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libChEBI/libChEBIpy | libchebipy/_parsers.py | __parse_chemical_data | def __parse_chemical_data():
'''Gets and parses file'''
filename = get_file('chemical_data.tsv')
with io.open(filename, 'r', encoding='cp1252') as textfile:
next(textfile)
for line in textfile:
tokens = line.strip().split('\t')
if tokens[3] == 'FORMULA':
... | python | def __parse_chemical_data():
'''Gets and parses file'''
filename = get_file('chemical_data.tsv')
with io.open(filename, 'r', encoding='cp1252') as textfile:
next(textfile)
for line in textfile:
tokens = line.strip().split('\t')
if tokens[3] == 'FORMULA':
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libChEBI/libChEBIpy | libchebipy/_parsers.py | get_all_comments | def get_all_comments(chebi_ids):
'''Returns all comments'''
all_comments = [get_comments(chebi_id) for chebi_id in chebi_ids]
return [x for sublist in all_comments for x in sublist] | python | def get_all_comments(chebi_ids):
'''Returns all comments'''
all_comments = [get_comments(chebi_id) for chebi_id in chebi_ids]
return [x for sublist in all_comments for x in sublist] | [
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libChEBI/libChEBIpy | libchebipy/_parsers.py | __parse_comments | def __parse_comments():
'''Gets and parses file'''
filename = get_file('comments.tsv')
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next(textfile)
for line in textfile:
tokens = line.strip().split('\t')
chebi_id = int(tokens[1])
if chebi_... | python | def __parse_comments():
'''Gets and parses file'''
filename = get_file('comments.tsv')
with io.open(filename, 'r', encoding='cp1252') as textfile:
next(textfile)
for line in textfile:
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libChEBI/libChEBIpy | libchebipy/_parsers.py | get_all_compound_origins | def get_all_compound_origins(chebi_ids):
'''Returns all compound origins'''
all_compound_origins = [get_compound_origins(chebi_id)
for chebi_id in chebi_ids]
return [x for sublist in all_compound_origins for x in sublist] | python | def get_all_compound_origins(chebi_ids):
'''Returns all compound origins'''
all_compound_origins = [get_compound_origins(chebi_id)
for chebi_id in chebi_ids]
return [x for sublist in all_compound_origins for x in sublist] | [
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libChEBI/libChEBIpy | libchebipy/_parsers.py | __parse_compound_origins | def __parse_compound_origins():
'''Gets and parses file'''
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'''Gets and parses file'''
filename = get_file('compound_origins.tsv')
with io.open(filename, 'r', encoding='cp1252') as textfile:
next(textfile)
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tokens = line.strip().split('\t')
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libChEBI/libChEBIpy | libchebipy/_parsers.py | get_parent_id | def get_parent_id(chebi_id):
'''Returns parent id'''
if len(__PARENT_IDS) == 0:
__parse_compounds()
return __PARENT_IDS[chebi_id] if chebi_id in __PARENT_IDS else float('NaN') | python | def get_parent_id(chebi_id):
'''Returns parent id'''
if len(__PARENT_IDS) == 0:
__parse_compounds()
return __PARENT_IDS[chebi_id] if chebi_id in __PARENT_IDS else float('NaN') | [
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libChEBI/libChEBIpy | libchebipy/_parsers.py | get_all_modified_on | def get_all_modified_on(chebi_ids):
'''Returns all modified on'''
all_modified_ons = [get_modified_on(chebi_id) for chebi_id in chebi_ids]
all_modified_ons = [modified_on for modified_on in all_modified_ons
if modified_on is not None]
return None if len(all_modified_ons) == 0 els... | python | def get_all_modified_on(chebi_ids):
'''Returns all modified on'''
all_modified_ons = [get_modified_on(chebi_id) for chebi_id in chebi_ids]
all_modified_ons = [modified_on for modified_on in all_modified_ons
if modified_on is not None]
return None if len(all_modified_ons) == 0 els... | [
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libChEBI/libChEBIpy | libchebipy/_parsers.py | get_star | def get_star(chebi_id):
'''Returns created by'''
if len(__STARS) == 0:
__parse_compounds()
return __STARS[chebi_id] if chebi_id in __STARS else float('NaN') | python | def get_star(chebi_id):
'''Returns created by'''
if len(__STARS) == 0:
__parse_compounds()
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libChEBI/libChEBIpy | libchebipy/_parsers.py | __parse_compounds | def __parse_compounds():
'''Gets and parses file'''
filename = get_file('compounds.tsv.gz')
with io.open(filename, 'r', encoding='cp1252') as textfile:
next(textfile)
for line in textfile:
tokens = line.strip().split('\t')
chebi_id = int(tokens[0])
__ST... | python | def __parse_compounds():
'''Gets and parses file'''
filename = get_file('compounds.tsv.gz')
with io.open(filename, 'r', encoding='cp1252') as textfile:
next(textfile)
for line in textfile:
tokens = line.strip().split('\t')
chebi_id = int(tokens[0])
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libChEBI/libChEBIpy | libchebipy/_parsers.py | __put_all_ids | def __put_all_ids(parent_id, child_id):
'''COMMENT'''
if parent_id in __ALL_IDS:
__ALL_IDS[parent_id].append(child_id)
else:
__ALL_IDS[parent_id] = [child_id] | python | def __put_all_ids(parent_id, child_id):
'''COMMENT'''
if parent_id in __ALL_IDS:
__ALL_IDS[parent_id].append(child_id)
else:
__ALL_IDS[parent_id] = [child_id] | [
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libChEBI/libChEBIpy | libchebipy/_parsers.py | get_all_database_accessions | def get_all_database_accessions(chebi_ids):
'''Returns all database accessions'''
all_database_accessions = [get_database_accessions(chebi_id)
for chebi_id in chebi_ids]
return [x for sublist in all_database_accessions for x in sublist] | python | def get_all_database_accessions(chebi_ids):
'''Returns all database accessions'''
all_database_accessions = [get_database_accessions(chebi_id)
for chebi_id in chebi_ids]
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libChEBI/libChEBIpy | libchebipy/_parsers.py | __parse_database_accessions | def __parse_database_accessions():
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... | python | def __parse_database_accessions():
'''Gets and parses file'''
filename = get_file('database_accession.tsv')
with io.open(filename, 'r', encoding='cp1252') as textfile:
next(textfile)
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libChEBI/libChEBIpy | libchebipy/_parsers.py | __parse_inchi | def __parse_inchi():
'''Gets and parses file'''
filename = get_file('chebiId_inchi.tsv')
with io.open(filename, 'r', encoding='cp1252') as textfile:
next(textfile)
for line in textfile:
tokens = line.strip().split('\t')
__INCHIS[int(tokens[0])] = tokens[1] | python | def __parse_inchi():
'''Gets and parses file'''
filename = get_file('chebiId_inchi.tsv')
with io.open(filename, 'r', encoding='cp1252') as textfile:
next(textfile)
for line in textfile:
tokens = line.strip().split('\t')
__INCHIS[int(tokens[0])] = tokens[1] | [
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libChEBI/libChEBIpy | libchebipy/_parsers.py | get_all_names | def get_all_names(chebi_ids):
'''Returns all names'''
all_names = [get_names(chebi_id) for chebi_id in chebi_ids]
return [x for sublist in all_names for x in sublist] | python | def get_all_names(chebi_ids):
'''Returns all names'''
all_names = [get_names(chebi_id) for chebi_id in chebi_ids]
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libChEBI/libChEBIpy | libchebipy/_parsers.py | __parse_names | def __parse_names():
'''Gets and parses file'''
filename = get_file('names.tsv.gz')
with io.open(filename, 'r', encoding='cp1252') as textfile:
next(textfile)
for line in textfile:
tokens = line.strip().split('\t')
chebi_id = int(tokens[1])
if chebi_id ... | python | def __parse_names():
'''Gets and parses file'''
filename = get_file('names.tsv.gz')
with io.open(filename, 'r', encoding='cp1252') as textfile:
next(textfile)
for line in textfile:
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chebi_id = int(tokens[1])
if chebi_id ... | [
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libChEBI/libChEBIpy | libchebipy/_parsers.py | get_references | def get_references(chebi_ids):
'''Returns references'''
references = []
chebi_ids = [str(chebi_id) for chebi_id in chebi_ids]
filename = get_file('reference.tsv.gz')
with io.open(filename, 'r', encoding='cp1252') as textfile:
next(textfile)
for line in textfile:
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'''Returns references'''
references = []
chebi_ids = [str(chebi_id) for chebi_id in chebi_ids]
filename = get_file('reference.tsv.gz')
with io.open(filename, 'r', encoding='cp1252') as textfile:
next(textfile)
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libChEBI/libChEBIpy | libchebipy/_parsers.py | get_all_outgoings | def get_all_outgoings(chebi_ids):
'''Returns all outgoings'''
all_outgoings = [get_outgoings(chebi_id) for chebi_id in chebi_ids]
return [x for sublist in all_outgoings for x in sublist] | python | def get_all_outgoings(chebi_ids):
'''Returns all outgoings'''
all_outgoings = [get_outgoings(chebi_id) for chebi_id in chebi_ids]
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libChEBI/libChEBIpy | libchebipy/_parsers.py | get_all_incomings | def get_all_incomings(chebi_ids):
'''Returns all incomings'''
all_incomings = [get_incomings(chebi_id) for chebi_id in chebi_ids]
return [x for sublist in all_incomings for x in sublist] | python | def get_all_incomings(chebi_ids):
'''Returns all incomings'''
all_incomings = [get_incomings(chebi_id) for chebi_id in chebi_ids]
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libChEBI/libChEBIpy | libchebipy/_parsers.py | __parse_relation | def __parse_relation():
'''Gets and parses file'''
relation_filename = get_file('relation.tsv')
vertice_filename = get_file('vertice.tsv')
relation_textfile = open(relation_filename, 'r')
vertice_textfile = open(vertice_filename, 'r')
# Parse vertice:
vertices = {}
next(vertice_textfil... | python | def __parse_relation():
'''Gets and parses file'''
relation_filename = get_file('relation.tsv')
vertice_filename = get_file('vertice.tsv')
relation_textfile = open(relation_filename, 'r')
vertice_textfile = open(vertice_filename, 'r')
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libChEBI/libChEBIpy | libchebipy/_parsers.py | get_mol | def get_mol(chebi_id):
'''Returns mol'''
chebi_id_regexp = '^\\d+\\,' + str(chebi_id) + '\\,.*'
mol_file_end_regexp = '\",mol,\\dD'
this_structure = []
filename = get_file('structures.csv.gz')
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in_chebi_id = False
next... | python | def get_mol(chebi_id):
'''Returns mol'''
chebi_id_regexp = '^\\d+\\,' + str(chebi_id) + '\\,.*'
mol_file_end_regexp = '\",mol,\\dD'
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libChEBI/libChEBIpy | libchebipy/_parsers.py | get_mol_filename | def get_mol_filename(chebi_id):
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mol = get_mol(chebi_id)
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file_descriptor, mol_filename = tempfile.mkstemp(str(chebi_id) +
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mol = get_mol(chebi_id)
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libChEBI/libChEBIpy | libchebipy/_parsers.py | __parse_structures | def __parse_structures():
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libChEBI/libChEBIpy | libchebipy/_parsers.py | __get_default_structure_ids | def __get_default_structure_ids():
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libChEBI/libChEBIpy | libchebipy/_parsers.py | get_file | def get_file(filename):
'''Downloads filename from ChEBI FTP site'''
destination = __DOWNLOAD_PARAMS['path']
filepath = os.path.join(destination, filename)
if not __is_current(filepath):
if not os.path.exists(destination):
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url = 'ftp://ftp.ebi.ac.u... | python | def get_file(filename):
'''Downloads filename from ChEBI FTP site'''
destination = __DOWNLOAD_PARAMS['path']
filepath = os.path.join(destination, filename)
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libChEBI/libChEBIpy | libchebipy/_parsers.py | __is_current | def __is_current(filepath):
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if not os.path.isfile(filepath):
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return datetime.datetime.utcfromtimestamp(os.path.getmtime(filepath)) \
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libChEBI/libChEBIpy | libchebipy/_parsers.py | __get_last_update_time | def __get_last_update_time():
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now = datetime.datetime.utcnow()
# Get the first Tuesday of the month
first_tuesday = __get_first_tuesday(now)
if first_tuesday < now:
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first_of_month = datetime.datetime(now.year, n... | python | def __get_last_update_time():
'''Returns last FTP site update time'''
now = datetime.datetime.utcnow()
# Get the first Tuesday of the month
first_tuesday = __get_first_tuesday(now)
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libChEBI/libChEBIpy | libchebipy/_parsers.py | __get_first_tuesday | def __get_first_tuesday(this_date):
'''Get the first Tuesday of the month'''
month_range = calendar.monthrange(this_date.year, this_date.month)
first_of_month = datetime.datetime(this_date.year, this_date.month, 1)
first_tuesday_day = (calendar.TUESDAY - month_range[0]) % 7
first_tuesday = first_of_... | python | def __get_first_tuesday(this_date):
'''Get the first Tuesday of the month'''
month_range = calendar.monthrange(this_date.year, this_date.month)
first_of_month = datetime.datetime(this_date.year, this_date.month, 1)
first_tuesday_day = (calendar.TUESDAY - month_range[0]) % 7
first_tuesday = first_of_... | [
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Turbo87/aerofiles | aerofiles/igc/writer.py | Writer.write_logger_id | def write_logger_id(self, manufacturer, logger_id, extension=None,
validate=True):
"""
Write the manufacturer and logger id header line::
writer.write_logger_id('XXX', 'ABC', extension='FLIGHT:1')
# -> AXXXABCFLIGHT:1
Some older loggers have deci... | python | def write_logger_id(self, manufacturer, logger_id, extension=None,
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"""
Write the manufacturer and logger id header line::
writer.write_logger_id('XXX', 'ABC', extension='FLIGHT:1')
# -> AXXXABCFLIGHT:1
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Turbo87/aerofiles | aerofiles/igc/writer.py | Writer.write_fix_accuracy | def write_fix_accuracy(self, accuracy=None):
"""
Write the GPS fix accuracy header::
writer.write_fix_accuracy()
# -> HFFXA500
writer.write_fix_accuracy(25)
# -> HFFXA025
:param accuracy: the estimated GPS fix accuracy in meters (optional)
... | python | def write_fix_accuracy(self, accuracy=None):
"""
Write the GPS fix accuracy header::
writer.write_fix_accuracy()
# -> HFFXA500
writer.write_fix_accuracy(25)
# -> HFFXA025
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Turbo87/aerofiles | aerofiles/igc/writer.py | Writer.write_gps_datum | def write_gps_datum(self, code=None, gps_datum=None):
"""
Write the mandatory GPS datum header::
writer.write_gps_datum()
# -> HFDTM100GPSDATUM:WGS-1984
writer.write_gps_datum(33, 'Guam-1963')
# -> HFDTM033GPSDATUM:Guam-1963
Note that the defaul... | python | def write_gps_datum(self, code=None, gps_datum=None):
"""
Write the mandatory GPS datum header::
writer.write_gps_datum()
# -> HFDTM100GPSDATUM:WGS-1984
writer.write_gps_datum(33, 'Guam-1963')
# -> HFDTM033GPSDATUM:Guam-1963
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Turbo87/aerofiles | aerofiles/igc/writer.py | Writer.write_headers | def write_headers(self, headers):
"""
Write all the necessary headers in the correct order::
writer.write_headers({
'manufacturer_code': 'XCS',
'logger_id': 'TBX',
'date': datetime.date(1987, 2, 24),
'fix_accuracy': 50,
... | python | def write_headers(self, headers):
"""
Write all the necessary headers in the correct order::
writer.write_headers({
'manufacturer_code': 'XCS',
'logger_id': 'TBX',
'date': datetime.date(1987, 2, 24),
'fix_accuracy': 50,
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Turbo87/aerofiles | aerofiles/igc/writer.py | Writer.write_task_metadata | def write_task_metadata(
self, declaration_datetime=None, flight_date=None,
task_number=None, turnpoints=None, text=None):
"""
Write the task declaration metadata record::
writer.write_task_metadata(
datetime.datetime(2014, 4, 13, 12, 53, 02),
... | python | def write_task_metadata(
self, declaration_datetime=None, flight_date=None,
task_number=None, turnpoints=None, text=None):
"""
Write the task declaration metadata record::
writer.write_task_metadata(
datetime.datetime(2014, 4, 13, 12, 53, 02),
... | [
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Turbo87/aerofiles | aerofiles/igc/writer.py | Writer.write_task_point | def write_task_point(self, latitude=None, longitude=None, text='',
distance_min=None, distance_max=None,
bearing1=None, bearing2=None):
"""
Write a task declaration point::
writer.write_task_point(
latitude=(51 + 7.345 / 60.)... | python | def write_task_point(self, latitude=None, longitude=None, text='',
distance_min=None, distance_max=None,
bearing1=None, bearing2=None):
"""
Write a task declaration point::
writer.write_task_point(
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Turbo87/aerofiles | aerofiles/igc/writer.py | Writer.write_task_points | def write_task_points(self, points):
"""
Write multiple task declaration points with one call::
writer.write_task_points([
(None, None, 'TAKEOFF'),
(51.40375, 6.41275, 'START'),
(50.38210, 8.82105, 'TURN 1'),
(50.59045, 7.03555... | python | def write_task_points(self, points):
"""
Write multiple task declaration points with one call::
writer.write_task_points([
(None, None, 'TAKEOFF'),
(51.40375, 6.41275, 'START'),
(50.38210, 8.82105, 'TURN 1'),
(50.59045, 7.03555... | [
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Turbo87/aerofiles | aerofiles/igc/writer.py | Writer.write_security | def write_security(self, security, bytes_per_line=75):
"""
Write the security signature::
writer.write_security('ABCDEF')
# -> GABCDEF
If a signature of more than 75 bytes is used the G record will be
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"""
Write the security signature::
writer.write_security('ABCDEF')
# -> GABCDEF
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Turbo87/aerofiles | aerofiles/igc/writer.py | Writer.write_fix | def write_fix(self, time=None, latitude=None, longitude=None, valid=False,
pressure_alt=None, gps_alt=None, extensions=None):
"""
Write a fix record::
writer.write_fix(
datetime.time(12, 34, 56),
latitude=51.40375,
longitude=... | python | def write_fix(self, time=None, latitude=None, longitude=None, valid=False,
pressure_alt=None, gps_alt=None, extensions=None):
"""
Write a fix record::
writer.write_fix(
datetime.time(12, 34, 56),
latitude=51.40375,
longitude=... | [
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Turbo87/aerofiles | aerofiles/igc/writer.py | Writer.write_event | def write_event(self, *args):
"""
Write an event record::
writer.write_event(datetime.time(12, 34, 56), 'PEV')
# -> B123456PEV
writer.write_event(datetime.time(12, 34, 56), 'PEV', 'Some Text')
# -> B123456PEVSome Text
writer.write_event('PEV... | python | def write_event(self, *args):
"""
Write an event record::
writer.write_event(datetime.time(12, 34, 56), 'PEV')
# -> B123456PEV
writer.write_event(datetime.time(12, 34, 56), 'PEV', 'Some Text')
# -> B123456PEVSome Text
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Turbo87/aerofiles | aerofiles/igc/writer.py | Writer.write_satellites | def write_satellites(self, *args):
"""
Write a satellite constellation record::
writer.write_satellites(datetime.time(12, 34, 56), [1, 2, 5, 22])
# -> F12345601020522
:param time: UTC time of the satellite constellation record (default:
:meth:`~datetime.date... | python | def write_satellites(self, *args):
"""
Write a satellite constellation record::
writer.write_satellites(datetime.time(12, 34, 56), [1, 2, 5, 22])
# -> F12345601020522
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Turbo87/aerofiles | aerofiles/igc/writer.py | Writer.write_k_record | def write_k_record(self, *args):
"""
Write a K record::
writer.write_k_record_extensions([
('FXA', 3), ('SIU', 2), ('ENL', 3),
])
writer.write_k_record(datetime.time(2, 3, 4), ['023', 13, 2])
# -> J030810FXA1112SIU1315ENL
# -... | python | def write_k_record(self, *args):
"""
Write a K record::
writer.write_k_record_extensions([
('FXA', 3), ('SIU', 2), ('ENL', 3),
])
writer.write_k_record(datetime.time(2, 3, 4), ['023', 13, 2])
# -> J030810FXA1112SIU1315ENL
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Turbo87/aerofiles | aerofiles/igc/writer.py | Writer.write_comment | def write_comment(self, code, text):
"""
Write a comment record::
writer.write_comment('PLT', 'Arrived at the first turnpoint')
# -> LPLTArrived at the first turnpoint
:param code: a three-letter-code describing the source of the comment
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"""
Write a comment record::
writer.write_comment('PLT', 'Arrived at the first turnpoint')
# -> LPLTArrived at the first turnpoint
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dreipol/djangocms-spa | djangocms_spa/content_helpers.py | get_frontend_data_dict_for_cms_page | def get_frontend_data_dict_for_cms_page(cms_page, cms_page_title, request, editable=False):
"""
Returns the data dictionary of a CMS page that is used by the frontend.
"""
placeholders = list(cms_page.placeholders.all())
placeholder_frontend_data_dict = get_frontend_data_dict_for_placeholders(
... | python | def get_frontend_data_dict_for_cms_page(cms_page, cms_page_title, request, editable=False):
"""
Returns the data dictionary of a CMS page that is used by the frontend.
"""
placeholders = list(cms_page.placeholders.all())
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dreipol/djangocms-spa | djangocms_spa/content_helpers.py | get_frontend_data_dict_for_placeholders | def get_frontend_data_dict_for_placeholders(placeholders, request, editable=False):
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dreipol/djangocms-spa | djangocms_spa/content_helpers.py | get_frontend_data_dict_for_plugin | def get_frontend_data_dict_for_plugin(request, plugin, editable):
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dreipol/djangocms-spa | djangocms_spa/content_helpers.py | get_frontend_data_dict_for_partials | def get_frontend_data_dict_for_partials(partials, request, editable=False, renderer=None):
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dreipol/djangocms-spa | djangocms_spa/content_helpers.py | get_global_placeholder_data | def get_global_placeholder_data(placeholder_frontend_data_dict):
"""
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object. Define your post-processor in the DJANGOCMS_SPA_VUE_JS_PLACEHOLDER_DATA_POST_PROCESSOR setting variable
(e.g. `my_app... | python | def get_global_placeholder_data(placeholder_frontend_data_dict):
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Turbo87/aerofiles | aerofiles/flarmcfg/writer.py | Writer.write_waypoint | def write_waypoint(self, latitude=None, longitude=None, description=None):
"""
Adds a waypoint to the current task declaration. The first and the
last waypoint added will be treated as takeoff and landing location,
respectively.
::
writer.write_waypoint(
... | python | def write_waypoint(self, latitude=None, longitude=None, description=None):
"""
Adds a waypoint to the current task declaration. The first and the
last waypoint added will be treated as takeoff and landing location,
respectively.
::
writer.write_waypoint(
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Turbo87/aerofiles | aerofiles/flarmcfg/writer.py | Writer.write_waypoints | def write_waypoints(self, points):
"""
Write multiple task declaration points with one call::
writer.write_waypoints([
(None, None, 'TAKEOFF'),
(51.40375, 6.41275, 'START'),
(50.38210, 8.82105, 'TURN 1'),
(50.59045, 7.03555, 'T... | python | def write_waypoints(self, points):
"""
Write multiple task declaration points with one call::
writer.write_waypoints([
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Turbo87/aerofiles | aerofiles/igc/reader.py | Reader.read | def read(self, file_obj):
"""
Read the specified file object and return a dictionary with the parsed data.
:param file_obj: a Python file object
"""
self.reader = LowLevelReader(file_obj)
logger_id = [[], None]
fix_records = [[], []]
task = [[], {"waypo... | python | def read(self, file_obj):
"""
Read the specified file object and return a dictionary with the parsed data.
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payu-org/payu | payu/models/model.py | Model.set_model_pathnames | def set_model_pathnames(self):
"""Define the paths associated with this model."""
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self.input_basepath = self.expt.lab.input_basepath
self.work_path = self.expt.work_path
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"""Define the paths associated with this model."""
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self.work_path = self.expt.work_path
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payu-org/payu | payu/models/model.py | Model.archive | def archive(self):
"""Store model output to laboratory archive."""
# Traverse the model directory deleting symlinks, zero length files
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payu-org/payu | payu/cli.py | parse | def parse():
"""Parse the command line inputs and execute the subcommand."""
# Build the list of subcommand modules
modnames = [mod for (_, mod, _)
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"""Parse the command line inputs and execute the subcommand."""
# Build the list of subcommand modules
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payu-org/payu | payu/cli.py | get_model_type | def get_model_type(model_type, config):
"""Determine and validate the active model type."""
# If no model type is given, then check the config file
if not model_type:
model_type = config.get('model')
# If there is still no model type, try the parent directory
if not model_type:
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payu-org/payu | payu/cli.py | set_env_vars | def set_env_vars(init_run=None, n_runs=None, lab_path=None, dir_path=None,
reproduce=None):
"""Construct the environment variables used by payu for resubmissions."""
payu_env_vars = {}
# Setup Python dynamic library link
lib_paths = sysconfig.get_config_vars('LIBDIR')
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"""Construct the environment variables used by payu for resubmissions."""
payu_env_vars = {}
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payu-org/payu | payu/cli.py | submit_job | def submit_job(pbs_script, pbs_config, pbs_vars=None):
"""Submit a userscript the scheduler."""
# Initialisation
if pbs_vars is None:
pbs_vars = {}
pbs_flags = []
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pbs_project = pb... | python | def submit_job(pbs_script, pbs_config, pbs_vars=None):
"""Submit a userscript the scheduler."""
# Initialisation
if pbs_vars is None:
pbs_vars = {}
pbs_flags = []
pbs_queue = pbs_config.get('queue', 'normal')
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payu-org/payu | payu/namcouple.py | Namcouple.substitute_timestep | def substitute_timestep(self, regex, timestep):
"""
Substitute a new timestep value using regex.
"""
# Make one change at a time, each change affects subsequent matches.
timestep_changed = False
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Substitute a new timestep value using regex.
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payu-org/payu | payu/calendar.py | int_to_date | def int_to_date(date):
"""
Convert an int of form yyyymmdd to a python date object.
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year = date // 10**4
month = date % 10**4 // 10**2
day = date % 10**2
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payu-org/payu | payu/calendar.py | runtime_from_date | def runtime_from_date(start_date, years, months, days, seconds, caltype):
"""
Get the number of seconds from start date to start date + date_delta.
Ignores Feb 29 for caltype == NOLEAP.
"""
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... | python | def runtime_from_date(start_date, years, months, days, seconds, caltype):
"""
Get the number of seconds from start date to start date + date_delta.
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payu-org/payu | payu/calendar.py | date_plus_seconds | def date_plus_seconds(init_date, seconds, caltype):
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payu-org/payu | payu/calendar.py | get_leapdays | def get_leapdays(init_date, final_date):
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payu-org/payu | payu/calendar.py | calculate_leapdays | def calculate_leapdays(init_date, final_date):
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payu-org/payu | payu/laboratory.py | Laboratory.get_default_lab_path | def get_default_lab_path(self, config):
"""Generate a default laboratory path based on user environment."""
# Default path settings
# Append project name if present (NCI-specific)
default_project = os.environ.get('PROJECT', '')
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payu-org/payu | payu/laboratory.py | Laboratory.initialize | def initialize(self):
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mkdir_p(self.input_basepath) | python | def initialize(self):
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mkdir_p(self.archive_path)
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payu-org/payu | payu/scheduler/pbs.py | get_job_id | def get_job_id(short=True):
"""
Return PBS job id
"""
jobid = os.environ.get('PBS_JOBID', '')
if short:
# Strip off '.rman2'
jobid = jobid.split('.')[0]
return(jobid) | python | def get_job_id(short=True):
"""
Return PBS job id
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payu-org/payu | payu/scheduler/pbs.py | get_job_info | def get_job_info():
"""
Get information about the job from the PBS server
"""
jobid = get_job_id()
if jobid == '':
return None
info = get_qstat_info('-ft {0}'.format(jobid), 'Job Id:')
# Select the dict for this job (there should only be one entry in any case)
info = info['Jo... | python | def get_job_info():
"""
Get information about the job from the PBS server
"""
jobid = get_job_id()
if jobid == '':
return None
info = get_qstat_info('-ft {0}'.format(jobid), 'Job Id:')
# Select the dict for this job (there should only be one entry in any case)
info = info['Jo... | [
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payu-org/payu | payu/experiment.py | Experiment.postprocess | def postprocess(self):
"""Submit a postprocessing script after collation"""
assert self.postscript
envmod.setup()
envmod.module('load', 'pbs')
cmd = 'qsub {script}'.format(script=self.postscript)
cmd = shlex.split(cmd)
rc = sp.call(cmd)
assert rc == 0, '... | python | def postprocess(self):
"""Submit a postprocessing script after collation"""
assert self.postscript
envmod.setup()
envmod.module('load', 'pbs')
cmd = 'qsub {script}'.format(script=self.postscript)
cmd = shlex.split(cmd)
rc = sp.call(cmd)
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payu-org/payu | payu/models/um.py | date_to_um_dump_date | def date_to_um_dump_date(date):
"""
Convert a time date object to a um dump format date which is
<decade><year><month><day>0
To accommodate two digit months and days the UM uses letters. e.g. 1st oct
is writing 01a10.
"""
assert(date.month <= 12)
decade = date.year // 10
# UM can ... | python | def date_to_um_dump_date(date):
"""
Convert a time date object to a um dump format date which is
<decade><year><month><day>0
To accommodate two digit months and days the UM uses letters. e.g. 1st oct
is writing 01a10.
"""
assert(date.month <= 12)
decade = date.year // 10
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payu-org/payu | payu/models/um.py | date_to_um_date | def date_to_um_date(date):
"""
Convert a date object to 'year, month, day, hour, minute, second.'
"""
assert date.hour == 0 and date.minute == 0 and date.second == 0
return [date.year, date.month, date.day, 0, 0, 0] | python | def date_to_um_date(date):
"""
Convert a date object to 'year, month, day, hour, minute, second.'
"""
assert date.hour == 0 and date.minute == 0 and date.second == 0
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payu-org/payu | payu/models/um.py | um_date_to_date | def um_date_to_date(d):
"""
Convert a string with format 'year, month, day, hour, minute, second'
to a datetime date.
"""
return datetime.datetime(year=d[0], month=d[1], day=d[2],
hour=d[3], minute=d[4], second=d[5]) | python | def um_date_to_date(d):
"""
Convert a string with format 'year, month, day, hour, minute, second'
to a datetime date.
"""
return datetime.datetime(year=d[0], month=d[1], day=d[2],
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payu-org/payu | payu/envmod.py | setup | def setup(basepath=DEFAULT_BASEPATH):
"""Set the environment modules used by the Environment Module system."""
module_version = os.environ.get('MODULE_VERSION', DEFAULT_VERSION)
moduleshome = os.path.join(basepath, module_version)
# Abort if MODULESHOME does not exist
if not os.path.isdir(modulesh... | python | def setup(basepath=DEFAULT_BASEPATH):
"""Set the environment modules used by the Environment Module system."""
module_version = os.environ.get('MODULE_VERSION', DEFAULT_VERSION)
moduleshome = os.path.join(basepath, module_version)
# Abort if MODULESHOME does not exist
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payu-org/payu | payu/envmod.py | module | def module(command, *args):
"""Run the modulecmd tool and use its Python-formatted output to set the
environment variables."""
if 'MODULESHOME' not in os.environ:
print('payu: warning: No Environment Modules found; skipping {0} call.'
''.format(command))
return
modulecmd ... | python | def module(command, *args):
"""Run the modulecmd tool and use its Python-formatted output to set the
environment variables."""
if 'MODULESHOME' not in os.environ:
print('payu: warning: No Environment Modules found; skipping {0} call.'
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return
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payu-org/payu | payu/models/mom6.py | Mom6.init_config | def init_config(self):
"""Patch input.nml as a new or restart run."""
input_fpath = os.path.join(self.work_path, 'input.nml')
input_nml = f90nml.read(input_fpath)
if self.expt.counter == 0 or self.expt.repeat_run:
input_type = 'n'
else:
input_type = 'r'... | python | def init_config(self):
"""Patch input.nml as a new or restart run."""
input_fpath = os.path.join(self.work_path, 'input.nml')
input_nml = f90nml.read(input_fpath)
if self.expt.counter == 0 or self.expt.repeat_run:
input_type = 'n'
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payu-org/payu | payu/fsops.py | mkdir_p | def mkdir_p(path):
"""Create a new directory; ignore if it already exists."""
try:
os.makedirs(path)
except EnvironmentError as exc:
if exc.errno != errno.EEXIST:
raise | python | def mkdir_p(path):
"""Create a new directory; ignore if it already exists."""
try:
os.makedirs(path)
except EnvironmentError as exc:
if exc.errno != errno.EEXIST:
raise | [
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payu-org/payu | payu/fsops.py | read_config | def read_config(config_fname=None):
"""Parse input configuration file and return a config dict."""
if not config_fname:
config_fname = DEFAULT_CONFIG_FNAME
try:
with open(config_fname, 'r') as config_file:
config = yaml.load(config_file)
except IOError as exc:
if ex... | python | def read_config(config_fname=None):
"""Parse input configuration file and return a config dict."""
if not config_fname:
config_fname = DEFAULT_CONFIG_FNAME
try:
with open(config_fname, 'r') as config_file:
config = yaml.load(config_file)
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payu-org/payu | payu/fsops.py | make_symlink | def make_symlink(src_path, lnk_path):
"""Safely create a symbolic link to an input field."""
# Check for Lustre 60-character symbolic link path bug
if CHECK_LUSTRE_PATH_LEN:
src_path = patch_lustre_path(src_path)
lnk_path = patch_lustre_path(lnk_path)
# os.symlink will happily make a s... | python | def make_symlink(src_path, lnk_path):
"""Safely create a symbolic link to an input field."""
# Check for Lustre 60-character symbolic link path bug
if CHECK_LUSTRE_PATH_LEN:
src_path = patch_lustre_path(src_path)
lnk_path = patch_lustre_path(lnk_path)
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payu-org/payu | payu/fsops.py | splitpath | def splitpath(path):
"""Recursively split a filepath into all directories and files."""
head, tail = os.path.split(path)
if tail == '':
return head,
elif head == '':
return tail,
else:
return splitpath(head) + (tail,) | python | def splitpath(path):
"""Recursively split a filepath into all directories and files."""
head, tail = os.path.split(path)
if tail == '':
return head,
elif head == '':
return tail,
else:
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payu-org/payu | payu/fsops.py | patch_lustre_path | def patch_lustre_path(f_path):
"""Patch any 60-character pathnames, to avoid a current Lustre bug."""
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f_path = './' + f_path
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payu-org/payu | payu/manifest.py | PayuManifest.check_fast | def check_fast(self, reproduce=False, **args):
"""
Check hash value for all filepaths using a fast hash function and fall
back to slower full hash functions if fast hashes fail to agree.
"""
hashvals = {}
fast_check = self.check_file(
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"""
Check hash value for all filepaths using a fast hash function and fall
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hashvals = {}
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Bespoke function to add filepath & fullpath to manifest
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Bespoke function to add filepath & fullpath to manifest
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payu-org/payu | payu/manifest.py | PayuManifest.add_fast | def add_fast(self, filepath, hashfn=None, force=False):
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payu-org/payu | payu/manifest.py | PayuManifest.copy_file | def copy_file(self, filepath):
"""
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return copy_file | python | def copy_file(self, filepath):
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Returns flag which says to copy rather than link a file.
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payu-org/payu | payu/manifest.py | PayuManifest.make_link | def make_link(self, filepath):
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Payu integration function for creating symlinks in work directories
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"""
# Check file exists. It may have been deleted but still in manifest
if not os.path.exists(self.fullpath(filepath)):
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"""
Payu integration function for creating symlinks in work directories
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# Check file exists. It may have been deleted but still in manifest
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payu-org/payu | payu/manifest.py | Manifest.add_filepath | def add_filepath(self, manifest, filepath, fullpath, copy=False):
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filepath = os.path.normpath(filepath)
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payu-org/payu | payu/runlog.py | commit_hash | def commit_hash(dir='.'):
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Return commit hash for HEAD of checked out branch of the
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"""
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"""
Return commit hash for HEAD of checked out branch of the
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"""
cmd = ['git', 'rev-parse', 'HEAD']
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payu-org/payu | payu/runlog.py | Runlog.create_manifest | def create_manifest(self):
"""Construct the list of files to be tracked by the runlog."""
config_path = os.path.join(self.expt.control_path,
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self.manifest = []
if os.path.isfile(config_path):
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payu-org/payu | payu/runlog.py | Runlog.push | def push(self):
"""Push the changes to the remote repository.
Usage: payu push
This command pushes local runlog changes to the remote runlog
repository, currently named `payu`, using the SSH key associated with
this experiment.
For an experiment `test`, it is equivalen... | python | def push(self):
"""Push the changes to the remote repository.
Usage: payu push
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payu-org/payu | payu/runlog.py | Runlog.github_setup | def github_setup(self):
"""Set up authentication keys and API tokens."""
github_auth = self.authenticate()
github_username = github_auth[0]
expt_name = self.config.get('name', self.expt.name)
expt_description = self.expt.config.get('description')
if not expt_description:... | python | def github_setup(self):
"""Set up authentication keys and API tokens."""
github_auth = self.authenticate()
github_username = github_auth[0]
expt_name = self.config.get('name', self.expt.name)
expt_description = self.expt.config.get('description')
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mozilla/python_moztelemetry | moztelemetry/shared_telemetry_utils.py | add_expiration_postfix | def add_expiration_postfix(expiration):
""" Formats the expiration version and adds a version postfix if needed.
:param expiration: the expiration version string.
:return: the modified expiration string.
"""
if re.match(r'^[1-9][0-9]*$', expiration):
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if re.ma... | python | def add_expiration_postfix(expiration):
""" Formats the expiration version and adds a version postfix if needed.
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:return: the modified expiration string.
"""
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mozilla/python_moztelemetry | moztelemetry/shared_telemetry_utils.py | load_yaml_file | def load_yaml_file(filename):
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return yaml.safe_load(f)
except IOError as e:
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except ValueError as e:
... | python | def load_yaml_file(filename):
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try:
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except IOError as e:
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mozilla/python_moztelemetry | moztelemetry/shared_telemetry_utils.py | StringTable.stringIndex | def stringIndex(self, string):
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:param string: the input string.
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if string in self.table:
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Karaage-Cluster/karaage | karaage/templatetags/karaage_tags.py | comments | def comments(context, obj):
""" Render comments for obj. """
content_type = ContentType.objects.get_for_model(obj.__class__)
comment_list = LogEntry.objects.filter(
content_type=content_type,
object_id=obj.pk,
action_flag=COMMENT
)
return {
'obj': obj,
'commen... | python | def comments(context, obj):
""" Render comments for obj. """
content_type = ContentType.objects.get_for_model(obj.__class__)
comment_list = LogEntry.objects.filter(
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Karaage-Cluster/karaage | karaage/machines/xmlrpc.py | get_disk_quota | def get_disk_quota(username, machine_name=None):
"""
Returns disk quota for username in KB
"""
try:
ua = Account.objects.get(
username=username,
date_deleted__isnull=True)
except Account.DoesNotExist:
return 'Account not found'
result = ua.get_disk_quota... | python | def get_disk_quota(username, machine_name=None):
"""
Returns disk quota for username in KB
"""
try:
ua = Account.objects.get(
username=username,
date_deleted__isnull=True)
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Karaage-Cluster/karaage | karaage/plugins/kgusage/tasks.py | _gen_project_trend_graph | def _gen_project_trend_graph(project, start, end, force_overwrite=False):
"""Generates a bar graph for a project
Keyword arguments:
project -- Project
start -- start date
end -- end date
"""
filename = graphs.get_project_trend_graph_filename(project, start, end)
csv_filename = os.path.... | python | def _gen_project_trend_graph(project, start, end, force_overwrite=False):
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project -- Project
start -- start date
end -- end date
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Karaage-Cluster/karaage | karaage/plugins/kgusage/tasks.py | _gen_institute_graph | def _gen_institute_graph(start, end, force_overwrite=False):
""" Pie chart comparing institutes usage. """
filename = graphs.get_institute_graph_filename(start, end)
csv_filename = os.path.join(GRAPH_ROOT, filename + '.csv')
png_filename = os.path.join(GRAPH_ROOT, filename + '.png')
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""" Pie chart comparing institutes usage. """
filename = graphs.get_institute_graph_filename(start, end)
csv_filename = os.path.join(GRAPH_ROOT, filename + '.csv')
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] | train | https://github.com/Karaage-Cluster/karaage/blob/2f4c8b4e2d728b3fcbb151160c49000f1c04f5c9/karaage/plugins/kgusage/tasks.py#L480-L521 |
Karaage-Cluster/karaage | karaage/plugins/kgusage/tasks.py | _gen_machine_graph | def _gen_machine_graph(start, end, force_overwrite=False):
""" Pie chart comparing machines usage. """
filename = graphs.get_machine_graph_filename(start, end)
csv_filename = os.path.join(GRAPH_ROOT, filename + '.csv')
png_filename = os.path.join(GRAPH_ROOT, filename + '.png')
_check_directory_exis... | python | def _gen_machine_graph(start, end, force_overwrite=False):
""" Pie chart comparing machines usage. """
filename = graphs.get_machine_graph_filename(start, end)
csv_filename = os.path.join(GRAPH_ROOT, filename + '.csv')
png_filename = os.path.join(GRAPH_ROOT, filename + '.png')
_check_directory_exis... | [
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Karaage-Cluster/karaage | karaage/plugins/kgusage/tasks.py | _gen_trend_graph | def _gen_trend_graph(start, end, force_overwrite=False):
""" Total trend graph for machine category. """
filename = graphs.get_trend_graph_filename(start, end)
csv_filename = os.path.join(GRAPH_ROOT, filename + '.csv')
png_filename = os.path.join(GRAPH_ROOT, filename + '.png')
_check_directory_exis... | python | def _gen_trend_graph(start, end, force_overwrite=False):
""" Total trend graph for machine category. """
filename = graphs.get_trend_graph_filename(start, end)
csv_filename = os.path.join(GRAPH_ROOT, filename + '.csv')
png_filename = os.path.join(GRAPH_ROOT, filename + '.png')
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mozilla/python_moztelemetry | moztelemetry/standards.py | daynum_to_date | def daynum_to_date(daynum, max_days=1000000):
""" Convert a number of days to a date. If it's out of range, default to a
max date. If it is not a number (or a numeric string), return None. Using
a max_days of more than 2932896 (9999-12-31) will throw an exception if the
specified daynum exceeds the max.... | python | def daynum_to_date(daynum, max_days=1000000):
""" Convert a number of days to a date. If it's out of range, default to a
max date. If it is not a number (or a numeric string), return None. Using
a max_days of more than 2932896 (9999-12-31) will throw an exception if the
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mozilla/python_moztelemetry | moztelemetry/standards.py | mau | def mau(dataframe, target_day, past_days=28, future_days=10, date_format="%Y%m%d"):
"""Compute Monthly Active Users (MAU) from the Executive Summary dataset.
See https://bugzilla.mozilla.org/show_bug.cgi?id=1240849
"""
target_day_date = datetime.strptime(target_day, date_format)
# Compute activity ... | python | def mau(dataframe, target_day, past_days=28, future_days=10, date_format="%Y%m%d"):
"""Compute Monthly Active Users (MAU) from the Executive Summary dataset.
See https://bugzilla.mozilla.org/show_bug.cgi?id=1240849
"""
target_day_date = datetime.strptime(target_day, date_format)
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mozilla/python_moztelemetry | moztelemetry/standards.py | snap_to_beginning_of_week | def snap_to_beginning_of_week(day, weekday_start="Sunday"):
""" Get the first day of the current week.
:param day: The input date to snap.
:param weekday_start: Either "Monday" or "Sunday", indicating the first day of the week.
:returns: A date representing the first day of the current week.
"""
... | python | def snap_to_beginning_of_week(day, weekday_start="Sunday"):
""" Get the first day of the current week.
:param day: The input date to snap.
:param weekday_start: Either "Monday" or "Sunday", indicating the first day of the week.
:returns: A date representing the first day of the current week.
"""
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mozilla/python_moztelemetry | moztelemetry/standards.py | get_last_week_range | def get_last_week_range(weekday_start="Sunday"):
""" Gets the date for the first and the last day of the previous complete week.
:param weekday_start: Either "Monday" or "Sunday", indicating the first day of the week.
:returns: A tuple containing two date objects, for the first and the last day of the week... | python | def get_last_week_range(weekday_start="Sunday"):
""" Gets the date for the first and the last day of the previous complete week.
:param weekday_start: Either "Monday" or "Sunday", indicating the first day of the week.
:returns: A tuple containing two date objects, for the first and the last day of the week... | [
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