id int32 0 252k | repo stringlengths 7 55 | path stringlengths 4 127 | func_name stringlengths 1 88 | original_string stringlengths 75 19.8k | language stringclasses 1
value | code stringlengths 51 19.8k | code_tokens list | docstring stringlengths 3 17.3k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 87 242 |
|---|---|---|---|---|---|---|---|---|---|---|---|
25,100 | wonambi-python/wonambi | wonambi/widgets/traces.py | Traces.next_event | def next_event(self, delete=False):
"""Go to next event."""
if delete:
msg = "Delete this event? This cannot be undone."
msgbox = QMessageBox(QMessageBox.Question, 'Delete event', msg)
msgbox.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
msgbox.setDefaultButton(QMessageBox.Yes)
response = msgbox.exec_()
if response == QMessageBox.No:
return
event_sel = self.event_sel
if event_sel is None:
return
notes = self.parent.notes
if not self.current_event_row:
row = notes.find_row(event_sel.marker.x(),
event_sel.marker.x() + event_sel.marker.width())
else:
row = self.current_event_row
same_type = self.action['next_of_same_type'].isChecked()
if same_type:
target = notes.idx_annot_list.item(row, 2).text()
if delete:
notes.delete_row()
msg = 'Deleted event from {} to {}.'.format(event_sel.marker.x(),
event_sel.marker.x() + event_sel.marker.width())
self.parent.statusBar().showMessage(msg)
row -= 1
if row + 1 == notes.idx_annot_list.rowCount():
return
if not same_type:
next_row = row + 1
else:
next_row = None
types = notes.idx_annot_list.property('name')[row + 1:]
for i, ty in enumerate(types):
if ty == target:
next_row = row + 1 + i
break
if next_row is None:
return
self.current_event_row = next_row
notes.go_to_marker(next_row, 0, 'annot')
notes.idx_annot_list.setCurrentCell(next_row, 0) | python | def next_event(self, delete=False):
if delete:
msg = "Delete this event? This cannot be undone."
msgbox = QMessageBox(QMessageBox.Question, 'Delete event', msg)
msgbox.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
msgbox.setDefaultButton(QMessageBox.Yes)
response = msgbox.exec_()
if response == QMessageBox.No:
return
event_sel = self.event_sel
if event_sel is None:
return
notes = self.parent.notes
if not self.current_event_row:
row = notes.find_row(event_sel.marker.x(),
event_sel.marker.x() + event_sel.marker.width())
else:
row = self.current_event_row
same_type = self.action['next_of_same_type'].isChecked()
if same_type:
target = notes.idx_annot_list.item(row, 2).text()
if delete:
notes.delete_row()
msg = 'Deleted event from {} to {}.'.format(event_sel.marker.x(),
event_sel.marker.x() + event_sel.marker.width())
self.parent.statusBar().showMessage(msg)
row -= 1
if row + 1 == notes.idx_annot_list.rowCount():
return
if not same_type:
next_row = row + 1
else:
next_row = None
types = notes.idx_annot_list.property('name')[row + 1:]
for i, ty in enumerate(types):
if ty == target:
next_row = row + 1 + i
break
if next_row is None:
return
self.current_event_row = next_row
notes.go_to_marker(next_row, 0, 'annot')
notes.idx_annot_list.setCurrentCell(next_row, 0) | [
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25,101 | wonambi-python/wonambi | wonambi/widgets/traces.py | Traces.resizeEvent | def resizeEvent(self, event):
"""Resize scene so that it fits the whole widget.
Parameters
----------
event : instance of QtCore.QEvent
not important
Notes
-----
This function overwrites Qt function, therefore the non-standard
name. Argument also depends on Qt.
The function is used to change the scale of view, so that the scene
fits the whole scene. There are two problems that I could not fix: 1)
how to give the width of the label in absolute width, 2) how to strech
scene just enough that it doesn't trigger a scrollbar. However, it's
pretty good as it is now.
"""
if self.scene is not None:
ratio = self.width() / (self.scene.width() * 1.1)
self.resetTransform()
self.scale(ratio, 1) | python | def resizeEvent(self, event):
if self.scene is not None:
ratio = self.width() / (self.scene.width() * 1.1)
self.resetTransform()
self.scale(ratio, 1) | [
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Parameters
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event : instance of QtCore.QEvent
not important
Notes
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name. Argument also depends on Qt.
The function is used to change the scale of view, so that the scene
fits the whole scene. There are two problems that I could not fix: 1)
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25,102 | wonambi-python/wonambi | wonambi/ioeeg/edf.py | Edf.return_dat | def return_dat(self, chan, begsam, endsam):
"""Read data from an EDF file.
Reads channel by channel, and adjusts the values by calibration.
Parameters
----------
chan : list of int
index (indices) of the channels to read
begsam : int
index of the first sample
endsam : int
index of the last sample
Returns
-------
numpy.ndarray
A 2d matrix, where the first dimension is the channels and the
second dimension are the samples.
"""
assert begsam < endsam
dat = empty((len(chan), endsam - begsam))
dat.fill(NaN)
with self.filename.open('rb') as f:
for i_dat, blk, i_blk in _select_blocks(self.blocks, begsam, endsam):
dat_in_rec = self._read_record(f, blk, chan)
dat[:, i_dat[0]:i_dat[1]] = dat_in_rec[:, i_blk[0]:i_blk[1]]
# calibration
dat = ((dat.astype('float64') - self.dig_min[chan, newaxis]) *
self.gain[chan, newaxis] + self.phys_min[chan, newaxis])
return dat | python | def return_dat(self, chan, begsam, endsam):
assert begsam < endsam
dat = empty((len(chan), endsam - begsam))
dat.fill(NaN)
with self.filename.open('rb') as f:
for i_dat, blk, i_blk in _select_blocks(self.blocks, begsam, endsam):
dat_in_rec = self._read_record(f, blk, chan)
dat[:, i_dat[0]:i_dat[1]] = dat_in_rec[:, i_blk[0]:i_blk[1]]
# calibration
dat = ((dat.astype('float64') - self.dig_min[chan, newaxis]) *
self.gain[chan, newaxis] + self.phys_min[chan, newaxis])
return dat | [
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Reads channel by channel, and adjusts the values by calibration.
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index (indices) of the channels to read
begsam : int
index of the first sample
endsam : int
index of the last sample
Returns
-------
numpy.ndarray
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25,103 | wonambi-python/wonambi | wonambi/ioeeg/edf.py | Edf._read_record | def _read_record(self, f, blk, chans):
"""Read raw data from a single EDF channel.
Parameters
----------
i_chan : int
index of the channel to read
begsam : int
index of the first sample
endsam : int
index of the last sample
Returns
-------
numpy.ndarray
A vector with the data as written on file, in 16-bit precision
"""
dat_in_rec = empty((len(chans), self.max_smp))
i_ch_in_dat = 0
for i_ch in chans:
offset, n_smp_per_chan = self._offset(blk, i_ch)
f.seek(offset)
x = fromfile(f, count=n_smp_per_chan, dtype=EDF_FORMAT)
ratio = int(self.max_smp / n_smp_per_chan)
dat_in_rec[i_ch_in_dat, :] = repeat(x, ratio)
i_ch_in_dat += 1
return dat_in_rec | python | def _read_record(self, f, blk, chans):
dat_in_rec = empty((len(chans), self.max_smp))
i_ch_in_dat = 0
for i_ch in chans:
offset, n_smp_per_chan = self._offset(blk, i_ch)
f.seek(offset)
x = fromfile(f, count=n_smp_per_chan, dtype=EDF_FORMAT)
ratio = int(self.max_smp / n_smp_per_chan)
dat_in_rec[i_ch_in_dat, :] = repeat(x, ratio)
i_ch_in_dat += 1
return dat_in_rec | [
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Parameters
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index of the channel to read
begsam : int
index of the first sample
endsam : int
index of the last sample
Returns
-------
numpy.ndarray
A vector with the data as written on file, in 16-bit precision | [
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25,104 | wonambi-python/wonambi | wonambi/ioeeg/brainvision.py | write_brainvision | def write_brainvision(data, filename, markers=None):
"""Export data in BrainVision format
Parameters
----------
data : instance of ChanTime
data with only one trial
filename : path to file
file to export to (use '.vhdr' as extension)
"""
filename = Path(filename).resolve().with_suffix('.vhdr')
if markers is None:
markers = []
with filename.open('w') as f:
f.write(_write_vhdr(data, filename))
with filename.with_suffix('.vmrk').open('w') as f:
f.write(_write_vmrk(data, filename, markers))
_write_eeg(data, filename) | python | def write_brainvision(data, filename, markers=None):
filename = Path(filename).resolve().with_suffix('.vhdr')
if markers is None:
markers = []
with filename.open('w') as f:
f.write(_write_vhdr(data, filename))
with filename.with_suffix('.vmrk').open('w') as f:
f.write(_write_vmrk(data, filename, markers))
_write_eeg(data, filename) | [
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Parameters
----------
data : instance of ChanTime
data with only one trial
filename : path to file
file to export to (use '.vhdr' as extension) | [
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25,105 | wonambi-python/wonambi | wonambi/source/linear.py | calc_xyz2surf | def calc_xyz2surf(surf, xyz, threshold=20, exponent=None, std=None):
"""Calculate transformation matrix from xyz values to vertices.
Parameters
----------
surf : instance of wonambi.attr.Surf
the surface of only one hemisphere.
xyz : numpy.ndarray
nChan x 3 matrix, with the locations in x, y, z.
std : float
distance in mm of the Gaussian kernel
exponent : int
inverse law (1-> direct inverse, 2-> inverse square, 3-> inverse cube)
threshold : float
distance in mm for a vertex to pick up electrode activity (if distance
is above the threshold, one electrode does not affect a vertex).
Returns
-------
numpy.ndarray
nVertices X xyz.shape[0] matrix
Notes
-----
This function is a helper when plotting onto brain surface, by creating a
transformation matrix from the values in space (f.e. at each electrode) to
the position of the vertices (used to show the brain surface).
There are many ways to move from values to vertices. The crucial parameter
is the function at which activity decreases in respect to the distance. You
can have an inverse relationship by specifying 'exponent'. If 'exponent' is
2, then the activity will decrease as inverse square of the distance. The
function can be a Gaussian. With std, you specify the width of the gaussian
kernel in mm.
For each vertex, it uses a threshold based on the distance ('threshold'
value, in mm). Finally, it normalizes the contribution of all the channels
to 1, so that the sum of the coefficients for each vertex is 1.
You can also create your own matrix (and skip calc_xyz2surf altogether) and
pass it as attribute to the main figure.
Because it's a loop over all the vertices, this function is pretty slow,
but if you calculate it once, you can reuse it.
We take advantage of multiprocessing, which speeds it up considerably.
"""
if exponent is None and std is None:
exponent = 1
if exponent is not None:
lg.debug('Vertex values based on inverse-law, with exponent ' +
str(exponent))
funct = partial(calc_one_vert_inverse, xyz=xyz, exponent=exponent)
elif std is not None:
lg.debug('Vertex values based on gaussian, with s.d. ' + str(std))
funct = partial(calc_one_vert_gauss, xyz=xyz, std=std)
with Pool() as p:
xyz2surf = p.map(funct, surf.vert)
xyz2surf = asarray(xyz2surf)
if exponent is not None:
threshold_value = (1 / (threshold ** exponent))
external_threshold_value = threshold_value
elif std is not None:
threshold_value = gauss(threshold, std)
external_threshold_value = gauss(std, std) # this is around 0.607
lg.debug('Values thresholded at ' + str(threshold_value))
xyz2surf[xyz2surf < threshold_value] = NaN
# here we deal with vertices that are within the threshold value but far
# from a single electrodes, so those remain empty
sumval = nansum(xyz2surf, axis=1)
sumval[sumval < external_threshold_value] = NaN
# normalize by the number of electrodes
xyz2surf /= atleast_2d(sumval).T
xyz2surf[isnan(xyz2surf)] = 0
return xyz2surf | python | def calc_xyz2surf(surf, xyz, threshold=20, exponent=None, std=None):
if exponent is None and std is None:
exponent = 1
if exponent is not None:
lg.debug('Vertex values based on inverse-law, with exponent ' +
str(exponent))
funct = partial(calc_one_vert_inverse, xyz=xyz, exponent=exponent)
elif std is not None:
lg.debug('Vertex values based on gaussian, with s.d. ' + str(std))
funct = partial(calc_one_vert_gauss, xyz=xyz, std=std)
with Pool() as p:
xyz2surf = p.map(funct, surf.vert)
xyz2surf = asarray(xyz2surf)
if exponent is not None:
threshold_value = (1 / (threshold ** exponent))
external_threshold_value = threshold_value
elif std is not None:
threshold_value = gauss(threshold, std)
external_threshold_value = gauss(std, std) # this is around 0.607
lg.debug('Values thresholded at ' + str(threshold_value))
xyz2surf[xyz2surf < threshold_value] = NaN
# here we deal with vertices that are within the threshold value but far
# from a single electrodes, so those remain empty
sumval = nansum(xyz2surf, axis=1)
sumval[sumval < external_threshold_value] = NaN
# normalize by the number of electrodes
xyz2surf /= atleast_2d(sumval).T
xyz2surf[isnan(xyz2surf)] = 0
return xyz2surf | [
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Parameters
----------
surf : instance of wonambi.attr.Surf
the surface of only one hemisphere.
xyz : numpy.ndarray
nChan x 3 matrix, with the locations in x, y, z.
std : float
distance in mm of the Gaussian kernel
exponent : int
inverse law (1-> direct inverse, 2-> inverse square, 3-> inverse cube)
threshold : float
distance in mm for a vertex to pick up electrode activity (if distance
is above the threshold, one electrode does not affect a vertex).
Returns
-------
numpy.ndarray
nVertices X xyz.shape[0] matrix
Notes
-----
This function is a helper when plotting onto brain surface, by creating a
transformation matrix from the values in space (f.e. at each electrode) to
the position of the vertices (used to show the brain surface).
There are many ways to move from values to vertices. The crucial parameter
is the function at which activity decreases in respect to the distance. You
can have an inverse relationship by specifying 'exponent'. If 'exponent' is
2, then the activity will decrease as inverse square of the distance. The
function can be a Gaussian. With std, you specify the width of the gaussian
kernel in mm.
For each vertex, it uses a threshold based on the distance ('threshold'
value, in mm). Finally, it normalizes the contribution of all the channels
to 1, so that the sum of the coefficients for each vertex is 1.
You can also create your own matrix (and skip calc_xyz2surf altogether) and
pass it as attribute to the main figure.
Because it's a loop over all the vertices, this function is pretty slow,
but if you calculate it once, you can reuse it.
We take advantage of multiprocessing, which speeds it up considerably. | [
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25,106 | wonambi-python/wonambi | wonambi/source/linear.py | calc_one_vert_inverse | def calc_one_vert_inverse(one_vert, xyz=None, exponent=None):
"""Calculate how many electrodes influence one vertex, using the inverse
function.
Parameters
----------
one_vert : ndarray
vector of xyz position of a vertex
xyz : ndarray
nChan X 3 with the position of all the channels
exponent : int
inverse law (1-> direct inverse, 2-> inverse square, 3-> inverse cube)
Returns
-------
ndarray
one vector with values for one vertex
"""
trans = empty(xyz.shape[0])
for i, one_xyz in enumerate(xyz):
trans[i] = 1 / (norm(one_vert - one_xyz) ** exponent)
return trans | python | def calc_one_vert_inverse(one_vert, xyz=None, exponent=None):
trans = empty(xyz.shape[0])
for i, one_xyz in enumerate(xyz):
trans[i] = 1 / (norm(one_vert - one_xyz) ** exponent)
return trans | [
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one_vert : ndarray
vector of xyz position of a vertex
xyz : ndarray
nChan X 3 with the position of all the channels
exponent : int
inverse law (1-> direct inverse, 2-> inverse square, 3-> inverse cube)
Returns
-------
ndarray
one vector with values for one vertex | [
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25,107 | wonambi-python/wonambi | wonambi/source/linear.py | calc_one_vert_gauss | def calc_one_vert_gauss(one_vert, xyz=None, std=None):
"""Calculate how many electrodes influence one vertex, using a Gaussian
function.
Parameters
----------
one_vert : ndarray
vector of xyz position of a vertex
xyz : ndarray
nChan X 3 with the position of all the channels
std : float
distance in mm of the Gaussian kernel
Returns
-------
ndarray
one vector with values for one vertex
"""
trans = empty(xyz.shape[0])
for i, one_xyz in enumerate(xyz):
trans[i] = gauss(norm(one_vert - one_xyz), std)
return trans | python | def calc_one_vert_gauss(one_vert, xyz=None, std=None):
trans = empty(xyz.shape[0])
for i, one_xyz in enumerate(xyz):
trans[i] = gauss(norm(one_vert - one_xyz), std)
return trans | [
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vector of xyz position of a vertex
xyz : ndarray
nChan X 3 with the position of all the channels
std : float
distance in mm of the Gaussian kernel
Returns
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ndarray
one vector with values for one vertex | [
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] | 1d8e3d7e53df8017c199f703bcab582914676e76 | https://github.com/wonambi-python/wonambi/blob/1d8e3d7e53df8017c199f703bcab582914676e76/wonambi/source/linear.py#L163-L184 |
25,108 | wonambi-python/wonambi | wonambi/ioeeg/micromed.py | _read_history | def _read_history(f, zone):
"""This matches the Matlab reader from Matlab Exchange but doesn't seem
correct.
"""
pos, length = zone
f.seek(pos, SEEK_SET)
histories = []
while f.tell() < (pos + length):
history = {
'nSample': unpack(MAX_SAMPLE * 'I', f.read(MAX_SAMPLE * 4)),
'lines': unpack('H', f.read(2)),
'sectors': unpack('H', f.read(2)),
'base_time': unpack('H', f.read(2)),
'notch': unpack('H', f.read(2)),
'colour': unpack(MAX_CAN_VIEW * 'B', f.read(MAX_CAN_VIEW)),
'selection': unpack(MAX_CAN_VIEW * 'B', f.read(MAX_CAN_VIEW)),
'description': f.read(64).strip(b'\x01\x00'),
'inputsNonInv': unpack(MAX_CAN_VIEW * 'H', f.read(MAX_CAN_VIEW * 2)), # NonInv : non inverting input
'inputsInv': unpack(MAX_CAN_VIEW * 'H', f.read(MAX_CAN_VIEW * 2)), # Inv : inverting input
'HiPass_Filter': unpack(MAX_CAN_VIEW * 'I', f.read(MAX_CAN_VIEW * 4)),
'LowPass_Filter': unpack(MAX_CAN_VIEW * 'I', f.read(MAX_CAN_VIEW * 4)),
'reference': unpack(MAX_CAN_VIEW * 'I', f.read(MAX_CAN_VIEW * 4)),
'free': f.read(1720).strip(b'\x01\x00'),
}
histories.append(history)
return histories | python | def _read_history(f, zone):
pos, length = zone
f.seek(pos, SEEK_SET)
histories = []
while f.tell() < (pos + length):
history = {
'nSample': unpack(MAX_SAMPLE * 'I', f.read(MAX_SAMPLE * 4)),
'lines': unpack('H', f.read(2)),
'sectors': unpack('H', f.read(2)),
'base_time': unpack('H', f.read(2)),
'notch': unpack('H', f.read(2)),
'colour': unpack(MAX_CAN_VIEW * 'B', f.read(MAX_CAN_VIEW)),
'selection': unpack(MAX_CAN_VIEW * 'B', f.read(MAX_CAN_VIEW)),
'description': f.read(64).strip(b'\x01\x00'),
'inputsNonInv': unpack(MAX_CAN_VIEW * 'H', f.read(MAX_CAN_VIEW * 2)), # NonInv : non inverting input
'inputsInv': unpack(MAX_CAN_VIEW * 'H', f.read(MAX_CAN_VIEW * 2)), # Inv : inverting input
'HiPass_Filter': unpack(MAX_CAN_VIEW * 'I', f.read(MAX_CAN_VIEW * 4)),
'LowPass_Filter': unpack(MAX_CAN_VIEW * 'I', f.read(MAX_CAN_VIEW * 4)),
'reference': unpack(MAX_CAN_VIEW * 'I', f.read(MAX_CAN_VIEW * 4)),
'free': f.read(1720).strip(b'\x01\x00'),
}
histories.append(history)
return histories | [
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25,109 | wonambi-python/wonambi | wonambi/widgets/video.py | Video.create_video | def create_video(self):
"""Create video widget."""
self.instance = vlc.Instance()
video_widget = QFrame()
self.mediaplayer = self.instance.media_player_new()
if system() == 'Linux':
self.mediaplayer.set_xwindow(video_widget.winId())
elif system() == 'Windows':
self.mediaplayer.set_hwnd(video_widget.winId())
elif system() == 'darwin': # to test
self.mediaplayer.set_nsobject(video_widget.winId())
else:
lg.warning('unsupported system for video widget')
return
self.medialistplayer = vlc.MediaListPlayer()
self.medialistplayer.set_media_player(self.mediaplayer)
event_manager = self.medialistplayer.event_manager()
event_manager.event_attach(vlc.EventType.MediaListPlayerNextItemSet,
self.next_video)
self.idx_button = QPushButton()
self.idx_button.setText('Start')
self.idx_button.clicked.connect(self.start_stop_video)
layout = QVBoxLayout()
layout.addWidget(video_widget)
layout.addWidget(self.idx_button)
self.setLayout(layout) | python | def create_video(self):
self.instance = vlc.Instance()
video_widget = QFrame()
self.mediaplayer = self.instance.media_player_new()
if system() == 'Linux':
self.mediaplayer.set_xwindow(video_widget.winId())
elif system() == 'Windows':
self.mediaplayer.set_hwnd(video_widget.winId())
elif system() == 'darwin': # to test
self.mediaplayer.set_nsobject(video_widget.winId())
else:
lg.warning('unsupported system for video widget')
return
self.medialistplayer = vlc.MediaListPlayer()
self.medialistplayer.set_media_player(self.mediaplayer)
event_manager = self.medialistplayer.event_manager()
event_manager.event_attach(vlc.EventType.MediaListPlayerNextItemSet,
self.next_video)
self.idx_button = QPushButton()
self.idx_button.setText('Start')
self.idx_button.clicked.connect(self.start_stop_video)
layout = QVBoxLayout()
layout.addWidget(video_widget)
layout.addWidget(self.idx_button)
self.setLayout(layout) | [
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25,110 | wonambi-python/wonambi | wonambi/widgets/video.py | Video.stop_video | def stop_video(self, tick):
"""Stop video if tick is more than the end, only for last file.
Parameters
----------
tick : int
time in ms from the beginning of the file
useless?
"""
if self.cnt_video == self.n_video:
if tick >= self.end_diff:
self.idx_button.setText('Start')
self.video.stop() | python | def stop_video(self, tick):
if self.cnt_video == self.n_video:
if tick >= self.end_diff:
self.idx_button.setText('Start')
self.video.stop() | [
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Parameters
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tick : int
time in ms from the beginning of the file
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25,111 | wonambi-python/wonambi | wonambi/widgets/video.py | Video.next_video | def next_video(self, _):
"""Also runs when file is loaded, so index starts at 2."""
self.cnt_video += 1
lg.info('Update video to ' + str(self.cnt_video)) | python | def next_video(self, _):
self.cnt_video += 1
lg.info('Update video to ' + str(self.cnt_video)) | [
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25,112 | wonambi-python/wonambi | wonambi/widgets/video.py | Video.start_stop_video | def start_stop_video(self):
"""Start and stop the video, and change the button.
"""
if self.parent.info.dataset is None:
self.parent.statusBar().showMessage('No Dataset Loaded')
return
# & is added automatically by PyQt, it seems
if 'Start' in self.idx_button.text().replace('&', ''):
try:
self.update_video()
except IndexError as er:
lg.debug(er)
self.idx_button.setText('Not Available / Start')
return
except OSError as er:
lg.debug(er)
self.idx_button.setText('NO VIDEO for this dataset')
return
self.idx_button.setText('Stop')
elif 'Stop' in self.idx_button.text():
self.idx_button.setText('Start')
self.medialistplayer.stop()
self.t.stop() | python | def start_stop_video(self):
if self.parent.info.dataset is None:
self.parent.statusBar().showMessage('No Dataset Loaded')
return
# & is added automatically by PyQt, it seems
if 'Start' in self.idx_button.text().replace('&', ''):
try:
self.update_video()
except IndexError as er:
lg.debug(er)
self.idx_button.setText('Not Available / Start')
return
except OSError as er:
lg.debug(er)
self.idx_button.setText('NO VIDEO for this dataset')
return
self.idx_button.setText('Stop')
elif 'Stop' in self.idx_button.text():
self.idx_button.setText('Start')
self.medialistplayer.stop()
self.t.stop() | [
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25,113 | wonambi-python/wonambi | wonambi/widgets/video.py | Video.update_video | def update_video(self):
"""Read list of files, convert to video time, and add video to queue.
"""
window_start = self.parent.value('window_start')
window_length = self.parent.value('window_length')
d = self.parent.info.dataset
videos, begsec, endsec = d.read_videos(window_start,
window_start + window_length)
lg.debug(f'Video: {begsec} - {endsec}')
self.endsec = endsec
videos = [str(v) for v in videos] # make sure it's a str (not path)
medialist = vlc.MediaList(videos)
self.medialistplayer.set_media_list(medialist)
self.cnt_video = 0
self.n_video = len(videos)
self.t = QTimer()
self.t.timeout.connect(self.check_if_finished)
self.t.start(100)
self.medialistplayer.play()
self.mediaplayer.set_time(int(begsec * 1000)) | python | def update_video(self):
window_start = self.parent.value('window_start')
window_length = self.parent.value('window_length')
d = self.parent.info.dataset
videos, begsec, endsec = d.read_videos(window_start,
window_start + window_length)
lg.debug(f'Video: {begsec} - {endsec}')
self.endsec = endsec
videos = [str(v) for v in videos] # make sure it's a str (not path)
medialist = vlc.MediaList(videos)
self.medialistplayer.set_media_list(medialist)
self.cnt_video = 0
self.n_video = len(videos)
self.t = QTimer()
self.t.timeout.connect(self.check_if_finished)
self.t.start(100)
self.medialistplayer.play()
self.mediaplayer.set_time(int(begsec * 1000)) | [
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25,114 | wonambi-python/wonambi | wonambi/trans/montage.py | montage | def montage(data, ref_chan=None, ref_to_avg=False, bipolar=None,
method='average'):
"""Apply linear transformation to the channels.
Parameters
----------
data : instance of DataRaw
the data to filter
ref_chan : list of str
list of channels used as reference
ref_to_avg : bool
if re-reference to average or not
bipolar : float
distance in mm to consider two channels as neighbors and then compute
the bipolar montage between them.
method : str
'average' or 'regression'. 'average' takes the
average across the channels selected as reference (it can be all) and
subtract it from each channel. 'regression' keeps the residuals after
regressing out the mean across channels.
Returns
-------
filtered_data : instance of DataRaw
filtered data
Notes
-----
If you don't change anything, it returns the same instance of data.
"""
if ref_to_avg and ref_chan is not None:
raise TypeError('You cannot specify reference to the average and '
'the channels to use as reference')
if ref_chan is not None:
if (not isinstance(ref_chan, (list, tuple)) or
not all(isinstance(x, str) for x in ref_chan)):
raise TypeError('chan should be a list of strings')
if ref_chan is None:
ref_chan = [] # TODO: check bool for ref_chan
if bipolar:
if not data.attr['chan']:
raise ValueError('Data should have Chan information in attr')
_assert_equal_channels(data.axis['chan'])
chan_in_data = data.axis['chan'][0]
chan = data.attr['chan']
chan = chan(lambda x: x.label in chan_in_data)
chan, trans = create_bipolar_chan(chan, bipolar)
data.attr['chan'] = chan
if ref_to_avg or ref_chan or bipolar:
mdata = data._copy()
idx_chan = mdata.index_of('chan')
for i in range(mdata.number_of('trial')):
if ref_to_avg or ref_chan:
if ref_to_avg:
ref_chan = data.axis['chan'][i]
ref_data = data(trial=i, chan=ref_chan)
if method == 'average':
mdata.data[i] = (data(trial=i) - mean(ref_data, axis=idx_chan))
elif method == 'regression':
mdata.data[i] = compute_average_regress(data(trial=i), idx_chan)
elif bipolar:
if not data.index_of('chan') == 0:
raise ValueError('For matrix multiplication to work, '
'the first dimension should be chan')
mdata.data[i] = dot(trans, data(trial=i))
mdata.axis['chan'][i] = asarray(chan.return_label(),
dtype='U')
else:
mdata = data
return mdata | python | def montage(data, ref_chan=None, ref_to_avg=False, bipolar=None,
method='average'):
if ref_to_avg and ref_chan is not None:
raise TypeError('You cannot specify reference to the average and '
'the channels to use as reference')
if ref_chan is not None:
if (not isinstance(ref_chan, (list, tuple)) or
not all(isinstance(x, str) for x in ref_chan)):
raise TypeError('chan should be a list of strings')
if ref_chan is None:
ref_chan = [] # TODO: check bool for ref_chan
if bipolar:
if not data.attr['chan']:
raise ValueError('Data should have Chan information in attr')
_assert_equal_channels(data.axis['chan'])
chan_in_data = data.axis['chan'][0]
chan = data.attr['chan']
chan = chan(lambda x: x.label in chan_in_data)
chan, trans = create_bipolar_chan(chan, bipolar)
data.attr['chan'] = chan
if ref_to_avg or ref_chan or bipolar:
mdata = data._copy()
idx_chan = mdata.index_of('chan')
for i in range(mdata.number_of('trial')):
if ref_to_avg or ref_chan:
if ref_to_avg:
ref_chan = data.axis['chan'][i]
ref_data = data(trial=i, chan=ref_chan)
if method == 'average':
mdata.data[i] = (data(trial=i) - mean(ref_data, axis=idx_chan))
elif method == 'regression':
mdata.data[i] = compute_average_regress(data(trial=i), idx_chan)
elif bipolar:
if not data.index_of('chan') == 0:
raise ValueError('For matrix multiplication to work, '
'the first dimension should be chan')
mdata.data[i] = dot(trans, data(trial=i))
mdata.axis['chan'][i] = asarray(chan.return_label(),
dtype='U')
else:
mdata = data
return mdata | [
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Parameters
----------
data : instance of DataRaw
the data to filter
ref_chan : list of str
list of channels used as reference
ref_to_avg : bool
if re-reference to average or not
bipolar : float
distance in mm to consider two channels as neighbors and then compute
the bipolar montage between them.
method : str
'average' or 'regression'. 'average' takes the
average across the channels selected as reference (it can be all) and
subtract it from each channel. 'regression' keeps the residuals after
regressing out the mean across channels.
Returns
-------
filtered_data : instance of DataRaw
filtered data
Notes
-----
If you don't change anything, it returns the same instance of data. | [
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25,115 | wonambi-python/wonambi | wonambi/trans/montage.py | _assert_equal_channels | def _assert_equal_channels(axis):
"""check that all the trials have the same channels, in the same order.
Parameters
----------
axis : ndarray of ndarray
one of the data axis
Raises
------
"""
for i0 in axis:
for i1 in axis:
if not all(i0 == i1):
raise ValueError('The channels for all the trials should have '
'the same labels, in the same order.') | python | def _assert_equal_channels(axis):
for i0 in axis:
for i1 in axis:
if not all(i0 == i1):
raise ValueError('The channels for all the trials should have '
'the same labels, in the same order.') | [
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axis : ndarray of ndarray
one of the data axis
Raises
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25,116 | wonambi-python/wonambi | wonambi/trans/montage.py | compute_average_regress | def compute_average_regress(x, idx_chan):
"""Take the mean across channels and regress out the mean from each channel
Parameters
----------
x : ndarray
2d array with channels on one dimension
idx_chan:
which axis contains channels
Returns
-------
ndarray
same as x, but with the mean being regressed out
"""
if x.ndim != 2:
raise ValueError(f'The number of dimensions must be 2, not {x.ndim}')
x = moveaxis(x, idx_chan, 0) # move axis to the front
avg = mean(x, axis=0)
x_o = []
for i in range(x.shape[0]):
r = lstsq(avg[:, None], x[i, :][:, None], rcond=0)[0]
x_o.append(
x[i, :] - r[0, 0] * avg
)
return moveaxis(asarray(x_o), 0, idx_chan) | python | def compute_average_regress(x, idx_chan):
if x.ndim != 2:
raise ValueError(f'The number of dimensions must be 2, not {x.ndim}')
x = moveaxis(x, idx_chan, 0) # move axis to the front
avg = mean(x, axis=0)
x_o = []
for i in range(x.shape[0]):
r = lstsq(avg[:, None], x[i, :][:, None], rcond=0)[0]
x_o.append(
x[i, :] - r[0, 0] * avg
)
return moveaxis(asarray(x_o), 0, idx_chan) | [
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which axis contains channels
Returns
-------
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25,117 | wonambi-python/wonambi | wonambi/widgets/utils.py | keep_recent_datasets | def keep_recent_datasets(max_dataset_history, info=None):
"""Keep track of the most recent recordings.
Parameters
----------
max_dataset_history : int
maximum number of datasets to remember
info : str, optional TODO
path to file
Returns
-------
list of str
paths to most recent datasets (only if you don't specify
new_dataset)
"""
history = settings.value('recent_recordings', [])
if isinstance(history, str):
history = [history]
if info is not None and info.filename is not None:
new_dataset = info.filename
if new_dataset in history:
lg.debug(new_dataset + ' already present, will be replaced')
history.remove(new_dataset)
if len(history) > max_dataset_history:
lg.debug('Removing last dataset ' + history[-1])
history.pop()
lg.debug('Adding ' + new_dataset + ' to list of recent datasets')
history.insert(0, new_dataset)
settings.setValue('recent_recordings', history)
return None
else:
return history | python | def keep_recent_datasets(max_dataset_history, info=None):
history = settings.value('recent_recordings', [])
if isinstance(history, str):
history = [history]
if info is not None and info.filename is not None:
new_dataset = info.filename
if new_dataset in history:
lg.debug(new_dataset + ' already present, will be replaced')
history.remove(new_dataset)
if len(history) > max_dataset_history:
lg.debug('Removing last dataset ' + history[-1])
history.pop()
lg.debug('Adding ' + new_dataset + ' to list of recent datasets')
history.insert(0, new_dataset)
settings.setValue('recent_recordings', history)
return None
else:
return history | [
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info : str, optional TODO
path to file
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-------
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25,118 | wonambi-python/wonambi | wonambi/widgets/utils.py | choose_file_or_dir | def choose_file_or_dir():
"""Create a simple message box to see if the user wants to open dir or file
Returns
-------
str
'dir' or 'file' or 'abort'
"""
question = QMessageBox(QMessageBox.Information, 'Open Dataset',
'Do you want to open a file or a directory?')
dir_button = question.addButton('Directory', QMessageBox.YesRole)
file_button = question.addButton('File', QMessageBox.NoRole)
question.addButton(QMessageBox.Cancel)
question.exec_()
response = question.clickedButton()
if response == dir_button:
return 'dir'
elif response == file_button:
return 'file'
else:
return 'abort' | python | def choose_file_or_dir():
question = QMessageBox(QMessageBox.Information, 'Open Dataset',
'Do you want to open a file or a directory?')
dir_button = question.addButton('Directory', QMessageBox.YesRole)
file_button = question.addButton('File', QMessageBox.NoRole)
question.addButton(QMessageBox.Cancel)
question.exec_()
response = question.clickedButton()
if response == dir_button:
return 'dir'
elif response == file_button:
return 'file'
else:
return 'abort' | [
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25,119 | wonambi-python/wonambi | wonambi/widgets/utils.py | convert_name_to_color | def convert_name_to_color(s):
"""Convert any string to an RGB color.
Parameters
----------
s : str
string to convert
selection : bool, optional
if an event is being selected, it's lighter
Returns
-------
instance of QColor
one of the possible color
Notes
-----
It takes any string and converts it to RGB color. The same string always
returns the same color. The numbers are a bit arbitrary but not completely.
h is the baseline color (keep it high to have brighter colors). Make sure
that the max module + h is less than 256 (RGB limit).
The number you multiply ord for is necessary to differentiate the letters
(otherwise 'r' and 's' are too close to each other).
"""
h = 100
v = [5 * ord(x) for x in s]
sum_mod = lambda x: sum(x) % 100
color = QColor(sum_mod(v[::3]) + h, sum_mod(v[1::3]) + h,
sum_mod(v[2::3]) + h)
return color | python | def convert_name_to_color(s):
h = 100
v = [5 * ord(x) for x in s]
sum_mod = lambda x: sum(x) % 100
color = QColor(sum_mod(v[::3]) + h, sum_mod(v[1::3]) + h,
sum_mod(v[2::3]) + h)
return color | [
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Returns
-------
instance of QColor
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Notes
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25,120 | wonambi-python/wonambi | wonambi/widgets/utils.py | freq_from_str | def freq_from_str(freq_str):
"""Obtain frequency ranges from input string, either as list or dynamic
notation.
Parameters
----------
freq_str : str
String with frequency ranges, either as a list:
e.g. [[1-3], [3-5], [5-8]];
or with a dynamic definition: (start, stop, width, step).
Returns
-------
list of tuple of float or None
Every tuple of float represents a frequency band. If input is invalid,
returns None.
"""
freq = []
as_list = freq_str[1:-1].replace(' ', '').split(',')
try:
if freq_str[0] == '[' and freq_str[-1] == ']':
for i in as_list:
one_band = i[1:-1].split('-')
one_band = float(one_band[0]), float(one_band[1])
freq.append(one_band)
elif freq_str[0] == '(' and freq_str[-1] == ')':
if len(as_list) == 4:
start = float(as_list[0])
stop = float(as_list[1])
halfwidth = float(as_list[2]) / 2
step = float(as_list[3])
centres = arange(start, stop, step)
for i in centres:
freq.append((i - halfwidth, i + halfwidth))
else:
return None
else:
return None
except:
return None
return freq | python | def freq_from_str(freq_str):
freq = []
as_list = freq_str[1:-1].replace(' ', '').split(',')
try:
if freq_str[0] == '[' and freq_str[-1] == ']':
for i in as_list:
one_band = i[1:-1].split('-')
one_band = float(one_band[0]), float(one_band[1])
freq.append(one_band)
elif freq_str[0] == '(' and freq_str[-1] == ')':
if len(as_list) == 4:
start = float(as_list[0])
stop = float(as_list[1])
halfwidth = float(as_list[2]) / 2
step = float(as_list[3])
centres = arange(start, stop, step)
for i in centres:
freq.append((i - halfwidth, i + halfwidth))
else:
return None
else:
return None
except:
return None
return freq | [
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25,121 | wonambi-python/wonambi | wonambi/widgets/utils.py | export_graphics_to_svg | def export_graphics_to_svg(widget, filename):
"""Export graphics to svg
Parameters
----------
widget : instance of QGraphicsView
traces or overview
filename : str
path to save svg
"""
generator = QSvgGenerator()
generator.setFileName(filename)
generator.setSize(widget.size())
generator.setViewBox(widget.rect())
painter = QPainter()
painter.begin(generator)
widget.render(painter)
painter.end() | python | def export_graphics_to_svg(widget, filename):
generator = QSvgGenerator()
generator.setFileName(filename)
generator.setSize(widget.size())
generator.setViewBox(widget.rect())
painter = QPainter()
painter.begin(generator)
widget.render(painter)
painter.end() | [
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filename : str
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25,122 | wonambi-python/wonambi | wonambi/widgets/utils.py | FormList.get_value | def get_value(self, default=None):
"""Get int from widget.
Parameters
----------
default : list
list with widgets
Returns
-------
list
list that might contain int or str or float etc
"""
if default is None:
default = []
try:
text = literal_eval(self.text())
if not isinstance(text, list):
pass
# raise ValueError
except ValueError:
lg.debug('Cannot convert "' + str(text) + '" to list. ' +
'Using default ' + str(default))
text = default
self.set_value(text)
return text | python | def get_value(self, default=None):
if default is None:
default = []
try:
text = literal_eval(self.text())
if not isinstance(text, list):
pass
# raise ValueError
except ValueError:
lg.debug('Cannot convert "' + str(text) + '" to list. ' +
'Using default ' + str(default))
text = default
self.set_value(text)
return text | [
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25,123 | wonambi-python/wonambi | wonambi/widgets/utils.py | FormDir.connect | def connect(self, funct):
"""Call funct when the text was changed.
Parameters
----------
funct : function
function that broadcasts a change.
Notes
-----
There is something wrong here. When you run this function, it calls
for opening a directory three or four times. This is obviously wrong
but I don't understand why this happens three times. Traceback did not
help.
"""
def get_directory():
rec = QFileDialog.getExistingDirectory(self,
'Path to Recording'
' Directory')
if rec == '':
return
self.setText(rec)
funct()
self.clicked.connect(get_directory) | python | def connect(self, funct):
def get_directory():
rec = QFileDialog.getExistingDirectory(self,
'Path to Recording'
' Directory')
if rec == '':
return
self.setText(rec)
funct()
self.clicked.connect(get_directory) | [
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25,124 | wonambi-python/wonambi | wonambi/widgets/utils.py | FormMenu.get_value | def get_value(self, default=None):
"""Get selection from widget.
Parameters
----------
default : str
str for use by widget
Returns
-------
str
selected item from the combobox
"""
if default is None:
default = ''
try:
text = self.currentText()
except ValueError:
lg.debug('Cannot convert "' + str(text) + '" to list. ' +
'Using default ' + str(default))
text = default
self.set_value(text)
return text | python | def get_value(self, default=None):
if default is None:
default = ''
try:
text = self.currentText()
except ValueError:
lg.debug('Cannot convert "' + str(text) + '" to list. ' +
'Using default ' + str(default))
text = default
self.set_value(text)
return text | [
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25,125 | wonambi-python/wonambi | wonambi/ioeeg/bids.py | _write_ieeg_json | def _write_ieeg_json(output_file):
"""Use only required fields
"""
dataset_info = {
"TaskName": "unknown",
"Manufacturer": "n/a",
"PowerLineFrequency": 50,
"iEEGReference": "n/a",
}
with output_file.open('w') as f:
dump(dataset_info, f, indent=' ') | python | def _write_ieeg_json(output_file):
dataset_info = {
"TaskName": "unknown",
"Manufacturer": "n/a",
"PowerLineFrequency": 50,
"iEEGReference": "n/a",
}
with output_file.open('w') as f:
dump(dataset_info, f, indent=' ') | [
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25,126 | wonambi-python/wonambi | wonambi/scroll_data.py | MainWindow.value | def value(self, parameter, new_value=None):
"""This function is a shortcut for any parameter. Instead of calling
the widget, its config and its values, you can call directly the
parameter.
Parameters
----------
parameter : str
name of the parameter of interest
new_value : str or float, optional
new value for the parameter
Returns
-------
str or float
if you didn't specify new_value, it returns the current value.
Notes
-----
It's important to maintain an organized dict in DEFAULTS which has to
correspond to the values in the widgets, also the name of the widget.
DEFAULTS is used like a look-up table.
"""
for widget_name, values in DEFAULTS.items():
if parameter in values.keys():
widget = getattr(self, widget_name)
if new_value is None:
return widget.config.value[parameter]
else:
lg.debug('setting value {0} of {1} to {2}'
''.format(parameter, widget_name, new_value))
widget.config.value[parameter] = new_value | python | def value(self, parameter, new_value=None):
for widget_name, values in DEFAULTS.items():
if parameter in values.keys():
widget = getattr(self, widget_name)
if new_value is None:
return widget.config.value[parameter]
else:
lg.debug('setting value {0} of {1} to {2}'
''.format(parameter, widget_name, new_value))
widget.config.value[parameter] = new_value | [
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25,127 | wonambi-python/wonambi | wonambi/scroll_data.py | MainWindow.update | def update(self):
"""Once you open a dataset, it activates all the widgets.
"""
self.info.display_dataset()
self.overview.update()
self.labels.update(labels=self.info.dataset.header['chan_name'])
self.channels.update()
try:
self.info.markers = self.info.dataset.read_markers()
except FileNotFoundError:
lg.info('No notes/markers present in the header of the file')
else:
self.notes.update_dataset_marker() | python | def update(self):
self.info.display_dataset()
self.overview.update()
self.labels.update(labels=self.info.dataset.header['chan_name'])
self.channels.update()
try:
self.info.markers = self.info.dataset.read_markers()
except FileNotFoundError:
lg.info('No notes/markers present in the header of the file')
else:
self.notes.update_dataset_marker() | [
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] | 1d8e3d7e53df8017c199f703bcab582914676e76 | https://github.com/wonambi-python/wonambi/blob/1d8e3d7e53df8017c199f703bcab582914676e76/wonambi/scroll_data.py#L121-L134 |
25,128 | wonambi-python/wonambi | wonambi/scroll_data.py | MainWindow.reset | def reset(self):
"""Remove all the information from previous dataset before loading a
new dataset.
"""
# store current dataset
max_dataset_history = self.value('max_dataset_history')
keep_recent_datasets(max_dataset_history, self.info)
# reset all the widgets
self.labels.reset()
self.channels.reset()
self.info.reset()
self.notes.reset()
self.overview.reset()
self.spectrum.reset()
self.traces.reset() | python | def reset(self):
# store current dataset
max_dataset_history = self.value('max_dataset_history')
keep_recent_datasets(max_dataset_history, self.info)
# reset all the widgets
self.labels.reset()
self.channels.reset()
self.info.reset()
self.notes.reset()
self.overview.reset()
self.spectrum.reset()
self.traces.reset() | [
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25,129 | wonambi-python/wonambi | wonambi/scroll_data.py | MainWindow.show_settings | def show_settings(self):
"""Open the Setting windows, after updating the values in GUI. """
self.notes.config.put_values()
self.overview.config.put_values()
self.settings.config.put_values()
self.spectrum.config.put_values()
self.traces.config.put_values()
self.video.config.put_values()
self.settings.show() | python | def show_settings(self):
self.notes.config.put_values()
self.overview.config.put_values()
self.settings.config.put_values()
self.spectrum.config.put_values()
self.traces.config.put_values()
self.video.config.put_values()
self.settings.show() | [
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25,130 | wonambi-python/wonambi | wonambi/scroll_data.py | MainWindow.show_spindle_dialog | def show_spindle_dialog(self):
"""Create the spindle detection dialog."""
self.spindle_dialog.update_groups()
self.spindle_dialog.update_cycles()
self.spindle_dialog.show() | python | def show_spindle_dialog(self):
self.spindle_dialog.update_groups()
self.spindle_dialog.update_cycles()
self.spindle_dialog.show() | [
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25,131 | wonambi-python/wonambi | wonambi/scroll_data.py | MainWindow.show_slow_wave_dialog | def show_slow_wave_dialog(self):
"""Create the SW detection dialog."""
self.slow_wave_dialog.update_groups()
self.slow_wave_dialog.update_cycles()
self.slow_wave_dialog.show() | python | def show_slow_wave_dialog(self):
self.slow_wave_dialog.update_groups()
self.slow_wave_dialog.update_cycles()
self.slow_wave_dialog.show() | [
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25,132 | wonambi-python/wonambi | wonambi/scroll_data.py | MainWindow.show_event_analysis_dialog | def show_event_analysis_dialog(self):
"""Create the event analysis dialog."""
self.event_analysis_dialog.update_types()
self.event_analysis_dialog.update_groups()
self.event_analysis_dialog.update_cycles()
self.event_analysis_dialog.show() | python | def show_event_analysis_dialog(self):
self.event_analysis_dialog.update_types()
self.event_analysis_dialog.update_groups()
self.event_analysis_dialog.update_cycles()
self.event_analysis_dialog.show() | [
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25,133 | wonambi-python/wonambi | wonambi/scroll_data.py | MainWindow.show_analysis_dialog | def show_analysis_dialog(self):
"""Create the analysis dialog."""
self.analysis_dialog.update_evt_types()
self.analysis_dialog.update_groups()
self.analysis_dialog.update_cycles()
self.analysis_dialog.show() | python | def show_analysis_dialog(self):
self.analysis_dialog.update_evt_types()
self.analysis_dialog.update_groups()
self.analysis_dialog.update_cycles()
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25,134 | wonambi-python/wonambi | wonambi/scroll_data.py | MainWindow.closeEvent | def closeEvent(self, event):
"""save the name of the last open dataset."""
max_dataset_history = self.value('max_dataset_history')
keep_recent_datasets(max_dataset_history, self.info)
settings.setValue('window/geometry', self.saveGeometry())
settings.setValue('window/state', self.saveState())
event.accept() | python | def closeEvent(self, event):
max_dataset_history = self.value('max_dataset_history')
keep_recent_datasets(max_dataset_history, self.info)
settings.setValue('window/geometry', self.saveGeometry())
settings.setValue('window/state', self.saveState())
event.accept() | [
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25,135 | wonambi-python/wonambi | wonambi/ioeeg/bci2000.py | _read_header | def _read_header(filename):
"""It's a pain to parse the header. It might be better to use the cpp code
but I would need to include it here.
"""
header = _read_header_text(filename)
first_row = header[0]
EXTRA_ROWS = 3 # drop DefaultValue1 LowRange1 HighRange1
hdr = {}
for group in finditer('(\w*)= ([\w.]*)', first_row):
hdr[group.group(1)] = group.group(2)
if first_row.startswith('BCI2000V'):
VERSION = hdr['BCI2000V']
else:
VERSION = '1'
hdr['DataFormat'] = 'int16'
for row in header[1:]:
if row.startswith('['): # remove '[ ... Definition ]'
section = row[2:-14].replace(' ', '')
if section == 'StateVector':
hdr[section] = []
else:
hdr[section] = {} # defaultdict(dict)
continue
if row == '':
continue
elif section == 'StateVector':
statevector = {key: value for key, value in list(zip(STATEVECTOR, row.split(' ')))}
hdr[section].append(statevector)
else:
group = match('(?P<subsection>[\w:%]*) (?P<format>\w*) (?P<key>\w*)= (?P<value>.*) // ', row)
onerow = group.groupdict()
values = onerow['value'].split(' ')
if len(values) > EXTRA_ROWS:
value = ' '.join(onerow['value'].split(' ')[:-EXTRA_ROWS])
else:
value = ' '.join(values)
hdr[section][onerow['key']] = value # similar to matlab's output
return hdr | python | def _read_header(filename):
header = _read_header_text(filename)
first_row = header[0]
EXTRA_ROWS = 3 # drop DefaultValue1 LowRange1 HighRange1
hdr = {}
for group in finditer('(\w*)= ([\w.]*)', first_row):
hdr[group.group(1)] = group.group(2)
if first_row.startswith('BCI2000V'):
VERSION = hdr['BCI2000V']
else:
VERSION = '1'
hdr['DataFormat'] = 'int16'
for row in header[1:]:
if row.startswith('['): # remove '[ ... Definition ]'
section = row[2:-14].replace(' ', '')
if section == 'StateVector':
hdr[section] = []
else:
hdr[section] = {} # defaultdict(dict)
continue
if row == '':
continue
elif section == 'StateVector':
statevector = {key: value for key, value in list(zip(STATEVECTOR, row.split(' ')))}
hdr[section].append(statevector)
else:
group = match('(?P<subsection>[\w:%]*) (?P<format>\w*) (?P<key>\w*)= (?P<value>.*) // ', row)
onerow = group.groupdict()
values = onerow['value'].split(' ')
if len(values) > EXTRA_ROWS:
value = ' '.join(onerow['value'].split(' ')[:-EXTRA_ROWS])
else:
value = ' '.join(values)
hdr[section][onerow['key']] = value # similar to matlab's output
return hdr | [
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25,136 | wonambi-python/wonambi | wonambi/trans/reject.py | remove_artf_evts | def remove_artf_evts(times, annot, chan=None, min_dur=0.1):
"""Correct times to remove events marked 'Artefact'.
Parameters
----------
times : list of tuple of float
the start and end times of each segment
annot : instance of Annotations
the annotation file containing events and epochs
chan : str, optional
full name of channel on which artefacts were marked. Channel format is
'chan_name (group_name)'. If None, artefacts from any channel will be
removed.
min_dur : float
resulting segments, after concatenation, are rejected if shorter than
this duration
Returns
-------
list of tuple of float
the new start and end times of each segment, with artefact periods
taken out
"""
new_times = times
beg = times[0][0]
end = times[-1][-1]
chan = (chan, '') if chan else None # '' is for channel-global artefacts
artefact = annot.get_events(name='Artefact', time=(beg, end), chan=chan,
qual='Good')
if artefact:
new_times = []
for seg in times:
reject = False
new_seg = True
while new_seg is not False:
if type(new_seg) is tuple:
seg = new_seg
end = seg[1]
for artf in artefact:
if artf['start'] <= seg[0] and seg[1] <= artf['end']:
reject = True
new_seg = False
break
a_starts_in_s = seg[0] <= artf['start'] <= seg[1]
a_ends_in_s = seg[0] <= artf['end'] <= seg[1]
if a_ends_in_s and not a_starts_in_s:
seg = artf['end'], seg[1]
elif a_starts_in_s:
seg = seg[0], artf['start']
if a_ends_in_s:
new_seg = artf['end'], end
else:
new_seg = False
break
new_seg = False
if reject is False and seg[1] - seg[0] >= min_dur:
new_times.append(seg)
return new_times | python | def remove_artf_evts(times, annot, chan=None, min_dur=0.1):
new_times = times
beg = times[0][0]
end = times[-1][-1]
chan = (chan, '') if chan else None # '' is for channel-global artefacts
artefact = annot.get_events(name='Artefact', time=(beg, end), chan=chan,
qual='Good')
if artefact:
new_times = []
for seg in times:
reject = False
new_seg = True
while new_seg is not False:
if type(new_seg) is tuple:
seg = new_seg
end = seg[1]
for artf in artefact:
if artf['start'] <= seg[0] and seg[1] <= artf['end']:
reject = True
new_seg = False
break
a_starts_in_s = seg[0] <= artf['start'] <= seg[1]
a_ends_in_s = seg[0] <= artf['end'] <= seg[1]
if a_ends_in_s and not a_starts_in_s:
seg = artf['end'], seg[1]
elif a_starts_in_s:
seg = seg[0], artf['start']
if a_ends_in_s:
new_seg = artf['end'], end
else:
new_seg = False
break
new_seg = False
if reject is False and seg[1] - seg[0] >= min_dur:
new_times.append(seg)
return new_times | [
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full name of channel on which artefacts were marked. Channel format is
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25,137 | SuLab/WikidataIntegrator | wikidataintegrator/wdi_core.py | WDBaseDataType.statement_ref_mode | def statement_ref_mode(self, value):
"""Set the reference mode for a statement, always overrides the global reference state."""
valid_values = ['STRICT_KEEP', 'STRICT_KEEP_APPEND', 'STRICT_OVERWRITE', 'KEEP_GOOD', 'CUSTOM']
if value not in valid_values:
raise ValueError('Not an allowed reference mode, allowed values {}'.format(' '.join(valid_values)))
self._statement_ref_mode = value | python | def statement_ref_mode(self, value):
valid_values = ['STRICT_KEEP', 'STRICT_KEEP_APPEND', 'STRICT_OVERWRITE', 'KEEP_GOOD', 'CUSTOM']
if value not in valid_values:
raise ValueError('Not an allowed reference mode, allowed values {}'.format(' '.join(valid_values)))
self._statement_ref_mode = value | [
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25,138 | SuLab/WikidataIntegrator | wikidataintegrator/wdi_core.py | WDBaseDataType.equals | def equals(self, that, include_ref=False, fref=None):
"""
Tests for equality of two statements.
If comparing references, the order of the arguments matters!!!
self is the current statement, the next argument is the new statement.
Allows passing in a function to use to compare the references 'fref'. Default is equality.
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return self == that
if include_ref and self != that:
return False
if include_ref and fref is None:
fref = WDBaseDataType.refs_equal
return fref(self, that) | python | def equals(self, that, include_ref=False, fref=None):
if not include_ref:
# return the result of WDBaseDataType.__eq__, which is testing for equality of value and qualifiers
return self == that
if include_ref and self != that:
return False
if include_ref and fref is None:
fref = WDBaseDataType.refs_equal
return fref(self, that) | [
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25,139 | SuLab/WikidataIntegrator | wikidataintegrator/wdi_core.py | WDBaseDataType.refs_equal | def refs_equal(olditem, newitem):
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oldrefs = olditem.references
newrefs = newitem.references
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oldrefs = olditem.references
newrefs = newitem.references
ref_equal = lambda oldref, newref: True if (len(oldref) == len(newref)) and all(
x in oldref for x in newref) else False
if len(oldrefs) == len(newrefs) and all(
any(ref_equal(oldref, newref) for oldref in oldrefs) for newref in newrefs):
return True
else:
return False | [
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25,140 | SuLab/WikidataIntegrator | wikidataintegrator/wdi_helpers/__init__.py | try_write | def try_write(wd_item, record_id, record_prop, login, edit_summary='', write=True):
"""
Write a PBB_core item. Log if item was created, updated, or skipped.
Catch and log all errors.
:param wd_item: A wikidata item that will be written
:type wd_item: PBB_Core.WDItemEngine
:param record_id: An external identifier, to be used for logging
:type record_id: str
:param record_prop: Property of the external identifier
:type record_prop: str
:param login: PBB_core login instance
:type login: PBB_login.WDLogin
:param edit_summary: passed directly to wd_item.write
:type edit_summary: str
:param write: If `False`, do not actually perform write. Action will be logged as if write had occured
:type write: bool
:return: True if write did not throw an exception, returns the exception otherwise
"""
if wd_item.require_write:
if wd_item.create_new_item:
msg = "CREATE"
else:
msg = "UPDATE"
else:
msg = "SKIP"
try:
if write:
wd_item.write(login=login, edit_summary=edit_summary)
wdi_core.WDItemEngine.log("INFO", format_msg(record_id, record_prop, wd_item.wd_item_id, msg) + ";" + str(
wd_item.lastrevid))
except wdi_core.WDApiError as e:
print(e)
wdi_core.WDItemEngine.log("ERROR",
format_msg(record_id, record_prop, wd_item.wd_item_id, json.dumps(e.wd_error_msg),
type(e)))
return e
except Exception as e:
print(e)
wdi_core.WDItemEngine.log("ERROR", format_msg(record_id, record_prop, wd_item.wd_item_id, str(e), type(e)))
return e
return True | python | def try_write(wd_item, record_id, record_prop, login, edit_summary='', write=True):
if wd_item.require_write:
if wd_item.create_new_item:
msg = "CREATE"
else:
msg = "UPDATE"
else:
msg = "SKIP"
try:
if write:
wd_item.write(login=login, edit_summary=edit_summary)
wdi_core.WDItemEngine.log("INFO", format_msg(record_id, record_prop, wd_item.wd_item_id, msg) + ";" + str(
wd_item.lastrevid))
except wdi_core.WDApiError as e:
print(e)
wdi_core.WDItemEngine.log("ERROR",
format_msg(record_id, record_prop, wd_item.wd_item_id, json.dumps(e.wd_error_msg),
type(e)))
return e
except Exception as e:
print(e)
wdi_core.WDItemEngine.log("ERROR", format_msg(record_id, record_prop, wd_item.wd_item_id, str(e), type(e)))
return e
return True | [
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25,141 | maykinmedia/django-admin-index | django_admin_index/compat/django18.py | _build_app_dict | def _build_app_dict(site, request, label=None):
"""
Builds the app dictionary. Takes an optional label parameters to filter
models of a specific app.
"""
app_dict = {}
if label:
models = {
m: m_a for m, m_a in site._registry.items()
if m._meta.app_label == label
}
else:
models = site._registry
for model, model_admin in models.items():
app_label = model._meta.app_label
has_module_perms = model_admin.has_module_permission(request)
if not has_module_perms:
continue
perms = model_admin.get_model_perms(request)
# Check whether user has any perm for this module.
# If so, add the module to the model_list.
if True not in perms.values():
continue
info = (app_label, model._meta.model_name)
model_dict = {
'name': capfirst(model._meta.verbose_name_plural),
'object_name': model._meta.object_name,
'perms': perms,
}
if perms.get('change'):
try:
model_dict['admin_url'] = reverse('admin:%s_%s_changelist' % info, current_app=site.name)
except NoReverseMatch:
pass
if perms.get('add'):
try:
model_dict['add_url'] = reverse('admin:%s_%s_add' % info, current_app=site.name)
except NoReverseMatch:
pass
if app_label in app_dict:
app_dict[app_label]['models'].append(model_dict)
else:
app_dict[app_label] = {
'name': apps.get_app_config(app_label).verbose_name,
'app_label': app_label,
'app_url': reverse(
'admin:app_list',
kwargs={'app_label': app_label},
current_app=site.name,
),
'has_module_perms': has_module_perms,
'models': [model_dict],
}
if label:
return app_dict.get(label)
return app_dict | python | def _build_app_dict(site, request, label=None):
app_dict = {}
if label:
models = {
m: m_a for m, m_a in site._registry.items()
if m._meta.app_label == label
}
else:
models = site._registry
for model, model_admin in models.items():
app_label = model._meta.app_label
has_module_perms = model_admin.has_module_permission(request)
if not has_module_perms:
continue
perms = model_admin.get_model_perms(request)
# Check whether user has any perm for this module.
# If so, add the module to the model_list.
if True not in perms.values():
continue
info = (app_label, model._meta.model_name)
model_dict = {
'name': capfirst(model._meta.verbose_name_plural),
'object_name': model._meta.object_name,
'perms': perms,
}
if perms.get('change'):
try:
model_dict['admin_url'] = reverse('admin:%s_%s_changelist' % info, current_app=site.name)
except NoReverseMatch:
pass
if perms.get('add'):
try:
model_dict['add_url'] = reverse('admin:%s_%s_add' % info, current_app=site.name)
except NoReverseMatch:
pass
if app_label in app_dict:
app_dict[app_label]['models'].append(model_dict)
else:
app_dict[app_label] = {
'name': apps.get_app_config(app_label).verbose_name,
'app_label': app_label,
'app_url': reverse(
'admin:app_list',
kwargs={'app_label': app_label},
current_app=site.name,
),
'has_module_perms': has_module_perms,
'models': [model_dict],
}
if label:
return app_dict.get(label)
return app_dict | [
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25,142 | maykinmedia/django-admin-index | django_admin_index/compat/django18.py | get_app_list | def get_app_list(site, request):
"""
Returns a sorted list of all the installed apps that have been
registered in this site.
"""
app_dict = _build_app_dict(site, request)
# Sort the apps alphabetically.
app_list = sorted(app_dict.values(), key=lambda x: x['name'].lower())
# Sort the models alphabetically within each app.
for app in app_list:
app['models'].sort(key=lambda x: x['name'])
return app_list | python | def get_app_list(site, request):
app_dict = _build_app_dict(site, request)
# Sort the apps alphabetically.
app_list = sorted(app_dict.values(), key=lambda x: x['name'].lower())
# Sort the models alphabetically within each app.
for app in app_list:
app['models'].sort(key=lambda x: x['name'])
return app_list | [
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25,143 | SuLab/WikidataIntegrator | wikidataintegrator/wdi_fastrun.py | FastRunContainer.format_query_results | def format_query_results(self, r, prop_nr):
"""
`r` is the results of the sparql query in _query_data and is modified in place
`prop_nr` is needed to get the property datatype to determine how to format the value
`r` is a list of dicts. The keys are:
item: the subject. the item this statement is on
v: the object. The value for this statement
sid: statement ID
pq: qualifier property
qval: qualifier value
ref: reference ID
pr: reference property
rval: reference value
"""
prop_dt = self.get_prop_datatype(prop_nr)
for i in r:
for value in {'item', 'sid', 'pq', 'pr', 'ref'}:
if value in i:
# these are always URIs for the local wikibase
i[value] = i[value]['value'].split('/')[-1]
# make sure datetimes are formatted correctly.
# the correct format is '+%Y-%m-%dT%H:%M:%SZ', but is sometimes missing the plus??
# some difference between RDF and xsd:dateTime that I don't understand
for value in {'v', 'qval', 'rval'}:
if value in i:
if i[value].get("datatype") == 'http://www.w3.org/2001/XMLSchema#dateTime' and not \
i[value]['value'][0] in '+-':
# if it is a dateTime and doesn't start with plus or minus, add a plus
i[value]['value'] = '+' + i[value]['value']
# these three ({'v', 'qval', 'rval'}) are values that can be any data type
# strip off the URI if they are wikibase-items
if 'v' in i:
if i['v']['type'] == 'uri' and prop_dt == 'wikibase-item':
i['v'] = i['v']['value'].split('/')[-1]
else:
i['v'] = i['v']['value']
# Note: no-value and some-value don't actually show up in the results here
# see for example: select * where { wd:Q7207 p:P40 ?c . ?c ?d ?e }
if type(i['v']) is not dict:
self.rev_lookup[i['v']].add(i['item'])
# handle qualifier value
if 'qval' in i:
qual_prop_dt = self.get_prop_datatype(prop_nr=i['pq'])
if i['qval']['type'] == 'uri' and qual_prop_dt == 'wikibase-item':
i['qval'] = i['qval']['value'].split('/')[-1]
else:
i['qval'] = i['qval']['value']
# handle reference value
if 'rval' in i:
ref_prop_dt = self.get_prop_datatype(prop_nr=i['pr'])
if i['rval']['type'] == 'uri' and ref_prop_dt == 'wikibase-item':
i['rval'] = i['rval']['value'].split('/')[-1]
else:
i['rval'] = i['rval']['value'] | python | def format_query_results(self, r, prop_nr):
prop_dt = self.get_prop_datatype(prop_nr)
for i in r:
for value in {'item', 'sid', 'pq', 'pr', 'ref'}:
if value in i:
# these are always URIs for the local wikibase
i[value] = i[value]['value'].split('/')[-1]
# make sure datetimes are formatted correctly.
# the correct format is '+%Y-%m-%dT%H:%M:%SZ', but is sometimes missing the plus??
# some difference between RDF and xsd:dateTime that I don't understand
for value in {'v', 'qval', 'rval'}:
if value in i:
if i[value].get("datatype") == 'http://www.w3.org/2001/XMLSchema#dateTime' and not \
i[value]['value'][0] in '+-':
# if it is a dateTime and doesn't start with plus or minus, add a plus
i[value]['value'] = '+' + i[value]['value']
# these three ({'v', 'qval', 'rval'}) are values that can be any data type
# strip off the URI if they are wikibase-items
if 'v' in i:
if i['v']['type'] == 'uri' and prop_dt == 'wikibase-item':
i['v'] = i['v']['value'].split('/')[-1]
else:
i['v'] = i['v']['value']
# Note: no-value and some-value don't actually show up in the results here
# see for example: select * where { wd:Q7207 p:P40 ?c . ?c ?d ?e }
if type(i['v']) is not dict:
self.rev_lookup[i['v']].add(i['item'])
# handle qualifier value
if 'qval' in i:
qual_prop_dt = self.get_prop_datatype(prop_nr=i['pq'])
if i['qval']['type'] == 'uri' and qual_prop_dt == 'wikibase-item':
i['qval'] = i['qval']['value'].split('/')[-1]
else:
i['qval'] = i['qval']['value']
# handle reference value
if 'rval' in i:
ref_prop_dt = self.get_prop_datatype(prop_nr=i['pr'])
if i['rval']['type'] == 'uri' and ref_prop_dt == 'wikibase-item':
i['rval'] = i['rval']['value'].split('/')[-1]
else:
i['rval'] = i['rval']['value'] | [
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item: the subject. the item this statement is on
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25,144 | SuLab/WikidataIntegrator | wikidataintegrator/wdi_fastrun.py | FastRunContainer.clear | def clear(self):
"""
convinience function to empty this fastrun container
"""
self.prop_dt_map = dict()
self.prop_data = dict()
self.rev_lookup = defaultdict(set) | python | def clear(self):
self.prop_dt_map = dict()
self.prop_data = dict()
self.rev_lookup = defaultdict(set) | [
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25,145 | sighingnow/parsec.py | src/parsec/__init__.py | times | def times(p, mint, maxt=None):
'''Repeat a parser between `mint` and `maxt` times. DO AS MUCH MATCH AS IT CAN.
Return a list of values.'''
maxt = maxt if maxt else mint
@Parser
def times_parser(text, index):
cnt, values, res = 0, Value.success(index, []), None
while cnt < maxt:
res = p(text, index)
if res.status:
values = values.aggregate(
Value.success(res.index, [res.value]))
index, cnt = res.index, cnt + 1
else:
if cnt >= mint:
break
else:
return res # failed, throw exception.
if cnt >= maxt: # finish.
break
# If we don't have any remaining text to start next loop, we need break.
#
# We cannot put the `index < len(text)` in where because some parser can
# success even when we have no any text. We also need to detect if the
# parser consume no text.
#
# See: #28
if index >= len(text):
if cnt >= mint:
break # we already have decent result to return
else:
r = p(text, index)
if index != r.index: # report error when the parser cannot success with no text
return Value.failure(index, "already meets the end, no enough text")
return values
return times_parser | python | def times(p, mint, maxt=None):
'''Repeat a parser between `mint` and `maxt` times. DO AS MUCH MATCH AS IT CAN.
Return a list of values.'''
maxt = maxt if maxt else mint
@Parser
def times_parser(text, index):
cnt, values, res = 0, Value.success(index, []), None
while cnt < maxt:
res = p(text, index)
if res.status:
values = values.aggregate(
Value.success(res.index, [res.value]))
index, cnt = res.index, cnt + 1
else:
if cnt >= mint:
break
else:
return res # failed, throw exception.
if cnt >= maxt: # finish.
break
# If we don't have any remaining text to start next loop, we need break.
#
# We cannot put the `index < len(text)` in where because some parser can
# success even when we have no any text. We also need to detect if the
# parser consume no text.
#
# See: #28
if index >= len(text):
if cnt >= mint:
break # we already have decent result to return
else:
r = p(text, index)
if index != r.index: # report error when the parser cannot success with no text
return Value.failure(index, "already meets the end, no enough text")
return values
return times_parser | [
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25,146 | sighingnow/parsec.py | src/parsec/__init__.py | optional | def optional(p, default_value=None):
'''`Make a parser as optional. If success, return the result, otherwise return
default_value silently, without raising any exception. If default_value is not
provided None is returned instead.
'''
@Parser
def optional_parser(text, index):
res = p(text, index)
if res.status:
return Value.success(res.index, res.value)
else:
# Return the maybe existing default value without doing anything.
return Value.success(res.index, default_value)
return optional_parser | python | def optional(p, default_value=None):
'''`Make a parser as optional. If success, return the result, otherwise return
default_value silently, without raising any exception. If default_value is not
provided None is returned instead.
'''
@Parser
def optional_parser(text, index):
res = p(text, index)
if res.status:
return Value.success(res.index, res.value)
else:
# Return the maybe existing default value without doing anything.
return Value.success(res.index, default_value)
return optional_parser | [
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25,147 | sighingnow/parsec.py | src/parsec/__init__.py | separated | def separated(p, sep, mint, maxt=None, end=None):
'''Repeat a parser `p` separated by `s` between `mint` and `maxt` times.
When `end` is None, a trailing separator is optional.
When `end` is True, a trailing separator is required.
When `end` is False, a trailing separator is not allowed.
MATCHES AS MUCH AS POSSIBLE.
Return list of values returned by `p`.'''
maxt = maxt if maxt else mint
@Parser
def sep_parser(text, index):
cnt, values, res = 0, Value.success(index, []), None
while cnt < maxt:
if end in [False, None] and cnt > 0:
res = sep(text, index)
if res.status: # `sep` found, consume it (advance index)
index, values = res.index, Value.success(
res.index, values.value)
elif cnt < mint:
return res # error: need more elemnts, but no `sep` found.
else:
break
res = p(text, index)
if res.status:
values = values.aggregate(
Value.success(res.index, [res.value]))
index, cnt = res.index, cnt + 1
elif cnt >= mint:
break
else:
return res # error: need more elements, but no `p` found.
if end is True:
res = sep(text, index)
if res.status:
index, values = res.index, Value.success(
res.index, values.value)
else:
return res # error: trailing `sep` not found
if cnt >= maxt:
break
return values
return sep_parser | python | def separated(p, sep, mint, maxt=None, end=None):
'''Repeat a parser `p` separated by `s` between `mint` and `maxt` times.
When `end` is None, a trailing separator is optional.
When `end` is True, a trailing separator is required.
When `end` is False, a trailing separator is not allowed.
MATCHES AS MUCH AS POSSIBLE.
Return list of values returned by `p`.'''
maxt = maxt if maxt else mint
@Parser
def sep_parser(text, index):
cnt, values, res = 0, Value.success(index, []), None
while cnt < maxt:
if end in [False, None] and cnt > 0:
res = sep(text, index)
if res.status: # `sep` found, consume it (advance index)
index, values = res.index, Value.success(
res.index, values.value)
elif cnt < mint:
return res # error: need more elemnts, but no `sep` found.
else:
break
res = p(text, index)
if res.status:
values = values.aggregate(
Value.success(res.index, [res.value]))
index, cnt = res.index, cnt + 1
elif cnt >= mint:
break
else:
return res # error: need more elements, but no `p` found.
if end is True:
res = sep(text, index)
if res.status:
index, values = res.index, Value.success(
res.index, values.value)
else:
return res # error: trailing `sep` not found
if cnt >= maxt:
break
return values
return sep_parser | [
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25,148 | sighingnow/parsec.py | src/parsec/__init__.py | one_of | def one_of(s):
'''Parser a char from specified string.'''
@Parser
def one_of_parser(text, index=0):
if index < len(text) and text[index] in s:
return Value.success(index + 1, text[index])
else:
return Value.failure(index, 'one of {}'.format(s))
return one_of_parser | python | def one_of(s):
'''Parser a char from specified string.'''
@Parser
def one_of_parser(text, index=0):
if index < len(text) and text[index] in s:
return Value.success(index + 1, text[index])
else:
return Value.failure(index, 'one of {}'.format(s))
return one_of_parser | [
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25,149 | sighingnow/parsec.py | src/parsec/__init__.py | none_of | def none_of(s):
'''Parser a char NOT from specified string.'''
@Parser
def none_of_parser(text, index=0):
if index < len(text) and text[index] not in s:
return Value.success(index + 1, text[index])
else:
return Value.failure(index, 'none of {}'.format(s))
return none_of_parser | python | def none_of(s):
'''Parser a char NOT from specified string.'''
@Parser
def none_of_parser(text, index=0):
if index < len(text) and text[index] not in s:
return Value.success(index + 1, text[index])
else:
return Value.failure(index, 'none of {}'.format(s))
return none_of_parser | [
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25,150 | sighingnow/parsec.py | src/parsec/__init__.py | space | def space():
'''Parser a whitespace character.'''
@Parser
def space_parser(text, index=0):
if index < len(text) and text[index].isspace():
return Value.success(index + 1, text[index])
else:
return Value.failure(index, 'one space')
return space_parser | python | def space():
'''Parser a whitespace character.'''
@Parser
def space_parser(text, index=0):
if index < len(text) and text[index].isspace():
return Value.success(index + 1, text[index])
else:
return Value.failure(index, 'one space')
return space_parser | [
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25,151 | sighingnow/parsec.py | src/parsec/__init__.py | letter | def letter():
'''Parse a letter in alphabet.'''
@Parser
def letter_parser(text, index=0):
if index < len(text) and text[index].isalpha():
return Value.success(index + 1, text[index])
else:
return Value.failure(index, 'a letter')
return letter_parser | python | def letter():
'''Parse a letter in alphabet.'''
@Parser
def letter_parser(text, index=0):
if index < len(text) and text[index].isalpha():
return Value.success(index + 1, text[index])
else:
return Value.failure(index, 'a letter')
return letter_parser | [
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25,152 | sighingnow/parsec.py | src/parsec/__init__.py | digit | def digit():
'''Parse a digit character.'''
@Parser
def digit_parser(text, index=0):
if index < len(text) and text[index].isdigit():
return Value.success(index + 1, text[index])
else:
return Value.failure(index, 'a digit')
return digit_parser | python | def digit():
'''Parse a digit character.'''
@Parser
def digit_parser(text, index=0):
if index < len(text) and text[index].isdigit():
return Value.success(index + 1, text[index])
else:
return Value.failure(index, 'a digit')
return digit_parser | [
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25,153 | sighingnow/parsec.py | src/parsec/__init__.py | eof | def eof():
'''Parser EOF flag of a string.'''
@Parser
def eof_parser(text, index=0):
if index >= len(text):
return Value.success(index, None)
else:
return Value.failure(index, 'EOF')
return eof_parser | python | def eof():
'''Parser EOF flag of a string.'''
@Parser
def eof_parser(text, index=0):
if index >= len(text):
return Value.success(index, None)
else:
return Value.failure(index, 'EOF')
return eof_parser | [
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25,154 | sighingnow/parsec.py | src/parsec/__init__.py | string | def string(s):
'''Parser a string.'''
@Parser
def string_parser(text, index=0):
slen, tlen = len(s), len(text)
if text[index:index + slen] == s:
return Value.success(index + slen, s)
else:
matched = 0
while matched < slen and index + matched < tlen and text[index + matched] == s[matched]:
matched = matched + 1
return Value.failure(index + matched, s)
return string_parser | python | def string(s):
'''Parser a string.'''
@Parser
def string_parser(text, index=0):
slen, tlen = len(s), len(text)
if text[index:index + slen] == s:
return Value.success(index + slen, s)
else:
matched = 0
while matched < slen and index + matched < tlen and text[index + matched] == s[matched]:
matched = matched + 1
return Value.failure(index + matched, s)
return string_parser | [
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25,155 | sighingnow/parsec.py | src/parsec/__init__.py | ParseError.loc_info | def loc_info(text, index):
'''Location of `index` in source code `text`.'''
if index > len(text):
raise ValueError('Invalid index.')
line, last_ln = text.count('\n', 0, index), text.rfind('\n', 0, index)
col = index - (last_ln + 1)
return (line, col) | python | def loc_info(text, index):
'''Location of `index` in source code `text`.'''
if index > len(text):
raise ValueError('Invalid index.')
line, last_ln = text.count('\n', 0, index), text.rfind('\n', 0, index)
col = index - (last_ln + 1)
return (line, col) | [
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25,156 | sighingnow/parsec.py | src/parsec/__init__.py | ParseError.loc | def loc(self):
'''Locate the error position in the source code text.'''
try:
return '{}:{}'.format(*ParseError.loc_info(self.text, self.index))
except ValueError:
return '<out of bounds index {!r}>'.format(self.index) | python | def loc(self):
'''Locate the error position in the source code text.'''
try:
return '{}:{}'.format(*ParseError.loc_info(self.text, self.index))
except ValueError:
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25,157 | sighingnow/parsec.py | src/parsec/__init__.py | Value.aggregate | def aggregate(self, other=None):
'''collect the furthest failure from self and other.'''
if not self.status:
return self
if not other:
return self
if not other.status:
return other
return Value(True, other.index, self.value + other.value, None) | python | def aggregate(self, other=None):
'''collect the furthest failure from self and other.'''
if not self.status:
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if not other:
return self
if not other.status:
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25,158 | sighingnow/parsec.py | src/parsec/__init__.py | Value.combinate | def combinate(values):
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out_values = tuple([v.value for v in values])
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'''aggregate multiple values into tuple'''
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25,159 | sighingnow/parsec.py | src/parsec/__init__.py | Parser.parse_partial | def parse_partial(self, text):
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'''Parse the longest possible prefix of a given string.
Return a tuple of the result value and the rest of the string.
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if not isinstance(text, str):
raise TypeError(
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25,160 | sighingnow/parsec.py | src/parsec/__init__.py | Parser.bind | def bind(self, fn):
'''This is the monadic binding operation. Returns a parser which, if
parser is successful, passes the result to fn, and continues with the
parser returned from fn.
'''
@Parser
def bind_parser(text, index):
res = self(text, index)
return res if not res.status else fn(res.value)(text, res.index)
return bind_parser | python | def bind(self, fn):
'''This is the monadic binding operation. Returns a parser which, if
parser is successful, passes the result to fn, and continues with the
parser returned from fn.
'''
@Parser
def bind_parser(text, index):
res = self(text, index)
return res if not res.status else fn(res.value)(text, res.index)
return bind_parser | [
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25,161 | sighingnow/parsec.py | src/parsec/__init__.py | Parser.parsecmap | def parsecmap(self, fn):
'''Returns a parser that transforms the produced value of parser with `fn`.'''
return self.bind(lambda res: Parser(lambda _, index: Value.success(index, fn(res)))) | python | def parsecmap(self, fn):
'''Returns a parser that transforms the produced value of parser with `fn`.'''
return self.bind(lambda res: Parser(lambda _, index: Value.success(index, fn(res)))) | [
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25,162 | sighingnow/parsec.py | src/parsec/__init__.py | Parser.parsecapp | def parsecapp(self, other):
'''Returns a parser that applies the produced value of this parser to the produced value of `other`.'''
# pylint: disable=unnecessary-lambda
return self.bind(lambda res: other.parsecmap(lambda x: res(x))) | python | def parsecapp(self, other):
'''Returns a parser that applies the produced value of this parser to the produced value of `other`.'''
# pylint: disable=unnecessary-lambda
return self.bind(lambda res: other.parsecmap(lambda x: res(x))) | [
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25,163 | sighingnow/parsec.py | src/parsec/__init__.py | Parser.result | def result(self, res):
'''Return a value according to the parameter `res` when parse successfully.'''
return self >> Parser(lambda _, index: Value.success(index, res)) | python | def result(self, res):
'''Return a value according to the parameter `res` when parse successfully.'''
return self >> Parser(lambda _, index: Value.success(index, res)) | [
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25,164 | sighingnow/parsec.py | src/parsec/__init__.py | Parser.mark | def mark(self):
'''Mark the line and column information of the result of this parser.'''
def pos(text, index):
return ParseError.loc_info(text, index)
@Parser
def mark_parser(text, index):
res = self(text, index)
if res.status:
return Value.success(res.index, (pos(text, index), res.value, pos(text, res.index)))
else:
return res # failed.
return mark_parser | python | def mark(self):
'''Mark the line and column information of the result of this parser.'''
def pos(text, index):
return ParseError.loc_info(text, index)
@Parser
def mark_parser(text, index):
res = self(text, index)
if res.status:
return Value.success(res.index, (pos(text, index), res.value, pos(text, res.index)))
else:
return res # failed.
return mark_parser | [
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25,165 | sighingnow/parsec.py | src/parsec/__init__.py | Parser.desc | def desc(self, description):
'''Describe a parser, when it failed, print out the description text.'''
return self | Parser(lambda _, index: Value.failure(index, description)) | python | def desc(self, description):
'''Describe a parser, when it failed, print out the description text.'''
return self | Parser(lambda _, index: Value.failure(index, description)) | [
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25,166 | pecan/pecan | pecan/routing.py | route | def route(*args):
"""
This function is used to define an explicit route for a path segment.
You generally only want to use this in situations where your desired path
segment is not a valid Python variable/function name.
For example, if you wanted to be able to route to:
/path/with-dashes/
...the following is invalid Python syntax::
class Controller(object):
with-dashes = SubController()
...so you would instead define the route explicitly::
class Controller(object):
pass
pecan.route(Controller, 'with-dashes', SubController())
"""
def _validate_route(route):
if not isinstance(route, six.string_types):
raise TypeError('%s must be a string' % route)
if route in ('.', '..') or not re.match(
'^[0-9a-zA-Z-_$\(\)\.~!,;:*+@=]+$', route
):
raise ValueError(
'%s must be a valid path segment. Keep in mind '
'that path segments should not contain path separators '
'(e.g., /) ' % route
)
if len(args) == 2:
# The handler in this situation is a @pecan.expose'd callable,
# and is generally only used by the @expose() decorator itself.
#
# This sets a special attribute, `custom_route` on the callable, which
# pecan's routing logic knows how to make use of (as a special case)
route, handler = args
if ismethod(handler):
handler = handler.__func__
if not iscontroller(handler):
raise TypeError(
'%s must be a callable decorated with @pecan.expose' % handler
)
obj, attr, value = handler, 'custom_route', route
if handler.__name__ in ('_lookup', '_default', '_route'):
raise ValueError(
'%s is a special method in pecan and cannot be used in '
'combination with custom path segments.' % handler.__name__
)
elif len(args) == 3:
# This is really just a setattr on the parent controller (with some
# additional validation for the path segment itself)
_, route, handler = args
obj, attr, value = args
if hasattr(obj, attr):
raise RuntimeError(
(
"%(module)s.%(class)s already has an "
"existing attribute named \"%(route)s\"." % {
'module': obj.__module__,
'class': obj.__name__,
'route': attr
}
),
)
else:
raise TypeError(
'pecan.route should be called in the format '
'route(ParentController, "path-segment", SubController())'
)
_validate_route(route)
setattr(obj, attr, value) | python | def route(*args):
def _validate_route(route):
if not isinstance(route, six.string_types):
raise TypeError('%s must be a string' % route)
if route in ('.', '..') or not re.match(
'^[0-9a-zA-Z-_$\(\)\.~!,;:*+@=]+$', route
):
raise ValueError(
'%s must be a valid path segment. Keep in mind '
'that path segments should not contain path separators '
'(e.g., /) ' % route
)
if len(args) == 2:
# The handler in this situation is a @pecan.expose'd callable,
# and is generally only used by the @expose() decorator itself.
#
# This sets a special attribute, `custom_route` on the callable, which
# pecan's routing logic knows how to make use of (as a special case)
route, handler = args
if ismethod(handler):
handler = handler.__func__
if not iscontroller(handler):
raise TypeError(
'%s must be a callable decorated with @pecan.expose' % handler
)
obj, attr, value = handler, 'custom_route', route
if handler.__name__ in ('_lookup', '_default', '_route'):
raise ValueError(
'%s is a special method in pecan and cannot be used in '
'combination with custom path segments.' % handler.__name__
)
elif len(args) == 3:
# This is really just a setattr on the parent controller (with some
# additional validation for the path segment itself)
_, route, handler = args
obj, attr, value = args
if hasattr(obj, attr):
raise RuntimeError(
(
"%(module)s.%(class)s already has an "
"existing attribute named \"%(route)s\"." % {
'module': obj.__module__,
'class': obj.__name__,
'route': attr
}
),
)
else:
raise TypeError(
'pecan.route should be called in the format '
'route(ParentController, "path-segment", SubController())'
)
_validate_route(route)
setattr(obj, attr, value) | [
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...the following is invalid Python syntax::
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25,167 | pecan/pecan | pecan/routing.py | lookup_controller | def lookup_controller(obj, remainder, request=None):
'''
Traverses the requested url path and returns the appropriate controller
object, including default routes.
Handles common errors gracefully.
'''
if request is None:
warnings.warn(
(
"The function signature for %s.lookup_controller is changing "
"in the next version of pecan.\nPlease update to: "
"`lookup_controller(self, obj, remainder, request)`." % (
__name__,
)
),
DeprecationWarning
)
notfound_handlers = []
while True:
try:
obj, remainder = find_object(obj, remainder, notfound_handlers,
request)
handle_security(obj)
return obj, remainder
except (exc.HTTPNotFound, exc.HTTPMethodNotAllowed,
PecanNotFound) as e:
if isinstance(e, PecanNotFound):
e = exc.HTTPNotFound()
while notfound_handlers:
name, obj, remainder = notfound_handlers.pop()
if name == '_default':
# Notfound handler is, in fact, a controller, so stop
# traversal
return obj, remainder
else:
# Notfound handler is an internal redirect, so continue
# traversal
result = handle_lookup_traversal(obj, remainder)
if result:
# If no arguments are passed to the _lookup, yet the
# argspec requires at least one, raise a 404
if (
remainder == [''] and
len(obj._pecan['argspec'].args) > 1
):
raise e
obj_, remainder_ = result
return lookup_controller(obj_, remainder_, request)
else:
raise e | python | def lookup_controller(obj, remainder, request=None):
'''
Traverses the requested url path and returns the appropriate controller
object, including default routes.
Handles common errors gracefully.
'''
if request is None:
warnings.warn(
(
"The function signature for %s.lookup_controller is changing "
"in the next version of pecan.\nPlease update to: "
"`lookup_controller(self, obj, remainder, request)`." % (
__name__,
)
),
DeprecationWarning
)
notfound_handlers = []
while True:
try:
obj, remainder = find_object(obj, remainder, notfound_handlers,
request)
handle_security(obj)
return obj, remainder
except (exc.HTTPNotFound, exc.HTTPMethodNotAllowed,
PecanNotFound) as e:
if isinstance(e, PecanNotFound):
e = exc.HTTPNotFound()
while notfound_handlers:
name, obj, remainder = notfound_handlers.pop()
if name == '_default':
# Notfound handler is, in fact, a controller, so stop
# traversal
return obj, remainder
else:
# Notfound handler is an internal redirect, so continue
# traversal
result = handle_lookup_traversal(obj, remainder)
if result:
# If no arguments are passed to the _lookup, yet the
# argspec requires at least one, raise a 404
if (
remainder == [''] and
len(obj._pecan['argspec'].args) > 1
):
raise e
obj_, remainder_ = result
return lookup_controller(obj_, remainder_, request)
else:
raise e | [
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25,168 | pecan/pecan | pecan/routing.py | find_object | def find_object(obj, remainder, notfound_handlers, request):
'''
'Walks' the url path in search of an action for which a controller is
implemented and returns that controller object along with what's left
of the remainder.
'''
prev_obj = None
while True:
if obj is None:
raise PecanNotFound
if iscontroller(obj):
if getattr(obj, 'custom_route', None) is None:
return obj, remainder
_detect_custom_path_segments(obj)
if remainder:
custom_route = __custom_routes__.get((obj.__class__, remainder[0]))
if custom_route:
return getattr(obj, custom_route), remainder[1:]
# are we traversing to another controller
cross_boundary(prev_obj, obj)
try:
next_obj, rest = remainder[0], remainder[1:]
if next_obj == '':
index = getattr(obj, 'index', None)
if iscontroller(index):
return index, rest
except IndexError:
# the URL has hit an index method without a trailing slash
index = getattr(obj, 'index', None)
if iscontroller(index):
raise NonCanonicalPath(index, [])
default = getattr(obj, '_default', None)
if iscontroller(default):
notfound_handlers.append(('_default', default, remainder))
lookup = getattr(obj, '_lookup', None)
if iscontroller(lookup):
notfound_handlers.append(('_lookup', lookup, remainder))
route = getattr(obj, '_route', None)
if iscontroller(route):
if len(getargspec(route).args) == 2:
warnings.warn(
(
"The function signature for %s.%s._route is changing "
"in the next version of pecan.\nPlease update to: "
"`def _route(self, args, request)`." % (
obj.__class__.__module__,
obj.__class__.__name__
)
),
DeprecationWarning
)
next_obj, next_remainder = route(remainder)
else:
next_obj, next_remainder = route(remainder, request)
cross_boundary(route, next_obj)
return next_obj, next_remainder
if not remainder:
raise PecanNotFound
prev_remainder = remainder
prev_obj = obj
remainder = rest
try:
obj = getattr(obj, next_obj, None)
except UnicodeEncodeError:
obj = None
# Last-ditch effort: if there's not a matching subcontroller, no
# `_default`, no `_lookup`, and no `_route`, look to see if there's
# an `index` that has a generic method defined for the current request
# method.
if not obj and not notfound_handlers and hasattr(prev_obj, 'index'):
if request.method in _cfg(prev_obj.index).get('generic_handlers',
{}):
return prev_obj.index, prev_remainder | python | def find_object(obj, remainder, notfound_handlers, request):
'''
'Walks' the url path in search of an action for which a controller is
implemented and returns that controller object along with what's left
of the remainder.
'''
prev_obj = None
while True:
if obj is None:
raise PecanNotFound
if iscontroller(obj):
if getattr(obj, 'custom_route', None) is None:
return obj, remainder
_detect_custom_path_segments(obj)
if remainder:
custom_route = __custom_routes__.get((obj.__class__, remainder[0]))
if custom_route:
return getattr(obj, custom_route), remainder[1:]
# are we traversing to another controller
cross_boundary(prev_obj, obj)
try:
next_obj, rest = remainder[0], remainder[1:]
if next_obj == '':
index = getattr(obj, 'index', None)
if iscontroller(index):
return index, rest
except IndexError:
# the URL has hit an index method without a trailing slash
index = getattr(obj, 'index', None)
if iscontroller(index):
raise NonCanonicalPath(index, [])
default = getattr(obj, '_default', None)
if iscontroller(default):
notfound_handlers.append(('_default', default, remainder))
lookup = getattr(obj, '_lookup', None)
if iscontroller(lookup):
notfound_handlers.append(('_lookup', lookup, remainder))
route = getattr(obj, '_route', None)
if iscontroller(route):
if len(getargspec(route).args) == 2:
warnings.warn(
(
"The function signature for %s.%s._route is changing "
"in the next version of pecan.\nPlease update to: "
"`def _route(self, args, request)`." % (
obj.__class__.__module__,
obj.__class__.__name__
)
),
DeprecationWarning
)
next_obj, next_remainder = route(remainder)
else:
next_obj, next_remainder = route(remainder, request)
cross_boundary(route, next_obj)
return next_obj, next_remainder
if not remainder:
raise PecanNotFound
prev_remainder = remainder
prev_obj = obj
remainder = rest
try:
obj = getattr(obj, next_obj, None)
except UnicodeEncodeError:
obj = None
# Last-ditch effort: if there's not a matching subcontroller, no
# `_default`, no `_lookup`, and no `_route`, look to see if there's
# an `index` that has a generic method defined for the current request
# method.
if not obj and not notfound_handlers and hasattr(prev_obj, 'index'):
if request.method in _cfg(prev_obj.index).get('generic_handlers',
{}):
return prev_obj.index, prev_remainder | [
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25,169 | pecan/pecan | pecan/secure.py | unlocked | def unlocked(func_or_obj):
"""
This method unlocks method or class attribute on a SecureController. Can
be used to decorate or wrap an attribute
"""
if ismethod(func_or_obj) or isfunction(func_or_obj):
return _unlocked_method(func_or_obj)
else:
return _UnlockedAttribute(func_or_obj) | python | def unlocked(func_or_obj):
if ismethod(func_or_obj) or isfunction(func_or_obj):
return _unlocked_method(func_or_obj)
else:
return _UnlockedAttribute(func_or_obj) | [
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25,170 | pecan/pecan | pecan/secure.py | secure | def secure(func_or_obj, check_permissions_for_obj=None):
"""
This method secures a method or class depending on invocation.
To decorate a method use one argument:
@secure(<check_permissions_method>)
To secure a class, invoke with two arguments:
secure(<obj instance>, <check_permissions_method>)
"""
if _allowed_check_permissions_types(func_or_obj):
return _secure_method(func_or_obj)
else:
if not _allowed_check_permissions_types(check_permissions_for_obj):
msg = "When securing an object, secure() requires the " + \
"second argument to be method"
raise TypeError(msg)
return _SecuredAttribute(func_or_obj, check_permissions_for_obj) | python | def secure(func_or_obj, check_permissions_for_obj=None):
if _allowed_check_permissions_types(func_or_obj):
return _secure_method(func_or_obj)
else:
if not _allowed_check_permissions_types(check_permissions_for_obj):
msg = "When securing an object, secure() requires the " + \
"second argument to be method"
raise TypeError(msg)
return _SecuredAttribute(func_or_obj, check_permissions_for_obj) | [
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To decorate a method use one argument:
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To secure a class, invoke with two arguments:
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25,171 | pecan/pecan | pecan/secure.py | _make_wrapper | def _make_wrapper(f):
"""return a wrapped function with a copy of the _pecan context"""
@wraps(f)
def wrapper(*args, **kwargs):
return f(*args, **kwargs)
wrapper._pecan = f._pecan.copy()
return wrapper | python | def _make_wrapper(f):
@wraps(f)
def wrapper(*args, **kwargs):
return f(*args, **kwargs)
wrapper._pecan = f._pecan.copy()
return wrapper | [
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25,172 | pecan/pecan | pecan/secure.py | handle_security | def handle_security(controller, im_self=None):
""" Checks the security of a controller. """
if controller._pecan.get('secured', False):
check_permissions = controller._pecan['check_permissions']
if isinstance(check_permissions, six.string_types):
check_permissions = getattr(
im_self or six.get_method_self(controller),
check_permissions
)
if not check_permissions():
raise exc.HTTPUnauthorized | python | def handle_security(controller, im_self=None):
if controller._pecan.get('secured', False):
check_permissions = controller._pecan['check_permissions']
if isinstance(check_permissions, six.string_types):
check_permissions = getattr(
im_self or six.get_method_self(controller),
check_permissions
)
if not check_permissions():
raise exc.HTTPUnauthorized | [
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25,173 | pecan/pecan | pecan/secure.py | cross_boundary | def cross_boundary(prev_obj, obj):
""" Check permissions as we move between object instances. """
if prev_obj is None:
return
if isinstance(obj, _SecuredAttribute):
# a secure attribute can live in unsecure class so we have to set
# while we walk the route
obj.parent = prev_obj
if hasattr(prev_obj, '_pecan'):
if obj not in prev_obj._pecan.get('unlocked', []):
handle_security(prev_obj) | python | def cross_boundary(prev_obj, obj):
if prev_obj is None:
return
if isinstance(obj, _SecuredAttribute):
# a secure attribute can live in unsecure class so we have to set
# while we walk the route
obj.parent = prev_obj
if hasattr(prev_obj, '_pecan'):
if obj not in prev_obj._pecan.get('unlocked', []):
handle_security(prev_obj) | [
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25,174 | pecan/pecan | pecan/scaffolds/__init__.py | makedirs | def makedirs(directory):
""" Resursively create a named directory. """
parent = os.path.dirname(os.path.abspath(directory))
if not os.path.exists(parent):
makedirs(parent)
os.mkdir(directory) | python | def makedirs(directory):
parent = os.path.dirname(os.path.abspath(directory))
if not os.path.exists(parent):
makedirs(parent)
os.mkdir(directory) | [
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25,175 | pecan/pecan | pecan/scaffolds/__init__.py | substitute_filename | def substitute_filename(fn, variables):
""" Substitute +variables+ in file directory names. """
for var, value in variables.items():
fn = fn.replace('+%s+' % var, str(value))
return fn | python | def substitute_filename(fn, variables):
for var, value in variables.items():
fn = fn.replace('+%s+' % var, str(value))
return fn | [
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25,176 | pecan/pecan | pecan/__init__.py | make_app | def make_app(root, **kw):
'''
Utility for creating the Pecan application object. This function should
generally be called from the ``setup_app`` function in your project's
``app.py`` file.
:param root: A string representing a root controller object (e.g.,
"myapp.controller.root.RootController")
:param static_root: The relative path to a directory containing static
files. Serving static files is only enabled when
debug mode is set.
:param debug: A flag to enable debug mode. This enables the debug
middleware and serving static files.
:param wrap_app: A function or middleware class to wrap the Pecan app.
This must either be a wsgi middleware class or a
function that returns a wsgi application. This wrapper
is applied first before wrapping the application in
other middlewares such as Pecan's debug middleware.
This should be used if you want to use middleware to
perform authentication or intercept all requests before
they are routed to the root controller.
:param logging: A dictionary used to configure logging. This uses
``logging.config.dictConfig``.
All other keyword arguments are passed in to the Pecan app constructor.
:returns: a ``Pecan`` object.
'''
# Pass logging configuration (if it exists) on to the Python logging module
logging = kw.get('logging', {})
debug = kw.get('debug', False)
if logging:
if debug:
try:
#
# By default, Python 2.7+ silences DeprecationWarnings.
# However, if conf.app.debug is True, we should probably ensure
# that users see these types of warnings.
#
from logging import captureWarnings
captureWarnings(True)
warnings.simplefilter("default", DeprecationWarning)
except ImportError:
# No captureWarnings on Python 2.6, DeprecationWarnings are on
pass
if isinstance(logging, Config):
logging = logging.to_dict()
if 'version' not in logging:
logging['version'] = 1
load_logging_config(logging)
# Instantiate the WSGI app by passing **kw onward
app = Pecan(root, **kw)
# Optionally wrap the app in another WSGI app
wrap_app = kw.get('wrap_app', None)
if wrap_app:
app = wrap_app(app)
# Configuration for serving custom error messages
errors = kw.get('errors', getattr(conf.app, 'errors', {}))
if errors:
app = middleware.errordocument.ErrorDocumentMiddleware(app, errors)
# Included for internal redirect support
app = middleware.recursive.RecursiveMiddleware(app)
# When in debug mode, load exception debugging middleware
static_root = kw.get('static_root', None)
if debug:
debug_kwargs = getattr(conf, 'debug', {})
debug_kwargs.setdefault('context_injectors', []).append(
lambda environ: {
'request': environ.get('pecan.locals', {}).get('request')
}
)
app = DebugMiddleware(
app,
**debug_kwargs
)
# Support for serving static files (for development convenience)
if static_root:
app = middleware.static.StaticFileMiddleware(app, static_root)
elif static_root:
warnings.warn(
"`static_root` is only used when `debug` is True, ignoring",
RuntimeWarning
)
if hasattr(conf, 'requestviewer'):
warnings.warn(''.join([
"`pecan.conf.requestviewer` is deprecated. To apply the ",
"`RequestViewerHook` to your application, add it to ",
"`pecan.conf.app.hooks` or manually in your project's `app.py` ",
"file."]),
DeprecationWarning
)
return app | python | def make_app(root, **kw):
'''
Utility for creating the Pecan application object. This function should
generally be called from the ``setup_app`` function in your project's
``app.py`` file.
:param root: A string representing a root controller object (e.g.,
"myapp.controller.root.RootController")
:param static_root: The relative path to a directory containing static
files. Serving static files is only enabled when
debug mode is set.
:param debug: A flag to enable debug mode. This enables the debug
middleware and serving static files.
:param wrap_app: A function or middleware class to wrap the Pecan app.
This must either be a wsgi middleware class or a
function that returns a wsgi application. This wrapper
is applied first before wrapping the application in
other middlewares such as Pecan's debug middleware.
This should be used if you want to use middleware to
perform authentication or intercept all requests before
they are routed to the root controller.
:param logging: A dictionary used to configure logging. This uses
``logging.config.dictConfig``.
All other keyword arguments are passed in to the Pecan app constructor.
:returns: a ``Pecan`` object.
'''
# Pass logging configuration (if it exists) on to the Python logging module
logging = kw.get('logging', {})
debug = kw.get('debug', False)
if logging:
if debug:
try:
#
# By default, Python 2.7+ silences DeprecationWarnings.
# However, if conf.app.debug is True, we should probably ensure
# that users see these types of warnings.
#
from logging import captureWarnings
captureWarnings(True)
warnings.simplefilter("default", DeprecationWarning)
except ImportError:
# No captureWarnings on Python 2.6, DeprecationWarnings are on
pass
if isinstance(logging, Config):
logging = logging.to_dict()
if 'version' not in logging:
logging['version'] = 1
load_logging_config(logging)
# Instantiate the WSGI app by passing **kw onward
app = Pecan(root, **kw)
# Optionally wrap the app in another WSGI app
wrap_app = kw.get('wrap_app', None)
if wrap_app:
app = wrap_app(app)
# Configuration for serving custom error messages
errors = kw.get('errors', getattr(conf.app, 'errors', {}))
if errors:
app = middleware.errordocument.ErrorDocumentMiddleware(app, errors)
# Included for internal redirect support
app = middleware.recursive.RecursiveMiddleware(app)
# When in debug mode, load exception debugging middleware
static_root = kw.get('static_root', None)
if debug:
debug_kwargs = getattr(conf, 'debug', {})
debug_kwargs.setdefault('context_injectors', []).append(
lambda environ: {
'request': environ.get('pecan.locals', {}).get('request')
}
)
app = DebugMiddleware(
app,
**debug_kwargs
)
# Support for serving static files (for development convenience)
if static_root:
app = middleware.static.StaticFileMiddleware(app, static_root)
elif static_root:
warnings.warn(
"`static_root` is only used when `debug` is True, ignoring",
RuntimeWarning
)
if hasattr(conf, 'requestviewer'):
warnings.warn(''.join([
"`pecan.conf.requestviewer` is deprecated. To apply the ",
"`RequestViewerHook` to your application, add it to ",
"`pecan.conf.app.hooks` or manually in your project's `app.py` ",
"file."]),
DeprecationWarning
)
return app | [
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:param root: A string representing a root controller object (e.g.,
"myapp.controller.root.RootController")
:param static_root: The relative path to a directory containing static
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:param debug: A flag to enable debug mode. This enables the debug
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other middlewares such as Pecan's debug middleware.
This should be used if you want to use middleware to
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:param logging: A dictionary used to configure logging. This uses
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All other keyword arguments are passed in to the Pecan app constructor.
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25,177 | pecan/pecan | pecan/configuration.py | conf_from_file | def conf_from_file(filepath):
'''
Creates a configuration dictionary from a file.
:param filepath: The path to the file.
'''
abspath = os.path.abspath(os.path.expanduser(filepath))
conf_dict = {}
if not os.path.isfile(abspath):
raise RuntimeError('`%s` is not a file.' % abspath)
# First, make sure the code will actually compile (and has no SyntaxErrors)
with open(abspath, 'rb') as f:
compiled = compile(f.read(), abspath, 'exec')
# Next, attempt to actually import the file as a module.
# This provides more verbose import-related error reporting than exec()
absname, _ = os.path.splitext(abspath)
basepath, module_name = absname.rsplit(os.sep, 1)
if six.PY3:
SourceFileLoader(module_name, abspath).load_module(module_name)
else:
imp.load_module(
module_name,
*imp.find_module(module_name, [basepath])
)
# If we were able to import as a module, actually exec the compiled code
exec(compiled, globals(), conf_dict)
conf_dict['__file__'] = abspath
return conf_from_dict(conf_dict) | python | def conf_from_file(filepath):
'''
Creates a configuration dictionary from a file.
:param filepath: The path to the file.
'''
abspath = os.path.abspath(os.path.expanduser(filepath))
conf_dict = {}
if not os.path.isfile(abspath):
raise RuntimeError('`%s` is not a file.' % abspath)
# First, make sure the code will actually compile (and has no SyntaxErrors)
with open(abspath, 'rb') as f:
compiled = compile(f.read(), abspath, 'exec')
# Next, attempt to actually import the file as a module.
# This provides more verbose import-related error reporting than exec()
absname, _ = os.path.splitext(abspath)
basepath, module_name = absname.rsplit(os.sep, 1)
if six.PY3:
SourceFileLoader(module_name, abspath).load_module(module_name)
else:
imp.load_module(
module_name,
*imp.find_module(module_name, [basepath])
)
# If we were able to import as a module, actually exec the compiled code
exec(compiled, globals(), conf_dict)
conf_dict['__file__'] = abspath
return conf_from_dict(conf_dict) | [
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25,178 | pecan/pecan | pecan/configuration.py | get_conf_path_from_env | def get_conf_path_from_env():
'''
If the ``PECAN_CONFIG`` environment variable exists and it points to
a valid path it will return that, otherwise it will raise
a ``RuntimeError``.
'''
config_path = os.environ.get('PECAN_CONFIG')
if not config_path:
error = "PECAN_CONFIG is not set and " \
"no config file was passed as an argument."
elif not os.path.isfile(config_path):
error = "PECAN_CONFIG was set to an invalid path: %s" % config_path
else:
return config_path
raise RuntimeError(error) | python | def get_conf_path_from_env():
'''
If the ``PECAN_CONFIG`` environment variable exists and it points to
a valid path it will return that, otherwise it will raise
a ``RuntimeError``.
'''
config_path = os.environ.get('PECAN_CONFIG')
if not config_path:
error = "PECAN_CONFIG is not set and " \
"no config file was passed as an argument."
elif not os.path.isfile(config_path):
error = "PECAN_CONFIG was set to an invalid path: %s" % config_path
else:
return config_path
raise RuntimeError(error) | [
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a ``RuntimeError``. | [
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25,179 | pecan/pecan | pecan/configuration.py | conf_from_dict | def conf_from_dict(conf_dict):
'''
Creates a configuration dictionary from a dictionary.
:param conf_dict: The configuration dictionary.
'''
conf = Config(filename=conf_dict.get('__file__', ''))
for k, v in six.iteritems(conf_dict):
if k.startswith('__'):
continue
elif inspect.ismodule(v):
continue
conf[k] = v
return conf | python | def conf_from_dict(conf_dict):
'''
Creates a configuration dictionary from a dictionary.
:param conf_dict: The configuration dictionary.
'''
conf = Config(filename=conf_dict.get('__file__', ''))
for k, v in six.iteritems(conf_dict):
if k.startswith('__'):
continue
elif inspect.ismodule(v):
continue
conf[k] = v
return conf | [
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25,180 | pecan/pecan | pecan/configuration.py | set_config | def set_config(config, overwrite=False):
'''
Updates the global configuration.
:param config: Can be a dictionary containing configuration, or a string
which represents a (relative) configuration filename.
'''
if config is None:
config = get_conf_path_from_env()
# must be after the fallback other a bad fallback will incorrectly clear
if overwrite is True:
_runtime_conf.empty()
if isinstance(config, six.string_types):
config = conf_from_file(config)
_runtime_conf.update(config)
if config.__file__:
_runtime_conf.__file__ = config.__file__
elif isinstance(config, dict):
_runtime_conf.update(conf_from_dict(config))
else:
raise TypeError('%s is neither a dictionary or a string.' % config) | python | def set_config(config, overwrite=False):
'''
Updates the global configuration.
:param config: Can be a dictionary containing configuration, or a string
which represents a (relative) configuration filename.
'''
if config is None:
config = get_conf_path_from_env()
# must be after the fallback other a bad fallback will incorrectly clear
if overwrite is True:
_runtime_conf.empty()
if isinstance(config, six.string_types):
config = conf_from_file(config)
_runtime_conf.update(config)
if config.__file__:
_runtime_conf.__file__ = config.__file__
elif isinstance(config, dict):
_runtime_conf.update(conf_from_dict(config))
else:
raise TypeError('%s is neither a dictionary or a string.' % config) | [
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25,181 | pecan/pecan | pecan/configuration.py | Config.update | def update(self, conf_dict):
'''
Updates this configuration with a dictionary.
:param conf_dict: A python dictionary to update this configuration
with.
'''
if isinstance(conf_dict, dict):
iterator = six.iteritems(conf_dict)
else:
iterator = iter(conf_dict)
for k, v in iterator:
if not IDENTIFIER.match(k):
raise ValueError('\'%s\' is not a valid indentifier' % k)
cur_val = self.__values__.get(k)
if isinstance(cur_val, Config):
cur_val.update(conf_dict[k])
else:
self[k] = conf_dict[k] | python | def update(self, conf_dict):
'''
Updates this configuration with a dictionary.
:param conf_dict: A python dictionary to update this configuration
with.
'''
if isinstance(conf_dict, dict):
iterator = six.iteritems(conf_dict)
else:
iterator = iter(conf_dict)
for k, v in iterator:
if not IDENTIFIER.match(k):
raise ValueError('\'%s\' is not a valid indentifier' % k)
cur_val = self.__values__.get(k)
if isinstance(cur_val, Config):
cur_val.update(conf_dict[k])
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self[k] = conf_dict[k] | [
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25,182 | pecan/pecan | pecan/configuration.py | Config.to_dict | def to_dict(self, prefix=None):
'''
Converts recursively the Config object into a valid dictionary.
:param prefix: A string to optionally prefix all key elements in the
returned dictonary.
'''
conf_obj = dict(self)
return self.__dictify__(conf_obj, prefix) | python | def to_dict(self, prefix=None):
'''
Converts recursively the Config object into a valid dictionary.
:param prefix: A string to optionally prefix all key elements in the
returned dictonary.
'''
conf_obj = dict(self)
return self.__dictify__(conf_obj, prefix) | [
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25,183 | pecan/pecan | pecan/core.py | override_template | def override_template(template, content_type=None):
'''
Call within a controller to override the template that is used in
your response.
:param template: a valid path to a template file, just as you would specify
in an ``@expose``.
:param content_type: a valid MIME type to use for the response.func_closure
'''
request.pecan['override_template'] = template
if content_type:
request.pecan['override_content_type'] = content_type | python | def override_template(template, content_type=None):
'''
Call within a controller to override the template that is used in
your response.
:param template: a valid path to a template file, just as you would specify
in an ``@expose``.
:param content_type: a valid MIME type to use for the response.func_closure
'''
request.pecan['override_template'] = template
if content_type:
request.pecan['override_content_type'] = content_type | [
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25,184 | pecan/pecan | pecan/core.py | abort | def abort(status_code, detail='', headers=None, comment=None, **kw):
'''
Raise an HTTP status code, as specified. Useful for returning status
codes like 401 Unauthorized or 403 Forbidden.
:param status_code: The HTTP status code as an integer.
:param detail: The message to send along, as a string.
:param headers: A dictionary of headers to send along with the response.
:param comment: A comment to include in the response.
'''
# If there is a traceback, we need to catch it for a re-raise
try:
_, _, traceback = sys.exc_info()
webob_exception = exc.status_map[status_code](
detail=detail,
headers=headers,
comment=comment,
**kw
)
if six.PY3:
raise webob_exception.with_traceback(traceback)
else:
# Using exec to avoid python 3 parsers from crashing
exec('raise webob_exception, None, traceback')
finally:
# Per the suggestion of the Python docs, delete the traceback object
del traceback | python | def abort(status_code, detail='', headers=None, comment=None, **kw):
'''
Raise an HTTP status code, as specified. Useful for returning status
codes like 401 Unauthorized or 403 Forbidden.
:param status_code: The HTTP status code as an integer.
:param detail: The message to send along, as a string.
:param headers: A dictionary of headers to send along with the response.
:param comment: A comment to include in the response.
'''
# If there is a traceback, we need to catch it for a re-raise
try:
_, _, traceback = sys.exc_info()
webob_exception = exc.status_map[status_code](
detail=detail,
headers=headers,
comment=comment,
**kw
)
if six.PY3:
raise webob_exception.with_traceback(traceback)
else:
# Using exec to avoid python 3 parsers from crashing
exec('raise webob_exception, None, traceback')
finally:
# Per the suggestion of the Python docs, delete the traceback object
del traceback | [
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25,185 | pecan/pecan | pecan/core.py | redirect | def redirect(location=None, internal=False, code=None, headers={},
add_slash=False, request=None):
'''
Perform a redirect, either internal or external. An internal redirect
performs the redirect server-side, while the external redirect utilizes
an HTTP 302 status code.
:param location: The HTTP location to redirect to.
:param internal: A boolean indicating whether the redirect should be
internal.
:param code: The HTTP status code to use for the redirect. Defaults to 302.
:param headers: Any HTTP headers to send with the response, as a
dictionary.
:param request: The :class:`pecan.Request` instance to use.
'''
request = request or state.request
if add_slash:
if location is None:
split_url = list(urlparse.urlsplit(request.url))
new_proto = request.environ.get(
'HTTP_X_FORWARDED_PROTO', split_url[0]
)
split_url[0] = new_proto
else:
split_url = urlparse.urlsplit(location)
split_url[2] = split_url[2].rstrip('/') + '/'
location = urlparse.urlunsplit(split_url)
if not headers:
headers = {}
if internal:
if code is not None:
raise ValueError('Cannot specify a code for internal redirects')
request.environ['pecan.recursive.context'] = request.context
raise ForwardRequestException(location)
if code is None:
code = 302
raise exc.status_map[code](location=location, headers=headers) | python | def redirect(location=None, internal=False, code=None, headers={},
add_slash=False, request=None):
'''
Perform a redirect, either internal or external. An internal redirect
performs the redirect server-side, while the external redirect utilizes
an HTTP 302 status code.
:param location: The HTTP location to redirect to.
:param internal: A boolean indicating whether the redirect should be
internal.
:param code: The HTTP status code to use for the redirect. Defaults to 302.
:param headers: Any HTTP headers to send with the response, as a
dictionary.
:param request: The :class:`pecan.Request` instance to use.
'''
request = request or state.request
if add_slash:
if location is None:
split_url = list(urlparse.urlsplit(request.url))
new_proto = request.environ.get(
'HTTP_X_FORWARDED_PROTO', split_url[0]
)
split_url[0] = new_proto
else:
split_url = urlparse.urlsplit(location)
split_url[2] = split_url[2].rstrip('/') + '/'
location = urlparse.urlunsplit(split_url)
if not headers:
headers = {}
if internal:
if code is not None:
raise ValueError('Cannot specify a code for internal redirects')
request.environ['pecan.recursive.context'] = request.context
raise ForwardRequestException(location)
if code is None:
code = 302
raise exc.status_map[code](location=location, headers=headers) | [
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25,186 | pecan/pecan | pecan/core.py | load_app | def load_app(config, **kwargs):
'''
Used to load a ``Pecan`` application and its environment based on passed
configuration.
:param config: Can be a dictionary containing configuration, a string which
represents a (relative) configuration filename
returns a pecan.Pecan object
'''
from .configuration import _runtime_conf, set_config
set_config(config, overwrite=True)
for package_name in getattr(_runtime_conf.app, 'modules', []):
module = __import__(package_name, fromlist=['app'])
if hasattr(module, 'app') and hasattr(module.app, 'setup_app'):
app = module.app.setup_app(_runtime_conf, **kwargs)
app.config = _runtime_conf
return app
raise RuntimeError(
'No app.setup_app found in any of the configured app.modules'
) | python | def load_app(config, **kwargs):
'''
Used to load a ``Pecan`` application and its environment based on passed
configuration.
:param config: Can be a dictionary containing configuration, a string which
represents a (relative) configuration filename
returns a pecan.Pecan object
'''
from .configuration import _runtime_conf, set_config
set_config(config, overwrite=True)
for package_name in getattr(_runtime_conf.app, 'modules', []):
module = __import__(package_name, fromlist=['app'])
if hasattr(module, 'app') and hasattr(module.app, 'setup_app'):
app = module.app.setup_app(_runtime_conf, **kwargs)
app.config = _runtime_conf
return app
raise RuntimeError(
'No app.setup_app found in any of the configured app.modules'
) | [
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25,187 | pecan/pecan | pecan/core.py | PecanBase.route | def route(self, req, node, path):
'''
Looks up a controller from a node based upon the specified path.
:param node: The node, such as a root controller object.
:param path: The path to look up on this node.
'''
path = path.split('/')[1:]
try:
node, remainder = lookup_controller(node, path, req)
return node, remainder
except NonCanonicalPath as e:
if self.force_canonical and \
not _cfg(e.controller).get('accept_noncanonical', False):
if req.method == 'POST':
raise RuntimeError(
"You have POSTed to a URL '%s' which "
"requires a slash. Most browsers will not maintain "
"POST data when redirected. Please update your code "
"to POST to '%s/' or set force_canonical to False" %
(req.pecan['routing_path'],
req.pecan['routing_path'])
)
redirect(code=302, add_slash=True, request=req)
return e.controller, e.remainder | python | def route(self, req, node, path):
'''
Looks up a controller from a node based upon the specified path.
:param node: The node, such as a root controller object.
:param path: The path to look up on this node.
'''
path = path.split('/')[1:]
try:
node, remainder = lookup_controller(node, path, req)
return node, remainder
except NonCanonicalPath as e:
if self.force_canonical and \
not _cfg(e.controller).get('accept_noncanonical', False):
if req.method == 'POST':
raise RuntimeError(
"You have POSTed to a URL '%s' which "
"requires a slash. Most browsers will not maintain "
"POST data when redirected. Please update your code "
"to POST to '%s/' or set force_canonical to False" %
(req.pecan['routing_path'],
req.pecan['routing_path'])
)
redirect(code=302, add_slash=True, request=req)
return e.controller, e.remainder | [
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25,188 | pecan/pecan | pecan/core.py | PecanBase.determine_hooks | def determine_hooks(self, controller=None):
'''
Determines the hooks to be run, in which order.
:param controller: If specified, includes hooks for a specific
controller.
'''
controller_hooks = []
if controller:
controller_hooks = _cfg(controller).get('hooks', [])
if controller_hooks:
return list(
sorted(
chain(controller_hooks, self.hooks),
key=operator.attrgetter('priority')
)
)
return self.hooks | python | def determine_hooks(self, controller=None):
'''
Determines the hooks to be run, in which order.
:param controller: If specified, includes hooks for a specific
controller.
'''
controller_hooks = []
if controller:
controller_hooks = _cfg(controller).get('hooks', [])
if controller_hooks:
return list(
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)
return self.hooks | [
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] | 833d0653fa0e6bbfb52545b091c30182105f4a82 | https://github.com/pecan/pecan/blob/833d0653fa0e6bbfb52545b091c30182105f4a82/pecan/core.py#L310-L328 |
25,189 | pecan/pecan | pecan/core.py | PecanBase.handle_hooks | def handle_hooks(self, hooks, hook_type, *args):
'''
Processes hooks of the specified type.
:param hook_type: The type of hook, including ``before``, ``after``,
``on_error``, and ``on_route``.
:param \*args: Arguments to pass to the hooks.
'''
if hook_type not in ['before', 'on_route']:
hooks = reversed(hooks)
for hook in hooks:
result = getattr(hook, hook_type)(*args)
# on_error hooks can choose to return a Response, which will
# be used instead of the standard error pages.
if hook_type == 'on_error' and isinstance(result, WebObResponse):
return result | python | def handle_hooks(self, hooks, hook_type, *args):
'''
Processes hooks of the specified type.
:param hook_type: The type of hook, including ``before``, ``after``,
``on_error``, and ``on_route``.
:param \*args: Arguments to pass to the hooks.
'''
if hook_type not in ['before', 'on_route']:
hooks = reversed(hooks)
for hook in hooks:
result = getattr(hook, hook_type)(*args)
# on_error hooks can choose to return a Response, which will
# be used instead of the standard error pages.
if hook_type == 'on_error' and isinstance(result, WebObResponse):
return result | [
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25,190 | pecan/pecan | pecan/core.py | PecanBase.get_args | def get_args(self, state, all_params, remainder, argspec, im_self):
'''
Determines the arguments for a controller based upon parameters
passed the argument specification for the controller.
'''
args = []
varargs = []
kwargs = dict()
valid_args = argspec.args[:]
if ismethod(state.controller) or im_self:
valid_args.pop(0) # pop off `self`
pecan_state = state.request.pecan
remainder = [x for x in remainder if x]
if im_self is not None:
args.append(im_self)
# grab the routing args from nested REST controllers
if 'routing_args' in pecan_state:
remainder = pecan_state['routing_args'] + list(remainder)
del pecan_state['routing_args']
# handle positional arguments
if valid_args and remainder:
args.extend(remainder[:len(valid_args)])
remainder = remainder[len(valid_args):]
valid_args = valid_args[len(args):]
# handle wildcard arguments
if [i for i in remainder if i]:
if not argspec[1]:
abort(404)
varargs.extend(remainder)
# get the default positional arguments
if argspec[3]:
defaults = dict(izip(argspec[0][-len(argspec[3]):], argspec[3]))
else:
defaults = dict()
# handle positional GET/POST params
for name in valid_args:
if name in all_params:
args.append(all_params.pop(name))
elif name in defaults:
args.append(defaults[name])
else:
break
# handle wildcard GET/POST params
if argspec[2]:
for name, value in six.iteritems(all_params):
if name not in argspec[0]:
kwargs[name] = value
return args, varargs, kwargs | python | def get_args(self, state, all_params, remainder, argspec, im_self):
'''
Determines the arguments for a controller based upon parameters
passed the argument specification for the controller.
'''
args = []
varargs = []
kwargs = dict()
valid_args = argspec.args[:]
if ismethod(state.controller) or im_self:
valid_args.pop(0) # pop off `self`
pecan_state = state.request.pecan
remainder = [x for x in remainder if x]
if im_self is not None:
args.append(im_self)
# grab the routing args from nested REST controllers
if 'routing_args' in pecan_state:
remainder = pecan_state['routing_args'] + list(remainder)
del pecan_state['routing_args']
# handle positional arguments
if valid_args and remainder:
args.extend(remainder[:len(valid_args)])
remainder = remainder[len(valid_args):]
valid_args = valid_args[len(args):]
# handle wildcard arguments
if [i for i in remainder if i]:
if not argspec[1]:
abort(404)
varargs.extend(remainder)
# get the default positional arguments
if argspec[3]:
defaults = dict(izip(argspec[0][-len(argspec[3]):], argspec[3]))
else:
defaults = dict()
# handle positional GET/POST params
for name in valid_args:
if name in all_params:
args.append(all_params.pop(name))
elif name in defaults:
args.append(defaults[name])
else:
break
# handle wildcard GET/POST params
if argspec[2]:
for name, value in six.iteritems(all_params):
if name not in argspec[0]:
kwargs[name] = value
return args, varargs, kwargs | [
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25,191 | pecan/pecan | pecan/commands/shell.py | ShellCommand.run | def run(self, args):
"""
Load the pecan app, prepare the locals, sets the
banner, and invokes the python shell.
"""
super(ShellCommand, self).run(args)
# load the application
app = self.load_app()
# prepare the locals
locs = dict(__name__='pecan-admin')
locs['wsgiapp'] = app
locs['app'] = TestApp(app)
model = self.load_model(app.config)
if model:
locs['model'] = model
# insert the pecan locals
from pecan import abort, conf, redirect, request, response
locs['abort'] = abort
locs['conf'] = conf
locs['redirect'] = redirect
locs['request'] = request
locs['response'] = response
# prepare the banner
banner = ' The following objects are available:\n'
banner += ' %-10s - This project\'s WSGI App instance\n' % 'wsgiapp'
banner += ' %-10s - The current configuration\n' % 'conf'
banner += ' %-10s - webtest.TestApp wrapped around wsgiapp\n' % 'app'
if model:
model_name = getattr(
model,
'__module__',
getattr(model, '__name__', 'model')
)
banner += ' %-10s - Models from %s\n' % ('model', model_name)
self.invoke_shell(locs, banner) | python | def run(self, args):
super(ShellCommand, self).run(args)
# load the application
app = self.load_app()
# prepare the locals
locs = dict(__name__='pecan-admin')
locs['wsgiapp'] = app
locs['app'] = TestApp(app)
model = self.load_model(app.config)
if model:
locs['model'] = model
# insert the pecan locals
from pecan import abort, conf, redirect, request, response
locs['abort'] = abort
locs['conf'] = conf
locs['redirect'] = redirect
locs['request'] = request
locs['response'] = response
# prepare the banner
banner = ' The following objects are available:\n'
banner += ' %-10s - This project\'s WSGI App instance\n' % 'wsgiapp'
banner += ' %-10s - The current configuration\n' % 'conf'
banner += ' %-10s - webtest.TestApp wrapped around wsgiapp\n' % 'app'
if model:
model_name = getattr(
model,
'__module__',
getattr(model, '__name__', 'model')
)
banner += ' %-10s - Models from %s\n' % ('model', model_name)
self.invoke_shell(locs, banner) | [
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25,192 | pecan/pecan | pecan/commands/shell.py | ShellCommand.load_model | def load_model(self, config):
"""
Load the model extension module
"""
for package_name in getattr(config.app, 'modules', []):
module = __import__(package_name, fromlist=['model'])
if hasattr(module, 'model'):
return module.model
return None | python | def load_model(self, config):
for package_name in getattr(config.app, 'modules', []):
module = __import__(package_name, fromlist=['model'])
if hasattr(module, 'model'):
return module.model
return None | [
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25,193 | pecan/pecan | pecan/rest.py | RestController._handle_bad_rest_arguments | def _handle_bad_rest_arguments(self, controller, remainder, request):
"""
Ensure that the argspec for a discovered controller actually matched
the positional arguments in the request path. If not, raise
a webob.exc.HTTPBadRequest.
"""
argspec = self._get_args_for_controller(controller)
fixed_args = len(argspec) - len(
request.pecan.get('routing_args', [])
)
if len(remainder) < fixed_args:
# For controllers that are missing intermediate IDs
# (e.g., /authors/books vs /authors/1/books), return a 404 for an
# invalid path.
abort(404) | python | def _handle_bad_rest_arguments(self, controller, remainder, request):
argspec = self._get_args_for_controller(controller)
fixed_args = len(argspec) - len(
request.pecan.get('routing_args', [])
)
if len(remainder) < fixed_args:
# For controllers that are missing intermediate IDs
# (e.g., /authors/books vs /authors/1/books), return a 404 for an
# invalid path.
abort(404) | [
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25,194 | pecan/pecan | pecan/rest.py | RestController._route | def _route(self, args, request=None):
'''
Routes a request to the appropriate controller and returns its result.
Performs a bit of validation - refuses to route delete and put actions
via a GET request).
'''
if request is None:
from pecan import request
# convention uses "_method" to handle browser-unsupported methods
method = request.params.get('_method', request.method).lower()
# make sure DELETE/PUT requests don't use GET
if request.method == 'GET' and method in ('delete', 'put'):
abort(405)
# check for nested controllers
result = self._find_sub_controllers(args, request)
if result:
return result
# handle the request
handler = getattr(
self,
'_handle_%s' % method,
self._handle_unknown_method
)
try:
if len(getargspec(handler).args) == 3:
result = handler(method, args)
else:
result = handler(method, args, request)
#
# If the signature of the handler does not match the number
# of remaining positional arguments, attempt to handle
# a _lookup method (if it exists)
#
argspec = self._get_args_for_controller(result[0])
num_args = len(argspec)
if num_args < len(args):
_lookup_result = self._handle_lookup(args, request)
if _lookup_result:
return _lookup_result
except (exc.HTTPClientError, exc.HTTPNotFound,
exc.HTTPMethodNotAllowed) as e:
#
# If the matching handler results in a 400, 404, or 405, attempt to
# handle a _lookup method (if it exists)
#
_lookup_result = self._handle_lookup(args, request)
if _lookup_result:
return _lookup_result
# Build a correct Allow: header
if isinstance(e, exc.HTTPMethodNotAllowed):
def method_iter():
for func in ('get', 'get_one', 'get_all', 'new', 'edit',
'get_delete'):
if self._find_controller(func):
yield 'GET'
break
for method in ('HEAD', 'POST', 'PUT', 'DELETE', 'TRACE',
'PATCH'):
func = method.lower()
if self._find_controller(func):
yield method
e.allow = sorted(method_iter())
raise
# return the result
return result | python | def _route(self, args, request=None):
'''
Routes a request to the appropriate controller and returns its result.
Performs a bit of validation - refuses to route delete and put actions
via a GET request).
'''
if request is None:
from pecan import request
# convention uses "_method" to handle browser-unsupported methods
method = request.params.get('_method', request.method).lower()
# make sure DELETE/PUT requests don't use GET
if request.method == 'GET' and method in ('delete', 'put'):
abort(405)
# check for nested controllers
result = self._find_sub_controllers(args, request)
if result:
return result
# handle the request
handler = getattr(
self,
'_handle_%s' % method,
self._handle_unknown_method
)
try:
if len(getargspec(handler).args) == 3:
result = handler(method, args)
else:
result = handler(method, args, request)
#
# If the signature of the handler does not match the number
# of remaining positional arguments, attempt to handle
# a _lookup method (if it exists)
#
argspec = self._get_args_for_controller(result[0])
num_args = len(argspec)
if num_args < len(args):
_lookup_result = self._handle_lookup(args, request)
if _lookup_result:
return _lookup_result
except (exc.HTTPClientError, exc.HTTPNotFound,
exc.HTTPMethodNotAllowed) as e:
#
# If the matching handler results in a 400, 404, or 405, attempt to
# handle a _lookup method (if it exists)
#
_lookup_result = self._handle_lookup(args, request)
if _lookup_result:
return _lookup_result
# Build a correct Allow: header
if isinstance(e, exc.HTTPMethodNotAllowed):
def method_iter():
for func in ('get', 'get_one', 'get_all', 'new', 'edit',
'get_delete'):
if self._find_controller(func):
yield 'GET'
break
for method in ('HEAD', 'POST', 'PUT', 'DELETE', 'TRACE',
'PATCH'):
func = method.lower()
if self._find_controller(func):
yield method
e.allow = sorted(method_iter())
raise
# return the result
return result | [
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25,195 | pecan/pecan | pecan/rest.py | RestController._find_controller | def _find_controller(self, *args):
'''
Returns the appropriate controller for routing a custom action.
'''
for name in args:
obj = self._lookup_child(name)
if obj and iscontroller(obj):
return obj
return None | python | def _find_controller(self, *args):
'''
Returns the appropriate controller for routing a custom action.
'''
for name in args:
obj = self._lookup_child(name)
if obj and iscontroller(obj):
return obj
return None | [
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25,196 | pecan/pecan | pecan/rest.py | RestController._find_sub_controllers | def _find_sub_controllers(self, remainder, request):
'''
Identifies the correct controller to route to by analyzing the
request URI.
'''
# need either a get_one or get to parse args
method = None
for name in ('get_one', 'get'):
if hasattr(self, name):
method = name
break
if not method:
return
# get the args to figure out how much to chop off
args = self._get_args_for_controller(getattr(self, method))
fixed_args = len(args) - len(
request.pecan.get('routing_args', [])
)
var_args = getargspec(getattr(self, method)).varargs
# attempt to locate a sub-controller
if var_args:
for i, item in enumerate(remainder):
controller = self._lookup_child(item)
if controller and not ismethod(controller):
self._set_routing_args(request, remainder[:i])
return lookup_controller(controller, remainder[i + 1:],
request)
elif fixed_args < len(remainder) and hasattr(
self, remainder[fixed_args]
):
controller = self._lookup_child(remainder[fixed_args])
if not ismethod(controller):
self._set_routing_args(request, remainder[:fixed_args])
return lookup_controller(
controller,
remainder[fixed_args + 1:],
request
) | python | def _find_sub_controllers(self, remainder, request):
'''
Identifies the correct controller to route to by analyzing the
request URI.
'''
# need either a get_one or get to parse args
method = None
for name in ('get_one', 'get'):
if hasattr(self, name):
method = name
break
if not method:
return
# get the args to figure out how much to chop off
args = self._get_args_for_controller(getattr(self, method))
fixed_args = len(args) - len(
request.pecan.get('routing_args', [])
)
var_args = getargspec(getattr(self, method)).varargs
# attempt to locate a sub-controller
if var_args:
for i, item in enumerate(remainder):
controller = self._lookup_child(item)
if controller and not ismethod(controller):
self._set_routing_args(request, remainder[:i])
return lookup_controller(controller, remainder[i + 1:],
request)
elif fixed_args < len(remainder) and hasattr(
self, remainder[fixed_args]
):
controller = self._lookup_child(remainder[fixed_args])
if not ismethod(controller):
self._set_routing_args(request, remainder[:fixed_args])
return lookup_controller(
controller,
remainder[fixed_args + 1:],
request
) | [
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25,197 | pecan/pecan | pecan/rest.py | RestController._handle_get | def _handle_get(self, method, remainder, request=None):
'''
Routes ``GET`` actions to the appropriate controller.
'''
if request is None:
self._raise_method_deprecation_warning(self._handle_get)
# route to a get_all or get if no additional parts are available
if not remainder or remainder == ['']:
remainder = list(six.moves.filter(bool, remainder))
controller = self._find_controller('get_all', 'get')
if controller:
self._handle_bad_rest_arguments(controller, remainder, request)
return controller, []
abort(405)
method_name = remainder[-1]
# check for new/edit/delete GET requests
if method_name in ('new', 'edit', 'delete'):
if method_name == 'delete':
method_name = 'get_delete'
controller = self._find_controller(method_name)
if controller:
return controller, remainder[:-1]
match = self._handle_custom_action(method, remainder, request)
if match:
return match
controller = self._lookup_child(remainder[0])
if controller and not ismethod(controller):
return lookup_controller(controller, remainder[1:], request)
# finally, check for the regular get_one/get requests
controller = self._find_controller('get_one', 'get')
if controller:
self._handle_bad_rest_arguments(controller, remainder, request)
return controller, remainder
abort(405) | python | def _handle_get(self, method, remainder, request=None):
'''
Routes ``GET`` actions to the appropriate controller.
'''
if request is None:
self._raise_method_deprecation_warning(self._handle_get)
# route to a get_all or get if no additional parts are available
if not remainder or remainder == ['']:
remainder = list(six.moves.filter(bool, remainder))
controller = self._find_controller('get_all', 'get')
if controller:
self._handle_bad_rest_arguments(controller, remainder, request)
return controller, []
abort(405)
method_name = remainder[-1]
# check for new/edit/delete GET requests
if method_name in ('new', 'edit', 'delete'):
if method_name == 'delete':
method_name = 'get_delete'
controller = self._find_controller(method_name)
if controller:
return controller, remainder[:-1]
match = self._handle_custom_action(method, remainder, request)
if match:
return match
controller = self._lookup_child(remainder[0])
if controller and not ismethod(controller):
return lookup_controller(controller, remainder[1:], request)
# finally, check for the regular get_one/get requests
controller = self._find_controller('get_one', 'get')
if controller:
self._handle_bad_rest_arguments(controller, remainder, request)
return controller, remainder
abort(405) | [
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"# route to a get_all or get if... | Routes ``GET`` actions to the appropriate controller. | [
"Routes",
"GET",
"actions",
"to",
"the",
"appropriate",
"controller",
"."
] | 833d0653fa0e6bbfb52545b091c30182105f4a82 | https://github.com/pecan/pecan/blob/833d0653fa0e6bbfb52545b091c30182105f4a82/pecan/rest.py#L270-L309 |
25,198 | pecan/pecan | pecan/rest.py | RestController._handle_delete | def _handle_delete(self, method, remainder, request=None):
'''
Routes ``DELETE`` actions to the appropriate controller.
'''
if request is None:
self._raise_method_deprecation_warning(self._handle_delete)
if remainder:
match = self._handle_custom_action(method, remainder, request)
if match:
return match
controller = self._lookup_child(remainder[0])
if controller and not ismethod(controller):
return lookup_controller(controller, remainder[1:], request)
# check for post_delete/delete requests first
controller = self._find_controller('post_delete', 'delete')
if controller:
return controller, remainder
# if no controller exists, try routing to a sub-controller; note that
# since this is a DELETE verb, any local exposes are 405'd
if remainder:
if self._find_controller(remainder[0]):
abort(405)
sub_controller = self._lookup_child(remainder[0])
if sub_controller:
return lookup_controller(sub_controller, remainder[1:],
request)
abort(405) | python | def _handle_delete(self, method, remainder, request=None):
'''
Routes ``DELETE`` actions to the appropriate controller.
'''
if request is None:
self._raise_method_deprecation_warning(self._handle_delete)
if remainder:
match = self._handle_custom_action(method, remainder, request)
if match:
return match
controller = self._lookup_child(remainder[0])
if controller and not ismethod(controller):
return lookup_controller(controller, remainder[1:], request)
# check for post_delete/delete requests first
controller = self._find_controller('post_delete', 'delete')
if controller:
return controller, remainder
# if no controller exists, try routing to a sub-controller; note that
# since this is a DELETE verb, any local exposes are 405'd
if remainder:
if self._find_controller(remainder[0]):
abort(405)
sub_controller = self._lookup_child(remainder[0])
if sub_controller:
return lookup_controller(sub_controller, remainder[1:],
request)
abort(405) | [
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":... | Routes ``DELETE`` actions to the appropriate controller. | [
"Routes",
"DELETE",
"actions",
"to",
"the",
"appropriate",
"controller",
"."
] | 833d0653fa0e6bbfb52545b091c30182105f4a82 | https://github.com/pecan/pecan/blob/833d0653fa0e6bbfb52545b091c30182105f4a82/pecan/rest.py#L311-L342 |
25,199 | pecan/pecan | pecan/rest.py | RestController._handle_post | def _handle_post(self, method, remainder, request=None):
'''
Routes ``POST`` requests.
'''
if request is None:
self._raise_method_deprecation_warning(self._handle_post)
# check for custom POST/PUT requests
if remainder:
match = self._handle_custom_action(method, remainder, request)
if match:
return match
controller = self._lookup_child(remainder[0])
if controller and not ismethod(controller):
return lookup_controller(controller, remainder[1:], request)
# check for regular POST/PUT requests
controller = self._find_controller(method)
if controller:
return controller, remainder
abort(405) | python | def _handle_post(self, method, remainder, request=None):
'''
Routes ``POST`` requests.
'''
if request is None:
self._raise_method_deprecation_warning(self._handle_post)
# check for custom POST/PUT requests
if remainder:
match = self._handle_custom_action(method, remainder, request)
if match:
return match
controller = self._lookup_child(remainder[0])
if controller and not ismethod(controller):
return lookup_controller(controller, remainder[1:], request)
# check for regular POST/PUT requests
controller = self._find_controller(method)
if controller:
return controller, remainder
abort(405) | [
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"_handle_post",
"(",
"self",
",",
"method",
",",
"remainder",
",",
"request",
"=",
"None",
")",
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"is",
"None",
":",
"self",
".",
"_raise_method_deprecation_warning",
"(",
"self",
".",
"_handle_post",
")",
"# check for custom POST/PUT ... | Routes ``POST`` requests. | [
"Routes",
"POST",
"requests",
"."
] | 833d0653fa0e6bbfb52545b091c30182105f4a82 | https://github.com/pecan/pecan/blob/833d0653fa0e6bbfb52545b091c30182105f4a82/pecan/rest.py#L344-L366 |
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