code
string | signature
string | docstring
string | loss_without_docstring
float64 | loss_with_docstring
float64 | factor
float64 |
|---|---|---|---|---|---|
file_dest: IO = file_dest_maybe or sys.stderr
def _print_progress(progress_min: float, rt_remaining: float, _mc: MeasureComparison) -> None:
nonlocal file_dest
percent_progress = progress_min * 100.0
time_remaining, unit = _display_time(rt_remaining)
print(
f"Progress: {percent_progress:.1f}% -- Time remaining: {time_remaining} {unit} ",
end="\r",
file=file_dest
)
return _print_progress
|
def capture_print(file_dest_maybe: Optional[IO] = None)
|
Progress capture that writes updated metrics to an interactive terminal.
| 4.652574
| 4.293502
| 1.083631
|
def measure_to_target() -> MeasureComparison:
return list(zip(measure(), target))
def is_finished(progress: MeasureComparison) -> bool:
return all(p >= t for p, t in progress)
capture = capture_maybe or capture_print()
rt_started = now_real()
while True:
advance(interval_check)
rt_elapsed = now_real() - rt_started
progress = measure_to_target()
ratio_progress_min = min(m / t for m, t in progress)
if ratio_progress_min == 0.0:
rt_total_projected = inf
else:
rt_total_projected = rt_elapsed / ratio_progress_min
capture(ratio_progress_min, rt_total_projected - rt_elapsed, progress)
if is_finished(progress):
stop()
break
|
def track_progress(
measure: MeasureProgress,
target: MetricProgress,
interval_check: float,
capture_maybe: Optional[CaptureProgress] = None
) -> None
|
Tracks progress against a certain end condition of the simulation (for instance, a certain duration on the simulated
clock), reporting this progress as the simulation chugs along. Stops the simulation once the target has been
reached. By default, the progress is reported as printout on standard output, in a manner that works best for
digital terminals.
| 4.268807
| 4.120729
| 1.035935
|
''' Return the tm of `seq` as a float.
'''
tm_meth = _tm_methods.get(tm_method)
if tm_meth is None:
raise ValueError('{} is not a valid tm calculation method'.format(
tm_method))
salt_meth = _salt_corrections_methods.get(salt_corrections_method)
if salt_meth is None:
raise ValueError('{} is not a valid salt correction method'.format(
salt_corrections_method))
# For whatever reason mv_conc and dna_conc have to be ints
args = [pjoin(PRIMER3_HOME, 'oligotm'),
'-mv', str(mv_conc),
'-dv', str(dv_conc),
'-n', str(dntp_conc),
'-d', str(dna_conc),
'-tp', str(tm_meth),
'-sc', str(salt_meth),
seq]
tm = subprocess.check_output(args, stderr=DEV_NULL,
env=os.environ)
return float(tm)
|
def calcTm(seq, mv_conc=50, dv_conc=0, dntp_conc=0.8, dna_conc=50,
max_nn_length=60, tm_method='santalucia',
salt_corrections_method='santalucia')
|
Return the tm of `seq` as a float.
| 3.147918
| 2.981231
| 1.055912
|
''' Helper method that uses regex to parse ntthal output. '''
parsed_vals = re.search(_ntthal_re, ntthal_output)
return THERMORESULT(
True, # Structure found
float(parsed_vals.group(1)), # dS
float(parsed_vals.group(2)), # dH
float(parsed_vals.group(3)), # dG
float(parsed_vals.group(4)) # tm
) if parsed_vals else NULLTHERMORESULT
|
def _parse_ntthal(ntthal_output)
|
Helper method that uses regex to parse ntthal output.
| 4.842437
| 4.308908
| 1.12382
|
args = [pjoin(PRIMER3_HOME, 'ntthal'),
'-a', str(calc_type),
'-mv', str(mv_conc),
'-dv', str(dv_conc),
'-n', str(dntp_conc),
'-d', str(dna_conc),
'-t', str(temp_c),
'-maxloop', str(max_loop),
'-path', THERMO_PATH,
'-s1', seq1,
'-s2', seq2]
if temp_only:
args += ['-r']
out = subprocess.check_output(args, stderr=DEV_NULL,
env=os.environ)
return _parse_ntthal(out)
|
def calcThermo(seq1, seq2, calc_type='ANY', mv_conc=50, dv_conc=0,
dntp_conc=0.8, dna_conc=50, temp_c=37, max_loop=30,
temp_only=False)
|
Main subprocess wrapper for calls to the ntthal executable.
Returns a named tuple with tm, ds, dh, and dg values or None if no
structure / complex could be computed.
| 3.021669
| 2.611908
| 1.156882
|
''' Return a namedtuple of the dS, dH, dG, and Tm of any hairpin struct
present.
'''
return calcThermo(seq, seq, 'HAIRPIN', mv_conc, dv_conc, dntp_conc,
dna_conc, temp_c, max_loop, temp_only)
|
def calcHairpin(seq, mv_conc=50, dv_conc=0, dntp_conc=0.8, dna_conc=50,
temp_c=37, max_loop=30, temp_only=False)
|
Return a namedtuple of the dS, dH, dG, and Tm of any hairpin struct
present.
| 7.038536
| 2.457143
| 2.86452
|
''' Return a tuple of the dS, dH, dG, and Tm of any predicted heterodimer.
'''
return calcThermo(seq1, seq2, 'ANY', mv_conc, dv_conc, dntp_conc,
dna_conc, temp_c, max_loop, temp_only)
|
def calcHeterodimer(seq1, seq2, mv_conc=50, dv_conc=0, dntp_conc=0.8,
dna_conc=50, temp_c=37, max_loop=30, temp_only=False)
|
Return a tuple of the dS, dH, dG, and Tm of any predicted heterodimer.
| 5.118137
| 2.371193
| 2.158465
|
'''
Return the thermodynamic characteristics of hairpin/homodimer structures.
Returns a tuple of namedtuples (hairpin data, homodimer data) in which each
individual tuple is structured (dS, dH, dG, Tm).
'''
hairpin_out = calcHairpin(seq)
homodimer_out = calcHomodimer(seq)
return (hairpin_out, homodimer_out)
|
def assessOligo(seq)
|
Return the thermodynamic characteristics of hairpin/homodimer structures.
Returns a tuple of namedtuples (hairpin data, homodimer data) in which each
individual tuple is structured (dS, dH, dG, Tm).
| 7.55983
| 1.822778
| 4.147422
|
''' Return the raw primer3_core output for the provided primer3 args.
Returns an ordered dict of the boulderIO-format primer3 output file
'''
sp = subprocess.Popen([pjoin(PRIMER3_HOME, 'primer3_core')],
stdout=subprocess.PIPE, stdin=subprocess.PIPE,
stderr=subprocess.STDOUT)
p3_args.setdefault('PRIMER_THERMODYNAMIC_PARAMETERS_PATH',
pjoin(PRIMER3_HOME, 'primer3_config/'))
in_str = _formatBoulderIO(p3_args)
if input_log:
input_log.write(in_str)
input_log.flush()
out_str, err_str = sp.communicate(input=in_str)
if output_log:
output_log.write(out_str)
output_log.flush()
if err_log and err_str is not None:
err_log.write(err_str)
err_log.flush()
return _parseBoulderIO(out_str)
|
def designPrimers(p3_args, input_log=None, output_log=None, err_log=None)
|
Return the raw primer3_core output for the provided primer3 args.
Returns an ordered dict of the boulderIO-format primer3 output file
| 3.335076
| 2.253005
| 1.480279
|
''' Adds the executable bit to the file at filepath `fp`
'''
mode = ((os.stat(fp).st_mode) | 0o555) & 0o7777
setup_log.info("Adding executable bit to %s (mode is now %o)", fp, mode)
os.chmod(fp, mode)
|
def makeExecutable(fp)
|
Adds the executable bit to the file at filepath `fp`
| 4.205443
| 3.744103
| 1.123218
|
''' Calculate the hairpin formation thermodynamics of a DNA sequence.
**Note that the maximum length of `seq` is 60 bp.** This is a cap suggested
by the Primer3 team as the longest reasonable sequence length for which
a two-state NN model produces reliable results (see primer3/src/libnano/thal.h:50).
Args:
seq (str): DNA sequence to analyze for hairpin formation
mv_conc (float/int, optional): Monovalent cation conc. (mM)
dv_conc (float/int, optional): Divalent cation conc. (mM)
dntp_conc (float/int, optional): dNTP conc. (mM)
dna_conc (float/int, optional): DNA conc. (nM)
temp_c (int, optional): Simulation temperature for dG (Celsius)
max_loop(int, optional): Maximum size of loops in the structure
Returns:
A `ThermoResult` object with thermodynamic characteristics of the
hairpin formation.
Raises:
``RuntimeError``
'''
_setThermoArgs(**locals())
return _THERMO_ANALYSIS.calcHairpin(seq).checkExc()
|
def calcHairpin(seq, mv_conc=50.0, dv_conc=0.0, dntp_conc=0.8, dna_conc=50.0,
temp_c=37, max_loop=30)
|
Calculate the hairpin formation thermodynamics of a DNA sequence.
**Note that the maximum length of `seq` is 60 bp.** This is a cap suggested
by the Primer3 team as the longest reasonable sequence length for which
a two-state NN model produces reliable results (see primer3/src/libnano/thal.h:50).
Args:
seq (str): DNA sequence to analyze for hairpin formation
mv_conc (float/int, optional): Monovalent cation conc. (mM)
dv_conc (float/int, optional): Divalent cation conc. (mM)
dntp_conc (float/int, optional): dNTP conc. (mM)
dna_conc (float/int, optional): DNA conc. (nM)
temp_c (int, optional): Simulation temperature for dG (Celsius)
max_loop(int, optional): Maximum size of loops in the structure
Returns:
A `ThermoResult` object with thermodynamic characteristics of the
hairpin formation.
Raises:
``RuntimeError``
| 6.813582
| 1.508293
| 4.517413
|
''' Calculate the 3' end stability of DNA sequence `seq1` against DNA
sequence `seq2`.
**Note that at least one of the two sequences must by <60 bp in length.**
This is a cap imposed by Primer3 as the longest reasonable sequence length
for which a two-state NN model produces reliable results (see
primer3/src/libnano/thal.h:50).
Args:
seq1 (str) : DNA sequence to analyze for 3' end
hybridization against the target
sequence
seq2 (str) : Target DNA sequence to analyze for
seq1 3' end hybridization
mv_conc (float/int, optional) : Monovalent cation conc. (mM)
dv_conc (float/int, optional) : Divalent cation conc. (mM)
dntp_conc (float/int, optional) : dNTP conc. (mM)
dna_conc (float/int, optional) : DNA conc. (nM)
temp_c (int, optional) : Simulation temperature for dG (C)
max_loop(int, optional) : Maximum size of loops in the
structure
Returns:
A `ThermoResult` object with thermodynamic characteristics of the
3' hybridization interaction.
Raises:
``RuntimeError``
'''
_setThermoArgs(**locals())
return _THERMO_ANALYSIS.calcEndStability(seq1, seq2).checkExc()
|
def calcEndStability(seq1, seq2, mv_conc=50, dv_conc=0, dntp_conc=0.8,
dna_conc=50, temp_c=37, max_loop=30)
|
Calculate the 3' end stability of DNA sequence `seq1` against DNA
sequence `seq2`.
**Note that at least one of the two sequences must by <60 bp in length.**
This is a cap imposed by Primer3 as the longest reasonable sequence length
for which a two-state NN model produces reliable results (see
primer3/src/libnano/thal.h:50).
Args:
seq1 (str) : DNA sequence to analyze for 3' end
hybridization against the target
sequence
seq2 (str) : Target DNA sequence to analyze for
seq1 3' end hybridization
mv_conc (float/int, optional) : Monovalent cation conc. (mM)
dv_conc (float/int, optional) : Divalent cation conc. (mM)
dntp_conc (float/int, optional) : dNTP conc. (mM)
dna_conc (float/int, optional) : DNA conc. (nM)
temp_c (int, optional) : Simulation temperature for dG (C)
max_loop(int, optional) : Maximum size of loops in the
structure
Returns:
A `ThermoResult` object with thermodynamic characteristics of the
3' hybridization interaction.
Raises:
``RuntimeError``
| 6.598808
| 1.384302
| 4.766885
|
''' Calculate the melting temperature (Tm) of a DNA sequence.
Note that NN thermodynamics will be used to calculate the Tm of sequences
up to 60 bp in length, after which point the following formula will be
used::
Tm = 81.5 + 16.6(log10([mv_conc])) + 0.41(%GC) - 600/length
Args:
seq (str) : DNA sequence
mv_conc (float/int, optional) : Monovalent cation conc. (mM)
dv_conc (float/int, optional) : Divalent cation conc. (mM)
dntp_conc (float/int, optional) : dNTP conc. (mM)
dna_conc (float/int, optional) : DNA conc. (nM)
max_nn_length (int, optional) : Maximum length for
nearest-neighbor calcs
tm_method (str, optional) : Tm calculation method
(breslauer or santalucia)
salt_corrections_method (str, optional) : Salt correction method
(schildkraut, owczarzy,
santalucia)
Returns:
The melting temperature in degrees Celsius (float).
'''
_setThermoArgs(**locals())
return _THERMO_ANALYSIS.calcTm(seq)
|
def calcTm(seq, mv_conc=50, dv_conc=0, dntp_conc=0.8, dna_conc=50,
max_nn_length=60, tm_method='santalucia',
salt_corrections_method='santalucia')
|
Calculate the melting temperature (Tm) of a DNA sequence.
Note that NN thermodynamics will be used to calculate the Tm of sequences
up to 60 bp in length, after which point the following formula will be
used::
Tm = 81.5 + 16.6(log10([mv_conc])) + 0.41(%GC) - 600/length
Args:
seq (str) : DNA sequence
mv_conc (float/int, optional) : Monovalent cation conc. (mM)
dv_conc (float/int, optional) : Divalent cation conc. (mM)
dntp_conc (float/int, optional) : dNTP conc. (mM)
dna_conc (float/int, optional) : DNA conc. (nM)
max_nn_length (int, optional) : Maximum length for
nearest-neighbor calcs
tm_method (str, optional) : Tm calculation method
(breslauer or santalucia)
salt_corrections_method (str, optional) : Salt correction method
(schildkraut, owczarzy,
santalucia)
Returns:
The melting temperature in degrees Celsius (float).
| 4.800038
| 1.351732
| 3.551028
|
''' Run the Primer3 design process.
If the global args have been previously set (either by a pervious
`designPrimers` call or by a `setGlobals` call), `designPrimers` may be
called with seqArgs alone (as a means of optimization).
Args:
seq_args (dict) : Primer3 sequence/design args as per
Primer3 docs
global_args (dict, optional) : Primer3 global args as per Primer3 docs
misprime_lib (dict, optional) : `Sequence name: sequence` dictionary
for mispriming checks.
mishyb_lib (dict, optional) : `Sequence name: sequence` dictionary
for mishybridization checks.
Returns:
A dictionary of Primer3 results (should be identical to the expected
BoulderIO output from primer3_main)
'''
if global_args:
primerdesign.setGlobals(global_args, misprime_lib, mishyb_lib)
primerdesign.setSeqArgs(seq_args)
return primerdesign.runDesign(debug)
|
def designPrimers(seq_args, global_args=None, misprime_lib=None,
mishyb_lib=None, debug=False)
|
Run the Primer3 design process.
If the global args have been previously set (either by a pervious
`designPrimers` call or by a `setGlobals` call), `designPrimers` may be
called with seqArgs alone (as a means of optimization).
Args:
seq_args (dict) : Primer3 sequence/design args as per
Primer3 docs
global_args (dict, optional) : Primer3 global args as per Primer3 docs
misprime_lib (dict, optional) : `Sequence name: sequence` dictionary
for mispriming checks.
mishyb_lib (dict, optional) : `Sequence name: sequence` dictionary
for mishybridization checks.
Returns:
A dictionary of Primer3 results (should be identical to the expected
BoulderIO output from primer3_main)
| 5.892588
| 1.406423
| 4.189769
|
sections = []
for type, subsection_list in section_data.items():
for section in subsection_list:
section['sectionType'] = type
sections.append(section)
return sections
|
def unravel_sections(section_data)
|
Unravels section type dictionary into flat list of sections with
section type set as an attribute.
Args:
section_data(dict): Data return from py:method::get_sections
Returns:
list: Flat list of sections with ``sectionType`` set to
type (i.e. recitation, lecture, etc)
| 3.498739
| 3.532932
| 0.990322
|
staff_list = []
for role, staff_members in staff_data['data'].items():
for member in staff_members:
member['role'] = role
staff_list.append(member)
return staff_list
|
def unravel_staff(staff_data)
|
Unravels staff role dictionary into flat list of staff
members with ``role`` set as an attribute.
Args:
staff_data(dict): Data return from py:method::get_staff
Returns:
list: Flat list of staff members with ``role`` set to
role type (i.e. course_admin, instructor, TA, etc)
| 3.066784
| 3.074008
| 0.99765
|
gradebook = self.get('gradebook', params={'uuid': gbuuid})
if 'data' not in gradebook:
failure_messsage = ('Error in get_gradebook_id '
'for {0} - no data'.format(
gradebook
))
log.error(failure_messsage)
raise PyLmodUnexpectedData(failure_messsage)
return gradebook['data']['gradebookId']
|
def get_gradebook_id(self, gbuuid)
|
Return gradebookid for a given gradebook uuid.
Args:
gbuuid (str): gradebook uuid, i.e. ``STELLAR:/project/gbngtest``
Raises:
PyLmodUnexpectedData: No gradebook id returned
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
str: value of gradebook id
| 5.023655
| 4.194726
| 1.197612
|
end_point = 'gradebook/options/{gradebookId}'.format(
gradebookId=gradebook_id or self.gradebook_id)
options = self.get(end_point)
return options['data']
|
def get_options(self, gradebook_id)
|
Get options for gradebook.
Get options dictionary for a gradebook. Options include gradebook
attributes.
Args:
gradebook_id (str): unique identifier for gradebook, i.e. ``2314``
Returns:
An example return value is:
.. code-block:: python
{
u'data':
{
u'accessLevel': u'class',
u'archived': False,
u'calc_on_approved_only': False,
u'configured': None,
u'courseName': u'',
u'courseNumber': u'mitxdemosite',
u'deriveOverallGrades': False,
u'gradebookEwsEnabled': False,
u'gradebookId': 1293808,
u'gradebookName': u'Gradebook for mitxdemosite',
u'gradebookReadOnly': False,
u'gradebookVisibleToAdvisors': False,
u'graders_change_approved': False,
u'hideExcuseButtonInUI': False,
u'homeworkBetaEnabled': False,
u'membershipQualifier': u'/project/mitxdemosite',
u'membershipSource': u'stellar',
u'student_sees_actual_grades': True,
u'student_sees_category_info': True,
u'student_sees_comments': True,
u'student_sees_cumulative_score': True,
u'student_sees_histograms': True,
u'student_sees_submissions': False,
u'ta_approves': False,
u'ta_change_approved': False,
u'ta_configures': False,
u'ta_edits': False,
u'use_grade_weighting': False,
u'usingAttendance': False,
u'versionCompatible': 4,
u'versionCompatibleString': u'General Availability'
},
}
| 3.639354
| 3.646085
| 0.998154
|
# These are parameters required for the remote API call, so
# there aren't too many arguments
# pylint: disable=too-many-arguments
params = dict(
includeMaxPoints=json.dumps(max_points),
includeAvgStats=json.dumps(avg_stats),
includeGradingStats=json.dumps(grading_stats)
)
assignments = self.get(
'assignments/{gradebookId}'.format(
gradebookId=gradebook_id or self.gradebook_id
),
params=params,
)
if simple:
return [{'AssignmentName': x['name']}
for x in assignments['data']]
return assignments['data']
|
def get_assignments(
self,
gradebook_id='',
simple=False,
max_points=True,
avg_stats=False,
grading_stats=False
)
|
Get assignments for a gradebook.
Return list of assignments for a given gradebook,
specified by a py:attribute::gradebook_id. You can control
if additional parameters are returned, but the response
time with py:attribute::avg_stats and py:attribute::grading_stats
enabled is significantly longer.
Args:
gradebook_id (str): unique identifier for gradebook, i.e. ``2314``
simple (bool): return just assignment names, default= ``False``
max_points (bool):
Max points is a property of the grading scheme for the
assignment rather than a property of the assignment itself,
default= ``True``
avg_stats (bool): return average grade, default= ``False``
grading_stats (bool):
return grading statistics, i.e. number of approved grades,
unapproved grades, etc., default= ``False``
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
list: list of assignment dictionaries
An example return value is:
.. code-block:: python
[
{
u'assignmentId': 2431240,
u'categoryId': 1293820,
u'description': u'',
u'dueDate': 1372392000000,
u'dueDateString': u'06-28-2013',
u'gradebookId': 1293808,
u'graderVisible': True,
u'gradingSchemeId': 2431243,
u'gradingSchemeType': u'NUMERIC',
u'isComposite': False,
u'isHomework': False,
u'maxPointsTotal': 10.0,
u'name': u'Homework 1',
u'shortName': u'HW1',
u'userDeleted': False,
u'weight': 1.0
},
{
u'assignmentId': 16708850,
u'categoryId': 1293820,
u'description': u'',
u'dueDate': 1383541200000,
u'dueDateString': u'11-04-2013',
u'gradebookId': 1293808,
u'graderVisible': False,
u'gradingSchemeId': 16708851,
u'gradingSchemeType': u'NUMERIC',
u'isComposite': False,
u'isHomework': False,
u'maxPointsTotal': 100.0,
u'name': u'midterm1',
u'shortName': u'mid1',
u'userDeleted': False,
u'weight': 1.0
},
]
| 3.207326
| 3.434667
| 0.93381
|
if assignments is None:
assignments = self.get_assignments()
for assignment in assignments:
if assignment['name'] == assignment_name:
return assignment['assignmentId'], assignment
return None, None
|
def get_assignment_by_name(self, assignment_name, assignments=None)
|
Get assignment by name.
Get an assignment by name. It works by retrieving all assignments
and returning the first assignment with a matching name. If the
optional parameter ``assignments`` is provided, it uses this
collection rather than retrieving all assignments from the service.
Args:
assignment_name (str): name of assignment
assignments (list): assignments to search, default: None
When ``assignments`` is unspecified, all assignments
are retrieved from the service.
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
tuple: tuple of assignment id and assignment dictionary
.. code-block:: python
(
16708850,
{
u'assignmentId': 16708850,
u'categoryId': 1293820,
u'description': u'',
u'dueDate': 1383541200000,
u'dueDateString': u'11-04-2013',
u'gradebookId': 1293808,
u'graderVisible': False,
u'gradingSchemeId': 16708851,
u'gradingSchemeType': u'NUMERIC',
u'isComposite': False,
u'isHomework': False,
u'maxPointsTotal': 100.0,
u'name': u'midterm1',
u'shortName': u'mid1',
u'userDeleted': False,
u'weight': 1.0
}
)
| 2.481967
| 2.325132
| 1.067452
|
data = {
'name': name,
'shortName': short_name,
'weight': weight,
'graderVisible': False,
'gradingSchemeType': 'NUMERIC',
'gradebookId': gradebook_id or self.gradebook_id,
'maxPointsTotal': max_points,
'dueDateString': due_date_str
}
data.update(kwargs)
log.info("Creating assignment %s", name)
response = self.post('assignment', data)
log.debug('Received response data: %s', response)
return response
|
def create_assignment( # pylint: disable=too-many-arguments
self,
name,
short_name,
weight,
max_points,
due_date_str,
gradebook_id='',
**kwargs
)
|
Create a new assignment.
Create a new assignment. By default, assignments are created
under the `Uncategorized` category.
Args:
name (str): descriptive assignment name,
i.e. ``new NUMERIC SIMPLE ASSIGNMENT``
short_name (str): short name of assignment, one word of
no more than 5 characters, i.e. ``SAnew``
weight (str): floating point value for weight, i.e. ``1.0``
max_points (str): floating point value for maximum point
total, i.e. ``100.0``
due_date_str (str): due date as string in ``mm-dd-yyyy``
format, i.e. ``08-21-2011``
gradebook_id (str): unique identifier for gradebook, i.e. ``2314``
kwargs (dict): dictionary containing additional parameters,
i.e. ``graderVisible``, ``totalAverage``, and ``categoryId``.
For example:
.. code-block:: python
{
u'graderVisible': True,
u'totalAverage': None
u'categoryId': 1007964,
}
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
dict: dictionary containing ``data``, ``status`` and ``message``
for example:
.. code-block:: python
{
u'data':
{
u'assignmentId': 18490492,
u'categoryId': 1293820,
u'description': u'',
u'dueDate': 1312171200000,
u'dueDateString': u'08-01-2011',
u'gradebookId': 1293808,
u'graderVisible': False,
u'gradingSchemeId': 18490493,
u'gradingSchemeType': u'NUMERIC',
u'isComposite': False,
u'isHomework': False,
u'maxPointsTotal': 100.0,
u'name': u'new NUMERIC SIMPLE ASSIGNMENT',
u'numStudentGradesToBeApproved': 0,
u'numStudentsToBeGraded': 614,
u'shortName': u'SAnew',
u'userDeleted': False,
u'weight': 1.0
},
u'message': u'assignment is created successfully',
u'status': 1
}
| 2.996242
| 2.415334
| 1.240508
|
# pylint: disable=too-many-arguments
# numericGradeValue stringified because 'x' is a possible
# value for excused grades.
grade_info = {
'studentId': student_id,
'assignmentId': assignment_id,
'mode': 2,
'comment': 'from MITx {0}'.format(time.ctime(time.time())),
'numericGradeValue': str(grade_value),
'isGradeApproved': False
}
grade_info.update(kwargs)
log.info(
"student %s set_grade=%s for assignment %s",
student_id,
grade_value,
assignment_id)
return self.post(
'grades/{gradebookId}'.format(
gradebookId=gradebook_id or self.gradebook_id
),
data=grade_info,
)
|
def set_grade(
self,
assignment_id,
student_id,
grade_value,
gradebook_id='',
**kwargs
)
|
Set numerical grade for student and assignment.
Set a numerical grade for for a student and assignment. Additional
options
for grade ``mode`` are: OVERALL_GRADE = ``1``, REGULAR_GRADE = ``2``
To set 'excused' as the grade, enter ``None`` for letter and
numeric grade values,
and pass ``x`` as the ``specialGradeValue``.
``ReturnAffectedValues`` flag determines whether or not to return
student cumulative points and
impacted assignment category grades (average and student grade).
Args:
assignment_id (str): numerical ID for assignment
student_id (str): numerical ID for student
grade_value (str): numerical grade value
gradebook_id (str): unique identifier for gradebook, i.e. ``2314``
kwargs (dict): dictionary of additional parameters
.. code-block:: python
{
u'letterGradeValue':None,
u'booleanGradeValue':None,
u'specialGradeValue':None,
u'mode':2,
u'isGradeApproved':False,
u'comment':None,
u'returnAffectedValues': True,
}
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
dict: dictionary containing response ``status`` and ``message``
.. code-block:: python
{
u'message': u'grade saved successfully',
u'status': 1
}
| 4.42379
| 3.933598
| 1.124617
|
log.info('Sending grades: %r', grade_array)
return self.post(
'multiGrades/{gradebookId}'.format(
gradebookId=gradebook_id or self.gradebook_id
),
data=grade_array,
)
|
def multi_grade(self, grade_array, gradebook_id='')
|
Set multiple grades for students.
Set multiple student grades for a gradebook. The grades are passed
as a list of dictionaries.
Each grade dictionary in ``grade_array`` must contain a
``studentId`` and a ``assignmentId``.
Options for grade mode are: OVERALL_GRADE = ``1``,
REGULAR_GRADE = ``2``
To set 'excused' as the grade, enter ``None`` for
``letterGradeValue`` and ``numericGradeValue``,
and pass ``x`` as the ``specialGradeValue``.
The ``ReturnAffectedValues`` flag determines whether to return
student cumulative points and impacted assignment category
grades (average and student grade)
.. code-block:: python
[
{
u'comment': None,
u'booleanGradeValue': None,
u'studentId': 1135,
u'assignmentId': 4522,
u'specialGradeValue': None,
u'returnAffectedValues': True,
u'letterGradeValue': None,
u'mode': 2,
u'numericGradeValue': 50,
u'isGradeApproved': False
},
{
u'comment': None,
u'booleanGradeValue': None,
u'studentId': 1135,
u'assignmentId': 4522,
u'specialGradeValue': u'x',
u'returnAffectedValues': True,
u'letterGradeValue': None,
u'mode': 2,
u'numericGradeValue': None,
u'isGradeApproved': False
},
{
u'comment': None,
u'booleanGradeValue': None,
u'studentId': 1135,
u'assignmentId': None,
u'specialGradeValue': None,
u'returnAffectedValues': True,
u'letterGradeValue': u'A',
u'mode': 1,
u'numericGradeValue': None,
u'isGradeApproved': False
}
]
Args:
grade_array (dict): an array of grades to save
gradebook_id (str): unique identifier for gradebook, i.e. ``2314``
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
dict: dictionary containing response ``status`` and ``message``
| 3.368426
| 3.831032
| 0.879248
|
params = dict(includeMembers='false')
section_data = self.get(
'sections/{gradebookId}'.format(
gradebookId=gradebook_id or self.gradebook_id
),
params=params
)
if simple:
sections = self.unravel_sections(section_data['data'])
return [{'SectionName': x['name']} for x in sections]
return section_data['data']
|
def get_sections(self, gradebook_id='', simple=False)
|
Get the sections for a gradebook.
Return a dictionary of types of sections containing a list of that
type for a given gradebook. Specified by a gradebookid.
If simple=True, a list of dictionaries is provided for each
section regardless of type. The dictionary only contains one
key ``SectionName``.
Args:
gradebook_id (str): unique identifier for gradebook, i.e. ``2314``
simple (bool): return a list of section names only
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
dict: Dictionary of section types where each type has a
list of sections
An example return value is:
.. code-block:: python
{
u'recitation':
[
{
u'editable': False,
u'groupId': 1293925,
u'groupingScheme': u'Recitation',
u'members': None,
u'name': u'Unassigned',
u'shortName': u'DefaultGroupNoCollisionPlease1234',
u'staffs': None
},
{
u'editable': True,
u'groupId': 1327565,
u'groupingScheme': u'Recitation',
u'members': None,
u'name': u'r01',
u'shortName': u'r01',
u'staffs': None},
{u'editable': True,
u'groupId': 1327555,
u'groupingScheme': u'Recitation',
u'members': None,
u'name': u'r02',
u'shortName': u'r02',
u'staffs': None
}
]
}
| 3.692487
| 3.653926
| 1.010553
|
sections = self.unravel_sections(self.get_sections())
for section in sections:
if section['name'] == section_name:
return section['groupId'], section
return None, None
|
def get_section_by_name(self, section_name)
|
Get a section by its name.
Get a list of sections for a given gradebook,
specified by a gradebookid.
Args:
section_name (str): The section's name.
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
tuple: tuple of group id, and section dictionary
An example return value is:
.. code-block:: python
(
1327565,
{
u'editable': True,
u'groupId': 1327565,
u'groupingScheme': u'Recitation',
u'members': None,
u'name': u'r01',
u'shortName': u'r01',
u'staffs': None
}
)
| 4.499897
| 4.280586
| 1.051234
|
# These are parameters required for the remote API call, so
# there aren't too many arguments, or too many variables
# pylint: disable=too-many-arguments,too-many-locals
# Set params by arguments
params = dict(
includePhoto=json.dumps(include_photo),
includeGradeInfo=json.dumps(include_grade_info),
includeGradeHistory=json.dumps(include_grade_history),
includeMakeupGrades=json.dumps(include_makeup_grades),
)
url = 'students/{gradebookId}'
if section_name:
group_id, _ = self.get_section_by_name(section_name)
if group_id is None:
failure_message = (
'in get_students -- Error: '
'No such section %s' % section_name
)
log.critical(failure_message)
raise PyLmodNoSuchSection(failure_message)
url += '/section/{0}'.format(group_id)
student_data = self.get(
url.format(
gradebookId=gradebook_id or self.gradebook_id
),
params=params,
)
if simple:
# just return dict with keys email, name, section
student_map = dict(
accountEmail='email',
displayName='name',
section='section'
)
def remap(students):
newx = dict((student_map[k], students[k]) for k in student_map)
# match certs
newx['email'] = newx['email'].replace('@mit.edu', '@MIT.EDU')
return newx
return [remap(x) for x in student_data['data']]
return student_data['data']
|
def get_students(
self,
gradebook_id='',
simple=False,
section_name='',
include_photo=False,
include_grade_info=False,
include_grade_history=False,
include_makeup_grades=False
)
|
Get students for a gradebook.
Get a list of students for a given gradebook,
specified by a gradebook id. Does not include grade data.
Args:
gradebook_id (str): unique identifier for gradebook, i.e. ``2314``
simple (bool):
if ``True``, just return dictionary with keys ``email``,
``name``, ``section``, default = ``False``
section_name (str): section name
include_photo (bool): include student photo, default= ``False``
include_grade_info (bool):
include student's grade info, default= ``False``
include_grade_history (bool):
include student's grade history, default= ``False``
include_makeup_grades (bool):
include student's makeup grades, default= ``False``
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
list: list of student dictionaries
.. code-block:: python
[{
u'accountEmail': u'stellar.test2@gmail.com',
u'displayName': u'Molly Parker',
u'photoUrl': None,
u'middleName': None,
u'section': u'Unassigned',
u'sectionId': 1293925,
u'editable': False,
u'overallGradeInformation': None,
u'studentId': 1145,
u'studentAssignmentInfo': None,
u'sortableName': u'Parker, Molly',
u'surname': u'Parker',
u'givenName': u'Molly',
u'nickName': u'Molly',
u'email': u'stellar.test2@gmail.com'
},]
| 3.607172
| 3.694577
| 0.976342
|
if students is None:
students = self.get_students()
email = email.lower()
for student in students:
if student['accountEmail'].lower() == email:
return student['studentId'], student
return None, None
|
def get_student_by_email(self, email, students=None)
|
Get a student based on an email address.
Calls ``self.get_students()`` to get list of all students,
if not passed as the ``students`` parameter.
Args:
email (str): student email
students (list): dictionary of students to search, default: None
When ``students`` is unspecified, all students in gradebook
are retrieved.
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
tuple: tuple of student id and student dictionary.
| 2.980893
| 2.97547
| 1.001823
|
non_assignment_fields = [
'ID', 'Username', 'Full Name', 'edX email', 'External email'
]
if max_points_column is not None:
non_assignment_fields.append(max_points_column)
if normalize_column is not None:
non_assignment_fields.append(normalize_column)
if email_field is not None:
non_assignment_fields.append(email_field)
else:
email_field = 'External email'
if not hasattr(csv_file, 'read'):
file_pointer = open(csv_file)
else:
file_pointer = csv_file
csv_reader = csv.DictReader(file_pointer, dialect='excel')
response = self._spreadsheet2gradebook_multi(
csv_reader,
email_field,
non_assignment_fields,
approve_grades=approve_grades,
use_max_points_column=use_max_points_column,
max_points_column=max_points_column,
normalize_column=normalize_column
)
return response
|
def spreadsheet2gradebook(
self,
csv_file,
email_field=None,
approve_grades=False,
use_max_points_column=False,
max_points_column=None,
normalize_column=None
)
|
Upload grade spreadsheet to gradebook.
Upload grades from CSV format spreadsheet file into the
Learning Modules gradebook. The spreadsheet must have a column
named ``External email`` which is used as the student's email
address (for looking up and matching studentId).
These columns are disregarded: ``ID``, ``Username``,
``Full Name``, ``edX email``, ``External email``,
as well as the strings passed in ``max_points_column``
and ``normalize_column``, if any.
All other columns are taken as assignments.
If ``email_field`` is specified, then that field name is taken as
the student's email.
.. code-block:: none
External email,AB Assignment 01,AB Assignment 02
jeannechiang@gmail.com,1.0,0.9
stellar.test2@gmail.com,0.2,0.4
stellar.test1@gmail.com,0.93,0.77
Args:
csv_reader (str): filename of csv data, or readable file object
email_field (str): student's email
approve_grades (bool): Should grades be auto approved?
use_max_points_column (bool):
If ``True``, read the max points and normalize values
from the CSV and use the max points value in place of
the default if normalized is ``False``.
max_points_column (str): The name of the max_pts column. All
rows contain the same number, the max points for
the assignment.
normalize_column (str): The name of the normalize column which
indicates whether to use the max points value.
Raises:
PyLmodFailedAssignmentCreation: Failed to create assignment
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
tuple: tuple of dictionary containing response ``status``
and ``message``, and duration of operation
| 2.093146
| 1.829984
| 1.143805
|
staff_data = self.get(
'staff/{gradebookId}'.format(
gradebookId=gradebook_id or self.gradebook_id
),
params=None,
)
if simple:
simple_list = []
unraveled_list = self.unravel_staff(staff_data)
for member in unraveled_list.__iter__():
simple_list.append({
'accountEmail': member['accountEmail'],
'displayName': member['displayName'],
'role': member['role'],
})
return simple_list
return staff_data['data']
|
def get_staff(self, gradebook_id, simple=False)
|
Get staff list for gradebook.
Get staff list for the gradebook specified. Optionally, return
a less detailed list by specifying ``simple = True``.
If simple=True, return a list of dictionaries, one dictionary
for each member. The dictionary contains a member's ``email``,
``displayName``, and ``role``. Members with multiple roles will
appear in the list once for each role.
Args:
gradebook_id (str): unique identifier for gradebook, i.e. ``2314``
simple (bool): Return a staff list with less detail. Default
is ``False``.
Returns:
An example return value is:
.. code-block:: python
{
u'data': {
u'COURSE_ADMIN': [
{
u'accountEmail': u'benfranklin@mit.edu',
u'displayName': u'Benjamin Franklin',
u'editable': False,
u'email': u'benfranklin@mit.edu',
u'givenName': u'Benjamin',
u'middleName': None,
u'mitId': u'921344431',
u'nickName': u'Benjamin',
u'personId': 10710616,
u'sortableName': u'Franklin, Benjamin',
u'surname': u'Franklin',
u'year': None
},
],
u'COURSE_PROF': [
{
u'accountEmail': u'dduck@mit.edu',
u'displayName': u'Donald Duck',
u'editable': False,
u'email': u'dduck@mit.edu',
u'givenName': u'Donald',
u'middleName': None,
u'mitId': u'916144889',
u'nickName': u'Donald',
u'personId': 8117160,
u'sortableName': u'Duck, Donald',
u'surname': u'Duck',
u'year': None
},
],
u'COURSE_TA': [
{
u'accountEmail': u'hduck@mit.edu',
u'displayName': u'Huey Duck',
u'editable': False,
u'email': u'hduck@mit.edu',
u'givenName': u'Huey',
u'middleName': None,
u'mitId': u'920445024',
u'nickName': u'Huey',
u'personId': 1299059,
u'sortableName': u'Duck, Huey',
u'surname': u'Duck',
u'year': None
},
]
},
}
| 3.180224
| 2.836851
| 1.12104
|
if uuid is None:
uuid = self.uuid
group_data = self.get('group', params={'uuid': uuid})
return group_data
|
def get_group(self, uuid=None)
|
Get group data based on uuid.
Args:
uuid (str): optional uuid. defaults to self.cuuid
Raises:
PyLmodUnexpectedData: No data was returned.
requests.RequestException: Exception connection error
Returns:
dict: group json
| 3.682507
| 5.244381
| 0.702181
|
group_data = self.get_group(uuid)
try:
return group_data['response']['docs'][0]['id']
except (KeyError, IndexError):
failure_message = ('Error in get_group response data - '
'got {0}'.format(group_data))
log.exception(failure_message)
raise PyLmodUnexpectedData(failure_message)
|
def get_group_id(self, uuid=None)
|
Get group id based on uuid.
Args:
uuid (str): optional uuid. defaults to self.cuuid
Raises:
PyLmodUnexpectedData: No group data was returned.
requests.RequestException: Exception connection error
Returns:
int: numeric group id
| 5.206519
| 4.29834
| 1.211286
|
group_id = self.get_group_id(uuid=uuid)
uri = 'group/{group_id}/member'
mbr_data = self.get(uri.format(group_id=group_id), params=None)
return mbr_data
|
def get_membership(self, uuid=None)
|
Get membership data based on uuid.
Args:
uuid (str): optional uuid. defaults to self.cuuid
Raises:
PyLmodUnexpectedData: No data was returned.
requests.RequestException: Exception connection error
Returns:
dict: membership json
| 3.55092
| 4.296917
| 0.826388
|
mbr_data = self.get_membership(uuid=uuid)
docs = []
try:
docs = mbr_data['response']['docs']
except KeyError:
failure_message = ('KeyError in membership data - '
'got {0}'.format(mbr_data))
log.exception(failure_message)
raise PyLmodUnexpectedData(failure_message)
if len(docs) == 0:
return False
has_role = any(
(x.get('email') == email and x.get('roleType') == role_name)
for x in docs
)
if has_role:
return True
return False
|
def email_has_role(self, email, role_name, uuid=None)
|
Determine if an email is associated with a role.
Args:
email (str): user email
role_name (str): user role
uuid (str): optional uuid. defaults to self.cuuid
Raises:
PyLmodUnexpectedData: Unexpected data was returned.
requests.RequestException: Exception connection error
Returns:
bool: True or False if email has role_name
| 3.88572
| 3.252995
| 1.194505
|
course_data = self.get(
'courseguide/course?uuid={uuid}'.format(
uuid=course_uuid or self.course_id
),
params=None
)
try:
return course_data['response']['docs'][0]['id']
except KeyError:
failure_message = ('KeyError in get_course_id - '
'got {0}'.format(course_data))
log.exception(failure_message)
raise PyLmodUnexpectedData(failure_message)
except TypeError:
failure_message = ('TypeError in get_course_id - '
'got {0}'.format(course_data))
log.exception(failure_message)
raise PyLmodUnexpectedData(failure_message)
|
def get_course_id(self, course_uuid)
|
Get course id based on uuid.
Args:
uuid (str): course uuid, i.e. /project/mitxdemosite
Raises:
PyLmodUnexpectedData: No course data was returned.
requests.RequestException: Exception connection error
Returns:
int: numeric course id
| 3.158559
| 2.863312
| 1.103114
|
staff_data = self.get(
'courseguide/course/{courseId}/staff'.format(
courseId=course_id or self.course_id
),
params=None
)
return staff_data['response']['docs']
|
def get_course_guide_staff(self, course_id='')
|
Get the staff roster for a course.
Get a list of staff members for a given course,
specified by a course id.
Args:
course_id (int): unique identifier for course, i.e. ``2314``
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
list: list of dictionaries containing staff data
An example return value is:
.. code-block:: python
[
{
u'displayName': u'Huey Duck',
u'role': u'TA',
u'sortableDisplayName': u'Duck, Huey'
},
{
u'displayName': u'Louie Duck',
u'role': u'CourseAdmin',
u'sortableDisplayName': u'Duck, Louie'
},
{
u'displayName': u'Benjamin Franklin',
u'role': u'CourseAdmin',
u'sortableDisplayName': u'Franklin, Benjamin'
},
{
u'displayName': u'George Washington',
u'role': u'Instructor',
u'sortableDisplayName': u'Washington, George'
},
]
| 4.255169
| 5.231843
| 0.813321
|
if type(data) not in [str, unicode]:
data = json.dumps(data)
return data
|
def _data_to_json(data)
|
Convert to json if it isn't already a string.
Args:
data (str): data to convert to json
| 4.412534
| 4.560666
| 0.96752
|
base_service_url = '{base}{service}'.format(
base=self.urlbase,
service=service
)
return base_service_url
|
def _url_format(self, service)
|
Generate URL from urlbase and service.
Args:
service (str): The endpoint service to use, i.e. gradebook
Returns:
str: URL to where the request should be made
| 4.613537
| 5.314881
| 0.868041
|
try:
response = func(url, timeout=self.TIMEOUT, **kwargs)
except requests.RequestException, err:
log.exception(
"[PyLmod] Error - connection error in "
"rest_action, err=%s", err
)
raise err
try:
return response.json()
except ValueError, err:
log.exception('Unable to decode %s', response.content)
raise err
|
def rest_action(self, func, url, **kwargs)
|
Routine to do low-level REST operation, with retry.
Args:
func (callable): API function to call
url (str): service URL endpoint
kwargs (dict): addition parameters
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
list: the json-encoded content of the response
| 5.021168
| 4.911558
| 1.022317
|
url = self._url_format(service)
if params is None:
params = {}
return self.rest_action(self._session.get, url, params=params)
|
def get(self, service, params=None)
|
Generic GET operation for retrieving data from Learning Modules API.
.. code-block:: python
gbk.get('students/{gradebookId}', params=params, gradebookId=gbid)
Args:
service (str): The endpoint service to use, i.e. gradebook
params (dict): additional parameters to add to the call
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
list: the json-encoded content of the response
| 4.150091
| 5.886729
| 0.704991
|
url = self._url_format(service)
data = Base._data_to_json(data)
# Add content-type for body in POST.
headers = {'content-type': 'application/json'}
return self.rest_action(self._session.post, url,
data=data, headers=headers)
|
def post(self, service, data)
|
Generic POST operation for sending data to Learning Modules API.
Data should be a JSON string or a dict. If it is not a string,
it is turned into a JSON string for the POST body.
Args:
service (str): The endpoint service to use, i.e. gradebook
data (json or dict): the data payload
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
list: the json-encoded content of the response
| 5.194209
| 5.784269
| 0.897989
|
url = self._url_format(service)
return self.rest_action(
self._session.delete, url
)
|
def delete(self, service)
|
Generic DELETE operation for Learning Modules API.
Args:
service (str): The endpoint service to use, i.e. gradebook
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
list: the json-encoded content of the response
| 9.96811
| 11.819184
| 0.843384
|
if not isinstance(secret, basestring):
raise ValueError("firebase_token_generator.create_token: secret must be a string.")
if not options and not data:
raise ValueError("firebase_token_generator.create_token: data is empty and no options are set. This token will have no effect on Firebase.");
if not options:
options = {}
is_admin_token = ('admin' in options and options['admin'] == True)
_validate_data(data, is_admin_token)
claims = _create_options_claims(options)
claims['v'] = TOKEN_VERSION
claims['iat'] = int(time.time())
claims['d'] = data
token = _encode_token(secret, claims)
if len(token) > 1024:
raise RuntimeError("firebase_token_generator.create_token: generated token is too long.")
return token
|
def create_token(secret, data, options=None)
|
Generates a secure authentication token.
Our token format follows the JSON Web Token (JWT) standard:
header.claims.signature
Where:
1) "header" is a stringified, base64-encoded JSON object containing version and algorithm information.
2) "claims" is a stringified, base64-encoded JSON object containing a set of claims:
Library-generated claims:
"iat" -> The issued at time in seconds since the epoch as a number
"d" -> The arbitrary JSON object supplied by the user.
User-supplied claims (these are all optional):
"exp" (optional) -> The expiration time of this token, as a number of seconds since the epoch.
"nbf" (optional) -> The "not before" time before which the token should be rejected (seconds since the epoch)
"admin" (optional) -> If set to true, this client will bypass all security rules (use this to authenticate servers)
"debug" (optional) -> "set to true to make this client receive debug information about security rule execution.
"simulate" (optional, internal-only for now) -> Set to true to neuter all API operations (listens / puts
will run security rules but not actually write or return data).
3) A signature that proves the validity of this token (see: http://tools.ietf.org/html/draft-ietf-jose-json-web-signature-07)
For base64-encoding we use URL-safe base64 encoding. This ensures that the entire token is URL-safe
and could, for instance, be placed as a query argument without any encoding (and this is what the JWT spec requires).
Args:
secret - the Firebase Application secret
data - a json serializable object of data to be included in the token
options - An optional dictionary of additional claims for the token. Possible keys include:
a) "expires" -- A datetime or timestamp (as a number of seconds since the epoch) denoting a time after
which this token should no longer be valid.
b) "notBefore" -- A datetime or timestamp (as a number of seconds since the epoch) denoting a time before
which this token should be rejected by the server.
c) "admin" -- Set to true to bypass all security rules (use this for your trusted servers).
d) "debug" -- Set to true to enable debug mode (so you can see the results of Rules API operations)
e) "simulate" -- (internal-only for now) Set to true to neuter all API operations (listens / puts
will run security rules but not actually write or return data)
Returns:
A signed Firebase Authentication Token
Raises:
ValueError: if an invalid key is specified in options
| 3.395159
| 3.182153
| 1.066938
|
parser = HTMLParser(encoding=encoding, remove_blank_text=True)
return parse(fileobj, parser)
|
def parse_html(fileobj, encoding)
|
Given a file object *fileobj*, get an ElementTree instance.
The *encoding* is assumed to be utf8.
| 3.925623
| 3.739974
| 1.049639
|
rec = self._db.execute(, [seq_id]).fetchone()
if rec is None:
raise KeyError(seq_id)
if self._writing and self._writing["relpath"] == rec["relpath"]:
logger.warning(.format(rec["relpath"]))
self.commit()
path = os.path.join(self._root_dir, rec["relpath"])
fabgz = self._open_for_reading(path)
return fabgz.fetch(seq_id, start, end)
|
def fetch(self, seq_id, start=None, end=None)
|
fetch sequence by seq_id, optionally with start, end bounds
| 5.551437
| 5.500643
| 1.009234
|
if not self._writeable:
raise RuntimeError("Cannot write -- opened read-only")
# open a file for writing if necessary
# path: <root_dir>/<reldir>/<basename>
# <---- relpath ---->
# <------ dir_ ----->
# <----------- path ----------->
if self._writing is None:
reldir = datetime.datetime.utcnow().strftime("%Y/%m%d/%H%M")
basename = str(time.time()) + ".fa.bgz"
relpath = os.path.join(reldir, basename)
dir_ = os.path.join(self._root_dir, reldir)
path = os.path.join(self._root_dir, reldir, basename)
makedirs(dir_, exist_ok=True)
fabgz = FabgzWriter(path)
self._writing = {"relpath": relpath, "fabgz": fabgz}
logger.info("Opened for writing: " + path)
self._writing["fabgz"].store(seq_id, seq)
alpha = "".join(sorted(set(seq)))
self._db.execute(, (seq_id, len(seq), alpha, self._writing["relpath"]))
return seq_id
|
def store(self, seq_id, seq)
|
store a sequence with key seq_id. The sequence itself is stored in
a fasta file and a reference to it in the sqlite3 database.
| 4.428299
| 4.380791
| 1.010845
|
dialect = postgresql.dialect()
statement = getattr(source, 'statement', source)
compiled = statement.compile(dialect=dialect)
conn, autoclose = raw_connection_from(engine_or_conn)
cursor = conn.cursor()
query = cursor.mogrify(compiled.string, compiled.params).decode()
formatted_flags = '({})'.format(format_flags(flags)) if flags else ''
copy = 'COPY ({}) TO STDOUT {}'.format(query, formatted_flags)
cursor.copy_expert(copy, dest)
if autoclose:
conn.close()
|
def copy_to(source, dest, engine_or_conn, **flags)
|
Export a query or select to a file. For flags, see the PostgreSQL
documentation at http://www.postgresql.org/docs/9.5/static/sql-copy.html.
Examples: ::
select = MyTable.select()
with open('/path/to/file.tsv', 'w') as fp:
copy_to(select, fp, conn)
query = session.query(MyModel)
with open('/path/to/file/csv', 'w') as fp:
copy_to(query, fp, engine, format='csv', null='.')
:param source: SQLAlchemy query or select
:param dest: Destination file pointer, in write mode
:param engine_or_conn: SQLAlchemy engine, connection, or raw_connection
:param **flags: Options passed through to COPY
If an existing connection is passed to `engine_or_conn`, it is the caller's
responsibility to commit and close.
| 3.639928
| 3.656322
| 0.995516
|
tbl = dest.__table__ if is_model(dest) else dest
conn, autoclose = raw_connection_from(engine_or_conn)
cursor = conn.cursor()
relation = '.'.join('"{}"'.format(part) for part in (tbl.schema, tbl.name) if part)
formatted_columns = '({})'.format(','.join(columns)) if columns else ''
formatted_flags = '({})'.format(format_flags(flags)) if flags else ''
copy = 'COPY {} {} FROM STDIN {}'.format(
relation,
formatted_columns,
formatted_flags,
)
cursor.copy_expert(copy, source)
if autoclose:
conn.commit()
conn.close()
|
def copy_from(source, dest, engine_or_conn, columns=(), **flags)
|
Import a table from a file. For flags, see the PostgreSQL documentation
at http://www.postgresql.org/docs/9.5/static/sql-copy.html.
Examples: ::
with open('/path/to/file.tsv') as fp:
copy_from(fp, MyTable, conn)
with open('/path/to/file.csv') as fp:
copy_from(fp, MyModel, engine, format='csv')
:param source: Source file pointer, in read mode
:param dest: SQLAlchemy model or table
:param engine_or_conn: SQLAlchemy engine, connection, or raw_connection
:param columns: Optional tuple of columns
:param **flags: Options passed through to COPY
If an existing connection is passed to `engine_or_conn`, it is the caller's
responsibility to commit and close.
The `columns` flag can be set to a tuple of strings to specify the column
order. Passing `header` alone will not handle out of order columns, it simply tells
postgres to ignore the first line of `source`.
| 3.565821
| 3.70046
| 0.963616
|
if hasattr(engine_or_conn, 'cursor'):
return engine_or_conn, False
if hasattr(engine_or_conn, 'connection'):
return engine_or_conn.connection, False
return engine_or_conn.raw_connection(), True
|
def raw_connection_from(engine_or_conn)
|
Extract a raw_connection and determine if it should be automatically closed.
Only connections opened by this package will be closed automatically.
| 2.400659
| 2.445205
| 0.981782
|
if os.path.exists(name):
if not exist_ok:
raise FileExistsError("File exists: " + name)
else:
os.makedirs(name, mode)
|
def makedirs(name, mode=0o777, exist_ok=False)
|
cheapo replacement for py3 makedirs with support for exist_ok
| 2.316233
| 2.178837
| 1.063059
|
def fetch_seq(q, nsa):
pid, ppid = os.getpid(), os.getppid()
q.put((pid, ppid, sr[nsa]))
q = Queue()
p = Process(target=fetch_seq, args=(q, nsa))
p.start()
pid, ppid, seq = q.get()
p.join()
assert pid != ppid, "sequence was not fetched from thread"
return pid, ppid, seq
|
def fetch_in_thread(sr, nsa)
|
fetch a sequence in a thread
| 3.325603
| 3.136495
| 1.060293
|
try:
self.linux.verify_system_status()
except InstallSkipError:
Log.info('Install skipped.')
return
work_dir = tempfile.mkdtemp(suffix='-rpm-py-installer')
Log.info("Created working directory '{0}'".format(work_dir))
with Cmd.pushd(work_dir):
self.rpm_py.download_and_install()
if not self.python.is_python_binding_installed():
message = (
'RPM Python binding failed to install '
'with unknown reason.'
)
raise InstallError(message)
# TODO: Print installed module name and version as INFO.
if self.is_work_dir_removed:
shutil.rmtree(work_dir)
Log.info("Removed working directory '{0}'".format(work_dir))
else:
Log.info("Saved working directory '{0}'".format(work_dir))
|
def run(self)
|
Run install process.
| 5.212046
| 4.898743
| 1.063956
|
if self.is_installed_from_bin:
try:
self.installer.install_from_rpm_py_package()
return
except RpmPyPackageNotFoundError as e:
Log.warn('RPM Py Package not found. reason: {0}'.format(e))
# Pass to try to install from the source.
pass
# Download and install from the source.
top_dir_name = self.downloader.download_and_expand()
rpm_py_dir = os.path.join(top_dir_name, 'python')
setup_py_in_found = False
with Cmd.pushd(rpm_py_dir):
if self.installer.setup_py.exists_in_path():
setup_py_in_found = True
self.installer.run()
if not setup_py_in_found:
self.installer.install_from_rpm_py_package()
|
def download_and_install(self)
|
Download and install RPM Python binding.
| 4.768725
| 4.393528
| 1.085398
|
info = self.info
return 'rpm-{major}.{minor}.x'.format(
major=info[0], minor=info[1])
|
def git_branch(self)
|
Git branch name.
| 8.753235
| 8.093161
| 1.08156
|
additional_patches = [
{
'src': r"pkgconfig\('--libs-only-L'\)",
'dest': "['{0}']".format(lib_dir),
},
# Considering -libs-only-l and -libs-only-L
# https://github.com/rpm-software-management/rpm/pull/327
{
'src': r"pkgconfig\('--libs(-only-l)?'\)",
'dest': "['rpm', 'rpmio']",
'required': True,
},
{
'src': r"pkgconfig\('--cflags'\)",
'dest': "['{0}']".format(include_dir),
'required': True,
},
]
self.patches.extend(additional_patches)
|
def add_patchs_to_build_without_pkg_config(self, lib_dir, include_dir)
|
Add patches to remove pkg-config command and rpm.pc part.
Replace with given library_path: lib_dir and include_path: include_dir
without rpm.pc file.
| 4.398304
| 4.310285
| 1.020421
|
patches = self.patches
content = None
with open(self.IN_PATH) as f_in:
# As setup.py.in file size is 2.4 KByte.
# it's fine to read entire content.
content = f_in.read()
# Replace words.
for key in self.replaced_word_dict:
content = content.replace(key, self.replaced_word_dict[key])
# Apply patches.
out_patches = []
for patch in patches:
pattern = re.compile(patch['src'], re.MULTILINE)
(content, subs_num) = re.subn(pattern, patch['dest'],
content)
if subs_num > 0:
patch['applied'] = True
out_patches.append(patch)
for patch in out_patches:
if patch.get('required') and not patch.get('applied'):
Log.warn('Patch not applied {0}'.format(patch['src']))
with open(self.OUT_PATH, 'w') as f_out:
f_out.write(content)
self.pathces = out_patches
# Release content data to make it released by GC quickly.
content = None
|
def apply_and_save(self)
|
Apply replaced words and patches, and save setup.py file.
| 4.466107
| 4.116834
| 1.08484
|
top_dir_name = None
if self.git_branch:
# Download a source by git clone.
top_dir_name = self._download_and_expand_by_git()
else:
# Download a source from the arcihve URL.
# Downloading the compressed archive is better than "git clone",
# because it is faster.
# If download failed due to URL not found, try "git clone".
try:
top_dir_name = self._download_and_expand_from_archive_url()
except RemoteFileNotFoundError:
Log.info('Try to download by git clone.')
top_dir_name = self._download_and_expand_by_git()
return top_dir_name
|
def download_and_expand(self)
|
Download and expand RPM Python binding.
| 5.171849
| 5.015609
| 1.031151
|
self._make_lib_file_symbolic_links()
self._copy_each_include_files_to_include_dir()
self._make_dep_lib_file_sym_links_and_copy_include_files()
self.setup_py.add_patchs_to_build_without_pkg_config(
self.rpm.lib_dir, self.rpm.include_dir
)
self.setup_py.apply_and_save()
self._build_and_install()
|
def run(self)
|
Run install main logic.
| 7.128586
| 6.728305
| 1.059492
|
so_file_dict = {
'rpmio': {
'sym_src_dir': self.rpm.lib_dir,
'sym_dst_dir': 'rpmio/.libs',
'require': True,
},
'rpm': {
'sym_src_dir': self.rpm.lib_dir,
'sym_dst_dir': 'lib/.libs',
'require': True,
},
'rpmbuild': {
'sym_src_dir': self.rpm.lib_dir,
'sym_dst_dir': 'build/.libs',
'require': True,
},
'rpmsign': {
'sym_src_dir': self.rpm.lib_dir,
'sym_dst_dir': 'sign/.libs',
},
}
self._update_sym_src_dirs_conditionally(so_file_dict)
for name in so_file_dict:
so_dict = so_file_dict[name]
pattern = 'lib{0}.so*'.format(name)
so_files = Cmd.find(so_dict['sym_src_dir'], pattern)
if not so_files:
is_required = so_dict.get('require', False)
if not is_required:
message_format = (
"Skip creating symbolic link of "
"not existing so file '{0}'"
)
Log.debug(message_format.format(name))
continue
message = 'so file pattern {0} not found at {1}'.format(
pattern, so_dict['sym_src_dir']
)
raise InstallError(message)
sym_dst_dir = os.path.abspath('../{0}'.format(
so_dict['sym_dst_dir']))
if not os.path.isdir(sym_dst_dir):
Cmd.mkdir_p(sym_dst_dir)
cmd = 'ln -sf {0} {1}/lib{2}.so'.format(so_files[0],
sym_dst_dir,
name)
Cmd.sh_e(cmd)
|
def _make_lib_file_symbolic_links(self)
|
Make symbolic links for lib files.
Make symbolic links from system library files or downloaded lib files
to downloaded source library files.
For example, case: Fedora x86_64
Make symbolic links
from
a. /usr/lib64/librpmio.so* (one of them)
b. /usr/lib64/librpm.so* (one of them)
c. If rpm-build-libs package is installed,
/usr/lib64/librpmbuild.so* (one of them)
otherwise, downloaded and extracted rpm-build-libs.
./usr/lib64/librpmbuild.so* (one of them)
c. If rpm-build-libs package is installed,
/usr/lib64/librpmsign.so* (one of them)
otherwise, downloaded and extracted rpm-build-libs.
./usr/lib64/librpmsign.so* (one of them)
to
a. rpm/rpmio/.libs/librpmio.so
b. rpm/lib/.libs/librpm.so
c. rpm/build/.libs/librpmbuild.so
d. rpm/sign/.libs/librpmsign.so
.
This is a status after running "make" on actual rpm build process.
| 2.721995
| 2.501853
| 1.087991
|
src_header_dirs = [
'rpmio',
'lib',
'build',
'sign',
]
with Cmd.pushd('..'):
src_include_dir = os.path.abspath('./include')
for header_dir in src_header_dirs:
if not os.path.isdir(header_dir):
message_format = "Skip not existing header directory '{0}'"
Log.debug(message_format.format(header_dir))
continue
header_files = Cmd.find(header_dir, '*.h')
for header_file in header_files:
pattern = '^{0}/'.format(header_dir)
(dst_header_file, subs_num) = re.subn(pattern,
'', header_file)
if subs_num == 0:
message = 'Failed to replace header_file: {0}'.format(
header_file)
raise ValueError(message)
dst_header_file = os.path.abspath(
os.path.join(src_include_dir, 'rpm', dst_header_file)
)
dst_dir = os.path.dirname(dst_header_file)
if not os.path.isdir(dst_dir):
Cmd.mkdir_p(dst_dir)
shutil.copyfile(header_file, dst_header_file)
|
def _copy_each_include_files_to_include_dir(self)
|
Copy include header files for each directory to include directory.
Copy include header files
from
rpm/
rpmio/*.h
lib/*.h
build/*.h
sign/*.h
to
rpm/
include/
rpm/*.h
.
This is a status after running "make" on actual rpm build process.
| 3.043634
| 2.59051
| 1.174917
|
if not self._rpm_py_has_popt_devel_dep():
message = (
'The RPM Python binding does not have popt-devel dependency'
)
Log.debug(message)
return
if self._is_popt_devel_installed():
message = '{0} package is installed.'.format(
self.pacakge_popt_devel_name)
Log.debug(message)
return
if not self._is_package_downloadable():
message = '''
Install a {0} download plugin or
install the {0} pacakge [{1}].
'''.format(self.package_sys_name, self.pacakge_popt_devel_name)
raise InstallError(message)
if not self._is_popt_installed():
message = '''
Required {0} not installed: [{1}],
Install the {0} package.
'''.format(self.package_sys_name, self.pacakge_popt_name)
raise InstallError(message)
self._download_and_extract_popt_devel()
# Copy libpopt.so to rpm_root/lib/.libs/.
popt_lib_dirs = [
self.rpm.lib_dir,
# /lib64/libpopt.so* installed at popt-1.13-7.el6.x86_64.
'/lib64',
# /lib/*/libpopt.so* installed at libpopt0-1.16-8ubuntu1
'/lib',
]
pattern = 'libpopt.so*'
popt_so_file = None
for popt_lib_dir in popt_lib_dirs:
so_files = Cmd.find(popt_lib_dir, pattern)
if so_files:
popt_so_file = so_files[0]
break
if not popt_so_file:
message = 'so file pattern {0} not found at {1}'.format(
pattern, str(popt_lib_dirs)
)
raise InstallError(message)
cmd = 'ln -sf {0} ../lib/.libs/libpopt.so'.format(
popt_so_file)
Cmd.sh_e(cmd)
# Copy popt.h to rpm_root/include
shutil.copy('./usr/include/popt.h', '../include')
|
def _make_dep_lib_file_sym_links_and_copy_include_files(self)
|
Make symbolick links for lib files and copy include files.
Do below steps for a dependency packages.
Dependency packages
- popt-devel
Steps
1. Make symbolic links from system library files or downloaded lib
files to downloaded source library files.
2. Copy include header files to include directory.
| 3.818412
| 3.744539
| 1.019728
|
found = False
with open('../include/rpm/rpmlib.h') as f_in:
for line in f_in:
if re.match(r'^#include .*popt.h.*$', line):
found = True
break
return found
|
def _rpm_py_has_popt_devel_dep(self)
|
Check if the RPM Python binding has a depndency to popt-devel.
Search include header files in the source code to check it.
| 4.117386
| 3.601273
| 1.143314
|
try:
if not self._is_rpm_all_lib_include_files_installed():
self._make_lib_file_symbolic_links()
self._copy_each_include_files_to_include_dir()
self._make_dep_lib_file_sym_links_and_copy_include_files()
self.setup_py.add_patchs_to_build_without_pkg_config(
self.rpm.lib_dir, self.rpm.include_dir
)
self.setup_py.apply_and_save()
self._build_and_install()
except InstallError as e:
if not self._is_rpm_all_lib_include_files_installed():
org_message = str(e)
message = '''
Install failed without rpm-devel package by below reason.
Can you install the RPM package, and run this installer again?
'''
message += org_message
raise InstallError(message)
else:
raise e
|
def run(self)
|
Run install main logic.
| 6.365664
| 6.065749
| 1.049444
|
self._download_and_extract_rpm_py_package()
# Find ./usr/lib64/pythonN.N/site-packages/rpm directory.
# A binary built by same version Python with used Python is target
# for the safe installation.
if self.rpm.has_set_up_py_in():
# If RPM has setup.py.in, this strict check is okay.
# Because we can still install from the source.
py_dir_name = 'python{0}.{1}'.format(
sys.version_info[0], sys.version_info[1])
else:
# If RPM does not have setup.py.in such as CentOS6,
# Only way to install is by different Python's RPM package.
py_dir_name = '*'
python_lib_dir_pattern = os.path.join(
'usr', '*', py_dir_name, 'site-packages')
rpm_dir_pattern = os.path.join(python_lib_dir_pattern, 'rpm')
downloaded_rpm_dirs = glob.glob(rpm_dir_pattern)
if not downloaded_rpm_dirs:
message = 'Directory with a pattern: {0} not found.'.format(
rpm_dir_pattern)
raise RpmPyPackageNotFoundError(message)
src_rpm_dir = downloaded_rpm_dirs[0]
# Remove rpm directory for the possible installed directories.
for rpm_dir in self.python.python_lib_rpm_dirs:
if os.path.isdir(rpm_dir):
Log.debug("Remove existing rpm directory {0}".format(rpm_dir))
shutil.rmtree(rpm_dir)
dst_rpm_dir = self.python.python_lib_rpm_dir
Log.debug("Copy directory from '{0}' to '{1}'".format(
src_rpm_dir, dst_rpm_dir))
shutil.copytree(src_rpm_dir, dst_rpm_dir)
file_name_pattern = 'rpm-*.egg-info'
rpm_egg_info_pattern = os.path.join(
python_lib_dir_pattern, file_name_pattern)
downloaded_rpm_egg_infos = glob.glob(rpm_egg_info_pattern)
if downloaded_rpm_egg_infos:
existing_rpm_egg_info_pattern = os.path.join(
self.python.python_lib_dir, file_name_pattern)
existing_rpm_egg_infos = glob.glob(existing_rpm_egg_info_pattern)
for existing_rpm_egg_info in existing_rpm_egg_infos:
Log.debug("Remove existing rpm egg info file '{0}'".format(
existing_rpm_egg_info))
os.remove(existing_rpm_egg_info)
Log.debug("Copy file from '{0}' to '{1}'".format(
downloaded_rpm_egg_infos[0], self.python.python_lib_dir))
shutil.copy2(downloaded_rpm_egg_infos[0],
self.python.python_lib_dir)
|
def install_from_rpm_py_package(self)
|
Run install from RPM Python binding RPM package.
| 3.082473
| 3.052965
| 1.009665
|
linux = None
if Cmd.which('apt-get'):
linux = DebianLinux(python, rpm_path, **kwargs)
else:
linux = FedoraLinux(python, rpm_path, **kwargs)
return linux
|
def get_instance(cls, python, rpm_path, **kwargs)
|
Get OS object.
| 3.879314
| 3.458202
| 1.121772
|
if not sys.platform.startswith('linux'):
raise InstallError('Supported platform is Linux only.')
if self.python.is_system_python():
if self.python.is_python_binding_installed():
message = '''
RPM Python binding already installed on system Python.
Nothing to do.
'''
Log.info(message)
raise InstallSkipError(message)
elif self.sys_installed:
pass
else:
message = '''
RPM Python binding on system Python should be installed manually.
Install the proper RPM package of python{,2,3}-rpm,
or set a environment variable RPM_PY_SYS=true
'''
raise InstallError(message)
if self.rpm.is_system_rpm():
self.verify_package_status()
|
def verify_system_status(self)
|
Verify system status.
| 7.251663
| 7.150516
| 1.014146
|
# rpm-libs is required for /usr/lib64/librpm*.so
self.rpm.verify_packages_installed(['rpm-libs'])
# Check RPM so files to build the Python binding.
message_format = '''
RPM: {0} or
RPM download tool (dnf-plugins-core (dnf) or yum-utils (yum)) required.
Install any of those.
'''
if self.rpm.has_composed_rpm_bulid_libs():
if (not self.rpm.is_package_installed('rpm-build-libs')
and not self.rpm.is_downloadable()):
raise InstallError(message_format.format('rpm-build-libs'))
else:
# All the needed so files are included in rpm-libs package.
pass
|
def verify_package_status(self)
|
Verify dependency RPM package status.
| 10.541012
| 10.086446
| 1.045067
|
return FedoraInstaller(rpm_py_version, self.python, self.rpm, **kwargs)
|
def create_installer(self, rpm_py_version, **kwargs)
|
Create Installer object.
| 6.939909
| 6.408188
| 1.082975
|
return DebianInstaller(rpm_py_version, self.python, self.rpm, **kwargs)
|
def create_installer(self, rpm_py_version, **kwargs)
|
Create Installer object.
| 7.734736
| 7.013157
| 1.102889
|
libs = [self.python_lib_arch_dir, self.python_lib_non_arch_dir]
def append_rpm(path):
return os.path.join(path, 'rpm')
return map(append_rpm, libs)
|
def python_lib_rpm_dirs(self)
|
Both arch and non-arch site-packages directories.
| 4.315709
| 3.476493
| 1.241397
|
is_installed = False
is_install_error = False
try:
is_installed = self.is_python_binding_installed_on_pip()
except InstallError:
# Consider a case of pip is not installed in old Python (<= 2.6).
is_install_error = True
if not is_installed or is_install_error:
for rpm_dir in self.python_lib_rpm_dirs:
init_py = os.path.join(rpm_dir, '__init__.py')
if os.path.isfile(init_py):
is_installed = True
break
return is_installed
|
def is_python_binding_installed(self)
|
Check if the Python binding has already installed.
Consider below cases.
- pip command is not installed.
- The installed RPM Python binding does not have information
showed as a result of pip list.
| 3.787623
| 3.482317
| 1.087673
|
pip_version = self._get_pip_version()
Log.debug('Pip version: {0}'.format(pip_version))
pip_major_version = int(pip_version.split('.')[0])
installed = False
# --format is from pip v9.0.0
# https://pip.pypa.io/en/stable/news/
if pip_major_version >= 9:
json_obj = self._get_pip_list_json_obj()
for package in json_obj:
Log.debug('pip list: {0}'.format(package))
if package['name'] in ('rpm-python', 'rpm'):
installed = True
Log.debug('Package installed: {0}, {1}'.format(
package['name'], package['version']))
break
else:
# Implementation for pip old version.
# It will be removed in the future.
lines = self._get_pip_list_lines()
for line in lines:
if re.match('^rpm(-python)? ', line):
installed = True
Log.debug('Package installed.')
break
return installed
|
def is_python_binding_installed_on_pip(self)
|
Check if the Python binding has already installed.
| 3.664224
| 3.595061
| 1.019238
|
stdout = Cmd.sh_e_out('{0} --version'.format(self.rpm_path))
rpm_version = stdout.split()[2]
return rpm_version
|
def version(self)
|
RPM vesion string.
| 9.956802
| 6.282162
| 1.584933
|
sys_rpm_paths = [
'/usr/bin/rpm',
# On CentOS6, system RPM is installed in this directory.
'/bin/rpm',
]
matched = False
for sys_rpm_path in sys_rpm_paths:
if self.rpm_path.startswith(sys_rpm_path):
matched = True
break
return matched
|
def is_system_rpm(self)
|
Check if the RPM is system RPM.
| 3.698923
| 3.416813
| 1.082565
|
if not package_name:
raise ValueError('package_name required.')
installed = True
try:
Cmd.sh_e('{0} --query {1} --quiet'.format(self.rpm_path,
package_name))
except InstallError:
installed = False
return installed
|
def is_package_installed(self, package_name)
|
Check if the RPM package is installed.
| 6.572613
| 5.274612
| 1.246085
|
if not package_names:
raise ValueError('package_names required.')
missing_packages = []
for package_name in package_names:
if not self.is_package_installed(package_name):
missing_packages.append(package_name)
if missing_packages:
comma_packages = ', '.join(missing_packages)
message = '''
Required RPM not installed: [{0}].
Install the RPM package.
'''.format(comma_packages)
raise InstallError(message)
|
def verify_packages_installed(self, package_names)
|
Check if the RPM packages are installed.
Raise InstallError if any of the packages is not installed.
| 3.352736
| 2.977933
| 1.12586
|
if not self._lib_dir:
rpm_lib_dir = None
cmd = '{0} -ql rpm-libs'.format(self.rpm_path)
out = Cmd.sh_e_out(cmd)
lines = out.split('\n')
for line in lines:
if 'librpm.so' in line:
rpm_lib_dir = os.path.dirname(line)
break
self._lib_dir = rpm_lib_dir
return self._lib_dir
|
def lib_dir(self)
|
Return standard library directory path used by RPM libs.
TODO: Support non-system RPM.
| 3.184533
| 2.905339
| 1.096097
|
is_plugin_avaiable = False
if self.is_dnf:
is_plugin_avaiable = self.is_package_installed(
'dnf-plugins-core')
else:
is_plugin_avaiable = self.is_package_installed(
'yum-utils')
return is_plugin_avaiable
|
def is_downloadable(self)
|
Return if rpm is downloadable by the package command.
Check if dnf or yum plugin package exists.
| 4.708537
| 3.536761
| 1.331313
|
if not package_name:
ValueError('package_name required.')
if self.is_dnf:
cmd = 'dnf download {0}.{1}'.format(package_name, self.arch)
else:
cmd = 'yumdownloader {0}.{1}'.format(package_name, self.arch)
try:
Cmd.sh_e(cmd, stdout=subprocess.PIPE)
except CmdError as e:
for out in (e.stdout, e.stderr):
for line in out.split('\n'):
if re.match(r'^No package [^ ]+ available', line) or \
re.match(r'^No Match for argument', line):
raise RemoteFileNotFoundError(
'Package {0} not found on remote'.format(
package_name
)
)
raise e
|
def download(self, package_name)
|
Download given package.
| 3.959386
| 3.848583
| 1.028791
|
for cmd in ['rpm2cpio', 'cpio']:
if not Cmd.which(cmd):
message = '{0} command not found. Install {0}.'.format(cmd)
raise InstallError(message)
pattern = '{0}*{1}.rpm'.format(package_name, self.arch)
rpm_files = Cmd.find('.', pattern)
if not rpm_files:
raise InstallError('PRM file not found.')
cmd = 'rpm2cpio {0} | cpio -idmv'.format(rpm_files[0])
Cmd.sh_e(cmd)
|
def extract(self, package_name)
|
Extract given package.
| 3.983257
| 3.841526
| 1.036894
|
if not self._lib_dir:
lib_files = glob.glob("/usr/lib/*/librpm.so*")
if not lib_files:
raise InstallError("Can not find lib directory.")
self._lib_dir = os.path.dirname(lib_files[0])
return self._lib_dir
|
def lib_dir(self)
|
Return standard library directory path used by RPM libs.
| 3.29697
| 2.60252
| 1.266838
|
Log.debug('CMD: {0}'.format(cmd))
cmd_kwargs = {
'shell': True,
}
cmd_kwargs.update(kwargs)
env = os.environ.copy()
# Better to parse English output
env['LC_ALL'] = 'en_US.utf-8'
if 'env' in kwargs:
env.update(kwargs['env'])
cmd_kwargs['env'] = env
# Capture stderr to show it on error message.
cmd_kwargs['stderr'] = subprocess.PIPE
proc = None
try:
proc = subprocess.Popen(cmd, **cmd_kwargs)
stdout, stderr = proc.communicate()
returncode = proc.returncode
message_format = (
'CMD Return Code: [{0}], Stdout: [{1}], Stderr: [{2}]'
)
Log.debug(message_format.format(returncode, stdout, stderr))
if stdout is not None:
stdout = stdout.decode('utf-8')
if stderr is not None:
stderr = stderr.decode('utf-8')
if returncode != 0:
message = 'CMD: [{0}], Return Code: [{1}] at [{2}]'.format(
cmd, returncode, os.getcwd())
if stderr is not None:
message += ' Stderr: [{0}]'.format(stderr)
ie = CmdError(message)
ie.stdout = stdout
ie.stderr = stderr
raise ie
return (stdout, stderr)
except Exception as e:
try:
proc.kill()
except Exception:
pass
raise e
|
def sh_e(cls, cmd, **kwargs)
|
Run the command. It behaves like "sh -e".
It raises InstallError if the command failed.
| 2.529401
| 2.522158
| 1.002872
|
cmd_kwargs = {
'stdout': subprocess.PIPE,
}
cmd_kwargs.update(kwargs)
return cls.sh_e(cmd, **cmd_kwargs)[0]
|
def sh_e_out(cls, cmd, **kwargs)
|
Run the command. and returns the stdout.
| 3.333672
| 2.96373
| 1.124823
|
Log.debug('CMD: cd {0}'.format(directory))
os.chdir(directory)
|
def cd(cls, directory)
|
Change directory. It behaves like "cd directory".
| 6.670444
| 5.810431
| 1.148012
|
previous_dir = os.getcwd()
try:
new_ab_dir = None
if os.path.isabs(new_dir):
new_ab_dir = new_dir
else:
new_ab_dir = os.path.join(previous_dir, new_dir)
# Use absolute path to show it on FileNotFoundError message.
cls.cd(new_ab_dir)
yield
finally:
cls.cd(previous_dir)
|
def pushd(cls, new_dir)
|
Change directory, and back to previous directory.
It behaves like "pushd directory; something; popd".
| 3.454486
| 3.527734
| 0.979236
|
abs_path_cmd = None
if sys.version_info >= (3, 3):
abs_path_cmd = shutil.which(cmd)
else:
abs_path_cmd = find_executable(cmd)
return abs_path_cmd
|
def which(cls, cmd)
|
Return an absolute path of the command.
It behaves like "which command".
| 2.749858
| 2.744659
| 1.001894
|
tar_gz_file_name = file_url.split('/')[-1]
if sys.version_info >= (3, 2):
from urllib.request import urlopen
from urllib.error import HTTPError
else:
from urllib2 import urlopen
from urllib2 import HTTPError
response = None
try:
response = urlopen(file_url)
except HTTPError as e:
message = 'Download failed: URL: {0}, reason: {1}'.format(
file_url, e)
if 'HTTP Error 404' in str(e):
raise RemoteFileNotFoundError(message)
else:
raise InstallError(message)
tar_gz_file_obj = io.BytesIO(response.read())
with open(tar_gz_file_name, 'wb') as f_out:
f_out.write(tar_gz_file_obj.read())
return tar_gz_file_name
|
def curl_remote_name(cls, file_url)
|
Download file_url, and save as a file name of the URL.
It behaves like "curl -O or --remote-name".
It raises HTTPError if the file_url not found.
| 2.213211
| 2.22318
| 0.995516
|
try:
with contextlib.closing(tarfile.open(tar_comp_file_path)) as tar:
tar.extractall()
except tarfile.ReadError as e:
message_format = (
'Extract failed: '
'tar_comp_file_path: {0}, reason: {1}'
)
raise InstallError(message_format.format(tar_comp_file_path, e))
|
def tar_extract(cls, tar_comp_file_path)
|
Extract tar.gz or tar bz2 file.
It behaves like
- tar xzf tar_gz_file_path
- tar xjf tar_bz2_file_path
It raises tarfile.ReadError if the file is broken.
| 2.741483
| 2.687602
| 1.020048
|
Log.debug('find {0} with pattern: {1}'.format(searched_dir, pattern))
matched_files = []
for root_dir, dir_names, file_names in os.walk(searched_dir,
followlinks=False):
for file_name in file_names:
if fnmatch.fnmatch(file_name, pattern):
file_path = os.path.join(root_dir, file_name)
if not os.path.islink(file_path):
matched_files.append(file_path)
matched_files.sort()
return matched_files
|
def find(cls, searched_dir, pattern)
|
Find matched files.
It does not include symbolic file in the result.
| 1.949984
| 1.866197
| 1.044897
|
if not isinstance(version_str, str):
ValueError('version_str invalid instance.')
version_info_list = re.findall(r'[0-9a-zA-Z]+', version_str)
def convert_to_int(string):
value = None
if re.match(r'^\d+$', string):
value = int(string)
else:
value = string
return value
version_info_list = [convert_to_int(s) for s in version_info_list]
return tuple(version_info_list)
|
def version_str2tuple(cls, version_str)
|
Version info.
tuple object. ex. ('4', '14', '0', 'rc1')
| 2.681875
| 2.568462
| 1.044156
|
header = None
for line in handle:
if line.startswith(">"):
if header is not None: # not the first record
yield header, "".join(seq_lines)
seq_lines = list()
header = line[1:].rstrip()
else:
if header is not None: # not the first record
seq_lines.append(line.strip())
if header is not None:
yield header, "".join(seq_lines)
else: # no FASTA records in file
return
|
def FastaIter(handle)
|
generator that returns (header, sequence) tuples from an open FASTA file handle
Lines before the start of the first record are ignored.
| 2.424237
| 2.284493
| 1.06117
|
for path in os.environ["PATH"].split(os.pathsep):
if os.path.exists(os.path.join(path, file)):
return os.path.join(path, file)
return None
|
def which(file)
|
>>> which("sh") is not None
True
>>> which("bogus-executable-that-doesn't-exist") is None
True
| 1.683786
| 2.080878
| 0.809171
|
python_path = sys.executable
cmd = '{0} install.py'.format(python_path)
exit_status = os.system(cmd)
if exit_status != 0:
raise Exception('Command failed: {0}'.format(cmd))
|
def install_rpm_py()
|
Install RPM Python binding.
| 3.103341
| 3.041469
| 1.020343
|
p = subprocess.Popen([exe, "-h"], stdout=subprocess.PIPE, stderr=subprocess.STDOUT, universal_newlines=True)
output = p.communicate()
version_line = output[0].splitlines()[1]
version = re.match(r"(?:Version:|bgzip \(htslib\))\s+(\d+\.\d+(\.\d+)?)", version_line).group(1)
return version
|
def _get_bgzip_version(exe)
|
return bgzip version as string
| 2.586228
| 2.505376
| 1.032271
|
missing_file_exception = OSError if six.PY2 else FileNotFoundError
min_bgzip_version = ".".join(map(str, min_bgzip_version_info))
exe = os.environ.get("SEQREPO_BGZIP_PATH", which("bgzip") or "/usr/bin/bgzip")
try:
bgzip_version = _get_bgzip_version(exe)
except AttributeError:
raise RuntimeError("Didn't find version string in bgzip executable ({exe})".format(exe=exe))
except missing_file_exception:
raise RuntimeError("{exe} doesn't exist; you need to install htslib (See https://github.com/biocommons/biocommons.seqrepo#requirements)".format(exe=exe))
except Exception:
raise RuntimeError("Unknown error while executing {exe}".format(exe=exe))
bgzip_version_info = tuple(map(int, bgzip_version.split(".")))
if bgzip_version_info < min_bgzip_version_info:
raise RuntimeError("bgzip ({exe}) {ev} is too old; >= {rv} is required; please upgrade".format(
exe=exe, ev=bgzip_version, rv=min_bgzip_version))
logger.info("Using bgzip {ev} ({exe})".format(ev=bgzip_version, exe=exe))
return exe
|
def _find_bgzip()
|
return path to bgzip if found and meets version requirements, else exception
| 3.069873
| 3.038451
| 1.010341
|
namespace, alias = uri_re.match(uri).groups()
return self.fetch(alias=alias, namespace=namespace, start=start, end=end)
|
def fetch_uri(self, uri, start=None, end=None)
|
fetch sequence for URI/CURIE of the form namespace:alias, such as
NCBI:NM_000059.3.
| 5.262537
| 4.087036
| 1.287617
|
if not self._writeable:
raise RuntimeError("Cannot write -- opened read-only")
if self._upcase:
seq = seq.upper()
try:
seqhash = bioutils.digests.seq_seqhash(seq)
except Exception as e:
import pprint
_logger.critical("Exception raised for " + pprint.pformat(nsaliases))
raise
seq_id = seqhash
# add sequence if not present
n_seqs_added = n_aliases_added = 0
msg = "sh{nsa_sep}{seq_id:.10s}... ({l} residues; {na} aliases {aliases})".format(
seq_id=seq_id,
l=len(seq),
na=len(nsaliases),
nsa_sep=nsa_sep,
aliases=", ".join("{nsa[namespace]}:{nsa[alias]}".format(nsa=nsa) for nsa in nsaliases))
if seq_id not in self.sequences:
_logger.info("Storing " + msg)
if len(seq) > ct_n_residues: # pragma: no cover
_logger.debug("Precommit for large sequence")
self.commit()
self.sequences.store(seq_id, seq)
n_seqs_added += 1
self._pending_sequences += 1
self._pending_sequences_len += len(seq)
self._pending_aliases += self._update_digest_aliases(seq_id, seq)
else:
_logger.debug("Sequence exists: " + msg)
# add/update external aliases for new and existing sequences
# updating is optimized to load only new <seq_id,ns,alias> tuples
existing_aliases = self.aliases.fetch_aliases(seq_id)
ea_tuples = [(r["seq_id"], r["namespace"], r["alias"]) for r in existing_aliases]
new_tuples = [(seq_id, r["namespace"], r["alias"]) for r in nsaliases]
upd_tuples = set(new_tuples) - set(ea_tuples)
if upd_tuples:
_logger.info("{} new aliases for {}".format(len(upd_tuples), msg))
for _, namespace, alias in upd_tuples:
self.aliases.store_alias(seq_id=seq_id, namespace=namespace, alias=alias)
self._pending_aliases += len(upd_tuples)
n_aliases_added += len(upd_tuples)
if (self._pending_sequences > ct_n_seqs or self._pending_aliases > ct_n_aliases
or self._pending_sequences_len > ct_n_residues): # pragma: no cover
_logger.info("Hit commit thresholds ({self._pending_sequences} sequences, "
"{self._pending_aliases} aliases, {self._pending_sequences_len} residues)".format(self=self))
self.commit()
return n_seqs_added, n_aliases_added
|
def store(self, seq, nsaliases)
|
nsaliases is a list of dicts, like:
[{"namespace": "en", "alias": "rose"},
{"namespace": "fr", "alias": "rose"},
{"namespace": "es", "alias": "rosa"}]
| 3.641512
| 3.567336
| 1.020793
|
if translate_ncbi_namespace is None:
translate_ncbi_namespace = self.translate_ncbi_namespace
seq_id = self._get_unique_seqid(alias=alias, namespace=namespace)
aliases = self.aliases.fetch_aliases(seq_id=seq_id,
translate_ncbi_namespace=translate_ncbi_namespace)
if target_namespaces:
aliases = [a for a in aliases if a["namespace"] in target_namespaces]
return aliases
|
def translate_alias(self, alias, namespace=None, target_namespaces=None, translate_ncbi_namespace=None)
|
given an alias and optional namespace, return a list of all other
aliases for same sequence
| 2.81918
| 2.448267
| 1.1515
|
namespace, alias = identifier.split(nsa_sep) if nsa_sep in identifier else (None, identifier)
aliases = self.translate_alias(alias=alias,
namespace=namespace,
target_namespaces=target_namespaces,
translate_ncbi_namespace=translate_ncbi_namespace)
return [nsa_sep.join((a["namespace"], a["alias"])) for a in aliases]
|
def translate_identifier(self, identifier, target_namespaces=None, translate_ncbi_namespace=None)
|
Given a string identifier, return a list of aliases (as
identifiers) that refer to the same sequence.
| 3.256133
| 3.050558
| 1.067389
|
recs = self.aliases.find_aliases(alias=alias, namespace=namespace)
seq_ids = set(r["seq_id"] for r in recs)
if len(seq_ids) == 0:
raise KeyError("Alias {} (namespace: {})".format(alias, namespace))
if len(seq_ids) > 1:
# This should only happen when namespace is None
raise KeyError("Alias {} (namespace: {}): not unique".format(alias, namespace))
return seq_ids.pop()
|
def _get_unique_seqid(self, alias, namespace)
|
given alias and namespace, return seq_id if exactly one distinct
sequence id is found, raise KeyError if there's no match, or
raise ValueError if there's more than one match.
| 2.990371
| 2.731774
| 1.094663
|
ir = bioutils.digests.seq_vmc_identifier(seq)
seq_aliases = [
{
"namespace": ir["namespace"],
"alias": ir["accession"],
},
{
"namespace": "SHA1",
"alias": bioutils.digests.seq_sha1(seq)
},
{
"namespace": "MD5",
"alias": bioutils.digests.seq_md5(seq)
},
{
"namespace": "SEGUID",
"alias": bioutils.digests.seq_seguid(seq)
},
]
for sa in seq_aliases:
self.aliases.store_alias(seq_id=seq_id, **sa)
return len(seq_aliases)
|
def _update_digest_aliases(self, seq_id, seq)
|
compute digest aliases for seq and update; returns number of digest
aliases (some of which may have already existed)
For the moment, sha512 is computed for seq_id separately from
the sha512 here. We should fix that.
| 3.332374
| 3.246712
| 1.026384
|
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.