src
stringlengths 75
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| cfg
stringlengths 32
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| ast
stringlengths 78
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|---|---|---|
def findArgs(args, prefixes):
"""
Extracts the list of arguments that start with any of the specified prefix values
"""
return list([
arg for arg in args
if len([p for p in prefixes if arg.lower().startswith(p.lower())]) > 0
]) | [2][SEP1][Return][SEP2][][SEP3][5] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_EXPR_CONSTANT_RETURN_CALL_NAME_LOAD_LISTCOMP_NAME_LOAD_COMPREHENSION_NAME_STORE_NAME_LOAD_COMPARE_CALL_NAME_LOAD_LISTCOMP_NAME_LOAD_COMPREHENSION_NAME_STORE_NAME_LOAD_CALL_ATTRIBUTE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_GT_CONSTANT |
def buildDescriptor(self, dir=os.getcwd(), configuration='Development', args=[], suppressOutput=False):
"""
Builds the editor modules for the Unreal project or plugin in the specified directory, using the specified build configuration
"""
# Verify that an Unreal project or plugin exists in the specified directory
descriptor = self.getDescriptor(dir)
descriptorType = 'project' if self.isProject(descriptor) else 'plugin'
# If the project or plugin is Blueprint-only, there is no C++ code to build
if os.path.exists(os.path.join(dir, 'Source')) == False:
Utility.printStderr('Pure Blueprint {}, nothing to build.'.format(descriptorType))
return
# Verify that the specified build configuration is valid
if configuration not in self.validBuildConfigurations():
raise UnrealManagerException('invalid build configuration "' + configuration + '"')
# Generate the arguments to pass to UBT
target = self.getDescriptorName(descriptor) + 'Editor' if self.isProject(descriptor) else 'UE4Editor'
baseArgs = ['-{}='.format(descriptorType) + descriptor]
# Perform the build
self._runUnrealBuildTool(target, self.getPlatformIdentifier(), configuration, baseArgs + args, capture=suppressOutput) | [5][SEP1][If][Return][If][None][None][SEP2][1,2][][3,4][][][SEP3][4][2][1][1][5] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_ARG_ARG_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_LIST_LOAD_CONSTANT_EXPR_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_IFEXP_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_CONSTANT_CONSTANT_IF_COMPARE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_NAME_LOAD_CONSTANT_EQ_CONSTANT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CALL_ATTRIBUTE_CONSTANT_LOAD_NAME_LOAD_RETURN_IF_COMPARE_NAME_LOAD_NOTIN_CALL_ATTRIBUTE_NAME_LOAD_LOAD_RAISE_CALL_NAME_LOAD_BINOP_BINOP_CONSTANT_ADD_NAME_LOAD_ADD_CONSTANT_ASSIGN_NAME_STORE_IFEXP_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_BINOP_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_ADD_CONSTANT_CONSTANT_ASSIGN_NAME_STORE_LIST_BINOP_CALL_ATTRIBUTE_CONSTANT_LOAD_NAME_LOAD_ADD_NAME_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_BINOP_NAME_LOAD_ADD_NAME_LOAD_KEYWORD_NAME_LOAD |
def _getThirdPartyLibs(self, platformIdentifier, configuration):
"""
Runs UnrealBuildTool in JSON export mode and extracts the list of third-party libraries
"""
# If we have previously cached the library list for the current engine version, use the cached data
cachedList = CachedDataManager.getCachedDataKey(self.engineVersionHash, 'ThirdPartyLibraries')
if cachedList != None:
return cachedList
# Create a temp directory to hold the JSON file
tempDir = tempfile.mkdtemp()
jsonFile = os.path.join(tempDir, 'ubt_output.json')
# Installed Builds of the Engine only contain a small handful of third-party libraries, rather than the full set
# included in a source build of the Engine. However, if the ThirdParty directory from a source build is copied
# into an Installed Build and the `InstalledBuild.txt` sentinel file is temporarily renamed, we can get the best
# of both worlds and utilise the full set of third-party libraries. Enable this sentinel renaming behaviour only
# if you have copied the ThirdParty directory from a source build into your Installed Build, or else the UBT
# command will fail trying to rebuild UnrealHeaderTool.
sentinelFile = os.path.join(self.engineRoot, 'Engine', 'Build', 'InstalledBuild.txt')
sentinelBackup = sentinelFile + '.bak'
renameSentinel = os.path.exists(sentinelFile) and os.environ.get('UE4CLI_SENTINEL_RENAME', '0') == '1'
if renameSentinel == True:
shutil.move(sentinelFile, sentinelBackup)
# Invoke UnrealBuildTool in JSON export mode (make sure we specify gathering mode, since this is a prerequisite of JSON export)
# (Ensure we always perform sentinel file cleanup even when errors occur)
try:
args = ['-Mode=JsonExport', '-OutputFile=' +jsonFile ] if self.engineVersion['MinorVersion'] >= 22 else ['-gather', '-jsonexport=' + jsonFile, '-SkipBuild']
self.runUBTFunc('UE4Editor', platformIdentifier, configuration, args)
finally:
if renameSentinel == True:
shutil.move(sentinelBackup, sentinelFile)
# Parse the JSON output
result = json.loads(Utility.readFile(jsonFile))
# Extract the list of third-party library modules
# (Note that since UE4.21, modules no longer have a "Type" field, so we must
# rely on the "Directory" field filter below to identify third-party libraries)
modules = [result['Modules'][key] for key in result['Modules']]
# Filter out any modules from outside the Engine/Source/ThirdParty directory
thirdPartyRoot = os.path.join(self.engineRoot, 'Engine', 'Source', 'ThirdParty')
thirdparty = list([m for m in modules if thirdPartyRoot in m['Directory']])
# Remove the temp directory
try:
shutil.rmtree(tempDir)
except:
pass
# Cache the list of libraries for use by subsequent runs
CachedDataManager.setCachedDataKey(self.engineVersionHash, 'ThirdPartyLibraries', thirdparty)
return thirdparty | [3][SEP1][If][Return][If][None][Try][None][Try][None][None][Return][SEP2][1,2][][3,4][4][5][6][7,8][9][9][][SEP3][1][0][5][1][1][1][4][1][0][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_IF_COMPARE_NAME_LOAD_NOTEQ_CONSTANT_RETURN_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_NAME_LOAD_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CONSTANT_CONSTANT_ASSIGN_NAME_STORE_BINOP_NAME_LOAD_ADD_CONSTANT_ASSIGN_NAME_STORE_BOOLOP_AND_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_NAME_LOAD_COMPARE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CONSTANT_CONSTANT_EQ_CONSTANT_IF_COMPARE_NAME_LOAD_EQ_CONSTANT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_NAME_LOAD_TRY_ASSIGN_NAME_STORE_IFEXP_COMPARE_SUBSCRIPT_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_LOAD_GTE_CONSTANT_LIST_CONSTANT_BINOP_CONSTANT_ADD_NAME_LOAD_LOAD_LIST_CONSTANT_BINOP_CONSTANT_ADD_NAME_LOAD_CONSTANT_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_NAME_LOAD_NAME_LOAD_NAME_LOAD_IF_COMPARE_NAME_LOAD_EQ_CONSTANT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_LISTCOMP_SUBSCRIPT_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_NAME_LOAD_LOAD_COMPREHENSION_NAME_STORE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CONSTANT_CONSTANT_ASSIGN_NAME_STORE_CALL_NAME_LOAD_LISTCOMP_NAME_LOAD_COMPREHENSION_NAME_STORE_NAME_LOAD_COMPARE_NAME_LOAD_IN_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_TRY_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_EXCEPTHANDLER_PASS_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_NAME_LOAD_RETURN_NAME_LOAD |
def set_command_attributes(self, name, attributes):
""" Sets the xml attributes of a specified command. """
if self.command_exists(name):
command = self.commands.get(name)
command['attributes'] = attributes | [3][SEP1][If][None][SEP2][1][][SEP3][1][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_EXPR_CONSTANT_IF_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_NAME_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_NAME_LOAD |
def start_scan(self, scan_id, targets, parallel=1):
""" Handle N parallel scans if 'parallel' is greater than 1. """
os.setsid()
multiscan_proc = []
logger.info("%s: Scan started.", scan_id)
target_list = targets
if target_list is None or not target_list:
raise OSPDError('Erroneous targets list', 'start_scan')
for index, target in enumerate(target_list):
while len(multiscan_proc) >= parallel:
progress = self.calculate_progress(scan_id)
self.set_scan_progress(scan_id, progress)
multiscan_proc = self.check_pending_target(scan_id,
multiscan_proc)
time.sleep(1)
#If the scan status is stopped, does not launch anymore target scans
if self.get_scan_status(scan_id) == ScanStatus.STOPPED:
return
logger.info("%s: Host scan started on ports %s.", target[0], target[1])
scan_process = multiprocessing.Process(target=self.parallel_scan,
args=(scan_id, target[0]))
multiscan_proc.append((scan_process, target[0]))
scan_process.start()
self.set_scan_status(scan_id, ScanStatus.RUNNING)
# Wait until all single target were scanned
while multiscan_proc:
multiscan_proc = self.check_pending_target(scan_id, multiscan_proc)
if multiscan_proc:
progress = self.calculate_progress(scan_id)
self.set_scan_progress(scan_id, progress)
time.sleep(1)
# Only set the scan as finished if the scan was not stopped.
if self.get_scan_status(scan_id) != ScanStatus.STOPPED:
self.finish_scan(scan_id) | [4][SEP1][If][None][For][While][While][None][If][If][If][Return][None][None][None][None][SEP2][1,2][][3,4][5,6][7,8][3][9,10][11,12][13][][2][12][4][][SEP3][2][1][7][1][1][4][1][1][1][0][5][2][1][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_ARG_CONSTANT_EXPR_CONSTANT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_LIST_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_NAME_LOAD_ASSIGN_NAME_STORE_NAME_LOAD_IF_BOOLOP_OR_COMPARE_NAME_LOAD_IS_CONSTANT_UNARYOP_NOT_NAME_LOAD_RAISE_CALL_NAME_LOAD_CONSTANT_CONSTANT_FOR_TUPLE_NAME_STORE_NAME_STORE_STORE_CALL_NAME_LOAD_NAME_LOAD_WHILE_COMPARE_CALL_NAME_LOAD_NAME_LOAD_GTE_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_IF_COMPARE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_EQ_ATTRIBUTE_NAME_LOAD_LOAD_RETURN_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_KEYWORD_ATTRIBUTE_NAME_LOAD_LOAD_KEYWORD_TUPLE_NAME_LOAD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_TUPLE_NAME_LOAD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_WHILE_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_NAME_LOAD_IF_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_IF_COMPARE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_NOTEQ_ATTRIBUTE_NAME_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD |
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)
return self.scan_collection.create_scan(scan_id, targets, options, vts) | [5][SEP1][If][None][Return][SEP2][1,2][2][][SEP3][1][1][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_ARG_ARG_EXPR_CONSTANT_IF_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_NAME_LOAD_RETURN_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_NAME_LOAD_NAME_LOAD_NAME_LOAD_NAME_LOAD |
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:
new_list = target_to_ipv4_cidr(target)
# Is it an IPv6 CIDR ?
if not new_list:
new_list = target_to_ipv6_cidr(target)
# Is it an IPv4 short-range ?
if not new_list:
new_list = target_to_ipv4_short(target)
# Is it an IPv4 long-range ?
if not new_list:
new_list = target_to_ipv4_long(target)
# Is it an IPv6 short-range ?
if not new_list:
new_list = target_to_ipv6_short(target)
# Is it an IPv6 long-range ?
if not new_list:
new_list = target_to_ipv6_long(target)
# Is it a hostname ?
if not new_list:
new_list = target_to_hostname(target)
return new_list | [1][SEP1][If][None][If][None][If][None][If][None][If][None][If][None][If][None][If][None][Return][SEP2][1,2][2][3,4][4][5,6][6][7,8][8][9,10][10][11,12][12][13,14][14][15,16][16][][SEP3][1][1][0][1][0][1][0][1][0][1][0][1][0][1][0][1][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_IF_UNARYOP_NOT_NAME_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_IF_UNARYOP_NOT_NAME_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_IF_UNARYOP_NOT_NAME_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_IF_UNARYOP_NOT_NAME_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_IF_UNARYOP_NOT_NAME_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_IF_UNARYOP_NOT_NAME_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_IF_UNARYOP_NOT_NAME_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_IF_UNARYOP_NOT_NAME_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_RETURN_NAME_LOAD |
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
# scan must be deleted from the scans_table.
if scan_id and self.id_exists(scan_id) and (
self.get_status(scan_id) == ScanStatus.STOPPED):
return self.resume_scan(scan_id, options)
if not options:
options = dict()
scan_info = self.data_manager.dict()
scan_info['results'] = list()
scan_info['finished_hosts'] = dict(
[[target, []] for target, _, _ in targets])
scan_info['progress'] = 0
scan_info['target_progress'] = dict(
[[target, {}] for target, _, _ in targets])
scan_info['targets'] = targets
scan_info['vts'] = vts
scan_info['options'] = options
scan_info['start_time'] = int(time.time())
scan_info['end_time'] = "0"
scan_info['status'] = ScanStatus.INIT
if scan_id is None or scan_id == '':
scan_id = str(uuid.uuid4())
scan_info['scan_id'] = scan_id
self.scans_table[scan_id] = scan_info
return scan_id | [5][SEP1][If][None][If][Return][If][None][If][None][Return][SEP2][1,2][2][3,4][][5,6][6][7,8][8][][SEP3][0][1][2][1][0][1][6][2][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_ARG_ARG_CONSTANT_CONSTANT_CONSTANT_CONSTANT_EXPR_CONSTANT_IF_COMPARE_ATTRIBUTE_NAME_LOAD_LOAD_IS_CONSTANT_ASSIGN_ATTRIBUTE_NAME_LOAD_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_IF_BOOLOP_AND_NAME_LOAD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_COMPARE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_EQ_ATTRIBUTE_NAME_LOAD_LOAD_RETURN_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_NAME_LOAD_IF_UNARYOP_NOT_NAME_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_CALL_NAME_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_CALL_NAME_LOAD_LISTCOMP_LIST_NAME_LOAD_LIST_LOAD_LOAD_COMPREHENSION_TUPLE_NAME_STORE_NAME_STORE_NAME_STORE_STORE_NAME_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_CONSTANT_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_CALL_NAME_LOAD_LISTCOMP_LIST_NAME_LOAD_DICT_LOAD_COMPREHENSION_TUPLE_NAME_STORE_NAME_STORE_NAME_STORE_STORE_NAME_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_NAME_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_NAME_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_NAME_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_CALL_NAME_LOAD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_CONSTANT_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_ATTRIBUTE_NAME_LOAD_LOAD_IF_BOOLOP_OR_COMPARE_NAME_LOAD_IS_CONSTANT_COMPARE_NAME_LOAD_EQ_CONSTANT_ASSIGN_NAME_STORE_CALL_NAME_LOAD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_NAME_LOAD_ASSIGN_SUBSCRIPT_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_STORE_NAME_LOAD_RETURN_NAME_LOAD |
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
# Exons of mRNA, sorted by start position (ascending)
exon_1
# Children of exon, sorted by start position
exon_child_1
exon_child_2
exon_2
...
# Non-exonic children here
...
mRNA_2
...
# Non-mRNA children here
...
Output records of a gene to a file, given a GFF database
and a gene_id. Outputs records in canonical order: gene record
first, then longest mRNA, followed by longest mRNA exons,
followed by rest, followed by next longest mRNA, and so on.
Includes the gene record itself in the output.
TODO: This probably doesn't handle deep GFF hierarchies.
"""
gene_rec = db[gene_id]
# Output gene record
self.write_rec(gene_rec)
# Get each mRNA's lengths
mRNA_lens = {}
c = list(db.children(gene_id, featuretype="mRNA"))
for mRNA in db.children(gene_id, featuretype="mRNA"):
mRNA_lens[mRNA.id] = \
sum(len(exon) for exon in db.children(mRNA,
featuretype="exon"))
# Sort mRNAs by length
sorted_mRNAs = \
sorted(mRNA_lens.items(), key=lambda x: x[1], reverse=True)
for curr_mRNA in sorted_mRNAs:
mRNA_id = curr_mRNA[0]
mRNA_rec = db[mRNA_id]
# Write mRNA record to file
self.write_rec(mRNA_rec)
# Write mRNA's children records to file
self.write_mRNA_children(db, mRNA_id)
# Write non-mRNA children of gene (only level1)
for gene_child in db.children(gene_id, level=1):
if gene_child.featuretype != "mRNA":
self.write_rec(gene_child) | [3][SEP1][None][For][None][None][For][None][For][If][None][SEP2][1][2,3][1][4][5,6][4][7][8,6][6][SEP3][3][1][3][2][0][2][1][0][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_SUBSCRIPT_NAME_LOAD_NAME_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_DICT_ASSIGN_NAME_STORE_CALL_NAME_LOAD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_KEYWORD_CONSTANT_FOR_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_KEYWORD_CONSTANT_ASSIGN_SUBSCRIPT_NAME_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_STORE_CALL_NAME_LOAD_GENERATOREXP_CALL_NAME_LOAD_NAME_LOAD_COMPREHENSION_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_KEYWORD_CONSTANT_ASSIGN_NAME_STORE_CALL_NAME_LOAD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_KEYWORD_LAMBDA_ARGUMENTS_ARG_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_KEYWORD_CONSTANT_FOR_NAME_STORE_NAME_LOAD_ASSIGN_NAME_STORE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_ASSIGN_NAME_STORE_SUBSCRIPT_NAME_LOAD_NAME_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_NAME_LOAD_FOR_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_KEYWORD_CONSTANT_IF_COMPARE_ATTRIBUTE_NAME_LOAD_LOAD_NOTEQ_CONSTANT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD |
def sequence(self, fasta, use_strand=True):
"""
Retrieves the sequence of this feature as a string.
Uses the pyfaidx package.
Parameters
----------
fasta : str
If str, then it's a FASTA-format filename; otherwise assume it's
a pyfaidx.Fasta object.
use_strand : bool
If True (default), the sequence returned will be
reverse-complemented for minus-strand features.
Returns
-------
string
"""
if isinstance(fasta, six.string_types):
fasta = Fasta(fasta, as_raw=False)
# recall GTF/GFF is 1-based closed; pyfaidx uses Python slice notation
# and is therefore 0-based half-open.
seq = fasta[self.chrom][self.start-1:self.stop]
if use_strand and self.strand == '-':
seq = seq.reverse.complement
return seq.seq | [3][SEP1][If][None][If][None][Return][SEP2][1,2][2][3,4][4][][SEP3][1][1][0][0][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_CONSTANT_EXPR_CONSTANT_IF_CALL_NAME_LOAD_NAME_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_KEYWORD_CONSTANT_ASSIGN_NAME_STORE_SUBSCRIPT_SUBSCRIPT_NAME_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_SLICE_BINOP_ATTRIBUTE_NAME_LOAD_LOAD_SUB_CONSTANT_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_IF_BOOLOP_AND_NAME_LOAD_COMPARE_ATTRIBUTE_NAME_LOAD_LOAD_EQ_CONSTANT_ASSIGN_NAME_STORE_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_RETURN_ATTRIBUTE_NAME_LOAD_LOAD |
def _replace(self, feature, cursor):
"""
Insert a feature into the database.
"""
try:
cursor.execute(
constants._UPDATE,
list(feature.astuple()) + [feature.id])
except sqlite3.ProgrammingError:
cursor.execute(
constants._INSERT,
list(feature.astuple(self.default_encoding)) + [feature.id]) | [3][SEP1][Try][None][None][SEP2][1,2][][][SEP3][0][3][3] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_EXPR_CONSTANT_TRY_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_BINOP_CALL_NAME_LOAD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ADD_LIST_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_EXCEPTHANDLER_ATTRIBUTE_NAME_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_BINOP_CALL_NAME_LOAD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_ADD_LIST_ATTRIBUTE_NAME_LOAD_LOAD_LOAD |
def _proxy_kwargs(browser_name, proxy, browser_kwargs={}): # pylint: disable=dangerous-default-value
"""
Determines the kwargs needed to set up a proxy based on the
browser type.
Returns: a dictionary of arguments needed to pass when
instantiating the WebDriver instance.
"""
proxy_dict = {
"httpProxy": proxy.proxy,
"proxyType": 'manual',
}
if browser_name == 'firefox' and 'desired_capabilities' not in browser_kwargs:
# This one works for firefox locally
wd_proxy = webdriver.common.proxy.Proxy(proxy_dict)
browser_kwargs['proxy'] = wd_proxy
else:
# This one works with chrome, both locally and remote
# This one works with firefox remote, but not locally
if 'desired_capabilities' not in browser_kwargs:
browser_kwargs['desired_capabilities'] = {}
browser_kwargs['desired_capabilities']['proxy'] = proxy_dict
return browser_kwargs | [3][SEP1][If][None][If][Return][None][None][SEP2][1,2][3][4,5][][5][3][SEP3][0][1][0][0][0][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_DICT_EXPR_CONSTANT_ASSIGN_NAME_STORE_DICT_CONSTANT_CONSTANT_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_IF_BOOLOP_AND_COMPARE_NAME_LOAD_EQ_CONSTANT_COMPARE_CONSTANT_NOTIN_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_LOAD_NAME_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_NAME_LOAD_IF_COMPARE_CONSTANT_NOTIN_NAME_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_DICT_ASSIGN_SUBSCRIPT_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_CONSTANT_STORE_NAME_LOAD_RETURN_NAME_LOAD |
def _parse_options(self, options):
"""Copy needed options to self"""
attributes = ('host', 'wapi_version', 'username', 'password',
'ssl_verify', 'http_request_timeout', 'max_retries',
'http_pool_connections', 'http_pool_maxsize',
'silent_ssl_warnings', 'log_api_calls_as_info',
'max_results', 'paging')
for attr in attributes:
if isinstance(options, dict) and attr in options:
setattr(self, attr, options[attr])
elif hasattr(options, attr):
value = getattr(options, attr)
setattr(self, attr, value)
elif attr in self.DEFAULT_OPTIONS:
setattr(self, attr, self.DEFAULT_OPTIONS[attr])
else:
msg = "WAPI config error. Option %s is not defined" % attr
raise ib_ex.InfobloxConfigException(msg=msg)
for attr in ('host', 'username', 'password'):
if not getattr(self, attr):
msg = "WAPI config error. Option %s can not be blank" % attr
raise ib_ex.InfobloxConfigException(msg=msg)
self.wapi_url = "https://%s/wapi/v%s/" % (self.host,
self.wapi_version)
self.cloud_api_enabled = self.is_cloud_wapi(self.wapi_version) | [2][SEP1][None][For][If][For][None][If][If][None][None][If][None][None][None][SEP2][1][2,3][4,5][6,7][1][8,9][10,3][][1][11,12][][1][][SEP3][0][0][1][0][1][1][1][1][2][0][1][1][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_TUPLE_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_LOAD_FOR_NAME_STORE_NAME_LOAD_IF_BOOLOP_AND_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_COMPARE_NAME_LOAD_IN_NAME_LOAD_EXPR_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_SUBSCRIPT_NAME_LOAD_NAME_LOAD_LOAD_IF_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_EXPR_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_NAME_LOAD_IF_COMPARE_NAME_LOAD_IN_ATTRIBUTE_NAME_LOAD_LOAD_EXPR_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_SUBSCRIPT_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_BINOP_CONSTANT_MOD_NAME_LOAD_RAISE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_KEYWORD_NAME_LOAD_FOR_NAME_STORE_TUPLE_CONSTANT_CONSTANT_CONSTANT_LOAD_IF_UNARYOP_NOT_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_BINOP_CONSTANT_MOD_NAME_LOAD_RAISE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_KEYWORD_NAME_LOAD_ASSIGN_ATTRIBUTE_NAME_LOAD_STORE_BINOP_CONSTANT_MOD_TUPLE_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_ASSIGN_ATTRIBUTE_NAME_LOAD_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD |
def _sincedb_update_position(self, lines=0, force_update=False):
"""Retrieves the starting position from the sincedb sql db for a given file
Returns a boolean representing whether or not it updated the record
"""
if not self._sincedb_path:
return False
self._line_count = self._line_count + lines
old_count = self._line_count_sincedb
lines = self._line_count
current_time = int(time.time())
if not force_update:
if self._last_sincedb_write and current_time - self._last_sincedb_write <= self._sincedb_write_interval:
return False
if old_count == lines:
return False
self._sincedb_init()
self._last_sincedb_write = current_time
self._log_debug('updating sincedb to {0}'.format(lines))
conn = sqlite3.connect(self._sincedb_path, isolation_level=None)
cursor = conn.cursor()
query = 'insert or replace into sincedb (fid, filename) values (:fid, :filename);'
cursor.execute(query, {
'fid': self._fid,
'filename': self._filename
})
query = 'update sincedb set position = :position where fid = :fid and filename = :filename'
cursor.execute(query, {
'fid': self._fid,
'filename': self._filename,
'position': lines,
})
conn.close()
self._line_count_sincedb = lines
return True | [3][SEP1][If][Return][If][If][Return][Return][If][Return][SEP2][1,2][][3,4][5,6][][][7,4][][SEP3][0][0][2][0][8][0][0][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_CONSTANT_CONSTANT_EXPR_CONSTANT_IF_UNARYOP_NOT_ATTRIBUTE_NAME_LOAD_LOAD_RETURN_CONSTANT_ASSIGN_ATTRIBUTE_NAME_LOAD_STORE_BINOP_ATTRIBUTE_NAME_LOAD_LOAD_ADD_NAME_LOAD_ASSIGN_NAME_STORE_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_IF_UNARYOP_NOT_NAME_LOAD_IF_BOOLOP_AND_ATTRIBUTE_NAME_LOAD_LOAD_COMPARE_BINOP_NAME_LOAD_SUB_ATTRIBUTE_NAME_LOAD_LOAD_LTE_ATTRIBUTE_NAME_LOAD_LOAD_RETURN_CONSTANT_IF_COMPARE_NAME_LOAD_EQ_NAME_LOAD_RETURN_CONSTANT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_ATTRIBUTE_NAME_LOAD_STORE_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CALL_ATTRIBUTE_CONSTANT_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_KEYWORD_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_CONSTANT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_DICT_CONSTANT_CONSTANT_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_CONSTANT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_DICT_CONSTANT_CONSTANT_CONSTANT_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_ATTRIBUTE_NAME_LOAD_STORE_NAME_LOAD_RETURN_CONSTANT |
def read(file_path):
""" Read a gmt file at the path specified by file_path.
Args:
file_path (string): path to gmt file
Returns:
gmt (GMT object): list of dicts, where each dict corresponds to one
line of the GMT file
"""
# Read in file
actual_file_path = os.path.expanduser(file_path)
with open(actual_file_path, 'r') as f:
lines = f.readlines()
# Create GMT object
gmt = []
# Iterate over each line
for line_num, line in enumerate(lines):
# Separate along tabs
fields = line.split('\t')
assert len(fields) > 2, (
"Each line must have at least 3 tab-delimited items. " +
"line_num: {}, fields: {}").format(line_num, fields)
# Get rid of trailing whitespace
fields[-1] = fields[-1].rstrip()
# Collect entries
entries = fields[2:]
# Remove empty entries
entries = [x for x in entries if x]
assert len(set(entries)) == len(entries), (
"There should not be duplicate entries for the same set. " +
"line_num: {}, entries: {}").format(line_num, entries)
# Store this line as a dictionary
line_dict = {SET_IDENTIFIER_FIELD: fields[0],
SET_DESC_FIELD: fields[1],
SET_MEMBERS_FIELD: entries}
gmt.append(line_dict)
verify_gmt_integrity(gmt)
return gmt | [1][SEP1][None][None][None][For][None][Return][None][None][SEP2][1][2][3][4,5][6][][7][3][SEP3][2][1][0][7][3][1][5][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_NAME_LOAD_WITH_WITHITEM_CALL_NAME_LOAD_NAME_LOAD_CONSTANT_NAME_STORE_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_LIST_LOAD_FOR_TUPLE_NAME_STORE_NAME_STORE_STORE_CALL_NAME_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_ASSERT_COMPARE_CALL_NAME_LOAD_NAME_LOAD_GT_CONSTANT_CALL_ATTRIBUTE_BINOP_CONSTANT_ADD_CONSTANT_LOAD_NAME_LOAD_NAME_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_UNARYOP_USUB_CONSTANT_STORE_CALL_ATTRIBUTE_SUBSCRIPT_NAME_LOAD_UNARYOP_USUB_CONSTANT_LOAD_LOAD_ASSIGN_NAME_STORE_SUBSCRIPT_NAME_LOAD_SLICE_CONSTANT_LOAD_ASSIGN_NAME_STORE_LISTCOMP_NAME_LOAD_COMPREHENSION_NAME_STORE_NAME_LOAD_NAME_LOAD_ASSERT_COMPARE_CALL_NAME_LOAD_CALL_NAME_LOAD_NAME_LOAD_EQ_CALL_NAME_LOAD_NAME_LOAD_CALL_ATTRIBUTE_BINOP_CONSTANT_ADD_CONSTANT_LOAD_NAME_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_DICT_NAME_LOAD_NAME_LOAD_NAME_LOAD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_EXPR_CALL_NAME_LOAD_NAME_LOAD_RETURN_NAME_LOAD |
def write_version_and_dims(version, dims, f):
"""Write first two lines of gct file.
Args:
version (string): 1.3 by default
dims (list of strings): length = 4
f (file handle): handle of output file
Returns:
nothing
"""
f.write(("#" + version + "\n"))
f.write((dims[0] + "\t" + dims[1] + "\t" + dims[2] + "\t" + dims[3] + "\n")) | [3][SEP1][None][SEP2][][SEP3][2] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_EXPR_CONSTANT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_BINOP_BINOP_CONSTANT_ADD_NAME_LOAD_ADD_CONSTANT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_BINOP_BINOP_BINOP_BINOP_BINOP_BINOP_BINOP_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_ADD_CONSTANT_ADD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_ADD_CONSTANT_ADD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_ADD_CONSTANT_ADD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_ADD_CONSTANT |
def read(in_path):
""" Read a grp file at the path specified by in_path.
Args:
in_path (string): path to GRP file
Returns:
grp (list)
"""
assert os.path.exists(in_path), "The following GRP file can't be found. in_path: {}".format(in_path)
with open(in_path, "r") as f:
lines = f.readlines()
# need the second conditional to ignore comment lines
grp = [line.strip() for line in lines if line and not re.match("^#", line)]
return grp | [1][SEP1][None][None][None][Return][SEP2][1][2][3][][SEP3][2][1][3][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_ASSERT_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_NAME_LOAD_CALL_ATTRIBUTE_CONSTANT_LOAD_NAME_LOAD_WITH_WITHITEM_CALL_NAME_LOAD_NAME_LOAD_CONSTANT_NAME_STORE_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_LISTCOMP_CALL_ATTRIBUTE_NAME_LOAD_LOAD_COMPREHENSION_NAME_STORE_NAME_LOAD_BOOLOP_AND_NAME_LOAD_UNARYOP_NOT_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_NAME_LOAD_RETURN_NAME_LOAD |
def timesince(when):
"""Returns string representing "time since" or "time until".
Examples:
3 days ago, 5 hours ago, 3 minutes from now, 5 hours from now, now.
"""
if not when:
return ''
now = datetime.datetime.utcnow()
if now > when:
diff = now - when
suffix = 'ago'
else:
diff = when - now
suffix = 'from now'
periods = (
(diff.days / 365, 'year', 'years'),
(diff.days / 30, 'month', 'months'),
(diff.days / 7, 'week', 'weeks'),
(diff.days, 'day', 'days'),
(diff.seconds / 3600, 'hour', 'hours'),
(diff.seconds / 60, 'minute', 'minutes'),
(diff.seconds, 'second', 'seconds'),
)
for period, singular, plural in periods:
if period:
return '%d %s %s' % (
period,
singular if period == 1 else plural,
suffix)
return 'now' | [1][SEP1][If][Return][If][None][None][None][For][If][Return][Return][SEP2][1,2][][3,4][5][5][6][7,8][9,6][][][SEP3][0][0][1][0][0][0][0][0][0][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_IF_UNARYOP_NOT_NAME_LOAD_RETURN_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_IF_COMPARE_NAME_LOAD_GT_NAME_LOAD_ASSIGN_NAME_STORE_BINOP_NAME_LOAD_SUB_NAME_LOAD_ASSIGN_NAME_STORE_CONSTANT_ASSIGN_NAME_STORE_BINOP_NAME_LOAD_SUB_NAME_LOAD_ASSIGN_NAME_STORE_CONSTANT_ASSIGN_NAME_STORE_TUPLE_TUPLE_BINOP_ATTRIBUTE_NAME_LOAD_LOAD_DIV_CONSTANT_CONSTANT_CONSTANT_LOAD_TUPLE_BINOP_ATTRIBUTE_NAME_LOAD_LOAD_DIV_CONSTANT_CONSTANT_CONSTANT_LOAD_TUPLE_BINOP_ATTRIBUTE_NAME_LOAD_LOAD_DIV_CONSTANT_CONSTANT_CONSTANT_LOAD_TUPLE_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CONSTANT_LOAD_TUPLE_BINOP_ATTRIBUTE_NAME_LOAD_LOAD_DIV_CONSTANT_CONSTANT_CONSTANT_LOAD_TUPLE_BINOP_ATTRIBUTE_NAME_LOAD_LOAD_DIV_CONSTANT_CONSTANT_CONSTANT_LOAD_TUPLE_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CONSTANT_LOAD_LOAD_FOR_TUPLE_NAME_STORE_NAME_STORE_NAME_STORE_STORE_NAME_LOAD_IF_NAME_LOAD_RETURN_BINOP_CONSTANT_MOD_TUPLE_NAME_LOAD_IFEXP_COMPARE_NAME_LOAD_EQ_CONSTANT_NAME_LOAD_NAME_LOAD_NAME_LOAD_LOAD_RETURN_CONSTANT |
def _get_artifact_context(run, file_type):
"""Gets the artifact details for the given run and file_type."""
sha1sum = None
image_file = False
log_file = False
config_file = False
if request.path == '/image':
image_file = True
if file_type == 'before':
sha1sum = run.ref_image
elif file_type == 'diff':
sha1sum = run.diff_image
elif file_type == 'after':
sha1sum = run.image
else:
abort(400)
elif request.path == '/log':
log_file = True
if file_type == 'before':
sha1sum = run.ref_log
elif file_type == 'diff':
sha1sum = run.diff_log
elif file_type == 'after':
sha1sum = run.log
else:
abort(400)
elif request.path == '/config':
config_file = True
if file_type == 'before':
sha1sum = run.ref_config
elif file_type == 'after':
sha1sum = run.config
else:
abort(400)
return image_file, log_file, config_file, sha1sum | [2][SEP1][If][If][If][None][If][If][If][Return][None][If][None][If][If][None][None][None][If][None][If][None][None][None][None][SEP2][1,2][3,4][5,6][7][8,9][10,11][12,7][][7][13,14][7][15,16][17,18][7][7][7][19,20][7][21,22][7][7][7][7][SEP3][0][0][0][0][0][0][0][0][0][0][0][0][0][0][1][0][0][0][0][0][1][0][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_CONSTANT_ASSIGN_NAME_STORE_CONSTANT_ASSIGN_NAME_STORE_CONSTANT_ASSIGN_NAME_STORE_CONSTANT_IF_COMPARE_ATTRIBUTE_NAME_LOAD_LOAD_EQ_CONSTANT_ASSIGN_NAME_STORE_CONSTANT_IF_COMPARE_NAME_LOAD_EQ_CONSTANT_ASSIGN_NAME_STORE_ATTRIBUTE_NAME_LOAD_LOAD_IF_COMPARE_NAME_LOAD_EQ_CONSTANT_ASSIGN_NAME_STORE_ATTRIBUTE_NAME_LOAD_LOAD_IF_COMPARE_NAME_LOAD_EQ_CONSTANT_ASSIGN_NAME_STORE_ATTRIBUTE_NAME_LOAD_LOAD_EXPR_CALL_NAME_LOAD_CONSTANT_IF_COMPARE_ATTRIBUTE_NAME_LOAD_LOAD_EQ_CONSTANT_ASSIGN_NAME_STORE_CONSTANT_IF_COMPARE_NAME_LOAD_EQ_CONSTANT_ASSIGN_NAME_STORE_ATTRIBUTE_NAME_LOAD_LOAD_IF_COMPARE_NAME_LOAD_EQ_CONSTANT_ASSIGN_NAME_STORE_ATTRIBUTE_NAME_LOAD_LOAD_IF_COMPARE_NAME_LOAD_EQ_CONSTANT_ASSIGN_NAME_STORE_ATTRIBUTE_NAME_LOAD_LOAD_EXPR_CALL_NAME_LOAD_CONSTANT_IF_COMPARE_ATTRIBUTE_NAME_LOAD_LOAD_EQ_CONSTANT_ASSIGN_NAME_STORE_CONSTANT_IF_COMPARE_NAME_LOAD_EQ_CONSTANT_ASSIGN_NAME_STORE_ATTRIBUTE_NAME_LOAD_LOAD_IF_COMPARE_NAME_LOAD_EQ_CONSTANT_ASSIGN_NAME_STORE_ATTRIBUTE_NAME_LOAD_LOAD_EXPR_CALL_NAME_LOAD_CONSTANT_RETURN_TUPLE_NAME_LOAD_NAME_LOAD_NAME_LOAD_NAME_LOAD_LOAD |
def verify_binary(flag_name, process_args=None):
"""Exits the program if the binary from the given flag doesn't run.
Args:
flag_name: Name of the flag that should be the path to the binary.
process_args: Args to pass to the binary to do nothing but verify
that it's working correctly (something like "--version") is good.
Optional. Defaults to no args.
Raises:
SystemExit with error if the process did not work.
"""
if process_args is None:
process_args = []
path = getattr(FLAGS, flag_name)
if not path:
logging.error('Flag %r not set' % flag_name)
sys.exit(1)
with open(os.devnull, 'w') as dev_null:
try:
subprocess.check_call(
[path] + process_args,
stdout=dev_null,
stderr=subprocess.STDOUT)
except:
logging.exception('--%s binary at path %r does not work',
flag_name, path)
sys.exit(1) | [2][SEP1][If][None][If][None][None][Try][None][None][SEP2][1,2][2][3,4][4][5][6,7][][][SEP3][0][0][1][2][1][0][1][2] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_CONSTANT_EXPR_CONSTANT_IF_COMPARE_NAME_LOAD_IS_CONSTANT_ASSIGN_NAME_STORE_LIST_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_IF_UNARYOP_NOT_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_BINOP_CONSTANT_MOD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_WITH_WITHITEM_CALL_NAME_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_NAME_STORE_TRY_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_BINOP_LIST_NAME_LOAD_LOAD_ADD_NAME_LOAD_KEYWORD_NAME_LOAD_KEYWORD_ATTRIBUTE_NAME_LOAD_LOAD_EXCEPTHANDLER_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_NAME_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT |
def list(self, detail=False):
"""
A generator that yields information about each file in the upload area
:param detail: return detailed file information (slower)
:return: a list of dicts containing at least 'name', or more of detail was requested
"""
creds_provider = CredentialsManager(upload_area=self)
s3agent = S3Agent(credentials_provider=creds_provider)
key_prefix = self.uuid + "/"
key_prefix_length = len(key_prefix)
for page in s3agent.list_bucket_by_page(bucket_name=self.uri.bucket_name, key_prefix=key_prefix):
file_list = [key[key_prefix_length:] for key in page] # cut off upload-area-id/
if detail:
files_info = self.upload_service.api_client.files_info(self.uuid, file_list)
else:
files_info = [{'name': filename} for filename in file_list]
for file_info in files_info:
yield file_info | [2][SEP1][None][For][If][None][None][For][None][SEP2][1][2][3,4][5][5][6,1][5][SEP3][3][1][0][1][0][0][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_CONSTANT_EXPR_CONSTANT_ASSIGN_NAME_STORE_CALL_NAME_LOAD_KEYWORD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_KEYWORD_NAME_LOAD_ASSIGN_NAME_STORE_BINOP_ATTRIBUTE_NAME_LOAD_LOAD_ADD_CONSTANT_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_FOR_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_KEYWORD_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_KEYWORD_NAME_LOAD_ASSIGN_NAME_STORE_LISTCOMP_SUBSCRIPT_NAME_LOAD_SLICE_NAME_LOAD_LOAD_COMPREHENSION_NAME_STORE_NAME_LOAD_IF_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_LISTCOMP_DICT_CONSTANT_NAME_LOAD_COMPREHENSION_NAME_STORE_NAME_LOAD_FOR_NAME_STORE_NAME_LOAD_EXPR_YIELD_NAME_LOAD |
def select_area(self, area_uuid):
"""
Update the "current area" to be the area with this UUID.
:param str area_uuid: The RFC4122-compliant UUID of the Upload Area.
"""
self._config.upload.current_area = area_uuid
self.save() | [2][SEP1][None][SEP2][][SEP3][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_EXPR_CONSTANT_ASSIGN_ATTRIBUTE_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_STORE_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD |
def safe_read_file(file_path: Path) -> str:
"""Read a text file. Several text encodings are tried until
the file content is correctly decoded.
:raise GuesslangError: when the file encoding is not supported
:param file_path: path to the input file
:return: text file content
"""
for encoding in FILE_ENCODINGS:
try:
return file_path.read_text(encoding=encoding)
except UnicodeError:
pass # Ignore encoding error
raise GuesslangError('Encoding not supported for {!s}'.format(file_path)) | [1][SEP1][None][For][Try][None][Return][None][SEP2][1][2,3][4,5][][][1][SEP3][0][0][0][2][1][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_NAME_LOAD_EXPR_CONSTANT_FOR_NAME_STORE_NAME_LOAD_TRY_RETURN_CALL_ATTRIBUTE_NAME_LOAD_LOAD_KEYWORD_NAME_LOAD_EXCEPTHANDLER_NAME_LOAD_PASS_RAISE_CALL_NAME_LOAD_CALL_ATTRIBUTE_CONSTANT_LOAD_NAME_LOAD_NAME_LOAD |
def make_relative(cls, course_locator, block_type, block_id):
"""
Return a new instance which has the given block_id in the given course
:param course_locator: may be a BlockUsageLocator in the same snapshot
"""
if hasattr(course_locator, 'course_key'):
course_locator = course_locator.course_key
return course_locator.make_usage_key(
block_type=block_type,
block_id=block_id
) | [4][SEP1][If][None][Return][SEP2][1,2][2][][SEP3][1][0][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_ARG_EXPR_CONSTANT_IF_CALL_NAME_LOAD_NAME_LOAD_CONSTANT_ASSIGN_NAME_STORE_ATTRIBUTE_NAME_LOAD_LOAD_RETURN_CALL_ATTRIBUTE_NAME_LOAD_LOAD_KEYWORD_NAME_LOAD_KEYWORD_NAME_LOAD |
def _clean(cls, value, invalid):
"""Deprecated. See BlockUsageLocator._clean"""
cls._deprecation_warning()
return BlockUsageLocator._clean(value, invalid) | [3][SEP1][Return][SEP2][][SEP3][2] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_EXPR_CONSTANT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_RETURN_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_NAME_LOAD |
def is_mutating(status):
"""Determines if the statement is mutating based on the status."""
if not status:
return False
mutating = set(['insert', 'update', 'delete', 'alter', 'create', 'drop',
'replace', 'truncate', 'load'])
return status.split(None, 1)[0].lower() in mutating | [1][SEP1][If][Return][Return][SEP2][1,2][][][SEP3][0][0][3] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_IF_UNARYOP_NOT_NAME_LOAD_RETURN_CONSTANT_ASSIGN_NAME_STORE_CALL_NAME_LOAD_LIST_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_LOAD_RETURN_COMPARE_CALL_ATTRIBUTE_SUBSCRIPT_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CONSTANT_CONSTANT_LOAD_LOAD_IN_NAME_LOAD |
def _get_vi_mode(cli):
"""Get the current vi mode for display."""
return {
InputMode.INSERT: 'I',
InputMode.NAVIGATION: 'N',
InputMode.REPLACE: 'R',
InputMode.INSERT_MULTIPLE: 'M'
}[cli.vi_state.input_mode] | [1][SEP1][Return][SEP2][][SEP3][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_RETURN_SUBSCRIPT_DICT_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CONSTANT_CONSTANT_CONSTANT_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_LOAD |
def _find_relevant_nodes(query_nodes, relevance_network, relevance_node_lim):
"""Return a list of nodes that are relevant for the query.
Parameters
----------
query_nodes : list[str]
A list of node names to query for.
relevance_network : str
The UUID of the NDEx network to query relevance in.
relevance_node_lim : int
The number of top relevant nodes to return.
Returns
-------
nodes : list[str]
A list of node names that are relevant for the query.
"""
all_nodes = relevance_client.get_relevant_nodes(relevance_network,
query_nodes)
nodes = [n[0] for n in all_nodes[:relevance_node_lim]]
return nodes | [3][SEP1][Return][SEP2][][SEP3][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_LISTCOMP_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_COMPREHENSION_NAME_STORE_SUBSCRIPT_NAME_LOAD_SLICE_NAME_LOAD_LOAD_RETURN_NAME_LOAD |
def extract_statements(self):
"""Extracts INDRA statements from the RDF graph via SPARQL queries.
"""
# Look for events that have an AGENT and an AFFECTED, and get the
# start and ending text indices for each.
query = prefixes + """
SELECT
?agent_start
?agent_end
?affected_start
?affected_end
WHERE {
?rel role:AGENT ?agent .
?rel role:AFFECTED ?affected .
?agent lf:start ?agent_start .
?agent lf:end ?agent_end .
?affected lf:start ?affected_start .
?affected lf:end ?affected_end .
}
"""
results = self.graph.query(query)
for res in results:
# Make a statement for each query match
self.extract_statement_from_query_result(res)
# Look for events that have an AGENT and a RESULT, and get the start
# and ending text indices for each.
query = query.replace('role:AFFECTED', 'role:RESULT')
results = self.graph.query(query)
for res in results:
# Make a statement for each query match
self.extract_statement_from_query_result(res) | [1][SEP1][None][For][None][None][For][None][SEP2][1][2,3][1][4][5][4][SEP3][1][0][1][2][0][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_BINOP_NAME_LOAD_ADD_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_NAME_LOAD_FOR_NAME_STORE_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_NAME_LOAD_FOR_NAME_STORE_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD |
def ungrounded_texts(stmts):
"""Return a list of all ungrounded entities ordered by number of mentions
Parameters
----------
stmts : list of :py:class:`indra.statements.Statement`
Returns
-------
ungroundc : list of tuple
list of tuples of the form (text: str, count: int) sorted in descending
order by count.
"""
ungrounded = [ag.db_refs['TEXT']
for s in stmts
for ag in s.agent_list()
if ag is not None and list(ag.db_refs.keys()) == ['TEXT']]
ungroundc = Counter(ungrounded)
ungroundc = ungroundc.items()
ungroundc = sorted(ungroundc, key=lambda x: x[1], reverse=True)
return ungroundc | [1][SEP1][Return][SEP2][][SEP3][6] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_LISTCOMP_SUBSCRIPT_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_LOAD_COMPREHENSION_NAME_STORE_NAME_LOAD_COMPREHENSION_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_BOOLOP_AND_COMPARE_NAME_LOAD_ISNOT_CONSTANT_COMPARE_CALL_NAME_LOAD_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_EQ_LIST_CONSTANT_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_KEYWORD_LAMBDA_ARGUMENTS_ARG_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_KEYWORD_CONSTANT_RETURN_NAME_LOAD |
def _is_physical_entity(pe):
"""Return True if the element is a physical entity"""
val = isinstance(pe, _bp('PhysicalEntity')) or \
isinstance(pe, _bpimpl('PhysicalEntity'))
return val | [1][SEP1][Return][SEP2][][SEP3][4] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_BOOLOP_OR_CALL_NAME_LOAD_NAME_LOAD_CALL_NAME_LOAD_CONSTANT_CALL_NAME_LOAD_NAME_LOAD_CALL_NAME_LOAD_CONSTANT_RETURN_NAME_LOAD |
def _get_db_refs(term):
"""Extract database references for a TERM."""
db_refs = {}
# Here we extract the text name of the Agent
# There are two relevant tags to consider here.
# The <text> tag typically contains a larger phrase surrounding the
# term but it contains the term in a raw, non-canonicalized form.
# The <name> tag only contains the name of the entity but it is
# canonicalized. For instance, MAP2K1 appears as MAP-2-K-1.
agent_text_tag = term.find('name')
if agent_text_tag is not None:
db_refs['TEXT'] = agent_text_tag.text
# If we have some drum-terms, the matched-name of the first
# drum-term (e.g. "MAP2K1") is a better value for TEXT than
# the name of the TERM (e.g. "MAP-2-K-1") so we put that in there
drum_terms = term.findall('drum-terms/drum-term')
if drum_terms:
matched_name = drum_terms[0].attrib.get('matched-name')
if matched_name:
db_refs['TEXT'] = matched_name
# We make a list of scored grounding terms from the DRUM terms
grounding_terms = _get_grounding_terms(term)
if not grounding_terms:
# This is for backwards compatibility with EKBs without drum-term
# scored entries. It is important to keep for Bioagents
# compatibility.
dbid = term.attrib.get('dbid')
if dbid:
dbids = dbid.split('|')
for dbname, dbid in [d.split(':') for d in dbids]:
if not db_refs.get(dbname):
db_refs[dbname] = dbid
return db_refs, None, []
# This is the INDRA prioritization of grounding name spaces. Lower score
# takes precedence.
ns_priority = {
'HGNC': 1,
'UP': 1,
'FPLX': 2,
'CHEBI': 3,
'PC': 3,
'GO': 4,
'FA': 5,
'XFAM': 5,
'NCIT': 5
}
# We get the top priority entry from each score group
score_groups = itertools.groupby(grounding_terms, lambda x: x['score'])
top_per_score_group = []
ambiguities = []
for score, group in score_groups:
entries = list(group)
for entry in entries:
priority = 100
for ref_ns, ref_id in entry['refs'].items():
# Skip etc UP entries
if ref_ns == 'UP' and ref_id == 'etc':
continue
try:
priority = min(priority, ns_priority[ref_ns])
except KeyError:
pass
if ref_ns == 'UP':
if not up_client.is_human(ref_id):
priority = 4
entry['priority'] = priority
if len(entries) > 1:
top_entry = entries[0]
top_idx = 0
for i, entry in enumerate(entries):
# We take the lowest priority entry within the score group
# as the top entry
if entry['priority'] < top_entry['priority']:
# This is a corner case in which a protein family
# should be prioritized over a specific protein,
# specifically when HGNC was mapped from NCIT but
# FPLX was not mapped from NCIT, the HGNC shouldn't
# take precedence.
if entry.get('comment') == 'HGNC_FROM_NCIT' and \
'FPLX' in top_entry['refs'] and \
top_entry.get('comment') != 'FPLX_FROM_NCIT':
continue
top_entry = entry
top_idx = i
for i, entry in enumerate(entries):
if i == top_idx:
continue
if (entry['priority'] - top_entry['priority']) <= 1:
ambiguities.append((top_entry, entry))
else:
top_entry = entries[0]
top_per_score_group.append(top_entry)
# Get the top priority for each score group
priorities = [entry['priority'] for entry in top_per_score_group]
# By default, we coose the top priority entry from the highest score group
top_grounding = top_per_score_group[0]
# Sometimes the top grounding has much lower priority and not much higher
# score than the second grounding. Typically 1.0 vs 0.82857 and 5 vs 2.
# In this case we take the second entry. A special case is handled where
# a FPLX entry was mapped from FA, in which case priority difference of < 2
# is also accepted.
if len(top_per_score_group) > 1:
score_diff = top_per_score_group[0]['score'] - \
top_per_score_group[1]['score']
priority_diff = top_per_score_group[0]['priority'] - \
top_per_score_group[1]['priority']
if score_diff < 0.2 and (priority_diff >= 2 or \
top_per_score_group[0].get('comment') == 'FPLX_FROM_FA'):
top_grounding = top_per_score_group[1]
relevant_ambiguities = []
for amb in ambiguities:
if top_grounding not in amb:
continue
if top_grounding == amb[0]:
relevant_ambiguities.append({'preferred': amb[0],
'alternative': amb[1]})
else:
relevant_ambiguities.append({'preferred': amb[1],
'alternative': amb[0]})
for k, v in top_grounding['refs'].items():
db_refs[k] = v
# Now standardize db_refs to the INDRA standards
# We need to add a prefix for CHEBI
chebi_id = db_refs.get('CHEBI')
if chebi_id and not chebi_id.startswith('CHEBI:'):
db_refs['CHEBI'] = 'CHEBI:%s' % chebi_id
# We need to strip the trailing version number for XFAM and rename to PF
pfam_id = db_refs.get('XFAM')
if pfam_id:
pfam_id = pfam_id.split('.')[0]
db_refs.pop('XFAM', None)
db_refs['PF'] = pfam_id
# We need to add GO prefix if it is missing
go_id = db_refs.get('GO')
if go_id:
if not go_id.startswith('GO:'):
db_refs['GO'] = 'GO:%s' % go_id
# We need to deal with Nextprot families
nxp_id = db_refs.get('FA')
if nxp_id:
db_refs.pop('FA', None)
db_refs['NXPFA'] = nxp_id
# We need to rename PC to PUBCHEM
pc_id = db_refs.get('PC')
if pc_id:
db_refs.pop('PC', None)
db_refs['PUBCHEM'] = pc_id
# Here we also get and return the type, which is a TRIPS
# ontology type. This is to be used in the context of
# Bioagents.
ont_type = top_grounding['type']
return db_refs, ont_type, relevant_ambiguities | [1][SEP1][If][If][If][If][If][None][None][None][Return][For][For][None][If][If][For][If][None][None][None][If][None][For][For][None][None][If][For][If][None][For][None][If][None][If][Try][If][For][None][None][None][If][None][None][If][If][None][If][If][None][If][If][If][If][None][None][None][If][None][None][Return][SEP2][1,2][3,2][4,5][6,2][7,8][9][2][10][][11,12][13,8][14][15,16][17,10][18,19][20,16][21][10][22][23,24][16][25,26][27,28][29][30][31,21][32,33][34,22][14][35,36][9][37,38][26][39,40][41,42][43,29][44,30][21][21][40][45,46][47][47][48,29][49,36][46][50,51][52,22][29][53,36][54,51][55,56][57,22][36][51][56][58,59][22][59][][SEP3][1][1][1][1][3][1][0][1][0][10][1][1][1][1][3][1][0][0][0][6][0][2][3][0][0][0][1][0][0][1][1][0][0][2][0][0][2][1][1][0][1][1][0][2][0][2][1][0][0][0][1][1][1][1][0][1][1][0][1][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_DICT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_IF_COMPARE_NAME_LOAD_ISNOT_CONSTANT_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_IF_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_LOAD_LOAD_CONSTANT_IF_NAME_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_NAME_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_IF_UNARYOP_NOT_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CONSTANT_IF_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_FOR_TUPLE_NAME_STORE_NAME_STORE_STORE_LISTCOMP_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_COMPREHENSION_NAME_STORE_NAME_LOAD_IF_UNARYOP_NOT_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_NAME_LOAD_STORE_NAME_LOAD_RETURN_TUPLE_NAME_LOAD_CONSTANT_LIST_LOAD_LOAD_ASSIGN_NAME_STORE_DICT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_LAMBDA_ARGUMENTS_ARG_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_ASSIGN_NAME_STORE_LIST_LOAD_ASSIGN_NAME_STORE_LIST_LOAD_FOR_TUPLE_NAME_STORE_NAME_STORE_STORE_NAME_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_FOR_NAME_STORE_NAME_LOAD_ASSIGN_NAME_STORE_CONSTANT_FOR_TUPLE_NAME_STORE_NAME_STORE_STORE_CALL_ATTRIBUTE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_LOAD_IF_BOOLOP_AND_COMPARE_NAME_LOAD_EQ_CONSTANT_COMPARE_NAME_LOAD_EQ_CONSTANT_CONTINUE_TRY_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_SUBSCRIPT_NAME_LOAD_NAME_LOAD_LOAD_EXCEPTHANDLER_NAME_LOAD_PASS_IF_COMPARE_NAME_LOAD_EQ_CONSTANT_IF_UNARYOP_NOT_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_CONSTANT_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_NAME_LOAD_IF_COMPARE_CALL_NAME_LOAD_NAME_LOAD_GT_CONSTANT_ASSIGN_NAME_STORE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_ASSIGN_NAME_STORE_CONSTANT_FOR_TUPLE_NAME_STORE_NAME_STORE_STORE_CALL_NAME_LOAD_NAME_LOAD_IF_COMPARE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_LT_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_IF_BOOLOP_AND_COMPARE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_EQ_CONSTANT_COMPARE_CONSTANT_IN_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_COMPARE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_NOTEQ_CONSTANT_CONTINUE_ASSIGN_NAME_STORE_NAME_LOAD_ASSIGN_NAME_STORE_NAME_LOAD_FOR_TUPLE_NAME_STORE_NAME_STORE_STORE_CALL_NAME_LOAD_NAME_LOAD_IF_COMPARE_NAME_LOAD_EQ_NAME_LOAD_CONTINUE_IF_COMPARE_BINOP_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_SUB_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_LTE_CONSTANT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_TUPLE_NAME_LOAD_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_LISTCOMP_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_COMPREHENSION_NAME_STORE_NAME_LOAD_ASSIGN_NAME_STORE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_IF_COMPARE_CALL_NAME_LOAD_NAME_LOAD_GT_CONSTANT_ASSIGN_NAME_STORE_BINOP_SUBSCRIPT_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_CONSTANT_LOAD_SUB_SUBSCRIPT_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_CONSTANT_LOAD_ASSIGN_NAME_STORE_BINOP_SUBSCRIPT_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_CONSTANT_LOAD_SUB_SUBSCRIPT_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_CONSTANT_LOAD_IF_BOOLOP_AND_COMPARE_NAME_LOAD_LT_CONSTANT_BOOLOP_OR_COMPARE_NAME_LOAD_GTE_CONSTANT_COMPARE_CALL_ATTRIBUTE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_LOAD_CONSTANT_EQ_CONSTANT_ASSIGN_NAME_STORE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_ASSIGN_NAME_STORE_LIST_LOAD_FOR_NAME_STORE_NAME_LOAD_IF_COMPARE_NAME_LOAD_NOTIN_NAME_LOAD_CONTINUE_IF_COMPARE_NAME_LOAD_EQ_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_DICT_CONSTANT_CONSTANT_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_DICT_CONSTANT_CONSTANT_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_FOR_TUPLE_NAME_STORE_NAME_STORE_STORE_CALL_ATTRIBUTE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_NAME_LOAD_STORE_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_IF_BOOLOP_AND_NAME_LOAD_UNARYOP_NOT_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_BINOP_CONSTANT_MOD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_IF_NAME_LOAD_ASSIGN_NAME_STORE_SUBSCRIPT_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CONSTANT_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CONSTANT_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_IF_NAME_LOAD_IF_UNARYOP_NOT_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_BINOP_CONSTANT_MOD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_IF_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CONSTANT_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_IF_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CONSTANT_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_NAME_LOAD_ASSIGN_NAME_STORE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_RETURN_TUPLE_NAME_LOAD_NAME_LOAD_NAME_LOAD_LOAD |
def _assemble_transphosphorylation(self, stmt):
"""Example: complex(p(HGNC:EGFR)) =>
p(HGNC:EGFR, pmod(Ph, Tyr, 1173))"""
# Check our assumptions about the bound condition of the enzyme
assert len(stmt.enz.bound_conditions) == 1
assert stmt.enz.bound_conditions[0].is_bound
# Create a modified protein node for the bound target
sub_agent = deepcopy(stmt.enz.bound_conditions[0].agent)
sub_agent.mods.append(stmt._get_mod_condition())
self._add_nodes_edges(stmt.enz, sub_agent, pc.DIRECTLY_INCREASES,
stmt.evidence) | [2][SEP1][None][None][None][SEP2][1][2][][SEP3][1][0][4] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_EXPR_CONSTANT_ASSERT_COMPARE_CALL_NAME_LOAD_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_EQ_CONSTANT_ASSERT_ATTRIBUTE_SUBSCRIPT_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CONSTANT_LOAD_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_ATTRIBUTE_SUBSCRIPT_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CONSTANT_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD |
def submit_curation():
"""Submit curations for a given corpus.
The submitted curations are handled to update the probability model but
there is no return value here. The update_belief function can be called
separately to calculate update belief scores.
Parameters
----------
corpus_id : str
The ID of the corpus for which the curation is submitted.
curations : dict
A set of curations where each key is a Statement UUID in the given
corpus and each key is 0 or 1 with 0 corresponding to incorrect and
1 corresponding to correct.
"""
if request.json is None:
abort(Response('Missing application/json header.', 415))
# Get input parameters
corpus_id = request.json.get('corpus_id')
curations = request.json.get('curations', {})
try:
curator.submit_curation(corpus_id, curations)
except InvalidCorpusError:
abort(Response('The corpus_id "%s" is unknown.' % corpus_id, 400))
return
return jsonify({}) | [0][SEP1][If][None][Try][None][Return][Return][SEP2][1,2][2][3,4][5][][][SEP3][0][2][2][1][2][1] | MODULE_FUNCTIONDEF_ARGUMENTS_EXPR_CONSTANT_IF_COMPARE_ATTRIBUTE_NAME_LOAD_LOAD_IS_CONSTANT_EXPR_CALL_NAME_LOAD_CALL_NAME_LOAD_CONSTANT_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CONSTANT_DICT_TRY_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_NAME_LOAD_EXCEPTHANDLER_NAME_LOAD_EXPR_CALL_NAME_LOAD_CALL_NAME_LOAD_BINOP_CONSTANT_MOD_NAME_LOAD_CONSTANT_RETURN_RETURN_CALL_NAME_LOAD_DICT |
def extract_statements(self):
"""Extract the statements from the json."""
for p_info in self._json:
para = RlimspParagraph(p_info, self.doc_id_type)
self.statements.extend(para.get_statements())
return | [1][SEP1][None][For][None][Return][SEP2][1][2,3][1][][SEP3][0][0][3][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_FOR_NAME_STORE_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_RETURN |
def process_nxml(nxml_filename, pmid=None, extra_annotations=None,
cleanup=True, add_grounding=True):
"""Process an NXML file using the ISI reader
First converts NXML to plain text and preprocesses it, then runs the ISI
reader, and processes the output to extract INDRA Statements.
Parameters
----------
nxml_filename : str
nxml file to process
pmid : Optional[str]
pmid of this nxml file, to be added to the Evidence object of the
extracted INDRA statements
extra_annotations : Optional[dict]
Additional annotations to add to the Evidence object of all extracted
INDRA statements. Extra annotations called 'interaction' are ignored
since this is used by the processor to store the corresponding
raw ISI output.
cleanup : Optional[bool]
If True, the temporary folders created for preprocessed reading input
and output are removed. Default: True
add_grounding : Optional[bool]
If True the extracted Statements' grounding is mapped
Returns
-------
ip : indra.sources.isi.processor.IsiProcessor
A processor containing extracted Statements
"""
if extra_annotations is None:
extra_annotations = {}
# Create a temporary directory to store the proprocessed input
pp_dir = tempfile.mkdtemp('indra_isi_pp_output')
pp = IsiPreprocessor(pp_dir)
extra_annotations = {}
pp.preprocess_nxml_file(nxml_filename, pmid, extra_annotations)
# Run the ISI reader and extract statements
ip = process_preprocessed(pp)
if add_grounding:
ip.add_grounding()
if cleanup:
# Remove temporary directory with processed input
shutil.rmtree(pp_dir)
else:
logger.info('Not cleaning up %s' % pp_dir)
return ip | [5][SEP1][If][None][If][None][If][None][None][Return][SEP2][1,2][2][3,4][4][5,6][7][7][][SEP3][0][0][4][1][0][1][1][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_ARG_ARG_CONSTANT_CONSTANT_CONSTANT_CONSTANT_EXPR_CONSTANT_IF_COMPARE_NAME_LOAD_IS_CONSTANT_ASSIGN_NAME_STORE_DICT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_DICT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_NAME_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_IF_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_IF_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_BINOP_CONSTANT_MOD_NAME_LOAD_RETURN_NAME_LOAD |
def _get_node_key(self, node_dict_item):
"""Return a tuple of sorted sources and targets given a node dict."""
s = tuple(sorted(node_dict_item['sources']))
t = tuple(sorted(node_dict_item['targets']))
return (s, t) | [2][SEP1][Return][SEP2][][SEP3][4] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_CALL_NAME_LOAD_CALL_NAME_LOAD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_CALL_NAME_LOAD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_RETURN_TUPLE_NAME_LOAD_NAME_LOAD_LOAD |
def process_pybel_graph(graph):
"""Return a PybelProcessor by processing a PyBEL graph.
Parameters
----------
graph : pybel.struct.BELGraph
A PyBEL graph to process
Returns
-------
bp : PybelProcessor
A PybelProcessor object which contains INDRA Statements in
bp.statements.
"""
bp = PybelProcessor(graph)
bp.get_statements()
if bp.annot_manager.failures:
logger.warning('missing %d annotation pairs',
sum(len(v)
for v in bp.annot_manager.failures.values()))
return bp | [1][SEP1][If][None][Return][SEP2][1,2][2][][SEP3][2][4][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_IF_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CALL_NAME_LOAD_GENERATOREXP_CALL_NAME_LOAD_NAME_LOAD_COMPREHENSION_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_LOAD_RETURN_NAME_LOAD |
def isa_or_partof(self, ns1, id1, ns2, id2):
"""Return True if two entities are in an "isa" or "partof" relationship
Parameters
----------
ns1 : str
Namespace code for an entity.
id1 : str
URI for an entity.
ns2 : str
Namespace code for an entity.
id2 : str
URI for an entity.
Returns
-------
bool
True if t1 has a "isa" or "partof" relationship with t2, either
directly or through a series of intermediates; False otherwise.
"""
rel_fun = lambda node, graph: self.isa_or_partof_objects(node)
return self.directly_or_indirectly_related(ns1, id1, ns2, id2,
self.isa_or_partof_closure,
rel_fun) | [5][SEP1][Return][SEP2][][SEP3][2] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_ARG_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_LAMBDA_ARGUMENTS_ARG_ARG_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_RETURN_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_NAME_LOAD_NAME_LOAD_NAME_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD |
def separate_reach_logs(log_str):
"""Get the list of reach logs from the overall logs."""
log_lines = log_str.splitlines()
reach_logs = []
reach_lines = []
adding_reach_lines = False
for l in log_lines[:]:
if not adding_reach_lines and 'Beginning reach' in l:
adding_reach_lines = True
elif adding_reach_lines and 'Reach finished' in l:
adding_reach_lines = False
reach_logs.append(('SUCCEEDED', '\n'.join(reach_lines)))
reach_lines = []
elif adding_reach_lines:
reach_lines.append(l.split('readers - ')[1])
log_lines.remove(l)
if adding_reach_lines:
reach_logs.append(('FAILURE', '\n'.join(reach_lines)))
return '\n'.join(log_lines), reach_logs | [1][SEP1][None][For][If][If][None][If][None][Return][None][If][None][SEP2][1][2,3][4,5][6,7][1][8,9][7][][1][10,1][1][SEP3][1][0][0][0][0][0][2][1][2][0][3] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_LIST_LOAD_ASSIGN_NAME_STORE_LIST_LOAD_ASSIGN_NAME_STORE_CONSTANT_FOR_NAME_STORE_SUBSCRIPT_NAME_LOAD_SLICE_LOAD_IF_BOOLOP_AND_UNARYOP_NOT_NAME_LOAD_COMPARE_CONSTANT_IN_NAME_LOAD_ASSIGN_NAME_STORE_CONSTANT_IF_BOOLOP_AND_NAME_LOAD_COMPARE_CONSTANT_IN_NAME_LOAD_ASSIGN_NAME_STORE_CONSTANT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_TUPLE_CONSTANT_CALL_ATTRIBUTE_CONSTANT_LOAD_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_LIST_LOAD_IF_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_SUBSCRIPT_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CONSTANT_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_IF_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_TUPLE_CONSTANT_CALL_ATTRIBUTE_CONSTANT_LOAD_NAME_LOAD_LOAD_RETURN_TUPLE_CALL_ATTRIBUTE_CONSTANT_LOAD_NAME_LOAD_NAME_LOAD_LOAD |
def _link_to_action_mentions(self, actionmention_filename):
"""Add action mentions"""
parser = GenewaysActionMentionParser(actionmention_filename)
self.action_mentions = parser.action_mentions
for action_mention in self.action_mentions:
hiid = action_mention.hiid
if hiid not in self.hiid_to_action_index:
m1 = 'Parsed action mention has hiid %d, which does not exist'
m2 = ' in table of action hiids'
raise Exception((m1 + m2) % hiid)
else:
idx = self.hiid_to_action_index[hiid]
self.actions[idx].action_mentions.append(action_mention) | [2][SEP1][None][For][If][None][None][SEP2][1][2][3,4][][1][SEP3][1][0][0][1][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_ASSIGN_ATTRIBUTE_NAME_LOAD_STORE_ATTRIBUTE_NAME_LOAD_LOAD_FOR_NAME_STORE_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_ATTRIBUTE_NAME_LOAD_LOAD_IF_COMPARE_NAME_LOAD_NOTIN_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_CONSTANT_ASSIGN_NAME_STORE_CONSTANT_RAISE_CALL_NAME_LOAD_BINOP_BINOP_NAME_LOAD_ADD_NAME_LOAD_MOD_NAME_LOAD_ASSIGN_NAME_STORE_SUBSCRIPT_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_ATTRIBUTE_SUBSCRIPT_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_LOAD_LOAD_LOAD_NAME_LOAD |
def get_uncond_agent(agent):
"""Construct the unconditional state of an Agent.
The unconditional Agent is a copy of the original agent but
without any bound conditions and modification conditions.
Mutation conditions, however, are preserved since they are static.
"""
agent_uncond = ist.Agent(_n(agent.name), mutations=agent.mutations)
return agent_uncond | [1][SEP1][Return][SEP2][][SEP3][2] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CALL_NAME_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_KEYWORD_ATTRIBUTE_NAME_LOAD_LOAD_RETURN_NAME_LOAD |
def get_statements(self):
"""Convert network edges into Statements.
Returns
-------
list of Statements
Converted INDRA Statements.
"""
edges = _get_dict_from_list('edges', self.cx)
for edge in edges:
edge_type = edge.get('i')
if not edge_type:
continue
stmt_type = _stmt_map.get(edge_type)
if stmt_type:
id = edge['@id']
source_agent = self._node_agents.get(edge['s'])
target_agent = self._node_agents.get(edge['t'])
if not source_agent or not target_agent:
logger.info("Skipping edge %s->%s: %s" %
(self._node_names[edge['s']],
self._node_names[edge['t']], edge))
continue
ev = self._create_evidence(id)
if stmt_type == Complex:
stmt = stmt_type([source_agent, target_agent], evidence=ev)
else:
stmt = stmt_type(source_agent, target_agent, evidence=ev)
self.statements.append(stmt)
return self.statements | [1][SEP1][None][For][If][Return][If][If][None][If][None][None][None][SEP2][1][2,3][4,1][][5,1][6,7][1][8,9][10][10][1][SEP3][1][8][1][0][5][2][1][1][1][1][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_CALL_NAME_LOAD_CONSTANT_ATTRIBUTE_NAME_LOAD_LOAD_FOR_NAME_STORE_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_IF_UNARYOP_NOT_NAME_LOAD_CONTINUE_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_IF_NAME_LOAD_ASSIGN_NAME_STORE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_IF_BOOLOP_OR_UNARYOP_NOT_NAME_LOAD_UNARYOP_NOT_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_BINOP_CONSTANT_MOD_TUPLE_SUBSCRIPT_ATTRIBUTE_NAME_LOAD_LOAD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_LOAD_SUBSCRIPT_ATTRIBUTE_NAME_LOAD_LOAD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_LOAD_NAME_LOAD_LOAD_CONTINUE_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_IF_COMPARE_NAME_LOAD_EQ_NAME_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_LIST_NAME_LOAD_NAME_LOAD_LOAD_KEYWORD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_KEYWORD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_NAME_LOAD_RETURN_ATTRIBUTE_NAME_LOAD_LOAD |
def process_from_web():
"""Return a TrrustProcessor based on the online interaction table.
Returns
-------
TrrustProcessor
A TrrustProcessor object that has a list of INDRA Statements in its
statements attribute.
"""
logger.info('Downloading table from %s' % trrust_human_url)
res = requests.get(trrust_human_url)
res.raise_for_status()
df = pandas.read_table(io.StringIO(res.text))
tp = TrrustProcessor(df)
tp.extract_statements()
return tp | [0][SEP1][Return][SEP2][][SEP3][7] | MODULE_FUNCTIONDEF_ARGUMENTS_EXPR_CONSTANT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_BINOP_CONSTANT_MOD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_RETURN_NAME_LOAD |
def _sanitize(text):
"""Return sanitized Eidos text field for human readability."""
d = {'-LRB-': '(', '-RRB-': ')'}
return re.sub('|'.join(d.keys()), lambda m: d[m.group(0)], text) | [1][SEP1][Return][SEP2][][SEP3][4] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_DICT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_RETURN_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CALL_ATTRIBUTE_CONSTANT_LOAD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_LAMBDA_ARGUMENTS_ARG_SUBSCRIPT_NAME_LOAD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_LOAD_NAME_LOAD |
def get_activating_mods(self):
"""Extract INDRA ActiveForm Statements with a single mod from BEL.
The SPARQL pattern used for extraction from BEL looks for a
ModifiedProteinAbundance as subject and an Activiy of a
ProteinAbundance as object.
Examples:
proteinAbundance(HGNC:INSR,proteinModification(P,Y))
directlyIncreases
kinaseActivity(proteinAbundance(HGNC:INSR))
"""
q_mods = prefixes + """
SELECT ?speciesName ?actType ?mod ?pos ?rel ?stmt ?species
WHERE {
?stmt a belvoc:Statement .
?stmt belvoc:hasRelationship ?rel .
?stmt belvoc:hasSubject ?subject .
?stmt belvoc:hasObject ?object .
?object belvoc:hasActivityType ?actType .
?object belvoc:hasChild ?species .
?species a belvoc:ProteinAbundance .
?species belvoc:hasConcept ?speciesName .
?subject a belvoc:ModifiedProteinAbundance .
?subject belvoc:hasModificationType ?mod .
?subject belvoc:hasChild ?species .
OPTIONAL { ?subject belvoc:hasModificationPosition ?pos . }
FILTER (?rel = belvoc:DirectlyIncreases ||
?rel = belvoc:DirectlyDecreases)
}
"""
# Now make the PySB for the phosphorylation
res_mods = self.g.query(q_mods)
for stmt in res_mods:
evidence = self._get_evidence(stmt[5])
# Parse out the elements of the query
species = self._get_agent(stmt[0], stmt[6])
act_type = term_from_uri(stmt[1]).lower()
mod = term_from_uri(stmt[2])
mod_pos = term_from_uri(stmt[3])
mc = self._get_mod_condition(mod, mod_pos)
species.mods = [mc]
rel = term_from_uri(stmt[4])
if rel == 'DirectlyDecreases':
is_active = False
else:
is_active = True
stmt_str = strip_statement(stmt[5])
# Mark this as a converted statement
self.converted_direct_stmts.append(stmt_str)
st = ActiveForm(species, act_type, is_active, evidence)
self.statements.append(st) | [1][SEP1][None][For][If][None][None][None][SEP2][1][2][3,4][5][5][1][SEP3][1][4][8][0][0][4] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_BINOP_NAME_LOAD_ADD_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_NAME_LOAD_FOR_NAME_STORE_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_CALL_NAME_LOAD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_NAME_LOAD_ASSIGN_ATTRIBUTE_NAME_LOAD_STORE_LIST_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_IF_COMPARE_NAME_LOAD_EQ_CONSTANT_ASSIGN_NAME_STORE_CONSTANT_ASSIGN_NAME_STORE_CONSTANT_ASSIGN_NAME_STORE_CALL_NAME_LOAD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_EXPR_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_NAME_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_NAME_LOAD |
def process_nxml_file(file_name, citation=None, offline=False,
output_fname=default_output_fname):
"""Return a ReachProcessor by processing the given NXML file.
NXML is the format used by PubmedCentral for papers in the open
access subset.
Parameters
----------
file_name : str
The name of the NXML file to be processed.
citation : Optional[str]
A PubMed ID passed to be used in the evidence for the extracted INDRA
Statements. Default: None
offline : Optional[bool]
If set to True, the REACH system is ran offline. Otherwise (by default)
the web service is called. Default: False
output_fname : Optional[str]
The file to output the REACH JSON output to.
Defaults to reach_output.json in current working directory.
Returns
-------
rp : ReachProcessor
A ReachProcessor containing the extracted INDRA Statements
in rp.statements.
"""
with open(file_name, 'rb') as f:
nxml_str = f.read().decode('utf-8')
return process_nxml_str(nxml_str, citation, False, output_fname) | [4][SEP1][None][Return][SEP2][1][][SEP3][1][3] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_ARG_CONSTANT_CONSTANT_NAME_LOAD_EXPR_CONSTANT_WITH_WITHITEM_CALL_NAME_LOAD_NAME_LOAD_CONSTANT_NAME_STORE_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CONSTANT_RETURN_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_CONSTANT_NAME_LOAD |
def process_json(json_dict):
"""Return an EidosProcessor by processing a Eidos JSON-LD dict.
Parameters
----------
json_dict : dict
The JSON-LD dict to be processed.
Returns
-------
ep : EidosProcessor
A EidosProcessor containing the extracted INDRA Statements
in its statements attribute.
"""
ep = EidosProcessor(json_dict)
ep.extract_causal_relations()
ep.extract_correlations()
ep.extract_events()
return ep | [1][SEP1][Return][SEP2][][SEP3][4] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_RETURN_NAME_LOAD |
def _remove_bound_conditions(agent, keep_criterion):
"""Removes bound conditions of agent such that keep_criterion is False.
Parameters
----------
agent: Agent
The agent whose bound conditions we evaluate
keep_criterion: function
Evaluates removal_criterion(a) for each agent a in a bound condition
and if it evaluates to False, removes a from agent's bound_conditions
"""
new_bc = []
for ind in range(len(agent.bound_conditions)):
if keep_criterion(agent.bound_conditions[ind].agent):
new_bc.append(agent.bound_conditions[ind])
agent.bound_conditions = new_bc | [2][SEP1][None][For][If][None][None][SEP2][1][2,3][4,1][][1][SEP3][0][2][1][0][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_LIST_LOAD_FOR_NAME_STORE_CALL_NAME_LOAD_CALL_NAME_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_IF_CALL_NAME_LOAD_ATTRIBUTE_SUBSCRIPT_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_SUBSCRIPT_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_LOAD_ASSIGN_ATTRIBUTE_NAME_LOAD_STORE_NAME_LOAD |
def export_kappa_cm(model, fname=None):
"""Return a networkx graph representing the model's Kappa contact map.
Parameters
----------
model : pysb.core.Model
A PySB model to be exported into a Kappa CM.
fname : Optional[str]
A file name, typically with .png or .pdf extension in which
the CM is rendered using pygraphviz.
Returns
-------
npygraphviz.Agraph
A graph object representing the contact map.
"""
from .kappa_util import cm_json_to_graph
kappa = _prepare_kappa(model)
cmap = kappa.analyses_contact_map()
cm = cm_json_to_graph(cmap)
if fname:
cm.draw(fname, prog='dot')
return cm | [2][SEP1][If][None][Return][SEP2][1,2][2][][SEP3][3][1][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_CONSTANT_EXPR_CONSTANT_IMPORTFROM_ALIAS_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_IF_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_KEYWORD_CONSTANT_RETURN_NAME_LOAD |
def assemble_pysb():
"""Assemble INDRA Statements and return PySB model string."""
if request.method == 'OPTIONS':
return {}
response = request.body.read().decode('utf-8')
body = json.loads(response)
stmts_json = body.get('statements')
export_format = body.get('export_format')
stmts = stmts_from_json(stmts_json)
pa = PysbAssembler()
pa.add_statements(stmts)
pa.make_model()
try:
for m in pa.model.monomers:
pysb_assembler.set_extended_initial_condition(pa.model, m, 0)
except Exception as e:
logger.exception(e)
if not export_format:
model_str = pa.print_model()
elif export_format in ('kappa_im', 'kappa_cm'):
fname = 'model_%s.png' % export_format
root = os.path.dirname(os.path.abspath(fname))
graph = pa.export_model(format=export_format, file_name=fname)
with open(fname, 'rb') as fh:
data = 'data:image/png;base64,%s' % \
base64.b64encode(fh.read()).decode()
return {'image': data}
else:
try:
model_str = pa.export_model(format=export_format)
except Exception as e:
logger.exception(e)
model_str = ''
res = {'model': model_str}
return res | [0][SEP1][If][Return][Try][For][None][None][If][None][If][Return][None][Try][Return][None][None][SEP2][1,2][][3,4][5,6][6][3][7,8][9][10,11][][12][13,14][][9][9][SEP3][0][0][9][0][1][1][0][1][0][0][4][0][3][1][1] | MODULE_FUNCTIONDEF_ARGUMENTS_EXPR_CONSTANT_IF_COMPARE_ATTRIBUTE_NAME_LOAD_LOAD_EQ_CONSTANT_RETURN_DICT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_LOAD_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_TRY_FOR_NAME_STORE_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_CONSTANT_EXCEPTHANDLER_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_IF_UNARYOP_NOT_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_IF_COMPARE_NAME_LOAD_IN_TUPLE_CONSTANT_CONSTANT_LOAD_ASSIGN_NAME_STORE_BINOP_CONSTANT_MOD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_KEYWORD_NAME_LOAD_KEYWORD_NAME_LOAD_WITH_WITHITEM_CALL_NAME_LOAD_NAME_LOAD_CONSTANT_NAME_STORE_ASSIGN_NAME_STORE_BINOP_CONSTANT_MOD_CALL_ATTRIBUTE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_RETURN_DICT_CONSTANT_NAME_LOAD_TRY_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_KEYWORD_NAME_LOAD_EXCEPTHANDLER_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_CONSTANT_ASSIGN_NAME_STORE_DICT_CONSTANT_NAME_LOAD_RETURN_NAME_LOAD |
def make_model(self, add_indra_json=True):
"""Assemble the CX network from the collected INDRA Statements.
This method assembles a CX network from the set of INDRA Statements.
The assembled network is set as the assembler's cx argument.
Parameters
----------
add_indra_json : Optional[bool]
If True, the INDRA Statement JSON annotation is added to each
edge in the network. Default: True
Returns
-------
cx_str : str
The json serialized CX model.
"""
self.add_indra_json = add_indra_json
for stmt in self.statements:
if isinstance(stmt, Modification):
self._add_modification(stmt)
if isinstance(stmt, SelfModification):
self._add_self_modification(stmt)
elif isinstance(stmt, RegulateActivity) or \
isinstance(stmt, RegulateAmount):
self._add_regulation(stmt)
elif isinstance(stmt, Complex):
self._add_complex(stmt)
elif isinstance(stmt, Gef):
self._add_gef(stmt)
elif isinstance(stmt, Gap):
self._add_gap(stmt)
elif isinstance(stmt, Influence):
self._add_influence(stmt)
network_description = ''
self.cx['networkAttributes'].append({'n': 'name',
'v': self.network_name})
self.cx['networkAttributes'].append({'n': 'description',
'v': network_description})
cx_str = self.print_cx()
return cx_str | [2][SEP1][None][For][If][Return][None][If][None][If][None][If][None][If][None][If][None][If][None][SEP2][1][2,3][4,5][][5][6,7][1][8,9][1][10,11][1][12,13][1][14,15][1][16,1][1][SEP3][0][13][1][3][1][1][1][2][1][1][1][1][1][1][1][1][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_CONSTANT_EXPR_CONSTANT_ASSIGN_ATTRIBUTE_NAME_LOAD_STORE_NAME_LOAD_FOR_NAME_STORE_ATTRIBUTE_NAME_LOAD_LOAD_IF_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_IF_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_IF_BOOLOP_OR_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_IF_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_IF_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_IF_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_IF_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_CONSTANT_EXPR_CALL_ATTRIBUTE_SUBSCRIPT_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_LOAD_LOAD_DICT_CONSTANT_CONSTANT_CONSTANT_ATTRIBUTE_NAME_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_SUBSCRIPT_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_LOAD_LOAD_DICT_CONSTANT_CONSTANT_CONSTANT_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_RETURN_NAME_LOAD |
def _get_edge_sign(im, edge):
"""Get the polarity of the influence by examining the edge sign."""
edge_data = im[edge[0]][edge[1]]
# Handle possible multiple edges between nodes
signs = list(set([v['sign'] for v in edge_data.values()
if v.get('sign')]))
if len(signs) > 1:
logger.warning("Edge %s has conflicting polarities; choosing "
"positive polarity by default" % str(edge))
sign = 1
else:
sign = signs[0]
if sign is None:
raise Exception('No sign attribute for edge.')
elif abs(sign) == 1:
return sign
else:
raise Exception('Unexpected edge sign: %s' % edge.attr['sign']) | [2][SEP1][If][None][None][If][None][If][Return][None][SEP2][1,2][3][3][4,5][][6,7][][][SEP3][5][2][0][0][1][1][0][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_SUBSCRIPT_SUBSCRIPT_NAME_LOAD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_LOAD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_CALL_NAME_LOAD_LISTCOMP_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_COMPREHENSION_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_IF_COMPARE_CALL_NAME_LOAD_NAME_LOAD_GT_CONSTANT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_BINOP_CONSTANT_MOD_CALL_NAME_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_CONSTANT_ASSIGN_NAME_STORE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_IF_COMPARE_NAME_LOAD_IS_CONSTANT_RAISE_CALL_NAME_LOAD_CONSTANT_IF_COMPARE_CALL_NAME_LOAD_NAME_LOAD_EQ_CONSTANT_RETURN_NAME_LOAD_RAISE_CALL_NAME_LOAD_BINOP_CONSTANT_MOD_SUBSCRIPT_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_LOAD |
def id_lookup(paper_id, idtype=None):
"""This function takes a Pubmed ID, Pubmed Central ID, or DOI
and use the Pubmed ID mapping
service and looks up all other IDs from one
of these. The IDs are returned in a dictionary."""
if idtype is not None and idtype not in ('pmid', 'pmcid', 'doi'):
raise ValueError("Invalid idtype %s; must be 'pmid', 'pmcid', "
"or 'doi'." % idtype)
if paper_id.upper().startswith('PMC'):
idtype = 'pmcid'
# Strip off any prefix
if paper_id.upper().startswith('PMID'):
paper_id = paper_id[4:]
elif paper_id.upper().startswith('DOI'):
paper_id = paper_id[3:]
data = {'ids': paper_id}
if idtype is not None:
data['idtype'] = idtype
try:
tree = pubmed_client.send_request(pmid_convert_url, data)
except Exception as e:
logger.error('Error looking up PMID in PMC: %s' % e)
return {}
if tree is None:
return {}
record = tree.find('record')
if record is None:
return {}
doi = record.attrib.get('doi')
pmid = record.attrib.get('pmid')
pmcid = record.attrib.get('pmcid')
ids = {'doi': doi,
'pmid': pmid,
'pmcid': pmcid}
return ids | [2][SEP1][If][None][If][None][If][None][If][If][None][None][Try][None][Return][If][Return][If][Return][Return][SEP2][1,2][][3,4][4][5,6][7][8,7][9,10][7][10][11,12][13][][14,15][][16,17][][][SEP3][0][1][2][0][2][0][2][0][0][0][0][1][1][0][0][1][0][3] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_CONSTANT_EXPR_CONSTANT_IF_BOOLOP_AND_COMPARE_NAME_LOAD_ISNOT_CONSTANT_COMPARE_NAME_LOAD_NOTIN_TUPLE_CONSTANT_CONSTANT_CONSTANT_LOAD_RAISE_CALL_NAME_LOAD_BINOP_CONSTANT_MOD_NAME_LOAD_IF_CALL_ATTRIBUTE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CONSTANT_ASSIGN_NAME_STORE_CONSTANT_IF_CALL_ATTRIBUTE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CONSTANT_ASSIGN_NAME_STORE_SUBSCRIPT_NAME_LOAD_SLICE_CONSTANT_LOAD_IF_CALL_ATTRIBUTE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CONSTANT_ASSIGN_NAME_STORE_SUBSCRIPT_NAME_LOAD_SLICE_CONSTANT_LOAD_ASSIGN_NAME_STORE_DICT_CONSTANT_NAME_LOAD_IF_COMPARE_NAME_LOAD_ISNOT_CONSTANT_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_NAME_LOAD_TRY_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_NAME_LOAD_EXCEPTHANDLER_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_BINOP_CONSTANT_MOD_NAME_LOAD_RETURN_DICT_IF_COMPARE_NAME_LOAD_IS_CONSTANT_RETURN_DICT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_IF_COMPARE_NAME_LOAD_IS_CONSTANT_RETURN_DICT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CONSTANT_ASSIGN_NAME_STORE_DICT_CONSTANT_CONSTANT_CONSTANT_NAME_LOAD_NAME_LOAD_NAME_LOAD_RETURN_NAME_LOAD |
def _make_sentence(txt):
"""Make a sentence from a piece of text."""
#Make sure first letter is capitalized
txt = txt.strip(' ')
txt = txt[0].upper() + txt[1:] + '.'
return txt | [1][SEP1][Return][SEP2][][SEP3][2] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_ASSIGN_NAME_STORE_BINOP_BINOP_CALL_ATTRIBUTE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_LOAD_ADD_SUBSCRIPT_NAME_LOAD_SLICE_CONSTANT_LOAD_ADD_CONSTANT_RETURN_NAME_LOAD |
def join_json_files(prefix):
"""Join different REACH output JSON files into a single JSON object.
The output of REACH is broken into three files that need to be joined
before processing. Specifically, there will be three files of the form:
`<prefix>.uaz.<subcategory>.json`.
Parameters
----------
prefix : str
The absolute path up to the extensions that reach will add.
Returns
-------
json_obj : dict
The result of joining the files, keyed by the three subcategories.
"""
try:
with open(prefix + '.uaz.entities.json', 'rt') as f:
entities = json.load(f)
with open(prefix + '.uaz.events.json', 'rt') as f:
events = json.load(f)
with open(prefix + '.uaz.sentences.json', 'rt') as f:
sentences = json.load(f)
except IOError as e:
logger.error(
'Failed to open JSON files for %s; REACH error?' % prefix
)
logger.exception(e)
return None
return {'events': events, 'entities': entities, 'sentences': sentences} | [1][SEP1][Try][None][Return][None][None][None][None][None][Return][SEP2][1,2][3][][4][5][6][7][8][][SEP3][4][1][2][1][1][1][1][1][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_TRY_WITH_WITHITEM_CALL_NAME_LOAD_BINOP_NAME_LOAD_ADD_CONSTANT_CONSTANT_NAME_STORE_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_WITH_WITHITEM_CALL_NAME_LOAD_BINOP_NAME_LOAD_ADD_CONSTANT_CONSTANT_NAME_STORE_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_WITH_WITHITEM_CALL_NAME_LOAD_BINOP_NAME_LOAD_ADD_CONSTANT_CONSTANT_NAME_STORE_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_EXCEPTHANDLER_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_BINOP_CONSTANT_MOD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_RETURN_CONSTANT_RETURN_DICT_CONSTANT_CONSTANT_CONSTANT_NAME_LOAD_NAME_LOAD_NAME_LOAD |
def _make_concept(self, entity):
"""Return Concept from a Hume entity."""
# Use the canonical name as the name of the Concept by default
name = self._sanitize(entity['canonicalName'])
# But if there is a trigger head text, we prefer that since
# it almost always results in a cleaner name
# This is removed for now since the head word seems to be too
# minimal for some concepts, e.g. it gives us only "security"
# for "food security".
"""
trigger = entity.get('trigger')
if trigger is not None:
head_text = trigger.get('head text')
if head_text is not None:
name = head_text
"""
# Save raw text and Hume scored groundings as db_refs
db_refs = _get_grounding(entity)
concept = Concept(name, db_refs=db_refs)
metadata = {arg['type']: arg['value']['@id']
for arg in entity['arguments']}
return concept, metadata | [2][SEP1][Return][SEP2][][SEP3][3] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_EXPR_CONSTANT_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_KEYWORD_NAME_LOAD_ASSIGN_NAME_STORE_DICTCOMP_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_SUBSCRIPT_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_CONSTANT_LOAD_COMPREHENSION_NAME_STORE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_RETURN_TUPLE_NAME_LOAD_NAME_LOAD_LOAD |
def preprocess_plain_text_file(self, filename, pmid, extra_annotations):
"""Preprocess a plain text file for use with ISI reder.
Preprocessing results in a new text file with one sentence
per line.
Parameters
----------
filename : str
The name of the plain text file
pmid : str
The PMID from which it comes, or None if not specified
extra_annotations : dict
Extra annotations to be added to each statement, possibly including
metadata about the source (annotations with the key "interaction"
will be overridden)
"""
with codecs.open(filename, 'r', encoding='utf-8') as f:
content = f.read()
self.preprocess_plain_text_string(content, pmid,
extra_annotations) | [4][SEP1][None][None][SEP2][1][][SEP3][1][2] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_ARG_EXPR_CONSTANT_WITH_WITHITEM_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_CONSTANT_KEYWORD_CONSTANT_NAME_STORE_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_NAME_LOAD_NAME_LOAD |
def comment_update(self, comment_id, body):
"""Function to update a comment (Requires login).
Parameters:
comment_id (int):
body (str):
"""
params = {'comment[body]': body}
return self._get('comments/{0}.json'.format(comment_id), params, 'PUT',
auth=True) | [3][SEP1][Return][SEP2][][SEP3][2] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_DICT_CONSTANT_NAME_LOAD_RETURN_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CALL_ATTRIBUTE_CONSTANT_LOAD_NAME_LOAD_NAME_LOAD_CONSTANT_KEYWORD_CONSTANT |
def note_list(self, body_matches=None, post_id=None, post_tags_match=None,
creator_name=None, creator_id=None, is_active=None):
"""Return list of notes.
Parameters:
body_matches (str): The note's body matches the given terms.
post_id (int): A specific post.
post_tags_match (str): The note's post's tags match the given terms.
creator_name (str): The creator's name. Exact match.
creator_id (int): The creator's user id.
is_active (bool): Can be: True, False.
"""
params = {
'search[body_matches]': body_matches,
'search[post_id]': post_id,
'search[post_tags_match]': post_tags_match,
'search[creator_name]': creator_name,
'search[creator_id]': creator_id,
'search[is_active]': is_active
}
return self._get('notes.json', params) | [7][SEP1][Return][SEP2][][SEP3][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_ARG_ARG_ARG_ARG_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_EXPR_CONSTANT_ASSIGN_NAME_STORE_DICT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_NAME_LOAD_NAME_LOAD_NAME_LOAD_NAME_LOAD_NAME_LOAD_NAME_LOAD_RETURN_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_NAME_LOAD |
def wiki_create(self, title, body, other_names=None):
"""Action to lets you create a wiki page (Requires login) (UNTESTED).
Parameters:
title (str): Page title.
body (str): Page content.
other_names (str): Other names.
"""
params = {
'wiki_page[title]': title,
'wiki_page[body]': body,
'wiki_page[other_names]': other_names
}
return self._get('wiki_pages.json', params, method='POST', auth=True) | [4][SEP1][Return][SEP2][][SEP3][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_ARG_CONSTANT_EXPR_CONSTANT_ASSIGN_NAME_STORE_DICT_CONSTANT_CONSTANT_CONSTANT_NAME_LOAD_NAME_LOAD_NAME_LOAD_RETURN_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_NAME_LOAD_KEYWORD_CONSTANT_KEYWORD_CONSTANT |
def artist_create(self, name, urls=None, alias=None, group=None):
"""Function to create an artist (Requires login) (UNTESTED).
Parameters:
name (str): The artist's name.
urls (str): A list of URLs associated with the artist, whitespace
delimited.
alias (str): The artist that this artist is an alias for. Simply
enter the alias artist's name.
group (str): The group or cicle that this artist is a member of.
Simply:param enter the group's name.
"""
params = {
'artist[name]': name,
'artist[urls]': urls,
'artist[alias]': alias,
'artist[group]': group
}
return self._get('artist/create', params, method='POST') | [5][SEP1][Return][SEP2][][SEP3][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_ARG_ARG_CONSTANT_CONSTANT_CONSTANT_EXPR_CONSTANT_ASSIGN_NAME_STORE_DICT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_NAME_LOAD_NAME_LOAD_NAME_LOAD_NAME_LOAD_RETURN_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_NAME_LOAD_KEYWORD_CONSTANT |
def user_can_edit_news(user):
"""
Check if the user has permission to edit any of the registered NewsItem
types.
"""
newsitem_models = [model.get_newsitem_model()
for model in NEWSINDEX_MODEL_CLASSES]
if user.is_active and user.is_superuser:
# admin can edit news iff any news types exist
return bool(newsitem_models)
for NewsItem in newsitem_models:
for perm in format_perms(NewsItem, ['add', 'change', 'delete']):
if user.has_perm(perm):
return True
return False | [1][SEP1][If][Return][For][For][Return][If][Return][SEP2][1,2][][3,4][5,2][][6,3][][SEP3][1][1][0][1][0][1][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_LISTCOMP_CALL_ATTRIBUTE_NAME_LOAD_LOAD_COMPREHENSION_NAME_STORE_NAME_LOAD_IF_BOOLOP_AND_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_RETURN_CALL_NAME_LOAD_NAME_LOAD_FOR_NAME_STORE_NAME_LOAD_FOR_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_LIST_CONSTANT_CONSTANT_CONSTANT_LOAD_IF_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_RETURN_CONSTANT_RETURN_CONSTANT |
def datetime_match(data, dts):
"""
matching of datetimes in time columns for data filtering
"""
dts = dts if islistable(dts) else [dts]
if any([not isinstance(i, datetime.datetime) for i in dts]):
error_msg = (
"`time` can only be filtered by datetimes"
)
raise TypeError(error_msg)
return data.isin(dts) | [2][SEP1][If][None][Return][SEP2][1,2][][][SEP3][3][1][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_IFEXP_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_LIST_NAME_LOAD_LOAD_IF_CALL_NAME_LOAD_LISTCOMP_UNARYOP_NOT_CALL_NAME_LOAD_NAME_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_COMPREHENSION_NAME_STORE_NAME_LOAD_ASSIGN_NAME_STORE_CONSTANT_RAISE_CALL_NAME_LOAD_NAME_LOAD_RETURN_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD |
def update(self, rc):
"""Add additional run control parameters
Parameters
----------
rc : string, file, dictionary, optional
a path to a YAML file, a file handle for a YAML file, or a
dictionary describing run control configuration
"""
rc = self._load_yaml(rc)
self.store = _recursive_update(self.store, rc) | [2][SEP1][None][SEP2][][SEP3][2] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_ASSIGN_ATTRIBUTE_NAME_LOAD_STORE_CALL_NAME_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD |
def mutate(self):
"""
Upgrades this Instance to the latest generation type
"""
self._client.post('{}/mutate'.format(Instance.api_endpoint), model=self)
return True | [1][SEP1][Return][SEP2][][SEP3][2] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_EXPR_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CALL_ATTRIBUTE_CONSTANT_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_KEYWORD_NAME_LOAD_RETURN_CONSTANT |
def events_mark_seen(self, event):
"""
Marks event as the last event we have seen. If event is an int, it is treated
as an event_id, otherwise it should be an event object whose id will be used.
"""
last_seen = event if isinstance(event, int) else event.id
self.client.post('{}/seen'.format(Event.api_endpoint), model=Event(self.client, last_seen)) | [2][SEP1][None][SEP2][][SEP3][4] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_IFEXP_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_NAME_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CALL_ATTRIBUTE_CONSTANT_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_KEYWORD_CALL_NAME_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD |
def iter_chain(cur):
"""Iterate over all of the chains in the database.
Args:
cur (:class:`sqlite3.Cursor`):
An sqlite3 cursor. This function is meant to be run within a :obj:`with` statement.
Yields:
list: The chain.
"""
select = "SELECT nodes FROM chain"
for nodes, in cur.execute(select):
yield json.loads(nodes) | [1][SEP1][None][For][None][SEP2][1][2][1][SEP3][0][1][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_CONSTANT_FOR_TUPLE_NAME_STORE_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_EXPR_YIELD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD |
def _contains_line(self, line):
"""Test if a chain of qubits is completely contained in ``self``. In
particular, test if all qubits are present and the couplers
connecting those qubits are also connected.
NOTE: this function assumes that ``line`` is a list or tuple of
qubits which satisfies the precondition that ``(line[i],line[i+1])``
is supposed to be a coupler for all ``i``.
INPUTS:
line: a list of qubits satisfying the above precondition
OUTPUT:
boolean
"""
return all(v in self for v in line) and all(u in self[v] for u, v in zip(line, line[1::])) | [2][SEP1][Return][SEP2][][SEP3][3] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_EXPR_CONSTANT_RETURN_BOOLOP_AND_CALL_NAME_LOAD_GENERATOREXP_COMPARE_NAME_LOAD_IN_NAME_LOAD_COMPREHENSION_NAME_STORE_NAME_LOAD_CALL_NAME_LOAD_GENERATOREXP_COMPARE_NAME_LOAD_IN_SUBSCRIPT_NAME_LOAD_NAME_LOAD_LOAD_COMPREHENSION_TUPLE_NAME_STORE_NAME_STORE_STORE_CALL_NAME_LOAD_NAME_LOAD_SUBSCRIPT_NAME_LOAD_SLICE_CONSTANT_LOAD |
def __related_categories(self, category_id):
""" Get all related categories to a given one """
related = []
for cat in self.categories_tree:
if category_id in self.categories_tree[cat]:
related.append(self.categories[cat])
return related | [2][SEP1][None][For][If][Return][None][SEP2][1][2,3][4,1][][1][SEP3][0][0][0][0][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_LIST_LOAD_FOR_NAME_STORE_ATTRIBUTE_NAME_LOAD_LOAD_IF_COMPARE_NAME_LOAD_IN_SUBSCRIPT_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_SUBSCRIPT_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_LOAD_RETURN_NAME_LOAD |
def get_identities(self, item):
""" Return the identities from an item """
data = item['data']
if 'assigned_to' in data:
user = self.get_sh_identity(data, 'assigned_to')
yield user
author = self.get_sh_identity(data, 'author')
yield author | [2][SEP1][If][None][None][SEP2][1,2][2][][SEP3][0][1][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_IF_COMPARE_CONSTANT_IN_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_CONSTANT_EXPR_YIELD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_CONSTANT_EXPR_YIELD_NAME_LOAD |
def delete_items(self, retention_time, time_field="metadata__updated_on"):
"""Delete documents updated before a given date
:param retention_time: maximum number of minutes wrt the current date to retain the data
:param time_field: time field to delete the data
"""
if retention_time is None:
logger.debug("[items retention] Retention policy disabled, no items will be deleted.")
return
if retention_time <= 0:
logger.debug("[items retention] Minutes to retain must be greater than 0.")
return
before_date = get_diff_current_date(minutes=retention_time)
before_date_str = before_date.isoformat()
es_query = '''
{
"query": {
"range": {
"%s": {
"lte": "%s"
}
}
}
}
''' % (time_field, before_date_str)
r = self.requests.post(self.index_url + "/_delete_by_query?refresh",
data=es_query, headers=HEADER_JSON, verify=False)
try:
r.raise_for_status()
r_json = r.json()
logger.debug("[items retention] %s items deleted from %s before %s.",
r_json['deleted'], self.anonymize_url(self.index_url), before_date)
except requests.exceptions.HTTPError as ex:
logger.error("[items retention] Error deleted items from %s.", self.anonymize_url(self.index_url))
logger.error(ex)
return | [3][SEP1][If][Return][If][Return][Try][None][Return][SEP2][1,2][][3,4][][5,6][][][SEP3][0][1][0][1][3][4][3] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_CONSTANT_EXPR_CONSTANT_IF_COMPARE_NAME_LOAD_IS_CONSTANT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_RETURN_IF_COMPARE_NAME_LOAD_LTE_CONSTANT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_RETURN_ASSIGN_NAME_STORE_CALL_NAME_LOAD_KEYWORD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_BINOP_CONSTANT_MOD_TUPLE_NAME_LOAD_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_BINOP_ATTRIBUTE_NAME_LOAD_LOAD_ADD_CONSTANT_KEYWORD_NAME_LOAD_KEYWORD_NAME_LOAD_KEYWORD_CONSTANT_TRY_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_EXCEPTHANDLER_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_RETURN |
def get_params_parser_create_dash():
"""Parse command line arguments"""
parser = argparse.ArgumentParser(usage="usage: e2k.py [options]",
description="Create a Kibana dashboard from a template")
ElasticOcean.add_params(parser)
parser.add_argument("-d", "--dashboard", help="dashboard to be used as template")
parser.add_argument("-i", "--index", help="enriched index to be used as data source")
parser.add_argument("--kibana", dest="kibana_index", default=".kibana",
help="Kibana index name (.kibana default)")
parser.add_argument('-g', '--debug', dest='debug', action='store_true')
return parser | [0][SEP1][Return][SEP2][][SEP3][6] | MODULE_FUNCTIONDEF_ARGUMENTS_EXPR_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_KEYWORD_CONSTANT_KEYWORD_CONSTANT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CONSTANT_KEYWORD_CONSTANT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CONSTANT_KEYWORD_CONSTANT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_KEYWORD_CONSTANT_KEYWORD_CONSTANT_KEYWORD_CONSTANT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CONSTANT_KEYWORD_CONSTANT_KEYWORD_CONSTANT_RETURN_NAME_LOAD |
def get_domain(self, identity):
""" Get the domain from a SH identity """
domain = None
if identity['email']:
try:
domain = identity['email'].split("@")[1]
except IndexError:
# logger.warning("Bad email format: %s" % (identity['email']))
pass
return domain | [2][SEP1][If][Try][Return][None][None][SEP2][1,2][3,4][][2][2][SEP3][0][0][0][1][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_CONSTANT_IF_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_TRY_ASSIGN_NAME_STORE_SUBSCRIPT_CALL_ATTRIBUTE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_LOAD_CONSTANT_CONSTANT_LOAD_EXCEPTHANDLER_NAME_LOAD_PASS_RETURN_NAME_LOAD |
def _fix_review_dates(self, item):
"""Convert dates so ES detect them"""
for date_field in ['timestamp', 'createdOn', 'lastUpdated']:
if date_field in item.keys():
date_ts = item[date_field]
item[date_field] = unixtime_to_datetime(date_ts).isoformat()
if 'patchSets' in item.keys():
for patch in item['patchSets']:
pdate_ts = patch['createdOn']
patch['createdOn'] = unixtime_to_datetime(pdate_ts).isoformat()
if 'approvals' in patch:
for approval in patch['approvals']:
adate_ts = approval['grantedOn']
approval['grantedOn'] = unixtime_to_datetime(adate_ts).isoformat()
if 'comments' in item.keys():
for comment in item['comments']:
cdate_ts = comment['timestamp']
comment['timestamp'] = unixtime_to_datetime(cdate_ts).isoformat() | [2][SEP1][None][For][If][If][None][For][If][If][For][For][None][None][SEP2][1][2,3][4,1][5,6][1][7,6][8][9,5][10][11,5][8][9][SEP3][0][0][1][1][2][0][1][2][0][0][2][2] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_EXPR_CONSTANT_FOR_NAME_STORE_LIST_CONSTANT_CONSTANT_CONSTANT_LOAD_IF_COMPARE_NAME_LOAD_IN_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_SUBSCRIPT_NAME_LOAD_NAME_LOAD_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_NAME_LOAD_STORE_CALL_ATTRIBUTE_CALL_NAME_LOAD_NAME_LOAD_LOAD_IF_COMPARE_CONSTANT_IN_CALL_ATTRIBUTE_NAME_LOAD_LOAD_FOR_NAME_STORE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_ASSIGN_NAME_STORE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_CALL_ATTRIBUTE_CALL_NAME_LOAD_NAME_LOAD_LOAD_IF_COMPARE_CONSTANT_IN_NAME_LOAD_FOR_NAME_STORE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_ASSIGN_NAME_STORE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_CALL_ATTRIBUTE_CALL_NAME_LOAD_NAME_LOAD_LOAD_IF_COMPARE_CONSTANT_IN_CALL_ATTRIBUTE_NAME_LOAD_LOAD_FOR_NAME_STORE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_ASSIGN_NAME_STORE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_CALL_ATTRIBUTE_CALL_NAME_LOAD_NAME_LOAD_LOAD |
def update_items(self, ocean_backend, enrich_backend):
"""Retrieve the commits not present in the original repository and delete
the corresponding documents from the raw and enriched indexes"""
fltr = {
'name': 'origin',
'value': [self.perceval_backend.origin]
}
logger.debug("[update-items] Checking commits for %s.", self.perceval_backend.origin)
git_repo = GitRepository(self.perceval_backend.uri, self.perceval_backend.gitpath)
try:
current_hashes = set([commit for commit in git_repo.rev_list()])
except Exception as e:
logger.error("Skip updating branch info for repo %s, git rev-list command failed: %s", git_repo.uri, e)
return
raw_hashes = set([item['data']['commit']
for item in ocean_backend.fetch(ignore_incremental=True, _filter=fltr)])
hashes_to_delete = list(raw_hashes.difference(current_hashes))
to_process = []
for _hash in hashes_to_delete:
to_process.append(_hash)
if len(to_process) != MAX_BULK_UPDATE_SIZE:
continue
# delete documents from the raw index
self.remove_commits(to_process, ocean_backend.elastic.index_url,
'data.commit', self.perceval_backend.origin)
# delete documents from the enriched index
self.remove_commits(to_process, enrich_backend.elastic.index_url,
'hash', self.perceval_backend.origin)
to_process = []
if to_process:
# delete documents from the raw index
self.remove_commits(to_process, ocean_backend.elastic.index_url,
'data.commit', self.perceval_backend.origin)
# delete documents from the enriched index
self.remove_commits(to_process, enrich_backend.elastic.index_url,
'hash', self.perceval_backend.origin)
logger.debug("[update-items] %s commits deleted from %s with origin %s.",
len(hashes_to_delete), ocean_backend.elastic.anonymize_url(ocean_backend.elastic.index_url),
self.perceval_backend.origin)
logger.debug("[update-items] %s commits deleted from %s with origin %s.",
len(hashes_to_delete), enrich_backend.elastic.anonymize_url(enrich_backend.elastic.index_url),
self.perceval_backend.origin)
# update branch info
self.delete_commit_branches(enrich_backend)
self.add_commit_branches(git_repo, enrich_backend) | [3][SEP1][Try][None][Return][None][For][If][If][None][None][None][SEP2][1,2][3][][4][5,6][7,4][8,9][4][9][][SEP3][2][2][1][4][2][2][0][2][2][8] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_DICT_CONSTANT_CONSTANT_CONSTANT_LIST_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_TRY_ASSIGN_NAME_STORE_CALL_NAME_LOAD_LISTCOMP_NAME_LOAD_COMPREHENSION_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_EXCEPTHANDLER_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_RETURN_ASSIGN_NAME_STORE_CALL_NAME_LOAD_LISTCOMP_SUBSCRIPT_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_CONSTANT_LOAD_COMPREHENSION_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_KEYWORD_CONSTANT_KEYWORD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_LIST_LOAD_FOR_NAME_STORE_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_IF_COMPARE_CALL_NAME_LOAD_NAME_LOAD_NOTEQ_NAME_LOAD_CONTINUE_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CONSTANT_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CONSTANT_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_ASSIGN_NAME_STORE_LIST_LOAD_IF_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CONSTANT_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CONSTANT_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CALL_NAME_LOAD_NAME_LOAD_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CALL_NAME_LOAD_NAME_LOAD_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_NAME_LOAD |
def _serialize_fields(point):
"""Field values can be floats, integers, strings, or Booleans."""
output = []
for k, v in point['fields'].items():
k = escape(k, key_escape)
if isinstance(v, bool):
output.append(f'{k}={v}')
elif isinstance(v, int):
output.append(f'{k}={v}i')
elif isinstance(v, str):
output.append(f'{k}="{v.translate(str_escape)}"')
elif v is None:
# Empty values
continue
else:
# Floats
output.append(f'{k}={v}')
return ','.join(output) | [1][SEP1][None][For][If][Return][None][If][None][If][None][If][None][SEP2][1][2,3][4,5][][1][6,7][1][8,9][1][10,1][1][SEP3][0][1][2][1][1][1][1][1][2][0][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_LIST_LOAD_FOR_TUPLE_NAME_STORE_NAME_STORE_STORE_CALL_ATTRIBUTE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_IF_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_JOINEDSTR_FORMATTEDVALUE_NAME_LOAD_CONSTANT_FORMATTEDVALUE_NAME_LOAD_IF_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_JOINEDSTR_FORMATTEDVALUE_NAME_LOAD_CONSTANT_FORMATTEDVALUE_NAME_LOAD_CONSTANT_IF_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_JOINEDSTR_FORMATTEDVALUE_NAME_LOAD_CONSTANT_FORMATTEDVALUE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_CONSTANT_IF_COMPARE_NAME_LOAD_IS_CONSTANT_CONTINUE_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_JOINEDSTR_FORMATTEDVALUE_NAME_LOAD_CONSTANT_FORMATTEDVALUE_NAME_LOAD_RETURN_CALL_ATTRIBUTE_CONSTANT_LOAD_NAME_LOAD |
def user_login(self, email=None, password=None):
"""Login with email, password and get back a session cookie
:type email: str
:param email: The email used for authentication
:type password: str
:param password: The password used for authentication
"""
email = six.moves.input("Email: ") if email is None else email
password = getpass.getpass() if password is None else password
login_data = {
"method": "user.login",
"params": {"email": email,
"pass": password}
}
# If the user/password match, the server respond will contain a
# session cookie that you can use to authenticate future requests.
r = self.session.post(
self.base_api_urls["logic"],
data=json.dumps(login_data),
)
if r.json()["result"] not in ["OK"]:
raise AuthenticationError("Could not authenticate.\n{}"
.format(r.json())) | [3][SEP1][If][None][SEP2][1][][SEP3][5][3] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_CONSTANT_CONSTANT_EXPR_CONSTANT_ASSIGN_NAME_STORE_IFEXP_COMPARE_NAME_LOAD_IS_CONSTANT_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CONSTANT_NAME_LOAD_ASSIGN_NAME_STORE_IFEXP_COMPARE_NAME_LOAD_IS_CONSTANT_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_DICT_CONSTANT_CONSTANT_CONSTANT_DICT_CONSTANT_CONSTANT_NAME_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_SUBSCRIPT_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_LOAD_KEYWORD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_IF_COMPARE_SUBSCRIPT_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_LOAD_NOTIN_LIST_CONSTANT_LOAD_RAISE_CALL_NAME_LOAD_CALL_ATTRIBUTE_CONSTANT_LOAD_CALL_ATTRIBUTE_NAME_LOAD_LOAD |
def resolve_post(self, post):
"""Mark post as resolved
:type post: dict|str|int
:param post: Either the post dict returned by another API method, or
the `cid` field of that post.
:returns: True if it is successful. False otherwise
"""
try:
cid = post["id"]
except KeyError:
cid = post
params = {
"cid": cid,
"resolved": "true"
}
return self._rpc.content_mark_resolved(params) | [2][SEP1][Try][None][None][Return][SEP2][1,2][3][3][][SEP3][0][0][0][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_EXPR_CONSTANT_TRY_ASSIGN_NAME_STORE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_EXCEPTHANDLER_NAME_LOAD_ASSIGN_NAME_STORE_NAME_LOAD_ASSIGN_NAME_STORE_DICT_CONSTANT_CONSTANT_NAME_LOAD_CONSTANT_RETURN_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_NAME_LOAD |
def metric_names(self, id, name=None, page=None):
"""
Return a list of known metrics and their value names for the given resource.
:type id: int
:param id: Server ID
:type name: str
:param name: Filter metrics by name
:type page: int
:param page: Pagination index
:rtype: dict
:return: The JSON response of the API, with an additional 'pages' key
if there are paginated results
::
{
"metrics": [
{
"name": "string",
"values": [
"string"
]
}
],
"pages": {
"last": {
"url": "https://api.newrelic.com/v2/servers/{server_id}/metrics.json?page=2",
"rel": "last"
},
"next": {
"url": "https://api.newrelic.com/v2/servers/{server_id}/metrics.json?page=2",
"rel": "next"
}
}
}
"""
params = [
'name={0}'.format(name) if name else None,
'page={0}'.format(page) if page else None
]
return self._get(
url='{0}servers/{1}/metrics.json'.format(self.URL, id),
headers=self.headers,
params=self.build_param_string(params)
) | [4][SEP1][Return][SEP2][][SEP3][5] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_ARG_CONSTANT_CONSTANT_EXPR_CONSTANT_ASSIGN_NAME_STORE_LIST_IFEXP_NAME_LOAD_CALL_ATTRIBUTE_CONSTANT_LOAD_NAME_LOAD_CONSTANT_IFEXP_NAME_LOAD_CALL_ATTRIBUTE_CONSTANT_LOAD_NAME_LOAD_CONSTANT_LOAD_RETURN_CALL_ATTRIBUTE_NAME_LOAD_LOAD_KEYWORD_CALL_ATTRIBUTE_CONSTANT_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_KEYWORD_ATTRIBUTE_NAME_LOAD_LOAD_KEYWORD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD |
def list(
self, application_id, filter_hostname=None, filter_ids=None,
page=None):
"""
This API endpoint returns a paginated list of instances associated with the
given application.
Application instances can be filtered by hostname, or the list of
application instance IDs.
:type application_id: int
:param application_id: Application ID
:type filter_hostname: str
:param filter_hostname: Filter by server hostname
:type filter_ids: list of ints
:param filter_ids: Filter by application instance ids
:type page: int
:param page: Pagination index
:rtype: dict
:return: The JSON response of the API, with an additional 'pages' key
if there are paginated results
::
{
"application_instances": [
{
"id": "integer",
"application_name": "string",
"host": "string",
"port": "integer",
"language": "integer",
"health_status": "string",
"application_summary": {
"response_time": "float",
"throughput": "float",
"error_rate": "float",
"apdex_score": "float"
},
"end_user_summary": {
"response_time": "float",
"throughput": "float",
"apdex_score": "float"
},
"links": {
"application": "integer",
"application_host": "integer",
"server": "integer"
}
}
],
"pages": {
"last": {
"url": "https://api.newrelic.com/v2/applications/{application_id}/instances.json?page=2",
"rel": "last"
},
"next": {
"url": "https://api.newrelic.com/v2/applications/{application_id}/instances.json?page=2",
"rel": "next"
}
}
}
"""
filters = [
'filter[hostname]={0}'.format(filter_hostname) if filter_hostname else None,
'filter[ids]={0}'.format(','.join([str(app_id) for app_id in filter_ids])) if filter_ids else None,
'page={0}'.format(page) if page else None
]
return self._get(
url='{root}applications/{application_id}/instances.json'.format(
root=self.URL,
application_id=application_id
),
headers=self.headers,
params=self.build_param_string(filters)
) | [5][SEP1][Return][SEP2][][SEP3][8] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_ARG_ARG_CONSTANT_CONSTANT_CONSTANT_EXPR_CONSTANT_ASSIGN_NAME_STORE_LIST_IFEXP_NAME_LOAD_CALL_ATTRIBUTE_CONSTANT_LOAD_NAME_LOAD_CONSTANT_IFEXP_NAME_LOAD_CALL_ATTRIBUTE_CONSTANT_LOAD_CALL_ATTRIBUTE_CONSTANT_LOAD_LISTCOMP_CALL_NAME_LOAD_NAME_LOAD_COMPREHENSION_NAME_STORE_NAME_LOAD_CONSTANT_IFEXP_NAME_LOAD_CALL_ATTRIBUTE_CONSTANT_LOAD_NAME_LOAD_CONSTANT_LOAD_RETURN_CALL_ATTRIBUTE_NAME_LOAD_LOAD_KEYWORD_CALL_ATTRIBUTE_CONSTANT_LOAD_KEYWORD_ATTRIBUTE_NAME_LOAD_LOAD_KEYWORD_NAME_LOAD_KEYWORD_ATTRIBUTE_NAME_LOAD_LOAD_KEYWORD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD |
def makeNodeTuple(citation, idVal, nodeInfo, fullInfo, nodeType, count, coreCitesDict, coreValues, detailedValues, addCR):
"""Makes a tuple of idVal and a dict of the selected attributes"""
d = {}
if nodeInfo:
if nodeType == 'full':
if coreValues:
if citation in coreCitesDict:
R = coreCitesDict[citation]
d['MK-ID'] = R.id
if not detailedValues:
infoVals = []
for tag in coreValues:
tagVal = R.get(tag)
if isinstance(tagVal, str):
infoVals.append(tagVal.replace(',',''))
elif isinstance(tagVal, list):
infoVals.append(tagVal[0].replace(',',''))
else:
pass
d['info'] = ', '.join(infoVals)
else:
for tag in coreValues:
v = R.get(tag, None)
if isinstance(v, list):
d[tag] = '|'.join(sorted(v))
else:
d[tag] = v
d['inCore'] = True
if addCR:
d['citations'] = '|'.join((str(c) for c in R.get('citations', [])))
else:
d['MK-ID'] = 'None'
d['info'] = citation.allButDOI()
d['inCore'] = False
if addCR:
d['citations'] = ''
else:
d['info'] = citation.allButDOI()
elif nodeType == 'journal':
if citation.isJournal():
d['info'] = str(citation.FullJournalName())
else:
d['info'] = "None"
elif nodeType == 'original':
d['info'] = str(citation)
else:
d['info'] = idVal
if fullInfo:
d['fullCite'] = str(citation)
if count:
d['count'] = 1
return (idVal, d) | [10][SEP1][If][If][If][If][If][None][If][If][None][If][If][None][Return][If][If][None][None][None][None][None][For][None][For][If][If][If][None][None][None][None][None][If][None][None][SEP2][1,2][3,4][5,6][7,8][9,10][6][11,12][13,14][2][15,16][17,18][12][][19,20][21,2][2][2][2][2][22][23,24][2][25,26][27,28][29,2][30,31][24][20][20][2][22][32,33][22][22][SEP3][0][0][0][0][0][1][0][3][1][1][0][0][0][8][1][2][0][1][0][0][0][0][0][2][0][2][1][2][0][3][2][1][2][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_ARG_ARG_ARG_ARG_ARG_ARG_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_DICT_IF_NAME_LOAD_IF_COMPARE_NAME_LOAD_EQ_CONSTANT_IF_NAME_LOAD_IF_COMPARE_NAME_LOAD_IN_NAME_LOAD_ASSIGN_NAME_STORE_SUBSCRIPT_NAME_LOAD_NAME_LOAD_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_ATTRIBUTE_NAME_LOAD_LOAD_IF_UNARYOP_NOT_NAME_LOAD_ASSIGN_NAME_STORE_LIST_LOAD_FOR_NAME_STORE_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_IF_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CONSTANT_IF_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CALL_ATTRIBUTE_SUBSCRIPT_NAME_LOAD_CONSTANT_LOAD_LOAD_CONSTANT_CONSTANT_PASS_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_CALL_ATTRIBUTE_CONSTANT_LOAD_NAME_LOAD_FOR_NAME_STORE_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_CONSTANT_IF_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_NAME_LOAD_STORE_CALL_ATTRIBUTE_CONSTANT_LOAD_CALL_NAME_LOAD_NAME_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_NAME_LOAD_STORE_NAME_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_CONSTANT_IF_NAME_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_CALL_ATTRIBUTE_CONSTANT_LOAD_GENERATOREXP_CALL_NAME_LOAD_NAME_LOAD_COMPREHENSION_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_LIST_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_CONSTANT_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_CONSTANT_IF_NAME_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_CONSTANT_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_IF_COMPARE_NAME_LOAD_EQ_CONSTANT_IF_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_CALL_NAME_LOAD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_CONSTANT_IF_COMPARE_NAME_LOAD_EQ_CONSTANT_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_CALL_NAME_LOAD_NAME_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_NAME_LOAD_IF_NAME_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_CALL_NAME_LOAD_NAME_LOAD_IF_NAME_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_CONSTANT_RETURN_TUPLE_NAME_LOAD_NAME_LOAD_LOAD |
def removeID(self, idVal):
"""Checks if the collected items contains the give _idVal_ and removes it if it is found, will raise a `KeyError` if item is not found
# Parameters
_idVal_ : `str`
> The removed id string
"""
for i in self:
if i.id == idVal:
self._collection.remove(i)
return
raise KeyError("A Record with the ID '{}' was not found in the RecordCollection: '{}'.".format(idVal, self)) | [2][SEP1][None][For][If][None][Return][SEP2][1][2,3][4,1][][][SEP3][0][0][0][2][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_EXPR_CONSTANT_FOR_NAME_STORE_NAME_LOAD_IF_COMPARE_ATTRIBUTE_NAME_LOAD_LOAD_EQ_NAME_LOAD_EXPR_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_NAME_LOAD_RETURN_RAISE_CALL_NAME_LOAD_CALL_ATTRIBUTE_CONSTANT_LOAD_NAME_LOAD_NAME_LOAD |
def j9urlGenerator(nameDict = False):
"""How to get all the urls for the WOS Journal Title Abbreviations. Each is varies by only a few characters. These are the currently in use urls they may change.
They are of the form:
> "https://images.webofknowledge.com/images/help/WOS/{VAL}_abrvjt.html"
> Where {VAL} is a capital letter or the string "0-9"
# Returns
`list[str]`
> A list of all the url's strings
"""
start = "https://images.webofknowledge.com/images/help/WOS/"
end = "_abrvjt.html"
if nameDict:
urls = {"0-9" : start + "0-9" + end}
for c in string.ascii_uppercase:
urls[c] = start + c + end
else:
urls = [start + "0-9" + end]
for c in string.ascii_uppercase:
urls.append(start + c + end)
return urls | [1][SEP1][If][None][None][For][For][None][Return][None][SEP2][1,2][3][4][5,6][7,6][3][][4][SEP3][1][0][0][0][0][0][0][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_CONSTANT_EXPR_CONSTANT_ASSIGN_NAME_STORE_CONSTANT_ASSIGN_NAME_STORE_CONSTANT_IF_NAME_LOAD_ASSIGN_NAME_STORE_DICT_CONSTANT_BINOP_BINOP_NAME_LOAD_ADD_CONSTANT_ADD_NAME_LOAD_FOR_NAME_STORE_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_NAME_LOAD_STORE_BINOP_BINOP_NAME_LOAD_ADD_NAME_LOAD_ADD_NAME_LOAD_ASSIGN_NAME_STORE_LIST_BINOP_BINOP_NAME_LOAD_ADD_CONSTANT_ADD_NAME_LOAD_LOAD_FOR_NAME_STORE_ATTRIBUTE_NAME_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_BINOP_BINOP_NAME_LOAD_ADD_NAME_LOAD_ADD_NAME_LOAD_RETURN_NAME_LOAD |
def _filter_pending_updates(self):
"""
Return all the updates that need to be applied, from a list of all the
updates that were called while the hold was active. This method is
meant to be overridden by subclasses that want to customize how held
updates are applied.
The `self._pending_updates` member variable is a list containing a
(method, args, kwargs) tuple for each update that was called while
updates were being held. This list is in the order that the updates
were actually called, and any updates that were called more than once
will appear in this list more than once.
This method should yield or return an list of the tuples in the same
format representing the updates that should be applied, in the order
they should be applied. The default implementation filters out
duplicate updates without changing their order. In cases where it
matters, the last call to each update is used to determine the order.
"""
from more_itertools import unique_everseen as unique
yield from reversed(list(unique(reversed(self._pending_updates)))) | [1][SEP1][None][SEP2][][SEP3][4] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_IMPORTFROM_ALIAS_EXPR_YIELDFROM_CALL_NAME_LOAD_CALL_NAME_LOAD_CALL_NAME_LOAD_CALL_NAME_LOAD_ATTRIBUTE_NAME_LOAD_LOAD |
def cli_main(pid, include_greenlet, debugger, verbose):
'''Print stack of python process.
$ pystack <pid>
'''
try:
print_stack(pid, include_greenlet, debugger, verbose)
except DebuggerNotFound as e:
click.echo('DebuggerNotFound: %s' % e.args[0], err=True)
click.get_current_context().exit(1) | [4][SEP1][Try][None][None][SEP2][1,2][][][SEP3][0][1][3] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_ARG_EXPR_CONSTANT_TRY_EXPR_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD_NAME_LOAD_NAME_LOAD_EXCEPTHANDLER_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_BINOP_CONSTANT_MOD_SUBSCRIPT_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_LOAD_KEYWORD_CONSTANT_EXPR_CALL_ATTRIBUTE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_CONSTANT |
def validate_email(addr):
"""Validate an email address.
This function raises ``ValueError`` if the email address is not valid.
>>> validate_email('foo@bar.com')
'foo@bar.com'
>>> validate_email('foo@bar com')
Traceback (most recent call last):
...
ValueError: Invalid domain: bar com
"""
if '@' not in addr:
raise ValueError('Invalid email address: %s' % addr)
node, domain = addr.split('@', 1)
try:
domain = idna.encode(force_text(domain))
except idna.core.IDNAError:
raise ValueError('Invalid domain: %s' % domain)
return '%s@%s' % (node, force_text(domain)) | [1][SEP1][If][None][Try][None][None][Return][SEP2][1,2][][3,4][5][][][SEP3][0][1][1][2][1][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_IF_COMPARE_CONSTANT_NOTIN_NAME_LOAD_RAISE_CALL_NAME_LOAD_BINOP_CONSTANT_MOD_NAME_LOAD_ASSIGN_TUPLE_NAME_STORE_NAME_STORE_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CONSTANT_TRY_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CALL_NAME_LOAD_NAME_LOAD_EXCEPTHANDLER_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_RAISE_CALL_NAME_LOAD_BINOP_CONSTANT_MOD_NAME_LOAD_RETURN_BINOP_CONSTANT_MOD_TUPLE_NAME_LOAD_CALL_NAME_LOAD_NAME_LOAD_LOAD |
def bundle(self):
"""A list of any parent CAs, including this CA.
The list is ordered so the Root CA will be the first.
"""
ca = self
bundle = [ca]
while ca.parent is not None:
bundle.append(ca.parent)
ca = ca.parent
return bundle | [1][SEP1][None][While][None][Return][SEP2][1][2,3][1][][SEP3][0][0][1][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_NAME_LOAD_ASSIGN_NAME_STORE_LIST_NAME_LOAD_LOAD_WHILE_COMPARE_ATTRIBUTE_NAME_LOAD_LOAD_ISNOT_CONSTANT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_ATTRIBUTE_NAME_LOAD_LOAD_RETURN_NAME_LOAD |
def include_theme_files(self, fragment):
"""
Gets theme configuration and renders theme css into fragment
"""
theme = self.get_theme()
if not theme or 'package' not in theme:
return
theme_package, theme_files = theme.get('package', None), theme.get('locations', [])
resource_loader = ResourceLoader(theme_package)
for theme_file in theme_files:
fragment.add_css(resource_loader.load_unicode(theme_file)) | [2][SEP1][If][Return][None][For][None][SEP2][1,2][][3][4][3][SEP3][1][0][3][0][2] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_IF_BOOLOP_OR_UNARYOP_NOT_NAME_LOAD_COMPARE_CONSTANT_NOTIN_NAME_LOAD_RETURN_ASSIGN_TUPLE_NAME_STORE_NAME_STORE_STORE_TUPLE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CONSTANT_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_LIST_LOAD_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_NAME_LOAD_FOR_NAME_STORE_NAME_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD |
def is_requirement(line):
"""
Return True if the requirement line is a package requirement;
that is, it is not blank, a comment, a URL, or an included file.
"""
return not (
line == '' or
line.startswith('-r') or
line.startswith('#') or
line.startswith('-e') or
line.startswith('git+')
) | [1][SEP1][Return][SEP2][][SEP3][4] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_RETURN_UNARYOP_NOT_BOOLOP_OR_COMPARE_NAME_LOAD_EQ_CONSTANT_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT |
def _find_content(self, cont_name):
"""Search for a content_name in the content data, if not found the parent is searched."""
try:
a = self.content_data[cont_name]
return a
except KeyError:
if self.parent:
return self.parent._find_content(cont_name)
else:
# Fallback for no content (Raise NoContent?)
return "" | [2][SEP1][Try][Return][If][Return][Return][SEP2][1,2][][3,4][][][SEP3][0][0][0][1][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_EXPR_CONSTANT_TRY_ASSIGN_NAME_STORE_SUBSCRIPT_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_LOAD_RETURN_NAME_LOAD_EXCEPTHANDLER_NAME_LOAD_IF_ATTRIBUTE_NAME_LOAD_LOAD_RETURN_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_NAME_LOAD_RETURN_CONSTANT |
def read_config(name):
"""
配置读取
"""
name = name.lower()
conf_list = _read_config_list()
for conf in conf_list:
if conf.startswith(name):
return conf.split('=')[1].split('#')[0].strip()
return None | [1][SEP1][None][For][If][Return][Return][SEP2][1][2,3][4,1][][][SEP3][2][0][1][0][3] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_CALL_NAME_LOAD_FOR_NAME_STORE_NAME_LOAD_IF_CALL_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_RETURN_CALL_ATTRIBUTE_SUBSCRIPT_CALL_ATTRIBUTE_SUBSCRIPT_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_CONSTANT_LOAD_LOAD_CONSTANT_CONSTANT_LOAD_LOAD_RETURN_CONSTANT |
def _dict_of_results(self):
"""
Get the dictionary representation of results
:return: dict (str -> dict (str -> str))
"""
result_json = {}
result_list = []
for r in self.results:
result_list.append({
'name': r.check_name,
'ok': r.ok,
'status': r.status,
'description': r.description,
'message': r.message,
'reference_url': r.reference_url,
'logs': r.logs,
})
result_json["checks"] = result_list
return result_json | [1][SEP1][None][For][None][Return][SEP2][1][2,3][1][][SEP3][0][0][1][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_DICT_ASSIGN_NAME_STORE_LIST_LOAD_FOR_NAME_STORE_ATTRIBUTE_NAME_LOAD_LOAD_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_DICT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_CONSTANT_STORE_NAME_LOAD_RETURN_NAME_LOAD |
def ostree_path(self):
""" ostree repository -- content """
if self._ostree_path is None:
self._ostree_path = os.path.join(self.tmpdir, "ostree-repo")
subprocess.check_call(["ostree", "init", "--mode", "bare-user-only",
"--repo", self._ostree_path])
return self._ostree_path | [1][SEP1][If][None][Return][SEP2][1,2][2][][SEP3][0][2][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_IF_COMPARE_ATTRIBUTE_NAME_LOAD_LOAD_IS_CONSTANT_ASSIGN_ATTRIBUTE_NAME_LOAD_STORE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_LIST_CONSTANT_CONSTANT_CONSTANT_CONSTANT_CONSTANT_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_RETURN_ATTRIBUTE_NAME_LOAD_LOAD |
def quick_add(self, text, note=None, reminder=None):
"""Add a task using the 'Quick Add Task' syntax.
:param text: The text of the task that is parsed. A project
name starts with the `#` character, a label starts with a `@`
and an assignee starts with a `+`.
:type text: str
:param note: The content of the note.
:type note: str
:param reminder: The date of the reminder, added in free form text.
:type reminder: str
:return: The added task.
:rtype: :class:`pytodoist.todoist.Task`
>>> from pytodoist import todoist
>>> user = todoist.login('john.doe@gmail.com', 'password')
>>> task = user.quick_add('Install Pytodoist #personal @app')
>>> print(task.content)
Install PyTodoist
"""
response = API.quick_add(self.api_token, text,
note=note, reminder=reminder)
_fail_if_contains_errors(response)
task_json = response.json()
return Task(task_json, self) | [4][SEP1][Return][SEP2][][SEP3][4] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_ARG_CONSTANT_CONSTANT_EXPR_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_KEYWORD_NAME_LOAD_KEYWORD_NAME_LOAD_EXPR_CALL_NAME_LOAD_NAME_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_RETURN_CALL_NAME_LOAD_NAME_LOAD_NAME_LOAD |
def delete_collaborator(self, email):
"""Remove a collaborating user from the shared project.
:param email: The collaborator's email address.
:type email: str
>>> from pytodoist import todoist
>>> user = todoist.login('john.doe@gmail.com', 'password')
>>> project = user.get_project('PyTodoist')
>>> project.delete_collaborator('jane.doe@gmail.com')
"""
args = {
'project_id': self.id,
'email': email,
}
_perform_command(self.owner, 'delete_collaborator', args) | [2][SEP1][None][SEP2][][SEP3][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_DICT_CONSTANT_CONSTANT_ATTRIBUTE_NAME_LOAD_LOAD_NAME_LOAD_EXPR_CALL_NAME_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_NAME_LOAD |
def rfind(self, sub, start=None, end=None):
"""Return the highest index where substring sub is found, such that sub is contained within string[start:end].
Optional arguments start and end are interpreted as in slice notation.
:param str sub: Substring to search.
:param int start: Beginning position.
:param int end: Stop comparison at this position.
"""
return self.value_no_colors.rfind(sub, start, end) | [4][SEP1][Return][SEP2][][SEP3][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_ARG_CONSTANT_CONSTANT_EXPR_CONSTANT_RETURN_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_NAME_LOAD_NAME_LOAD_NAME_LOAD |
def white(cls, string, auto=False):
"""Color-code entire string.
:param str string: String to colorize.
:param bool auto: Enable auto-color (dark/light terminal).
:return: Class instance for colorized string.
:rtype: Color
"""
return cls.colorize('white', string, auto=auto) | [3][SEP1][Return][SEP2][][SEP3][1] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_ARG_ARG_CONSTANT_EXPR_CONSTANT_RETURN_CALL_ATTRIBUTE_NAME_LOAD_LOAD_CONSTANT_NAME_LOAD_KEYWORD_NAME_LOAD |
def linked_parameters(self):
"""
Get a dictionary with all parameters in this model in a linked status. A parameter is in a linked status
if it is linked to another parameter (i.e. it is forced to have the same value of the other parameter), or
if it is linked with another parameter or an independent variable through a law.
:return: dictionary of linked parameters
"""
# Refresh the list
self._update_parameters()
# Filter selecting only free parameters
linked_parameter_dictionary = collections.OrderedDict()
for parameter_name, parameter in self._parameters.iteritems():
if parameter.has_auxiliary_variable():
linked_parameter_dictionary[parameter_name] = parameter
return linked_parameter_dictionary | [1][SEP1][None][For][If][Return][None][SEP2][1][2,3][4,1][][1][SEP3][2][1][1][0][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_EXPR_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_FOR_TUPLE_NAME_STORE_NAME_STORE_STORE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_IF_CALL_ATTRIBUTE_NAME_LOAD_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_NAME_LOAD_STORE_NAME_LOAD_RETURN_NAME_LOAD |
def parameters(self):
"""
Returns a dictionary of all parameters for this source.
We use the parameter path as the key because it's
guaranteed to be unique, unlike the parameter name.
:return:
"""
all_parameters = collections.OrderedDict()
for component in self._components.values():
for par in component.shape.parameters.values():
all_parameters[par.path] = par
return all_parameters | [1][SEP1][None][For][For][Return][None][SEP2][1][2,3][4,1][][2][SEP3][1][1][1][0][0] | MODULE_FUNCTIONDEF_ARGUMENTS_ARG_EXPR_CONSTANT_ASSIGN_NAME_STORE_CALL_ATTRIBUTE_NAME_LOAD_LOAD_FOR_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_FOR_NAME_STORE_CALL_ATTRIBUTE_ATTRIBUTE_ATTRIBUTE_NAME_LOAD_LOAD_LOAD_LOAD_ASSIGN_SUBSCRIPT_NAME_LOAD_ATTRIBUTE_NAME_LOAD_LOAD_STORE_NAME_LOAD_RETURN_NAME_LOAD |