Bio.SeqFeature object to a gffutils.Feature object.
The GFF fields `source`, `score`, `seqid`, and `frame` are assumed to be
stored as qualifiers. Any other qualifiers will be assumed to be GFF
attributes.
"""
source = s.qualifiers.get('sour... | python | def from_seqfeature(s, **kwargs):
"""
Converts a Bio.SeqFeature object to a gffutils.Feature object.
The GFF fields `source`, `score`, `seqid`, and `frame` are assumed to be
stored as qualifiers. Any other qualifiers will be assumed to be GFF
attributes.
"""
source = s.qualifiers.get('sour... | [
"def",
"from_seqfeature",
"(",
"s",
",",
"*",
"*",
"kwargs",
")",
":",
"source",
"=",
"s",
".",
"qualifiers",
".",
"get",
"(",
"'source'",
",",
"'.'",
")",
"[",
"0",
"]",
"score",
"=",
"s",
".",
"qualifiers",
".",
"get",
"(",
"'score'",
",",
"'.'... | Converts a Bio.SeqFeature object to a gffutils.Feature object.
The GFF fields `source`, `score`, `seqid`, and `frame` are assumed to be
stored as qualifiers. Any other qualifiers will be assumed to be GFF
attributes. | [
"Converts",
"a",
"Bio",
".",
"SeqFeature",
"object",
"to",
"a",
"gffutils",
".",
"Feature",
"object",
"."
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/biopython_integration.py#L55-L81 |
daler/gffutils | gffutils/interface.py | FeatureDB.set_pragmas | def set_pragmas(self, pragmas):
"""
Set pragmas for the current database connection.
Parameters
----------
pragmas : dict
Dictionary of pragmas; see constants.default_pragmas for a template
and http://www.sqlite.org/pragma.html for a full list.
""... | python | def set_pragmas(self, pragmas):
"""
Set pragmas for the current database connection.
Parameters
----------
pragmas : dict
Dictionary of pragmas; see constants.default_pragmas for a template
and http://www.sqlite.org/pragma.html for a full list.
""... | [
"def",
"set_pragmas",
"(",
"self",
",",
"pragmas",
")",
":",
"self",
".",
"pragmas",
"=",
"pragmas",
"c",
"=",
"self",
".",
"conn",
".",
"cursor",
"(",
")",
"c",
".",
"executescript",
"(",
"';\\n'",
".",
"join",
"(",
"[",
"'PRAGMA %s=%s'",
"%",
"i",
... | Set pragmas for the current database connection.
Parameters
----------
pragmas : dict
Dictionary of pragmas; see constants.default_pragmas for a template
and http://www.sqlite.org/pragma.html for a full list. | [
"Set",
"pragmas",
"for",
"the",
"current",
"database",
"connection",
"."
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/interface.py#L163-L180 |
daler/gffutils | gffutils/interface.py | FeatureDB._feature_returner | def _feature_returner(self, **kwargs):
"""
Returns a feature, adding additional database-specific defaults
"""
kwargs.setdefault('dialect', self.dialect)
kwargs.setdefault('keep_order', self.keep_order)
kwargs.setdefault('sort_attribute_values', self.sort_attribute_values... | python | def _feature_returner(self, **kwargs):
"""
Returns a feature, adding additional database-specific defaults
"""
kwargs.setdefault('dialect', self.dialect)
kwargs.setdefault('keep_order', self.keep_order)
kwargs.setdefault('sort_attribute_values', self.sort_attribute_values... | [
"def",
"_feature_returner",
"(",
"self",
",",
"*",
"*",
"kwargs",
")",
":",
"kwargs",
".",
"setdefault",
"(",
"'dialect'",
",",
"self",
".",
"dialect",
")",
"kwargs",
".",
"setdefault",
"(",
"'keep_order'",
",",
"self",
".",
"keep_order",
")",
"kwargs",
... | Returns a feature, adding additional database-specific defaults | [
"Returns",
"a",
"feature",
"adding",
"additional",
"database",
"-",
"specific",
"defaults"
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/interface.py#L182-L189 |
daler/gffutils | gffutils/interface.py | FeatureDB.schema | def schema(self):
"""
Returns the database schema as a string.
"""
c = self.conn.cursor()
c.execute(
'''
SELECT sql FROM sqlite_master
''')
results = []
for i, in c:
if i is not None:
results.append(i... | python | def schema(self):
"""
Returns the database schema as a string.
"""
c = self.conn.cursor()
c.execute(
'''
SELECT sql FROM sqlite_master
''')
results = []
for i, in c:
if i is not None:
results.append(i... | [
"def",
"schema",
"(",
"self",
")",
":",
"c",
"=",
"self",
".",
"conn",
".",
"cursor",
"(",
")",
"c",
".",
"execute",
"(",
"'''\n SELECT sql FROM sqlite_master\n '''",
")",
"results",
"=",
"[",
"]",
"for",
"i",
",",
"in",
"c",
":",
"... | Returns the database schema as a string. | [
"Returns",
"the",
"database",
"schema",
"as",
"a",
"string",
"."
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/interface.py#L199-L212 |
daler/gffutils | gffutils/interface.py | FeatureDB.count_features_of_type | def count_features_of_type(self, featuretype=None):
"""
Simple count of features.
Can be faster than "grep", and is faster than checking the length of
results from :meth:`gffutils.FeatureDB.features_of_type`.
Parameters
----------
featuretype : string
... | python | def count_features_of_type(self, featuretype=None):
"""
Simple count of features.
Can be faster than "grep", and is faster than checking the length of
results from :meth:`gffutils.FeatureDB.features_of_type`.
Parameters
----------
featuretype : string
... | [
"def",
"count_features_of_type",
"(",
"self",
",",
"featuretype",
"=",
"None",
")",
":",
"c",
"=",
"self",
".",
"conn",
".",
"cursor",
"(",
")",
"if",
"featuretype",
"is",
"not",
"None",
":",
"c",
".",
"execute",
"(",
"'''\n SELECT count() FRO... | Simple count of features.
Can be faster than "grep", and is faster than checking the length of
results from :meth:`gffutils.FeatureDB.features_of_type`.
Parameters
----------
featuretype : string
Feature type (e.g., "gene") to count. If None, then count *all*
... | [
"Simple",
"count",
"of",
"features",
"."
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/interface.py#L230-L266 |
daler/gffutils | gffutils/interface.py | FeatureDB.features_of_type | def features_of_type(self, featuretype, limit=None, strand=None,
order_by=None, reverse=False,
completely_within=False):
"""
Returns an iterator of :class:`gffutils.Feature` objects.
Parameters
----------
{_method_doc}
""... | python | def features_of_type(self, featuretype, limit=None, strand=None,
order_by=None, reverse=False,
completely_within=False):
"""
Returns an iterator of :class:`gffutils.Feature` objects.
Parameters
----------
{_method_doc}
""... | [
"def",
"features_of_type",
"(",
"self",
",",
"featuretype",
",",
"limit",
"=",
"None",
",",
"strand",
"=",
"None",
",",
"order_by",
"=",
"None",
",",
"reverse",
"=",
"False",
",",
"completely_within",
"=",
"False",
")",
":",
"query",
",",
"args",
"=",
... | Returns an iterator of :class:`gffutils.Feature` objects.
Parameters
----------
{_method_doc} | [
"Returns",
"an",
"iterator",
"of",
":",
"class",
":",
"gffutils",
".",
"Feature",
"objects",
"."
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/interface.py#L268-L289 |
daler/gffutils | gffutils/interface.py | FeatureDB.iter_by_parent_childs | def iter_by_parent_childs(self, featuretype="gene", level=None,
order_by=None, reverse=False,
completely_within=False):
"""
For each parent of type `featuretype`, yield a list L of that parent
and all of its children (`[parent] + list(c... | python | def iter_by_parent_childs(self, featuretype="gene", level=None,
order_by=None, reverse=False,
completely_within=False):
"""
For each parent of type `featuretype`, yield a list L of that parent
and all of its children (`[parent] + list(c... | [
"def",
"iter_by_parent_childs",
"(",
"self",
",",
"featuretype",
"=",
"\"gene\"",
",",
"level",
"=",
"None",
",",
"order_by",
"=",
"None",
",",
"reverse",
"=",
"False",
",",
"completely_within",
"=",
"False",
")",
":",
"# Get all the parent records of the requeste... | For each parent of type `featuretype`, yield a list L of that parent
and all of its children (`[parent] + list(children)`). The parent will
always be L[0].
This is useful for "sanitizing" a GFF file for downstream tools.
Additional kwargs are passed to :meth:`FeatureDB.children`, and w... | [
"For",
"each",
"parent",
"of",
"type",
"featuretype",
"yield",
"a",
"list",
"L",
"of",
"that",
"parent",
"and",
"all",
"of",
"its",
"children",
"(",
"[",
"parent",
"]",
"+",
"list",
"(",
"children",
")",
")",
".",
"The",
"parent",
"will",
"always",
"... | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/interface.py#L292-L312 |
daler/gffutils | gffutils/interface.py | FeatureDB.featuretypes | def featuretypes(self):
"""
Iterate over feature types found in the database.
Returns
-------
A generator object that yields featuretypes (as strings)
"""
c = self.conn.cursor()
c.execute(
'''
SELECT DISTINCT featuretype from featu... | python | def featuretypes(self):
"""
Iterate over feature types found in the database.
Returns
-------
A generator object that yields featuretypes (as strings)
"""
c = self.conn.cursor()
c.execute(
'''
SELECT DISTINCT featuretype from featu... | [
"def",
"featuretypes",
"(",
"self",
")",
":",
"c",
"=",
"self",
".",
"conn",
".",
"cursor",
"(",
")",
"c",
".",
"execute",
"(",
"'''\n SELECT DISTINCT featuretype from features\n '''",
")",
"for",
"i",
",",
"in",
"c",
":",
"yield",
"i"
] | Iterate over feature types found in the database.
Returns
-------
A generator object that yields featuretypes (as strings) | [
"Iterate",
"over",
"feature",
"types",
"found",
"in",
"the",
"database",
"."
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/interface.py#L339-L353 |
daler/gffutils | gffutils/interface.py | FeatureDB._relation | def _relation(self, id, join_on, join_to, level=None, featuretype=None,
order_by=None, reverse=False, completely_within=False,
limit=None):
# The following docstring will be included in the parents() and
# children() docstrings to maintain consistency, since they bot... | python | def _relation(self, id, join_on, join_to, level=None, featuretype=None,
order_by=None, reverse=False, completely_within=False,
limit=None):
# The following docstring will be included in the parents() and
# children() docstrings to maintain consistency, since they bot... | [
"def",
"_relation",
"(",
"self",
",",
"id",
",",
"join_on",
",",
"join_to",
",",
"level",
"=",
"None",
",",
"featuretype",
"=",
"None",
",",
"order_by",
"=",
"None",
",",
"reverse",
"=",
"False",
",",
"completely_within",
"=",
"False",
",",
"limit",
"=... | Parameters
----------
id : string or a Feature object
level : None or int
If `level=None` (default), then return all children regardless
of level. If `level` is an integer, then constrain to just that
level.
{_method_doc}
Returns
-... | [
"Parameters",
"----------"
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/interface.py#L355-L409 |
daler/gffutils | gffutils/interface.py | FeatureDB.parents | def parents(self, id, level=None, featuretype=None, order_by=None,
reverse=False, completely_within=False, limit=None):
"""
Return parents of feature `id`.
{_relation_docstring}
"""
return self._relation(
id, join_on='parent', join_to='child', level=le... | python | def parents(self, id, level=None, featuretype=None, order_by=None,
reverse=False, completely_within=False, limit=None):
"""
Return parents of feature `id`.
{_relation_docstring}
"""
return self._relation(
id, join_on='parent', join_to='child', level=le... | [
"def",
"parents",
"(",
"self",
",",
"id",
",",
"level",
"=",
"None",
",",
"featuretype",
"=",
"None",
",",
"order_by",
"=",
"None",
",",
"reverse",
"=",
"False",
",",
"completely_within",
"=",
"False",
",",
"limit",
"=",
"None",
")",
":",
"return",
"... | Return parents of feature `id`.
{_relation_docstring} | [
"Return",
"parents",
"of",
"feature",
"id",
".",
"{",
"_relation_docstring",
"}"
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/interface.py#L422-L431 |
daler/gffutils | gffutils/interface.py | FeatureDB.execute | def execute(self, query):
"""
Execute arbitrary queries on the db.
.. seealso::
:class:`FeatureDB.schema` may be helpful when writing your own
queries.
Parameters
----------
query : str
Query to execute -- trailing ";" opti... | python | def execute(self, query):
"""
Execute arbitrary queries on the db.
.. seealso::
:class:`FeatureDB.schema` may be helpful when writing your own
queries.
Parameters
----------
query : str
Query to execute -- trailing ";" opti... | [
"def",
"execute",
"(",
"self",
",",
"query",
")",
":",
"c",
"=",
"self",
".",
"conn",
".",
"cursor",
"(",
")",
"return",
"c",
".",
"execute",
"(",
"query",
")"
] | Execute arbitrary queries on the db.
.. seealso::
:class:`FeatureDB.schema` may be helpful when writing your own
queries.
Parameters
----------
query : str
Query to execute -- trailing ";" optional.
Returns
-------
... | [
"Execute",
"arbitrary",
"queries",
"on",
"the",
"db",
"."
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/interface.py#L440-L461 |
daler/gffutils | gffutils/interface.py | FeatureDB.region | def region(self, region=None, seqid=None, start=None, end=None,
strand=None, featuretype=None, completely_within=False):
"""
Return features within specified genomic coordinates.
Specifying genomic coordinates can be done in a flexible manner
Parameters
---------... | python | def region(self, region=None, seqid=None, start=None, end=None,
strand=None, featuretype=None, completely_within=False):
"""
Return features within specified genomic coordinates.
Specifying genomic coordinates can be done in a flexible manner
Parameters
---------... | [
"def",
"region",
"(",
"self",
",",
"region",
"=",
"None",
",",
"seqid",
"=",
"None",
",",
"start",
"=",
"None",
",",
"end",
"=",
"None",
",",
"strand",
"=",
"None",
",",
"featuretype",
"=",
"None",
",",
"completely_within",
"=",
"False",
")",
":",
... | Return features within specified genomic coordinates.
Specifying genomic coordinates can be done in a flexible manner
Parameters
----------
region : string, tuple, or Feature instance
If string, then of the form "seqid:start-end". If tuple, then
(seqid, start, ... | [
"Return",
"features",
"within",
"specified",
"genomic",
"coordinates",
"."
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/interface.py#L471-L648 |
daler/gffutils | gffutils/interface.py | FeatureDB.interfeatures | def interfeatures(self, features, new_featuretype=None,
merge_attributes=True, dialect=None,
attribute_func=None, update_attributes=None):
"""
Construct new features representing the space between features.
For example, if `features` is a list of exon... | python | def interfeatures(self, features, new_featuretype=None,
merge_attributes=True, dialect=None,
attribute_func=None, update_attributes=None):
"""
Construct new features representing the space between features.
For example, if `features` is a list of exon... | [
"def",
"interfeatures",
"(",
"self",
",",
"features",
",",
"new_featuretype",
"=",
"None",
",",
"merge_attributes",
"=",
"True",
",",
"dialect",
"=",
"None",
",",
"attribute_func",
"=",
"None",
",",
"update_attributes",
"=",
"None",
")",
":",
"for",
"i",
"... | Construct new features representing the space between features.
For example, if `features` is a list of exons, then this method will
return the introns. If `features` is a list of genes, then this method
will return the intergenic regions.
Providing N features will return N - 1 new fe... | [
"Construct",
"new",
"features",
"representing",
"the",
"space",
"between",
"features",
"."
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/interface.py#L650-L766 |
daler/gffutils | gffutils/interface.py | FeatureDB.delete | def delete(self, features, make_backup=True, **kwargs):
"""
Delete features from database.
features : str, iterable, FeatureDB instance
If FeatureDB, all features will be used. If string, assume it's the
ID of the feature to remove. Otherwise, assume it's an iterable of
... | python | def delete(self, features, make_backup=True, **kwargs):
"""
Delete features from database.
features : str, iterable, FeatureDB instance
If FeatureDB, all features will be used. If string, assume it's the
ID of the feature to remove. Otherwise, assume it's an iterable of
... | [
"def",
"delete",
"(",
"self",
",",
"features",
",",
"make_backup",
"=",
"True",
",",
"*",
"*",
"kwargs",
")",
":",
"if",
"make_backup",
":",
"if",
"isinstance",
"(",
"self",
".",
"dbfn",
",",
"six",
".",
"string_types",
")",
":",
"shutil",
".",
"copy... | Delete features from database.
features : str, iterable, FeatureDB instance
If FeatureDB, all features will be used. If string, assume it's the
ID of the feature to remove. Otherwise, assume it's an iterable of
Feature objects. The classes in gffutils.iterators may be helpfu... | [
"Delete",
"features",
"from",
"database",
"."
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/interface.py#L768-L812 |
daler/gffutils | gffutils/interface.py | FeatureDB.update | def update(self, data, make_backup=True, **kwargs):
"""
Update database with features in `data`.
data : str, iterable, FeatureDB instance
If FeatureDB, all data will be used. If string, assume it's
a filename of a GFF or GTF file. Otherwise, assume it's an
i... | python | def update(self, data, make_backup=True, **kwargs):
"""
Update database with features in `data`.
data : str, iterable, FeatureDB instance
If FeatureDB, all data will be used. If string, assume it's
a filename of a GFF or GTF file. Otherwise, assume it's an
i... | [
"def",
"update",
"(",
"self",
",",
"data",
",",
"make_backup",
"=",
"True",
",",
"*",
"*",
"kwargs",
")",
":",
"from",
"gffutils",
"import",
"create",
"from",
"gffutils",
"import",
"iterators",
"if",
"make_backup",
":",
"if",
"isinstance",
"(",
"self",
"... | Update database with features in `data`.
data : str, iterable, FeatureDB instance
If FeatureDB, all data will be used. If string, assume it's
a filename of a GFF or GTF file. Otherwise, assume it's an
iterable of Feature objects. The classes in gffutils.iterators may
... | [
"Update",
"database",
"with",
"features",
"in",
"data",
"."
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/interface.py#L814-L871 |
daler/gffutils | gffutils/interface.py | FeatureDB.add_relation | def add_relation(self, parent, child, level, parent_func=None,
child_func=None):
"""
Manually add relations to the database.
Parameters
----------
parent : str or Feature instance
Parent feature to add.
child : str or Feature instance
... | python | def add_relation(self, parent, child, level, parent_func=None,
child_func=None):
"""
Manually add relations to the database.
Parameters
----------
parent : str or Feature instance
Parent feature to add.
child : str or Feature instance
... | [
"def",
"add_relation",
"(",
"self",
",",
"parent",
",",
"child",
",",
"level",
",",
"parent_func",
"=",
"None",
",",
"child_func",
"=",
"None",
")",
":",
"if",
"isinstance",
"(",
"parent",
",",
"six",
".",
"string_types",
")",
":",
"parent",
"=",
"self... | Manually add relations to the database.
Parameters
----------
parent : str or Feature instance
Parent feature to add.
child : str or Feature instance
Child feature to add
level : int
Level of the relation. For example, if parent is a gene ... | [
"Manually",
"add",
"relations",
"to",
"the",
"database",
"."
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/interface.py#L873-L928 |
daler/gffutils | gffutils/interface.py | FeatureDB._insert | def _insert(self, feature, cursor):
"""
Insert a feature into the database.
"""
try:
cursor.execute(constants._INSERT, feature.astuple())
except sqlite3.ProgrammingError:
cursor.execute(
constants._INSERT, feature.astuple(self.default_encod... | python | def _insert(self, feature, cursor):
"""
Insert a feature into the database.
"""
try:
cursor.execute(constants._INSERT, feature.astuple())
except sqlite3.ProgrammingError:
cursor.execute(
constants._INSERT, feature.astuple(self.default_encod... | [
"def",
"_insert",
"(",
"self",
",",
"feature",
",",
"cursor",
")",
":",
"try",
":",
"cursor",
".",
"execute",
"(",
"constants",
".",
"_INSERT",
",",
"feature",
".",
"astuple",
"(",
")",
")",
"except",
"sqlite3",
".",
"ProgrammingError",
":",
"cursor",
... | Insert a feature into the database. | [
"Insert",
"a",
"feature",
"into",
"the",
"database",
"."
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/interface.py#L935-L943 |
daler/gffutils | gffutils/interface.py | FeatureDB.create_introns | def create_introns(self, exon_featuretype='exon',
grandparent_featuretype='gene', parent_featuretype=None,
new_featuretype='intron', merge_attributes=True):
"""
Create introns from existing annotations.
Parameters
----------
exon_fe... | python | def create_introns(self, exon_featuretype='exon',
grandparent_featuretype='gene', parent_featuretype=None,
new_featuretype='intron', merge_attributes=True):
"""
Create introns from existing annotations.
Parameters
----------
exon_fe... | [
"def",
"create_introns",
"(",
"self",
",",
"exon_featuretype",
"=",
"'exon'",
",",
"grandparent_featuretype",
"=",
"'gene'",
",",
"parent_featuretype",
"=",
"None",
",",
"new_featuretype",
"=",
"'intron'",
",",
"merge_attributes",
"=",
"True",
")",
":",
"if",
"(... | Create introns from existing annotations.
Parameters
----------
exon_featuretype : string
Feature type to use in order to infer introns. Typically `"exon"`.
grandparent_featuretype : string
If `grandparent_featuretype` is not None, then group exons by
... | [
"Create",
"introns",
"from",
"existing",
"annotations",
"."
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/interface.py#L945-L1017 |
daler/gffutils | gffutils/interface.py | FeatureDB.merge | def merge(self, features, ignore_strand=False):
"""
Merge overlapping features together.
Parameters
----------
features : iterator of Feature instances
ignore_strand : bool
If True, features on multiple strands will be merged, and the final
stra... | python | def merge(self, features, ignore_strand=False):
"""
Merge overlapping features together.
Parameters
----------
features : iterator of Feature instances
ignore_strand : bool
If True, features on multiple strands will be merged, and the final
stra... | [
"def",
"merge",
"(",
"self",
",",
"features",
",",
"ignore_strand",
"=",
"False",
")",
":",
"# Consume iterator up front...",
"features",
"=",
"list",
"(",
"features",
")",
"if",
"len",
"(",
"features",
")",
"==",
"0",
":",
"raise",
"StopIteration",
"# Eithe... | Merge overlapping features together.
Parameters
----------
features : iterator of Feature instances
ignore_strand : bool
If True, features on multiple strands will be merged, and the final
strand will be set to '.'. Otherwise, ValueError will be raised if
... | [
"Merge",
"overlapping",
"features",
"together",
"."
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/interface.py#L1019-L1112 |
daler/gffutils | gffutils/interface.py | FeatureDB.children_bp | def children_bp(self, feature, child_featuretype='exon', merge=False,
ignore_strand=False):
"""
Total bp of all children of a featuretype.
Useful for getting the exonic bp of an mRNA.
Parameters
----------
feature : str or Feature instance
... | python | def children_bp(self, feature, child_featuretype='exon', merge=False,
ignore_strand=False):
"""
Total bp of all children of a featuretype.
Useful for getting the exonic bp of an mRNA.
Parameters
----------
feature : str or Feature instance
... | [
"def",
"children_bp",
"(",
"self",
",",
"feature",
",",
"child_featuretype",
"=",
"'exon'",
",",
"merge",
"=",
"False",
",",
"ignore_strand",
"=",
"False",
")",
":",
"children",
"=",
"self",
".",
"children",
"(",
"feature",
",",
"featuretype",
"=",
"child_... | Total bp of all children of a featuretype.
Useful for getting the exonic bp of an mRNA.
Parameters
----------
feature : str or Feature instance
child_featuretype : str
Which featuretype to consider. For example, to get exonic bp of an
mRNA, use `child... | [
"Total",
"bp",
"of",
"all",
"children",
"of",
"a",
"featuretype",
"."
] | train | https://github.com/daler/gffutils/blob/6f7f547cad898738a1bd0a999fd68ba68db2c524/gffutils/interface.py#L1114-L1152 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.