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kata198/AdvancedHTMLParser
|
AdvancedHTMLParser/SpecialAttributes.py
|
StyleAttribute.styleToDict
|
def styleToDict(styleStr):
'''
getStyleDict - Gets a dictionary of style attribute/value pairs.
NOTE: dash-names (like padding-top) are used here
@return - OrderedDict of "style" attribute.
'''
styleStr = styleStr.strip()
styles = styleStr.split(';') # Won't work for strings containing semicolon..
styleDict = OrderedDict()
for item in styles:
try:
splitIdx = item.index(':')
name = item[:splitIdx].strip().lower()
value = item[splitIdx+1:].strip()
styleDict[name] = value
except:
continue
return styleDict
|
python
|
def styleToDict(styleStr):
'''
getStyleDict - Gets a dictionary of style attribute/value pairs.
NOTE: dash-names (like padding-top) are used here
@return - OrderedDict of "style" attribute.
'''
styleStr = styleStr.strip()
styles = styleStr.split(';') # Won't work for strings containing semicolon..
styleDict = OrderedDict()
for item in styles:
try:
splitIdx = item.index(':')
name = item[:splitIdx].strip().lower()
value = item[splitIdx+1:].strip()
styleDict[name] = value
except:
continue
return styleDict
|
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train
|
https://github.com/kata198/AdvancedHTMLParser/blob/06aeea5d8e2ea86e155aae0fc237623d3e9b7f9d/AdvancedHTMLParser/SpecialAttributes.py#L638-L659
|
kata198/AdvancedHTMLParser
|
AdvancedHTMLParser/SpecialAttributes.py
|
StyleAttribute._asStr
|
def _asStr(self):
'''
_asStr - Get the string representation of this style
@return <str> - A string representation of this style (semicolon separated, key: value format)
'''
styleDict = self._styleDict
if styleDict:
return '; '.join([name + ': ' + value for name, value in styleDict.items()])
return ''
|
python
|
def _asStr(self):
'''
_asStr - Get the string representation of this style
@return <str> - A string representation of this style (semicolon separated, key: value format)
'''
styleDict = self._styleDict
if styleDict:
return '; '.join([name + ': ' + value for name, value in styleDict.items()])
return ''
|
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_asStr - Get the string representation of this style
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|
[
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"-",
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train
|
https://github.com/kata198/AdvancedHTMLParser/blob/06aeea5d8e2ea86e155aae0fc237623d3e9b7f9d/AdvancedHTMLParser/SpecialAttributes.py#L738-L748
|
kata198/AdvancedHTMLParser
|
AdvancedHTMLParser/constants.py
|
_special_value_rows
|
def _special_value_rows(em):
'''
_special_value_rows - Handle "rows" special attribute, which differs if tagName is a textarea or frameset
'''
if em.tagName == 'textarea':
return convertToIntRange(em.getAttribute('rows', 2), minValue=1, maxValue=None, invalidDefault=2)
else:
# frameset
return em.getAttribute('rows', '')
|
python
|
def _special_value_rows(em):
'''
_special_value_rows - Handle "rows" special attribute, which differs if tagName is a textarea or frameset
'''
if em.tagName == 'textarea':
return convertToIntRange(em.getAttribute('rows', 2), minValue=1, maxValue=None, invalidDefault=2)
else:
# frameset
return em.getAttribute('rows', '')
|
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_special_value_rows - Handle "rows" special attribute, which differs if tagName is a textarea or frameset
|
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train
|
https://github.com/kata198/AdvancedHTMLParser/blob/06aeea5d8e2ea86e155aae0fc237623d3e9b7f9d/AdvancedHTMLParser/constants.py#L248-L256
|
kata198/AdvancedHTMLParser
|
AdvancedHTMLParser/constants.py
|
_special_value_cols
|
def _special_value_cols(em):
'''
_special_value_cols - Handle "cols" special attribute, which differs if tagName is a textarea or frameset
'''
if em.tagName == 'textarea':
return convertToIntRange(em.getAttribute('cols', 20), minValue=1, maxValue=None, invalidDefault=20)
else:
# frameset
return em.getAttribute('cols', '')
|
python
|
def _special_value_cols(em):
'''
_special_value_cols - Handle "cols" special attribute, which differs if tagName is a textarea or frameset
'''
if em.tagName == 'textarea':
return convertToIntRange(em.getAttribute('cols', 20), minValue=1, maxValue=None, invalidDefault=20)
else:
# frameset
return em.getAttribute('cols', '')
|
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_special_value_cols - Handle "cols" special attribute, which differs if tagName is a textarea or frameset
|
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] |
train
|
https://github.com/kata198/AdvancedHTMLParser/blob/06aeea5d8e2ea86e155aae0fc237623d3e9b7f9d/AdvancedHTMLParser/constants.py#L258-L266
|
kata198/AdvancedHTMLParser
|
AdvancedHTMLParser/constants.py
|
_special_value_autocomplete
|
def _special_value_autocomplete(em):
'''
handle "autocomplete" property, which has different behaviour for form vs input"
'''
if em.tagName == 'form':
return convertPossibleValues(em.getAttribute('autocomplete', 'on'), POSSIBLE_VALUES_ON_OFF, invalidDefault='on', emptyValue=EMPTY_IS_INVALID)
# else: input
return convertPossibleValues(em.getAttribute('autocomplete', ''), POSSIBLE_VALUES_ON_OFF, invalidDefault="", emptyValue='')
|
python
|
def _special_value_autocomplete(em):
'''
handle "autocomplete" property, which has different behaviour for form vs input"
'''
if em.tagName == 'form':
return convertPossibleValues(em.getAttribute('autocomplete', 'on'), POSSIBLE_VALUES_ON_OFF, invalidDefault='on', emptyValue=EMPTY_IS_INVALID)
# else: input
return convertPossibleValues(em.getAttribute('autocomplete', ''), POSSIBLE_VALUES_ON_OFF, invalidDefault="", emptyValue='')
|
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train
|
https://github.com/kata198/AdvancedHTMLParser/blob/06aeea5d8e2ea86e155aae0fc237623d3e9b7f9d/AdvancedHTMLParser/constants.py#L268-L275
|
kata198/AdvancedHTMLParser
|
AdvancedHTMLParser/constants.py
|
_special_value_size
|
def _special_value_size(em):
'''
handle "size" property, which has different behaviour for input vs everything else
'''
if em.tagName == 'input':
# TODO: "size" on an input is implemented very weirdly. Negative values are treated as invalid,
# A value of "0" raises an exception (and does not set HTML attribute)
# No upper limit.
return convertToPositiveInt(em.getAttribute('size', 20), invalidDefault=20)
return em.getAttribute('size', '')
|
python
|
def _special_value_size(em):
'''
handle "size" property, which has different behaviour for input vs everything else
'''
if em.tagName == 'input':
# TODO: "size" on an input is implemented very weirdly. Negative values are treated as invalid,
# A value of "0" raises an exception (and does not set HTML attribute)
# No upper limit.
return convertToPositiveInt(em.getAttribute('size', 20), invalidDefault=20)
return em.getAttribute('size', '')
|
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train
|
https://github.com/kata198/AdvancedHTMLParser/blob/06aeea5d8e2ea86e155aae0fc237623d3e9b7f9d/AdvancedHTMLParser/constants.py#L277-L286
|
kata198/AdvancedHTMLParser
|
AdvancedHTMLParser/constants.py
|
_special_value_maxLength
|
def _special_value_maxLength(em, newValue=NOT_PROVIDED):
'''
_special_value_maxLength - Handle the special "maxLength" property
@param em <AdvancedTag> - The tag element
@param newValue - Default NOT_PROVIDED, if provided will use that value instead of the
current .getAttribute value on the tag. This is because this method can be used for both validation
and getting/setting
'''
if newValue is NOT_PROVIDED:
if not em.hasAttribute('maxlength'):
return -1
curValue = em.getAttribute('maxlength', '-1')
# If we are accessing, the invalid default should be negative
invalidDefault = -1
else:
curValue = newValue
# If we are setting, we should raise an exception upon invalid value
invalidDefault = IndexSizeErrorException
return convertToIntRange(curValue, minValue=0, maxValue=None, emptyValue='0', invalidDefault=invalidDefault)
|
python
|
def _special_value_maxLength(em, newValue=NOT_PROVIDED):
'''
_special_value_maxLength - Handle the special "maxLength" property
@param em <AdvancedTag> - The tag element
@param newValue - Default NOT_PROVIDED, if provided will use that value instead of the
current .getAttribute value on the tag. This is because this method can be used for both validation
and getting/setting
'''
if newValue is NOT_PROVIDED:
if not em.hasAttribute('maxlength'):
return -1
curValue = em.getAttribute('maxlength', '-1')
# If we are accessing, the invalid default should be negative
invalidDefault = -1
else:
curValue = newValue
# If we are setting, we should raise an exception upon invalid value
invalidDefault = IndexSizeErrorException
return convertToIntRange(curValue, minValue=0, maxValue=None, emptyValue='0', invalidDefault=invalidDefault)
|
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|
[
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train
|
https://github.com/kata198/AdvancedHTMLParser/blob/06aeea5d8e2ea86e155aae0fc237623d3e9b7f9d/AdvancedHTMLParser/constants.py#L300-L327
|
StanfordBioinformatics/loom
|
server/loomengine_server/api/models/data_objects.py
|
DataObject.get_by_value
|
def get_by_value(cls, value, type):
""" Converts a value into a corresponding data object.
For files, this looks up a file DataObject by name, uuid, and/or md5.
For other types, it creates a new DataObject.
"""
if type == 'file':
return cls._get_file_by_value(value)
else:
data_object = DataObject(data={
'value': cls._type_cast(value, type)}, type=type)
data_object.full_clean()
data_object.save()
return data_object
|
python
|
def get_by_value(cls, value, type):
""" Converts a value into a corresponding data object.
For files, this looks up a file DataObject by name, uuid, and/or md5.
For other types, it creates a new DataObject.
"""
if type == 'file':
return cls._get_file_by_value(value)
else:
data_object = DataObject(data={
'value': cls._type_cast(value, type)}, type=type)
data_object.full_clean()
data_object.save()
return data_object
|
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train
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https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/server/loomengine_server/api/models/data_objects.py#L55-L67
|
StanfordBioinformatics/loom
|
server/loomengine_server/api/models/data_objects.py
|
DataObject._get_file_by_value
|
def _get_file_by_value(cls, value):
"""Look up a file DataObject by name, uuid, and/or md5.
"""
# Ignore any FileResource with no DataObject. This is a typical state
# for a deleted file that has not yet been cleaned up.
queryset = FileResource.objects.exclude(data_object__isnull=True)
matches = FileResource.filter_by_name_or_id_or_tag_or_hash(
value, queryset=queryset)
if matches.count() == 0:
raise ValidationError(
'No file found that matches value "%s"' % value)
elif matches.count() > 1:
match_id_list = ['%s@%s' % (match.filename, match.get_uuid())
for match in matches]
match_id_string = ('", "'.join(match_id_list))
raise ValidationError(
'Multiple files were found matching value "%s": "%s". '\
'Use a more precise identifier to select just one file.' % (
value, match_id_string))
return matches.first().data_object
|
python
|
def _get_file_by_value(cls, value):
"""Look up a file DataObject by name, uuid, and/or md5.
"""
# Ignore any FileResource with no DataObject. This is a typical state
# for a deleted file that has not yet been cleaned up.
queryset = FileResource.objects.exclude(data_object__isnull=True)
matches = FileResource.filter_by_name_or_id_or_tag_or_hash(
value, queryset=queryset)
if matches.count() == 0:
raise ValidationError(
'No file found that matches value "%s"' % value)
elif matches.count() > 1:
match_id_list = ['%s@%s' % (match.filename, match.get_uuid())
for match in matches]
match_id_string = ('", "'.join(match_id_list))
raise ValidationError(
'Multiple files were found matching value "%s": "%s". '\
'Use a more precise identifier to select just one file.' % (
value, match_id_string))
return matches.first().data_object
|
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/server/loomengine_server/api/models/data_objects.py#L87-L106
|
StanfordBioinformatics/loom
|
server/loomengine_server/api/models/data_objects.py
|
FileResource._get_run_breadcrumbs
|
def _get_run_breadcrumbs(cls, source_type, data_object, task_attempt):
"""Create a path for a given file, in such a way
that files end up being organized and browsable by run
"""
# We cannot generate the path unless connect to a TaskAttempt
# and a run
if not task_attempt:
return []
# If multiple tasks exist, use the original.
task = task_attempt.tasks.earliest('datetime_created')
if task is None:
return []
run = task.run
if run is None:
return []
breadcrumbs = [
run.name,
"task-%s" % str(task.uuid)[0:8],
"attempt-%s" % str(task_attempt.uuid)[0:8],
]
# Include any ancestors if run is nested
while run.parent is not None:
run = run.parent
breadcrumbs = [run.name] + breadcrumbs
# Prepend first breadcrumb with datetime and id
breadcrumbs[0] = "%s-%s-%s" % (
run.datetime_created.strftime('%Y-%m-%dT%H.%M.%SZ'),
str(run.uuid)[0:8],
breadcrumbs[0])
breadcrumbs = ['runs'] + breadcrumbs
return breadcrumbs
|
python
|
def _get_run_breadcrumbs(cls, source_type, data_object, task_attempt):
"""Create a path for a given file, in such a way
that files end up being organized and browsable by run
"""
# We cannot generate the path unless connect to a TaskAttempt
# and a run
if not task_attempt:
return []
# If multiple tasks exist, use the original.
task = task_attempt.tasks.earliest('datetime_created')
if task is None:
return []
run = task.run
if run is None:
return []
breadcrumbs = [
run.name,
"task-%s" % str(task.uuid)[0:8],
"attempt-%s" % str(task_attempt.uuid)[0:8],
]
# Include any ancestors if run is nested
while run.parent is not None:
run = run.parent
breadcrumbs = [run.name] + breadcrumbs
# Prepend first breadcrumb with datetime and id
breadcrumbs[0] = "%s-%s-%s" % (
run.datetime_created.strftime('%Y-%m-%dT%H.%M.%SZ'),
str(run.uuid)[0:8],
breadcrumbs[0])
breadcrumbs = ['runs'] + breadcrumbs
return breadcrumbs
|
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/server/loomengine_server/api/models/data_objects.py#L384-L418
|
StanfordBioinformatics/loom
|
server/loomengine_server/api/models/base.py
|
FilterHelper.filter_by_name_or_id_or_tag
|
def filter_by_name_or_id_or_tag(self, query_string, queryset = None):
"""Find objects that match the identifier of form {name}@{ID}, {name},
or @{ID}, where ID may be truncated
"""
assert self.Model.NAME_FIELD, \
'NAME_FIELD is missing on model %s' % self.Model.__name__
assert self.Model.ID_FIELD, \
'ID_FIELD is missing on model %s' % self.Model.__name__
assert self.Model.TAG_FIELD, \
'TAG_FIELD is missing on model %s' % self.Model.__name__
filter_args = {}
name, uuid, tag = self._parse_as_name_or_id_or_tag(query_string)
if name is not None:
filter_args[self.Model.NAME_FIELD] = name
if uuid is not None:
filter_args[self.Model.ID_FIELD+'__startswith'] = uuid
if tag is not None:
filter_args[self.Model.TAG_FIELD] = tag
if queryset is None:
queryset = self.Model.objects.all()
return queryset.filter(**filter_args)
|
python
|
def filter_by_name_or_id_or_tag(self, query_string, queryset = None):
"""Find objects that match the identifier of form {name}@{ID}, {name},
or @{ID}, where ID may be truncated
"""
assert self.Model.NAME_FIELD, \
'NAME_FIELD is missing on model %s' % self.Model.__name__
assert self.Model.ID_FIELD, \
'ID_FIELD is missing on model %s' % self.Model.__name__
assert self.Model.TAG_FIELD, \
'TAG_FIELD is missing on model %s' % self.Model.__name__
filter_args = {}
name, uuid, tag = self._parse_as_name_or_id_or_tag(query_string)
if name is not None:
filter_args[self.Model.NAME_FIELD] = name
if uuid is not None:
filter_args[self.Model.ID_FIELD+'__startswith'] = uuid
if tag is not None:
filter_args[self.Model.TAG_FIELD] = tag
if queryset is None:
queryset = self.Model.objects.all()
return queryset.filter(**filter_args)
|
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/server/loomengine_server/api/models/base.py#L126-L147
|
StanfordBioinformatics/loom
|
server/loomengine_server/api/models/base.py
|
BaseModel.save
|
def save(self, *args, **kwargs):
"""
This save method protects against two processesses concurrently modifying
the same object. Normally the second save would silently overwrite the
changes from the first. Instead we raise a ConcurrentModificationError.
"""
cls = self.__class__
if self.pk:
rows = cls.objects.filter(
pk=self.pk, _change=self._change).update(
_change=self._change + 1)
if not rows:
raise ConcurrentModificationError(cls.__name__, self.pk)
self._change += 1
count = 0
max_retries=3
while True:
try:
return super(BaseModel, self).save(*args, **kwargs)
except django.db.utils.OperationalError:
if count >= max_retries:
raise
count += 1
|
python
|
def save(self, *args, **kwargs):
"""
This save method protects against two processesses concurrently modifying
the same object. Normally the second save would silently overwrite the
changes from the first. Instead we raise a ConcurrentModificationError.
"""
cls = self.__class__
if self.pk:
rows = cls.objects.filter(
pk=self.pk, _change=self._change).update(
_change=self._change + 1)
if not rows:
raise ConcurrentModificationError(cls.__name__, self.pk)
self._change += 1
count = 0
max_retries=3
while True:
try:
return super(BaseModel, self).save(*args, **kwargs)
except django.db.utils.OperationalError:
if count >= max_retries:
raise
count += 1
|
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|
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/server/loomengine_server/api/models/base.py#L225-L248
|
StanfordBioinformatics/loom
|
server/loomengine_server/api/models/base.py
|
BaseModel.setattrs_and_save_with_retries
|
def setattrs_and_save_with_retries(self, assignments, max_retries=5):
"""
If the object is being edited by other processes,
save may fail due to concurrent modification.
This method recovers and retries the edit.
assignments is a dict of {attribute: value}
"""
count = 0
obj=self
while True:
for attribute, value in assignments.iteritems():
setattr(obj, attribute, value)
try:
obj.full_clean()
obj.save()
except ConcurrentModificationError:
if count >= max_retries:
raise SaveRetriesExceededError(
'Exceeded retries when saving "%s" of id "%s" '\
'with assigned values "%s"' %
(self.__class__, self.id, assignments))
count += 1
obj = self.__class__.objects.get(id=self.id)
continue
return obj
|
python
|
def setattrs_and_save_with_retries(self, assignments, max_retries=5):
"""
If the object is being edited by other processes,
save may fail due to concurrent modification.
This method recovers and retries the edit.
assignments is a dict of {attribute: value}
"""
count = 0
obj=self
while True:
for attribute, value in assignments.iteritems():
setattr(obj, attribute, value)
try:
obj.full_clean()
obj.save()
except ConcurrentModificationError:
if count >= max_retries:
raise SaveRetriesExceededError(
'Exceeded retries when saving "%s" of id "%s" '\
'with assigned values "%s"' %
(self.__class__, self.id, assignments))
count += 1
obj = self.__class__.objects.get(id=self.id)
continue
return obj
|
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/server/loomengine_server/api/models/base.py#L250-L275
|
StanfordBioinformatics/loom
|
server/loomengine_server/api/models/base.py
|
BaseModel.delete
|
def delete(self, *args, **kwargs):
"""
This method implements retries for object deletion.
"""
count = 0
max_retries=3
while True:
try:
return super(BaseModel, self).delete(*args, **kwargs)
except django.db.utils.OperationalError:
if count >= max_retries:
raise
count += 1
|
python
|
def delete(self, *args, **kwargs):
"""
This method implements retries for object deletion.
"""
count = 0
max_retries=3
while True:
try:
return super(BaseModel, self).delete(*args, **kwargs)
except django.db.utils.OperationalError:
if count >= max_retries:
raise
count += 1
|
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|
[
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/server/loomengine_server/api/models/base.py#L277-L289
|
StanfordBioinformatics/loom
|
client/loomengine/common.py
|
get_server_type
|
def get_server_type():
"""Checks server.ini for server type."""
server_location_file = os.path.expanduser(SERVER_LOCATION_FILE)
if not os.path.exists(server_location_file):
raise Exception(
"%s not found. Please run 'loom server set "
"<servertype>' first." % server_location_file)
config = ConfigParser.SafeConfigParser()
config.read(server_location_file)
server_type = config.get('server', 'type')
return server_type
|
python
|
def get_server_type():
"""Checks server.ini for server type."""
server_location_file = os.path.expanduser(SERVER_LOCATION_FILE)
if not os.path.exists(server_location_file):
raise Exception(
"%s not found. Please run 'loom server set "
"<servertype>' first." % server_location_file)
config = ConfigParser.SafeConfigParser()
config.read(server_location_file)
server_type = config.get('server', 'type')
return server_type
|
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Checks server.ini for server type.
|
[
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/client/loomengine/common.py#L110-L120
|
StanfordBioinformatics/loom
|
utils/loomengine_utils/import_manager.py
|
ImportManager._set_upload_status
|
def _set_upload_status(self, file_data_object, upload_status):
""" Set file_data_object.file_resource.upload_status
"""
uuid = file_data_object['uuid']
return self.connection.update_data_object(
uuid,
{'uuid': uuid, 'value': { 'upload_status': upload_status}}
)
|
python
|
def _set_upload_status(self, file_data_object, upload_status):
""" Set file_data_object.file_resource.upload_status
"""
uuid = file_data_object['uuid']
return self.connection.update_data_object(
uuid,
{'uuid': uuid, 'value': { 'upload_status': upload_status}}
)
|
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Set file_data_object.file_resource.upload_status
|
[
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/utils/loomengine_utils/import_manager.py#L406-L413
|
StanfordBioinformatics/loom
|
utils/loomengine_utils/import_manager.py
|
ImportManager._substitute_file_uuids_throughout_template
|
def _substitute_file_uuids_throughout_template(self, template, file_dependencies):
"""Anywhere in "template" that refers to a data object but does not
give a specific UUID, if a matching file can be found in "file_dependencies",
we will change the data object reference to use that UUID. That way templates
have a preference to connect to files nested under their ".dependencies" over
files that were previously imported to the server.
"""
if not isinstance(template, dict):
# Nothing to do if this is a reference to a previously imported template.
return
for input in template.get('inputs', []):
self._substitute_file_uuids_in_input(input, file_dependencies)
for step in template.get('steps', []):
self._substitute_file_uuids_throughout_template(step, file_dependencies)
|
python
|
def _substitute_file_uuids_throughout_template(self, template, file_dependencies):
"""Anywhere in "template" that refers to a data object but does not
give a specific UUID, if a matching file can be found in "file_dependencies",
we will change the data object reference to use that UUID. That way templates
have a preference to connect to files nested under their ".dependencies" over
files that were previously imported to the server.
"""
if not isinstance(template, dict):
# Nothing to do if this is a reference to a previously imported template.
return
for input in template.get('inputs', []):
self._substitute_file_uuids_in_input(input, file_dependencies)
for step in template.get('steps', []):
self._substitute_file_uuids_throughout_template(step, file_dependencies)
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https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/utils/loomengine_utils/import_manager.py#L614-L627
|
StanfordBioinformatics/loom
|
client/loomengine/run.py
|
RunStart._get_inputs
|
def _get_inputs(self):
"""Converts command line args into a list of template inputs
"""
# Convert file inputs to a dict, to make it easier to override
# them with commandline inputs
file_inputs = self._get_file_inputs()
try:
jsonschema.validate(file_inputs, file_input_schema)
except jsonschema.ValidationError:
raise SystemExit("ERROR! Input file was invalid")
input_dict = {}
for (channel, input_id) in file_inputs.iteritems():
input_dict[channel] = input_id
if self.args.inputs:
for kv_pair in self.args.inputs:
(channel, input_id) = kv_pair.split('=')
input_dict[channel] = self._parse_string_to_nested_lists(
input_id)
inputs = []
for (channel, contents) in input_dict.iteritems():
inputs.append({
'channel': channel,
'data': {
'contents': contents
}
})
return inputs
|
python
|
def _get_inputs(self):
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# Convert file inputs to a dict, to make it easier to override
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file_inputs = self._get_file_inputs()
try:
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input_dict = {}
for (channel, input_id) in file_inputs.iteritems():
input_dict[channel] = input_id
if self.args.inputs:
for kv_pair in self.args.inputs:
(channel, input_id) = kv_pair.split('=')
input_dict[channel] = self._parse_string_to_nested_lists(
input_id)
inputs = []
for (channel, contents) in input_dict.iteritems():
inputs.append({
'channel': channel,
'data': {
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})
return inputs
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/client/loomengine/run.py#L113-L141
|
StanfordBioinformatics/loom
|
client/loomengine/run.py
|
RunStart._parse_string_to_nested_lists
|
def _parse_string_to_nested_lists(self, value):
"""e.g., convert "[[a,b,c],[d,e],[f,g]]"
into [["a","b","c"],["d","e"],["f","g"]]
"""
if not re.match(r'\[.*\]', value.strip()):
if '[' in value or ']' in value or ',' in value:
raise Exception('Missing outer brace')
elif len(value.strip()) == 0:
raise Exception('Missing value')
else:
terms = value.split(',')
terms = [term.strip() for term in terms]
if len(terms) == 1:
return terms[0]
else:
return terms
# remove outer braces
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terms = []
depth = 0
leftmost = 0
first_open_brace = None
break_on_commas = False
for i in range(len(value)):
if value[i] == ',' and depth == 0:
terms.append(
self._parse_string_to_nested_lists(value[leftmost:i]))
leftmost = i+1
if value[i] == '[':
if first_open_brace is None:
first_open_brace = i
depth += 1
if value[i] == ']':
depth -= 1
if depth < 0:
raise Exception('Unbalanced close brace')
i += i
if depth > 0:
raise Exception('Expected "]"')
terms.append(
self._parse_string_to_nested_lists(value[leftmost:len(value)]))
return terms
|
python
|
def _parse_string_to_nested_lists(self, value):
"""e.g., convert "[[a,b,c],[d,e],[f,g]]"
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"""
if not re.match(r'\[.*\]', value.strip()):
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raise Exception('Missing value')
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terms = value.split(',')
terms = [term.strip() for term in terms]
if len(terms) == 1:
return terms[0]
else:
return terms
# remove outer braces
value = value[1:-1]
terms = []
depth = 0
leftmost = 0
first_open_brace = None
break_on_commas = False
for i in range(len(value)):
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terms.append(
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leftmost = i+1
if value[i] == '[':
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depth += 1
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terms.append(
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/client/loomengine/run.py#L179-L221
|
StanfordBioinformatics/loom
|
client/loomengine/run.py
|
RunRestart._get_inputs
|
def _get_inputs(self, old_inputs):
"""Converts command line args into a list of template inputs
"""
# Convert inputs to dict to facilitate overriding by channel name
# Also, drop DataNode ID and keep only contents.
input_dict = {}
for input in old_inputs:
# Strip out DataNode UUID and URL
input['data'] = {'contents': input['data']['contents']}
input_dict[input['channel']] = input
file_inputs = self._get_file_inputs()
try:
jsonschema.validate(file_inputs, file_input_schema)
except jsonschema.ValidationError:
raise SystemExit("ERROR! User inputs file is not valid")
for (channel, input_id) in file_inputs.iteritems():
input_dict[channel] = {
'channel': channel,
'data': {'contents': input_id}
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# Override with cli user inputs if specified
if self.args.inputs:
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(channel, input_id) = kv_pair.split('=')
input_dict[channel] = {
'channel': channel,
'data': {
'contents':
self._parse_string_to_nested_lists(input_id)}
}
return input_dict.values()
|
python
|
def _get_inputs(self, old_inputs):
"""Converts command line args into a list of template inputs
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# Convert inputs to dict to facilitate overriding by channel name
# Also, drop DataNode ID and keep only contents.
input_dict = {}
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input_dict[input['channel']] = input
file_inputs = self._get_file_inputs()
try:
jsonschema.validate(file_inputs, file_input_schema)
except jsonschema.ValidationError:
raise SystemExit("ERROR! User inputs file is not valid")
for (channel, input_id) in file_inputs.iteritems():
input_dict[channel] = {
'channel': channel,
'data': {'contents': input_id}
}
# Override with cli user inputs if specified
if self.args.inputs:
for kv_pair in self.args.inputs:
(channel, input_id) = kv_pair.split('=')
input_dict[channel] = {
'channel': channel,
'data': {
'contents':
self._parse_string_to_nested_lists(input_id)}
}
return input_dict.values()
|
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/client/loomengine/run.py#L285-L316
|
StanfordBioinformatics/loom
|
server/loomengine_server/api/serializers/__init__.py
|
CreateWithParentModelSerializer.create
|
def create(self, validated_data):
""" This is a standard method called indirectly by calling
'save' on the serializer.
This method expects the 'parent_field' and 'parent_instance' to
be included in the Serializer context.
"""
if self.context.get('parent_field') \
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validated_data.update({
self.context.get('parent_field'):
self.context.get('parent_instance')})
instance = self.Meta.model(**validated_data)
instance.full_clean()
instance.save()
return instance
|
python
|
def create(self, validated_data):
""" This is a standard method called indirectly by calling
'save' on the serializer.
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be included in the Serializer context.
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if self.context.get('parent_field') \
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instance.full_clean()
instance.save()
return instance
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/server/loomengine_server/api/serializers/__init__.py#L42-L57
|
StanfordBioinformatics/loom
|
utils/loomengine_utils/connection.py
|
disable_insecure_request_warning
|
def disable_insecure_request_warning():
"""Suppress warning about untrusted SSL certificate."""
import requests
from requests.packages.urllib3.exceptions import InsecureRequestWarning
requests.packages.urllib3.disable_warnings(InsecureRequestWarning)
|
python
|
def disable_insecure_request_warning():
"""Suppress warning about untrusted SSL certificate."""
import requests
from requests.packages.urllib3.exceptions import InsecureRequestWarning
requests.packages.urllib3.disable_warnings(InsecureRequestWarning)
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")"
] |
Suppress warning about untrusted SSL certificate.
|
[
"Suppress",
"warning",
"about",
"untrusted",
"SSL",
"certificate",
"."
] |
train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/utils/loomengine_utils/connection.py#L14-L18
|
StanfordBioinformatics/loom
|
utils/loomengine_utils/connection.py
|
Connection._make_request_to_server
|
def _make_request_to_server(self, query_function, raise_for_status=True,
time_limit_seconds=2, retry_delay_seconds=0.2):
"""Retry sending request until timeout or until receiving a response.
"""
start_time = datetime.datetime.now()
while datetime.datetime.now() - start_time < datetime.timedelta(
0, time_limit_seconds):
error = None
response = None
try:
response = query_function()
except requests.exceptions.ConnectionError as e:
error = ServerConnectionError(
"No response from server.\n%s" % e)
except:
if response:
logger.info(response.text)
raise
if response is not None and raise_for_status:
# raises requests.exceptions.HTTPError
self._raise_for_status(response)
if error:
time.sleep(retry_delay_seconds)
continue
else:
return response
raise error
|
python
|
def _make_request_to_server(self, query_function, raise_for_status=True,
time_limit_seconds=2, retry_delay_seconds=0.2):
"""Retry sending request until timeout or until receiving a response.
"""
start_time = datetime.datetime.now()
while datetime.datetime.now() - start_time < datetime.timedelta(
0, time_limit_seconds):
error = None
response = None
try:
response = query_function()
except requests.exceptions.ConnectionError as e:
error = ServerConnectionError(
"No response from server.\n%s" % e)
except:
if response:
logger.info(response.text)
raise
if response is not None and raise_for_status:
# raises requests.exceptions.HTTPError
self._raise_for_status(response)
if error:
time.sleep(retry_delay_seconds)
continue
else:
return response
raise error
|
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"(",
"retry_delay_seconds",
")",
"continue",
"else",
":",
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"raise",
"error"
] |
Retry sending request until timeout or until receiving a response.
|
[
"Retry",
"sending",
"request",
"until",
"timeout",
"or",
"until",
"receiving",
"a",
"response",
"."
] |
train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/utils/loomengine_utils/connection.py#L108-L134
|
StanfordBioinformatics/loom
|
utils/loomengine_utils/connection.py
|
Connection._get_resource
|
def _get_resource(self, relative_url, params=None):
"""Convenience function for retrieving a resource.
If resource does not exist, return None.
"""
response = self._get(relative_url, params=params, raise_for_status=False)
if response.status_code == 404:
return None
self._raise_for_status(response)
return response.json()
|
python
|
def _get_resource(self, relative_url, params=None):
"""Convenience function for retrieving a resource.
If resource does not exist, return None.
"""
response = self._get(relative_url, params=params, raise_for_status=False)
if response.status_code == 404:
return None
self._raise_for_status(response)
return response.json()
|
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Convenience function for retrieving a resource.
If resource does not exist, return None.
|
[
"Convenience",
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"for",
"retrieving",
"a",
"resource",
".",
"If",
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"does",
"not",
"exist",
"return",
"None",
"."
] |
train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/utils/loomengine_utils/connection.py#L172-L180
|
StanfordBioinformatics/loom
|
worker/loomengine_worker/inputs.py
|
TaskAttemptInput
|
def TaskAttemptInput(input, task_attempt):
"""Returns the correct Input class for a given
data type and gather mode
"""
(data_type, mode) = _get_input_info(input)
if data_type != 'file':
return NoOpInput(None, task_attempt)
if mode == 'no_gather':
return FileInput(input['data']['contents'], task_attempt)
else:
assert mode.startswith('gather')
return FileListInput(input['data']['contents'], task_attempt)
|
python
|
def TaskAttemptInput(input, task_attempt):
"""Returns the correct Input class for a given
data type and gather mode
"""
(data_type, mode) = _get_input_info(input)
if data_type != 'file':
return NoOpInput(None, task_attempt)
if mode == 'no_gather':
return FileInput(input['data']['contents'], task_attempt)
else:
assert mode.startswith('gather')
return FileListInput(input['data']['contents'], task_attempt)
|
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"FileListInput",
"(",
"input",
"[",
"'data'",
"]",
"[",
"'contents'",
"]",
",",
"task_attempt",
")"
] |
Returns the correct Input class for a given
data type and gather mode
|
[
"Returns",
"the",
"correct",
"Input",
"class",
"for",
"a",
"given",
"data",
"type",
"and",
"gather",
"mode"
] |
train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/worker/loomengine_worker/inputs.py#L83-L97
|
StanfordBioinformatics/loom
|
server/loomengine_server/api/async.py
|
execute
|
def execute(task_function, *args, **kwargs):
"""Run a task asynchronously
"""
if get_setting('TEST_DISABLE_ASYNC_DELAY'):
# Delay disabled, run synchronously
logger.debug('Running function "%s" synchronously because '\
'TEST_DISABLE_ASYNC_DELAY is True'
% task_function.__name__)
return task_function(*args, **kwargs)
db.connections.close_all()
task_function.delay(*args, **kwargs)
|
python
|
def execute(task_function, *args, **kwargs):
"""Run a task asynchronously
"""
if get_setting('TEST_DISABLE_ASYNC_DELAY'):
# Delay disabled, run synchronously
logger.debug('Running function "%s" synchronously because '\
'TEST_DISABLE_ASYNC_DELAY is True'
% task_function.__name__)
return task_function(*args, **kwargs)
db.connections.close_all()
task_function.delay(*args, **kwargs)
|
[
"def",
"execute",
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"task_function",
",",
"*",
"args",
",",
"*",
"*",
"kwargs",
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":",
"if",
"get_setting",
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"'TEST_DISABLE_ASYNC_DELAY'",
")",
":",
"# Delay disabled, run synchronously",
"logger",
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"debug",
"(",
"'Running function \"%s\" synchronously because '",
"'TEST_DISABLE_ASYNC_DELAY is True'",
"%",
"task_function",
".",
"__name__",
")",
"return",
"task_function",
"(",
"*",
"args",
",",
"*",
"*",
"kwargs",
")",
"db",
".",
"connections",
".",
"close_all",
"(",
")",
"task_function",
".",
"delay",
"(",
"*",
"args",
",",
"*",
"*",
"kwargs",
")"
] |
Run a task asynchronously
|
[
"Run",
"a",
"task",
"asynchronously"
] |
train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/server/loomengine_server/api/async.py#L24-L36
|
StanfordBioinformatics/loom
|
server/loomengine_server/api/async.py
|
execute_with_delay
|
def execute_with_delay(task_function, *args, **kwargs):
"""Run a task asynchronously after at least delay_seconds
"""
delay = kwargs.pop('delay', 0)
if get_setting('TEST_DISABLE_ASYNC_DELAY'):
# Delay disabled, run synchronously
logger.debug('Running function "%s" synchronously because '\
'TEST_DISABLE_ASYNC_DELAY is True'
% task_function.__name__)
return task_function(*args, **kwargs)
db.connections.close_all()
task_function.apply_async(args=args, kwargs=kwargs, countdown=delay)
|
python
|
def execute_with_delay(task_function, *args, **kwargs):
"""Run a task asynchronously after at least delay_seconds
"""
delay = kwargs.pop('delay', 0)
if get_setting('TEST_DISABLE_ASYNC_DELAY'):
# Delay disabled, run synchronously
logger.debug('Running function "%s" synchronously because '\
'TEST_DISABLE_ASYNC_DELAY is True'
% task_function.__name__)
return task_function(*args, **kwargs)
db.connections.close_all()
task_function.apply_async(args=args, kwargs=kwargs, countdown=delay)
|
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"logger",
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"'TEST_DISABLE_ASYNC_DELAY is True'",
"%",
"task_function",
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"__name__",
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"task_function",
"(",
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",",
"*",
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"connections",
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"(",
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"apply_async",
"(",
"args",
"=",
"args",
",",
"kwargs",
"=",
"kwargs",
",",
"countdown",
"=",
"delay",
")"
] |
Run a task asynchronously after at least delay_seconds
|
[
"Run",
"a",
"task",
"asynchronously",
"after",
"at",
"least",
"delay_seconds"
] |
train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/server/loomengine_server/api/async.py#L38-L50
|
StanfordBioinformatics/loom
|
server/loomengine_server/api/async.py
|
check_for_stalled_tasks
|
def check_for_stalled_tasks():
"""Check for tasks that are no longer sending a heartbeat
"""
from api.models.tasks import Task
for task in Task.objects.filter(status_is_running=True):
if not task.is_responsive():
task.system_error()
if task.is_timed_out():
task.timeout_error()
|
python
|
def check_for_stalled_tasks():
"""Check for tasks that are no longer sending a heartbeat
"""
from api.models.tasks import Task
for task in Task.objects.filter(status_is_running=True):
if not task.is_responsive():
task.system_error()
if task.is_timed_out():
task.timeout_error()
|
[
"def",
"check_for_stalled_tasks",
"(",
")",
":",
"from",
"api",
".",
"models",
".",
"tasks",
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"task",
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")",
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"if",
"task",
".",
"is_timed_out",
"(",
")",
":",
"task",
".",
"timeout_error",
"(",
")"
] |
Check for tasks that are no longer sending a heartbeat
|
[
"Check",
"for",
"tasks",
"that",
"are",
"no",
"longer",
"sending",
"a",
"heartbeat"
] |
train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/server/loomengine_server/api/async.py#L55-L63
|
StanfordBioinformatics/loom
|
server/loomengine_server/api/async.py
|
check_for_missed_cleanup
|
def check_for_missed_cleanup():
"""Check for TaskAttempts that were never cleaned up
"""
if get_setting('PRESERVE_ALL'):
return
from api.models.tasks import TaskAttempt
if get_setting('PRESERVE_ON_FAILURE'):
for task_attempt in TaskAttempt.objects.filter(
status_is_running=False).filter(
status_is_cleaned_up=False).exclude(
status_is_failed=True):
task_attempt.cleanup()
else:
for task_attempt in TaskAttempt.objects.filter(
status_is_running=False).filter(status_is_cleaned_up=False):
task_attempt.cleanup()
|
python
|
def check_for_missed_cleanup():
"""Check for TaskAttempts that were never cleaned up
"""
if get_setting('PRESERVE_ALL'):
return
from api.models.tasks import TaskAttempt
if get_setting('PRESERVE_ON_FAILURE'):
for task_attempt in TaskAttempt.objects.filter(
status_is_running=False).filter(
status_is_cleaned_up=False).exclude(
status_is_failed=True):
task_attempt.cleanup()
else:
for task_attempt in TaskAttempt.objects.filter(
status_is_running=False).filter(status_is_cleaned_up=False):
task_attempt.cleanup()
|
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Check for TaskAttempts that were never cleaned up
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[
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/server/loomengine_server/api/async.py#L66-L81
|
StanfordBioinformatics/loom
|
utils/loomengine_utils/__init__.py
|
execute_with_retries
|
def execute_with_retries(retryable_function,
retryable_errors,
logger,
human_readable_action_name='Action',
nonretryable_errors=None):
"""This attempts to execute "retryable_function" with exponential backoff
on delay time.
10 retries adds up to about 34 minutes total delay before the last attempt.
"human_readable_action_name" is an option input to customize retry message.
"""
max_retries = 10
attempt = 0
if not nonretryable_errors:
nonretryable_errors = ()
while True:
try:
return retryable_function()
except tuple(nonretryable_errors):
raise
except tuple(retryable_errors) as e:
attempt += 1
if attempt > max_retries:
raise
# Exponentional backoff on retry delay as suggested by
# https://cloud.google.com/storage/docs/exponential-backoff
delay = 2**attempt + random.random()
logger.info('"%s" failed with error "%s". '\
'Retry number %s of %s in %s seconds'
% (human_readable_action_name, str(e),
attempt, max_retries, delay))
time.sleep(delay)
|
python
|
def execute_with_retries(retryable_function,
retryable_errors,
logger,
human_readable_action_name='Action',
nonretryable_errors=None):
"""This attempts to execute "retryable_function" with exponential backoff
on delay time.
10 retries adds up to about 34 minutes total delay before the last attempt.
"human_readable_action_name" is an option input to customize retry message.
"""
max_retries = 10
attempt = 0
if not nonretryable_errors:
nonretryable_errors = ()
while True:
try:
return retryable_function()
except tuple(nonretryable_errors):
raise
except tuple(retryable_errors) as e:
attempt += 1
if attempt > max_retries:
raise
# Exponentional backoff on retry delay as suggested by
# https://cloud.google.com/storage/docs/exponential-backoff
delay = 2**attempt + random.random()
logger.info('"%s" failed with error "%s". '\
'Retry number %s of %s in %s seconds'
% (human_readable_action_name, str(e),
attempt, max_retries, delay))
time.sleep(delay)
|
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This attempts to execute "retryable_function" with exponential backoff
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10 retries adds up to about 34 minutes total delay before the last attempt.
"human_readable_action_name" is an option input to customize retry message.
|
[
"This",
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"retryable_function",
"with",
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"an",
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"input",
"to",
"customize",
"retry",
"message",
"."
] |
train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/utils/loomengine_utils/__init__.py#L18-L48
|
StanfordBioinformatics/loom
|
utils/loomengine_utils/export_manager.py
|
ExportManager.export_file
|
def export_file(self, data_object, destination_directory=None,
destination_filename=None, retry=False,
export_metadata=False, export_raw_file=True):
"""Export a file from Loom to some file storage location.
Default destination_directory is cwd. Default destination_filename is the
filename from the file data object associated with the given file_id.
"""
if not destination_directory:
destination_directory = os.getcwd()
# We get filename from the dataobject
if not destination_filename:
destination_filename = data_object['value']['filename']
destination_file_url = os.path.join(destination_directory,
destination_filename)
logger.info('Exporting file %s@%s ...' % (
data_object['value']['filename'],
data_object['uuid']))
if export_raw_file:
destination = File(
destination_file_url, self.storage_settings, retry=retry)
if destination.exists():
raise FileAlreadyExistsError(
'File already exists at %s' % destination_file_url)
logger.info('...copying file to %s' % (
destination.get_url()))
# Copy from the first file location
file_resource = data_object.get('value')
md5 = file_resource.get('md5')
source_url = data_object['value']['file_url']
File(source_url, self.storage_settings, retry=retry).copy_to(
destination, expected_md5=md5)
data_object['value'] = self._create_new_file_resource(
data_object['value'], destination.get_url())
else:
logger.info('...skipping raw file')
if export_metadata:
data_object['value'].pop('link', None)
data_object['value'].pop('upload_status', None)
destination_metadata_url = os.path.join(
destination_file_url + '.metadata.yaml')
logger.info('...writing metadata to %s' % destination_metadata_url)
metadata = yaml.safe_dump(data_object, default_flow_style=False)
metadata_file = File(destination_metadata_url,
self.storage_settings, retry=retry)
metadata_file.write(metadata)
else:
logger.info('...skipping metadata')
logger.info('...finished file export')
|
python
|
def export_file(self, data_object, destination_directory=None,
destination_filename=None, retry=False,
export_metadata=False, export_raw_file=True):
"""Export a file from Loom to some file storage location.
Default destination_directory is cwd. Default destination_filename is the
filename from the file data object associated with the given file_id.
"""
if not destination_directory:
destination_directory = os.getcwd()
# We get filename from the dataobject
if not destination_filename:
destination_filename = data_object['value']['filename']
destination_file_url = os.path.join(destination_directory,
destination_filename)
logger.info('Exporting file %s@%s ...' % (
data_object['value']['filename'],
data_object['uuid']))
if export_raw_file:
destination = File(
destination_file_url, self.storage_settings, retry=retry)
if destination.exists():
raise FileAlreadyExistsError(
'File already exists at %s' % destination_file_url)
logger.info('...copying file to %s' % (
destination.get_url()))
# Copy from the first file location
file_resource = data_object.get('value')
md5 = file_resource.get('md5')
source_url = data_object['value']['file_url']
File(source_url, self.storage_settings, retry=retry).copy_to(
destination, expected_md5=md5)
data_object['value'] = self._create_new_file_resource(
data_object['value'], destination.get_url())
else:
logger.info('...skipping raw file')
if export_metadata:
data_object['value'].pop('link', None)
data_object['value'].pop('upload_status', None)
destination_metadata_url = os.path.join(
destination_file_url + '.metadata.yaml')
logger.info('...writing metadata to %s' % destination_metadata_url)
metadata = yaml.safe_dump(data_object, default_flow_style=False)
metadata_file = File(destination_metadata_url,
self.storage_settings, retry=retry)
metadata_file.write(metadata)
else:
logger.info('...skipping metadata')
logger.info('...finished file export')
|
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Export a file from Loom to some file storage location.
Default destination_directory is cwd. Default destination_filename is the
filename from the file data object associated with the given file_id.
|
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/utils/loomengine_utils/export_manager.py#L47-L101
|
StanfordBioinformatics/loom
|
utils/loomengine_utils/file_utils.py
|
_urlparse
|
def _urlparse(path):
"""Like urlparse except it assumes 'file://' if no scheme is specified
"""
url = urlparse.urlparse(path)
_validate_url(url)
if not url.scheme or url.scheme == 'file://':
# Normalize path, and set scheme to "file" if missing
path = os.path.abspath(
os.path.expanduser(path))
url = urlparse.urlparse('file://'+path)
return url
|
python
|
def _urlparse(path):
"""Like urlparse except it assumes 'file://' if no scheme is specified
"""
url = urlparse.urlparse(path)
_validate_url(url)
if not url.scheme or url.scheme == 'file://':
# Normalize path, and set scheme to "file" if missing
path = os.path.abspath(
os.path.expanduser(path))
url = urlparse.urlparse('file://'+path)
return url
|
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Like urlparse except it assumes 'file://' if no scheme is specified
|
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"file",
":",
"//",
"if",
"no",
"scheme",
"is",
"specified"
] |
train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/utils/loomengine_utils/file_utils.py#L68-L78
|
StanfordBioinformatics/loom
|
utils/loomengine_utils/file_utils.py
|
FilePattern
|
def FilePattern(pattern, settings, **kwargs):
"""Factory method returns LocalFilePattern or GoogleStorageFilePattern
"""
url = _urlparse(pattern)
if url.scheme == 'gs':
return GoogleStorageFilePattern(pattern, settings, **kwargs)
else:
assert url.scheme == 'file'
return LocalFilePattern(pattern, settings, **kwargs)
|
python
|
def FilePattern(pattern, settings, **kwargs):
"""Factory method returns LocalFilePattern or GoogleStorageFilePattern
"""
url = _urlparse(pattern)
if url.scheme == 'gs':
return GoogleStorageFilePattern(pattern, settings, **kwargs)
else:
assert url.scheme == 'file'
return LocalFilePattern(pattern, settings, **kwargs)
|
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",",
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Factory method returns LocalFilePattern or GoogleStorageFilePattern
|
[
"Factory",
"method",
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"LocalFilePattern",
"or",
"GoogleStorageFilePattern"
] |
train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/utils/loomengine_utils/file_utils.py#L119-L127
|
StanfordBioinformatics/loom
|
utils/loomengine_utils/file_utils.py
|
File
|
def File(url, settings, retry=False):
"""Factory method
"""
parsed_url = _urlparse(url)
if parsed_url.scheme == 'gs':
return GoogleStorageFile(url, settings, retry=retry)
elif parsed_url.scheme == 'file':
if parsed_url.hostname == 'localhost' or parsed_url.hostname is None:
return LocalFile(url, settings, retry=retry)
else:
raise FileUtilsError(
"Cannot process file url %s. Remote file hosts not supported."
% url)
else:
raise FileUtilsError('Unsupported scheme "%s" in file "%s"'
% (parsed_url.scheme, url))
|
python
|
def File(url, settings, retry=False):
"""Factory method
"""
parsed_url = _urlparse(url)
if parsed_url.scheme == 'gs':
return GoogleStorageFile(url, settings, retry=retry)
elif parsed_url.scheme == 'file':
if parsed_url.hostname == 'localhost' or parsed_url.hostname is None:
return LocalFile(url, settings, retry=retry)
else:
raise FileUtilsError(
"Cannot process file url %s. Remote file hosts not supported."
% url)
else:
raise FileUtilsError('Unsupported scheme "%s" in file "%s"'
% (parsed_url.scheme, url))
|
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")",
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] |
Factory method
|
[
"Factory",
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] |
train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/utils/loomengine_utils/file_utils.py#L291-L307
|
StanfordBioinformatics/loom
|
utils/loomengine_utils/file_utils.py
|
Copier
|
def Copier(source, destination):
"""Factory method to select the right copier for a given source and destination.
"""
if source.type == 'local' and destination.type == 'local':
return LocalCopier(source, destination)
elif source.type == 'local' and destination.type == 'google_storage':
return Local2GoogleStorageCopier(source, destination)
elif source.type == 'google_storage' and destination.type == 'local':
return GoogleStorage2LocalCopier(source, destination)
elif source.type == 'google_storage' and destination.type == 'google_storage':
return GoogleStorageCopier(source, destination)
else:
raise FileUtilsError('Could not find method to copy from source '\
'"%s" to destination "%s".' % (source, destination))
|
python
|
def Copier(source, destination):
"""Factory method to select the right copier for a given source and destination.
"""
if source.type == 'local' and destination.type == 'local':
return LocalCopier(source, destination)
elif source.type == 'local' and destination.type == 'google_storage':
return Local2GoogleStorageCopier(source, destination)
elif source.type == 'google_storage' and destination.type == 'local':
return GoogleStorage2LocalCopier(source, destination)
elif source.type == 'google_storage' and destination.type == 'google_storage':
return GoogleStorageCopier(source, destination)
else:
raise FileUtilsError('Could not find method to copy from source '\
'"%s" to destination "%s".' % (source, destination))
|
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Factory method to select the right copier for a given source and destination.
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/utils/loomengine_utils/file_utils.py#L496-L510
|
StanfordBioinformatics/loom
|
server/loomengine_server/api/models/input_calculator.py
|
InputSetGeneratorNode.create_from_data_channel
|
def create_from_data_channel(cls, data_channel):
"""Scan the data tree on the given data_channel to create a corresponding
InputSetGenerator tree.
"""
gather_depth = cls._get_gather_depth(data_channel)
generator = InputSetGeneratorNode()
for (data_path, data_node) in data_channel.get_ready_data_nodes(
[], gather_depth):
flat_data_node = data_node.flattened_clone(save=False)
input_item = InputItem(
flat_data_node, data_channel.channel,
data_channel.as_channel, mode=data_channel.mode)
generator._add_input_item(data_path, input_item)
return generator
|
python
|
def create_from_data_channel(cls, data_channel):
"""Scan the data tree on the given data_channel to create a corresponding
InputSetGenerator tree.
"""
gather_depth = cls._get_gather_depth(data_channel)
generator = InputSetGeneratorNode()
for (data_path, data_node) in data_channel.get_ready_data_nodes(
[], gather_depth):
flat_data_node = data_node.flattened_clone(save=False)
input_item = InputItem(
flat_data_node, data_channel.channel,
data_channel.as_channel, mode=data_channel.mode)
generator._add_input_item(data_path, input_item)
return generator
|
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Scan the data tree on the given data_channel to create a corresponding
InputSetGenerator tree.
|
[
"Scan",
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"on",
"the",
"given",
"data_channel",
"to",
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] |
train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/server/loomengine_server/api/models/input_calculator.py#L119-L133
|
StanfordBioinformatics/loom
|
worker/loomengine_worker/outputs.py
|
TaskAttemptOutput
|
def TaskAttemptOutput(output, task_attempt):
"""Returns the correct Output class for a given
data type, source type, and scatter mode
"""
(data_type, mode, source_type) = _get_output_info(output)
if data_type == 'file':
if mode == 'scatter':
assert source_type in ['filenames', 'glob'], \
'source type "%s" not allowed' % source_type
if source_type == 'filenames':
return FileListScatterOutput(output, task_attempt)
return GlobScatterOutput(output, task_attempt)
else:
assert mode == 'no_scatter'
assert source_type == 'filename', \
'source type "%s" not allowed' % source_type
return FileOutput(output, task_attempt)
else: # data_type is non-file
if mode == 'scatter':
assert source_type in [
'filename', 'filenames', 'glob', 'stream'], \
'source type "%s" not allowed' % source_type
if source_type == 'filename':
return FileContentsScatterOutput(output, task_attempt)
if source_type == 'filenames':
return FileListContentsScatterOutput(output, task_attempt)
if source_type == 'glob':
return GlobContentsScatterOutput(output, task_attempt)
assert source_type == 'stream'
return StreamScatterOutput(output, task_attempt)
else:
assert mode == 'no_scatter'
assert source_type in ['filename', 'stream'], \
'source type "%s" not allowed' % source_type
if source_type == 'filename':
return FileContentsOutput(output, task_attempt)
assert source_type == 'stream'
return StreamOutput(output, task_attempt)
|
python
|
def TaskAttemptOutput(output, task_attempt):
"""Returns the correct Output class for a given
data type, source type, and scatter mode
"""
(data_type, mode, source_type) = _get_output_info(output)
if data_type == 'file':
if mode == 'scatter':
assert source_type in ['filenames', 'glob'], \
'source type "%s" not allowed' % source_type
if source_type == 'filenames':
return FileListScatterOutput(output, task_attempt)
return GlobScatterOutput(output, task_attempt)
else:
assert mode == 'no_scatter'
assert source_type == 'filename', \
'source type "%s" not allowed' % source_type
return FileOutput(output, task_attempt)
else: # data_type is non-file
if mode == 'scatter':
assert source_type in [
'filename', 'filenames', 'glob', 'stream'], \
'source type "%s" not allowed' % source_type
if source_type == 'filename':
return FileContentsScatterOutput(output, task_attempt)
if source_type == 'filenames':
return FileListContentsScatterOutput(output, task_attempt)
if source_type == 'glob':
return GlobContentsScatterOutput(output, task_attempt)
assert source_type == 'stream'
return StreamScatterOutput(output, task_attempt)
else:
assert mode == 'no_scatter'
assert source_type in ['filename', 'stream'], \
'source type "%s" not allowed' % source_type
if source_type == 'filename':
return FileContentsOutput(output, task_attempt)
assert source_type == 'stream'
return StreamOutput(output, task_attempt)
|
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Returns the correct Output class for a given
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|
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/worker/loomengine_worker/outputs.py#L181-L220
|
StanfordBioinformatics/loom
|
server/loomengine_server/api/models/data_nodes.py
|
DataNode.add_leaf
|
def add_leaf(self, index, data_object, save=False):
"""Adds a new leaf node at the given index with the given data_object
"""
assert self.type == data_object.type, 'data type mismatch'
if self._get_child_by_index(index) is not None:
raise NodeAlreadyExistsError(
'Leaf data node already exists at this index')
else:
data_node = DataNode(
parent=self,
index=index,
data_object=data_object,
type=self.type)
if save:
data_node.full_clean()
data_node.save()
self._add_unsaved_child(data_node)
return data_node
|
python
|
def add_leaf(self, index, data_object, save=False):
"""Adds a new leaf node at the given index with the given data_object
"""
assert self.type == data_object.type, 'data type mismatch'
if self._get_child_by_index(index) is not None:
raise NodeAlreadyExistsError(
'Leaf data node already exists at this index')
else:
data_node = DataNode(
parent=self,
index=index,
data_object=data_object,
type=self.type)
if save:
data_node.full_clean()
data_node.save()
self._add_unsaved_child(data_node)
return data_node
|
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/server/loomengine_server/api/models/data_nodes.py#L103-L120
|
StanfordBioinformatics/loom
|
server/loomengine_server/api/models/data_nodes.py
|
DataNode.get_ready_data_nodes
|
def get_ready_data_nodes(self, seed_path, gather_depth):
"""Returns a list [(path1,data_node1),...]
with entries only for existing nodes with DataObjects where is_ready==True.
Missing nodes or those with non-ready or non-existing data are ignored.
"""
try:
seed_node = self.get_node(seed_path)
except MissingBranchError:
return []
all_paths = seed_node._get_all_paths(seed_path, gather_depth)
ready_data_nodes = []
for path in all_paths:
if self.is_ready(data_path=path):
ready_data_nodes.append((path, self.get_node(path)))
return ready_data_nodes
|
python
|
def get_ready_data_nodes(self, seed_path, gather_depth):
"""Returns a list [(path1,data_node1),...]
with entries only for existing nodes with DataObjects where is_ready==True.
Missing nodes or those with non-ready or non-existing data are ignored.
"""
try:
seed_node = self.get_node(seed_path)
except MissingBranchError:
return []
all_paths = seed_node._get_all_paths(seed_path, gather_depth)
ready_data_nodes = []
for path in all_paths:
if self.is_ready(data_path=path):
ready_data_nodes.append((path, self.get_node(path)))
return ready_data_nodes
|
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/server/loomengine_server/api/models/data_nodes.py#L183-L197
|
StanfordBioinformatics/loom
|
server/loomengine_server/api/models/data_nodes.py
|
DataNode._check_index
|
def _check_index(self, index):
"""Verify that the given index is consistent with the degree of the node.
"""
if self.degree is None:
raise UnknownDegreeError(
'Cannot access child DataNode on a parent with degree of None. '\
'Set the degree on the parent first.')
if index < 0 or index >= self.degree:
raise IndexOutOfRangeError(
'Out of range index %s. DataNode parent has degree %s, so index '\
'should be in the range 0 to %s' % (
index, self.degree, self.degree-1))
|
python
|
def _check_index(self, index):
"""Verify that the given index is consistent with the degree of the node.
"""
if self.degree is None:
raise UnknownDegreeError(
'Cannot access child DataNode on a parent with degree of None. '\
'Set the degree on the parent first.')
if index < 0 or index >= self.degree:
raise IndexOutOfRangeError(
'Out of range index %s. DataNode parent has degree %s, so index '\
'should be in the range 0 to %s' % (
index, self.degree, self.degree-1))
|
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/server/loomengine_server/api/models/data_nodes.py#L328-L339
|
StanfordBioinformatics/loom
|
client/loomengine/playbooks/files/gcloud_utils.py
|
on_gcloud_vm
|
def on_gcloud_vm():
""" Determines if we're running on a GCE instance."""
r = None
try:
r = requests.get('http://metadata.google.internal')
except requests.ConnectionError:
return False
try:
if r.headers['Metadata-Flavor'] == 'Google' and \
r.headers['Server'] == 'Metadata Server for VM':
return True
except KeyError:
return False
|
python
|
def on_gcloud_vm():
""" Determines if we're running on a GCE instance."""
r = None
try:
r = requests.get('http://metadata.google.internal')
except requests.ConnectionError:
return False
try:
if r.headers['Metadata-Flavor'] == 'Google' and \
r.headers['Server'] == 'Metadata Server for VM':
return True
except KeyError:
return False
|
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/client/loomengine/playbooks/files/gcloud_utils.py#L11-L24
|
StanfordBioinformatics/loom
|
client/loomengine/playbooks/files/gcloud_utils.py
|
get_cheapest_instance_type
|
def get_cheapest_instance_type(cores, memory):
"""Determine the cheapest instance type given a minimum
number of cores and minimum amount of RAM (in GB).
"""
pricelist = get_gcloud_pricelist()
# Filter out preemptible, shared-CPU, and non-US instance types
us_instance_types = {k: v for k, v in pricelist.items()
if k.startswith('CP-COMPUTEENGINE-VMIMAGE-')
and not k.endswith('-PREEMPTIBLE')
and 'us' in v and v['cores'] != 'shared'}
# Convert to array and add keys (instance type names) as type names
price_array = []
for key in us_instance_types:
value = us_instance_types[key]
value.update({'name': key.replace(
'CP-COMPUTEENGINE-VMIMAGE-', '').lower()})
price_array.append(value)
# Sort by price in US
price_array.sort(None, lambda x: x['us'])
# Look for an instance type that satisfies requested
# cores and memory; first will be cheapest
for instance_type in price_array:
if int(instance_type['cores']) >= int(cores) \
and float(instance_type['memory']) >= float(memory):
print instance_type['name']
return instance_type['name']
# No instance type found that can fulfill requested cores and memory
raise Exception('No instance type found with at least %d cores '
'and %f GB of RAM.' % (cores, memory))
|
python
|
def get_cheapest_instance_type(cores, memory):
"""Determine the cheapest instance type given a minimum
number of cores and minimum amount of RAM (in GB).
"""
pricelist = get_gcloud_pricelist()
# Filter out preemptible, shared-CPU, and non-US instance types
us_instance_types = {k: v for k, v in pricelist.items()
if k.startswith('CP-COMPUTEENGINE-VMIMAGE-')
and not k.endswith('-PREEMPTIBLE')
and 'us' in v and v['cores'] != 'shared'}
# Convert to array and add keys (instance type names) as type names
price_array = []
for key in us_instance_types:
value = us_instance_types[key]
value.update({'name': key.replace(
'CP-COMPUTEENGINE-VMIMAGE-', '').lower()})
price_array.append(value)
# Sort by price in US
price_array.sort(None, lambda x: x['us'])
# Look for an instance type that satisfies requested
# cores and memory; first will be cheapest
for instance_type in price_array:
if int(instance_type['cores']) >= int(cores) \
and float(instance_type['memory']) >= float(memory):
print instance_type['name']
return instance_type['name']
# No instance type found that can fulfill requested cores and memory
raise Exception('No instance type found with at least %d cores '
'and %f GB of RAM.' % (cores, memory))
|
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/client/loomengine/playbooks/files/gcloud_utils.py#L27-L61
|
StanfordBioinformatics/loom
|
client/loomengine/playbooks/files/gcloud_utils.py
|
get_gcloud_pricelist
|
def get_gcloud_pricelist():
"""Retrieve latest pricelist from Google Cloud, or use
cached copy if not reachable.
"""
try:
r = requests.get('http://cloudpricingcalculator.appspot.com'
'/static/data/pricelist.json')
content = json.loads(r.content)
except ConnectionError:
logger.warning(
"Couldn't get updated pricelist from "
"http://cloudpricingcalculator.appspot.com"
"/static/data/pricelist.json. Falling back to cached "
"copy, but prices may be out of date.")
with open('gcloudpricelist.json') as infile:
content = json.load(infile)
pricelist = content['gcp_price_list']
return pricelist
|
python
|
def get_gcloud_pricelist():
"""Retrieve latest pricelist from Google Cloud, or use
cached copy if not reachable.
"""
try:
r = requests.get('http://cloudpricingcalculator.appspot.com'
'/static/data/pricelist.json')
content = json.loads(r.content)
except ConnectionError:
logger.warning(
"Couldn't get updated pricelist from "
"http://cloudpricingcalculator.appspot.com"
"/static/data/pricelist.json. Falling back to cached "
"copy, but prices may be out of date.")
with open('gcloudpricelist.json') as infile:
content = json.load(infile)
pricelist = content['gcp_price_list']
return pricelist
|
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/client/loomengine/playbooks/files/gcloud_utils.py#L64-L82
|
StanfordBioinformatics/loom
|
client/loomengine/playbooks/files/gcloud_utils.py
|
_get_base_name
|
def _get_base_name(hostname, step_name, attempt_id, max_length):
"""Create a base name for the worker instance that will run the specified
task run attempt, from this server. Since hostname and step name will be
duplicated across workers (reruns, etc.), ensure that at least
MIN_TASK_ID_CHARS are preserved in the instance name. Also, prevent names
from ending with dashes.
"""
max_length = int(max_length)
if len(hostname)+len(step_name)+MIN_TASK_ID_CHARS+2 > max_length:
# round with ceil/floor such that extra char goes to hostname if odd
hostname_chars = int(math.ceil(
(max_length-MIN_TASK_ID_CHARS-2)/float(2)))
step_name_chars = int(math.floor(
(max_length-MIN_TASK_ID_CHARS-2)/float(2)))
hostname = hostname[:hostname_chars]
step_name = step_name[:step_name_chars]
name_base = '-'.join([hostname, step_name, attempt_id])
return _sanitize_instance_name(name_base, max_length)
|
python
|
def _get_base_name(hostname, step_name, attempt_id, max_length):
"""Create a base name for the worker instance that will run the specified
task run attempt, from this server. Since hostname and step name will be
duplicated across workers (reruns, etc.), ensure that at least
MIN_TASK_ID_CHARS are preserved in the instance name. Also, prevent names
from ending with dashes.
"""
max_length = int(max_length)
if len(hostname)+len(step_name)+MIN_TASK_ID_CHARS+2 > max_length:
# round with ceil/floor such that extra char goes to hostname if odd
hostname_chars = int(math.ceil(
(max_length-MIN_TASK_ID_CHARS-2)/float(2)))
step_name_chars = int(math.floor(
(max_length-MIN_TASK_ID_CHARS-2)/float(2)))
hostname = hostname[:hostname_chars]
step_name = step_name[:step_name_chars]
name_base = '-'.join([hostname, step_name, attempt_id])
return _sanitize_instance_name(name_base, max_length)
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train
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https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/client/loomengine/playbooks/files/gcloud_utils.py#L88-L105
|
StanfordBioinformatics/loom
|
client/loomengine/playbooks/files/gcloud_utils.py
|
_sanitize_instance_name
|
def _sanitize_instance_name(name, max_length):
"""Instance names must start with a lowercase letter.
All following characters must be a dash, lowercase letter,
or digit.
"""
name = str(name).lower() # make all letters lowercase
name = re.sub(r'[^-a-z0-9]', '', name) # remove invalid characters
# remove non-lowercase letters from the beginning
name = re.sub(r'^[^a-z]+', '', name)
name = name[:max_length]
name = re.sub(r'-+$', '', name) # remove hyphens from the end
return name
|
python
|
def _sanitize_instance_name(name, max_length):
"""Instance names must start with a lowercase letter.
All following characters must be a dash, lowercase letter,
or digit.
"""
name = str(name).lower() # make all letters lowercase
name = re.sub(r'[^-a-z0-9]', '', name) # remove invalid characters
# remove non-lowercase letters from the beginning
name = re.sub(r'^[^a-z]+', '', name)
name = name[:max_length]
name = re.sub(r'-+$', '', name) # remove hyphens from the end
return name
|
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/client/loomengine/playbooks/files/gcloud_utils.py#L115-L126
|
StanfordBioinformatics/loom
|
client/loomengine/playbooks/gce.py
|
CloudInventoryCache.is_valid
|
def is_valid(self, max_age=None):
''' Determines if the cache files have expired, or if it is still valid '''
if max_age is None:
max_age = self.cache_max_age
if os.path.isfile(self.cache_path_cache):
mod_time = os.path.getmtime(self.cache_path_cache)
current_time = time()
if (mod_time + max_age) > current_time:
return True
return False
|
python
|
def is_valid(self, max_age=None):
''' Determines if the cache files have expired, or if it is still valid '''
if max_age is None:
max_age = self.cache_max_age
if os.path.isfile(self.cache_path_cache):
mod_time = os.path.getmtime(self.cache_path_cache)
current_time = time()
if (mod_time + max_age) > current_time:
return True
return False
|
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/client/loomengine/playbooks/gce.py#L123-L135
|
StanfordBioinformatics/loom
|
client/loomengine/playbooks/gce.py
|
CloudInventoryCache.get_all_data_from_cache
|
def get_all_data_from_cache(self, filename=''):
''' Reads the JSON inventory from the cache file. Returns Python dictionary. '''
data = ''
if not filename:
filename = self.cache_path_cache
with open(filename, 'r') as cache:
data = cache.read()
return json.loads(data)
|
python
|
def get_all_data_from_cache(self, filename=''):
''' Reads the JSON inventory from the cache file. Returns Python dictionary. '''
data = ''
if not filename:
filename = self.cache_path_cache
with open(filename, 'r') as cache:
data = cache.read()
return json.loads(data)
|
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/client/loomengine/playbooks/gce.py#L137-L145
|
StanfordBioinformatics/loom
|
client/loomengine/playbooks/gce.py
|
CloudInventoryCache.write_to_cache
|
def write_to_cache(self, data, filename=''):
''' Writes data to file as JSON. Returns True. '''
if not filename:
filename = self.cache_path_cache
json_data = json.dumps(data)
with open(filename, 'w') as cache:
cache.write(json_data)
return True
|
python
|
def write_to_cache(self, data, filename=''):
''' Writes data to file as JSON. Returns True. '''
if not filename:
filename = self.cache_path_cache
json_data = json.dumps(data)
with open(filename, 'w') as cache:
cache.write(json_data)
return True
|
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train
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https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/client/loomengine/playbooks/gce.py#L147-L154
|
StanfordBioinformatics/loom
|
client/loomengine/playbooks/gce.py
|
GceInventory.get_config
|
def get_config(self):
"""
Reads the settings from the gce.ini file.
Populates a SafeConfigParser object with defaults and
attempts to read an .ini-style configuration from the filename
specified in GCE_INI_PATH. If the environment variable is
not present, the filename defaults to gce.ini in the current
working directory.
"""
gce_ini_default_path = os.path.join(
os.path.dirname(os.path.realpath(__file__)), "gce.ini")
gce_ini_path = os.environ.get('GCE_INI_PATH', gce_ini_default_path)
# Create a ConfigParser.
# This provides empty defaults to each key, so that environment
# variable configuration (as opposed to INI configuration) is able
# to work.
config = ConfigParser.SafeConfigParser(defaults={
'gce_service_account_email_address': '',
'gce_service_account_pem_file_path': '',
'gce_project_id': '',
'libcloud_secrets': '',
'inventory_ip_type': '',
'cache_path': '~/.ansible/tmp',
'cache_max_age': '300'
})
if 'gce' not in config.sections():
config.add_section('gce')
if 'inventory' not in config.sections():
config.add_section('inventory')
if 'cache' not in config.sections():
config.add_section('cache')
config.read(gce_ini_path)
#########
# Section added for processing ini settings
#########
# Set the instance_states filter based on config file options
self.instance_states = []
if config.has_option('gce', 'instance_states'):
states = config.get('gce', 'instance_states')
# Ignore if instance_states is an empty string.
if states:
self.instance_states = states.split(',')
# Caching
cache_path = config.get('cache', 'cache_path')
cache_max_age = config.getint('cache', 'cache_max_age')
# TOOD(supertom): support project-specific caches
cache_name = 'ansible-gce.cache'
self.cache = CloudInventoryCache(cache_path=cache_path,
cache_max_age=cache_max_age,
cache_name=cache_name)
return config
|
python
|
def get_config(self):
"""
Reads the settings from the gce.ini file.
Populates a SafeConfigParser object with defaults and
attempts to read an .ini-style configuration from the filename
specified in GCE_INI_PATH. If the environment variable is
not present, the filename defaults to gce.ini in the current
working directory.
"""
gce_ini_default_path = os.path.join(
os.path.dirname(os.path.realpath(__file__)), "gce.ini")
gce_ini_path = os.environ.get('GCE_INI_PATH', gce_ini_default_path)
# Create a ConfigParser.
# This provides empty defaults to each key, so that environment
# variable configuration (as opposed to INI configuration) is able
# to work.
config = ConfigParser.SafeConfigParser(defaults={
'gce_service_account_email_address': '',
'gce_service_account_pem_file_path': '',
'gce_project_id': '',
'libcloud_secrets': '',
'inventory_ip_type': '',
'cache_path': '~/.ansible/tmp',
'cache_max_age': '300'
})
if 'gce' not in config.sections():
config.add_section('gce')
if 'inventory' not in config.sections():
config.add_section('inventory')
if 'cache' not in config.sections():
config.add_section('cache')
config.read(gce_ini_path)
#########
# Section added for processing ini settings
#########
# Set the instance_states filter based on config file options
self.instance_states = []
if config.has_option('gce', 'instance_states'):
states = config.get('gce', 'instance_states')
# Ignore if instance_states is an empty string.
if states:
self.instance_states = states.split(',')
# Caching
cache_path = config.get('cache', 'cache_path')
cache_max_age = config.getint('cache', 'cache_max_age')
# TOOD(supertom): support project-specific caches
cache_name = 'ansible-gce.cache'
self.cache = CloudInventoryCache(cache_path=cache_path,
cache_max_age=cache_max_age,
cache_name=cache_name)
return config
|
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/client/loomengine/playbooks/gce.py#L198-L254
|
StanfordBioinformatics/loom
|
client/loomengine/playbooks/gce.py
|
GceInventory.get_inventory_options
|
def get_inventory_options(self):
"""Determine inventory options. Environment variables always
take precedence over configuration files."""
ip_type = self.config.get('inventory', 'inventory_ip_type')
# If the appropriate environment variables are set, they override
# other configuration
ip_type = os.environ.get('INVENTORY_IP_TYPE', ip_type)
return ip_type
|
python
|
def get_inventory_options(self):
"""Determine inventory options. Environment variables always
take precedence over configuration files."""
ip_type = self.config.get('inventory', 'inventory_ip_type')
# If the appropriate environment variables are set, they override
# other configuration
ip_type = os.environ.get('INVENTORY_IP_TYPE', ip_type)
return ip_type
|
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Determine inventory options. Environment variables always
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|
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/client/loomengine/playbooks/gce.py#L256-L263
|
StanfordBioinformatics/loom
|
client/loomengine/playbooks/gce.py
|
GceInventory.get_gce_driver
|
def get_gce_driver(self):
"""Determine the GCE authorization settings and return a
libcloud driver.
"""
# Attempt to get GCE params from a configuration file, if one
# exists.
secrets_path = self.config.get('gce', 'libcloud_secrets')
secrets_found = False
try:
import secrets
args = list(getattr(secrets, 'GCE_PARAMS', []))
kwargs = getattr(secrets, 'GCE_KEYWORD_PARAMS', {})
secrets_found = True
except:
pass
if not secrets_found and secrets_path:
if not secrets_path.endswith('secrets.py'):
err = "Must specify libcloud secrets file as "
err += "/absolute/path/to/secrets.py"
sys.exit(err)
sys.path.append(os.path.dirname(secrets_path))
try:
import secrets
args = list(getattr(secrets, 'GCE_PARAMS', []))
kwargs = getattr(secrets, 'GCE_KEYWORD_PARAMS', {})
secrets_found = True
except:
pass
if not secrets_found:
args = [
self.config.get('gce','gce_service_account_email_address'),
self.config.get('gce','gce_service_account_pem_file_path')
]
kwargs = {'project': self.config.get('gce', 'gce_project_id')}
# If the appropriate environment variables are set, they override
# other configuration; process those into our args and kwargs.
args[0] = os.environ.get('GCE_EMAIL', args[0])
args[1] = os.environ.get('GCE_PEM_FILE_PATH', args[1])
kwargs['project'] = os.environ.get('GCE_PROJECT', kwargs['project'])
# Retrieve and return the GCE driver.
gce = get_driver(Provider.GCE)(*args, **kwargs)
gce.connection.user_agent_append(
'%s/%s' % (USER_AGENT_PRODUCT, USER_AGENT_VERSION),
)
return gce
|
python
|
def get_gce_driver(self):
"""Determine the GCE authorization settings and return a
libcloud driver.
"""
# Attempt to get GCE params from a configuration file, if one
# exists.
secrets_path = self.config.get('gce', 'libcloud_secrets')
secrets_found = False
try:
import secrets
args = list(getattr(secrets, 'GCE_PARAMS', []))
kwargs = getattr(secrets, 'GCE_KEYWORD_PARAMS', {})
secrets_found = True
except:
pass
if not secrets_found and secrets_path:
if not secrets_path.endswith('secrets.py'):
err = "Must specify libcloud secrets file as "
err += "/absolute/path/to/secrets.py"
sys.exit(err)
sys.path.append(os.path.dirname(secrets_path))
try:
import secrets
args = list(getattr(secrets, 'GCE_PARAMS', []))
kwargs = getattr(secrets, 'GCE_KEYWORD_PARAMS', {})
secrets_found = True
except:
pass
if not secrets_found:
args = [
self.config.get('gce','gce_service_account_email_address'),
self.config.get('gce','gce_service_account_pem_file_path')
]
kwargs = {'project': self.config.get('gce', 'gce_project_id')}
# If the appropriate environment variables are set, they override
# other configuration; process those into our args and kwargs.
args[0] = os.environ.get('GCE_EMAIL', args[0])
args[1] = os.environ.get('GCE_PEM_FILE_PATH', args[1])
kwargs['project'] = os.environ.get('GCE_PROJECT', kwargs['project'])
# Retrieve and return the GCE driver.
gce = get_driver(Provider.GCE)(*args, **kwargs)
gce.connection.user_agent_append(
'%s/%s' % (USER_AGENT_PRODUCT, USER_AGENT_VERSION),
)
return gce
|
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] |
train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/client/loomengine/playbooks/gce.py#L265-L312
|
StanfordBioinformatics/loom
|
client/loomengine/playbooks/gce.py
|
GceInventory.parse_env_zones
|
def parse_env_zones(self):
'''returns a list of comma separated zones parsed from the GCE_ZONE environment variable.
If provided, this will be used to filter the results of the grouped_instances call'''
import csv
reader = csv.reader([os.environ.get('GCE_ZONE',"")], skipinitialspace=True)
zones = [r for r in reader]
return [z for z in zones[0]]
|
python
|
def parse_env_zones(self):
'''returns a list of comma separated zones parsed from the GCE_ZONE environment variable.
If provided, this will be used to filter the results of the grouped_instances call'''
import csv
reader = csv.reader([os.environ.get('GCE_ZONE',"")], skipinitialspace=True)
zones = [r for r in reader]
return [z for z in zones[0]]
|
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returns a list of comma separated zones parsed from the GCE_ZONE environment variable.
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|
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/client/loomengine/playbooks/gce.py#L314-L320
|
StanfordBioinformatics/loom
|
client/loomengine/playbooks/gce.py
|
GceInventory.parse_cli_args
|
def parse_cli_args(self):
''' Command line argument processing '''
parser = argparse.ArgumentParser(
description='Produce an Ansible Inventory file based on GCE')
parser.add_argument('--list', action='store_true', default=True,
help='List instances (default: True)')
parser.add_argument('--host', action='store',
help='Get all information about an instance')
parser.add_argument('--pretty', action='store_true', default=False,
help='Pretty format (default: False)')
parser.add_argument(
'--refresh-cache', action='store_true', default=False,
help='Force refresh of cache by making API requests (default: False - use cache files)')
self.args = parser.parse_args()
|
python
|
def parse_cli_args(self):
''' Command line argument processing '''
parser = argparse.ArgumentParser(
description='Produce an Ansible Inventory file based on GCE')
parser.add_argument('--list', action='store_true', default=True,
help='List instances (default: True)')
parser.add_argument('--host', action='store',
help='Get all information about an instance')
parser.add_argument('--pretty', action='store_true', default=False,
help='Pretty format (default: False)')
parser.add_argument(
'--refresh-cache', action='store_true', default=False,
help='Force refresh of cache by making API requests (default: False - use cache files)')
self.args = parser.parse_args()
|
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Command line argument processing
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[
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/client/loomengine/playbooks/gce.py#L322-L336
|
StanfordBioinformatics/loom
|
client/loomengine/playbooks/gce.py
|
GceInventory.load_inventory_from_cache
|
def load_inventory_from_cache(self):
''' Loads inventory from JSON on disk. '''
try:
self.inventory = self.cache.get_all_data_from_cache()
hosts = self.inventory['_meta']['hostvars']
except Exception as e:
print(
"Invalid inventory file %s. Please rebuild with -refresh-cache option."
% (self.cache.cache_path_cache))
raise
|
python
|
def load_inventory_from_cache(self):
''' Loads inventory from JSON on disk. '''
try:
self.inventory = self.cache.get_all_data_from_cache()
hosts = self.inventory['_meta']['hostvars']
except Exception as e:
print(
"Invalid inventory file %s. Please rebuild with -refresh-cache option."
% (self.cache.cache_path_cache))
raise
|
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[
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/client/loomengine/playbooks/gce.py#L374-L384
|
StanfordBioinformatics/loom
|
client/loomengine/playbooks/gce.py
|
GceInventory.do_api_calls_update_cache
|
def do_api_calls_update_cache(self):
''' Do API calls and save data in cache. '''
zones = self.parse_env_zones()
data = self.group_instances(zones)
self.cache.write_to_cache(data)
self.inventory = data
|
python
|
def do_api_calls_update_cache(self):
''' Do API calls and save data in cache. '''
zones = self.parse_env_zones()
data = self.group_instances(zones)
self.cache.write_to_cache(data)
self.inventory = data
|
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/client/loomengine/playbooks/gce.py#L386-L391
|
StanfordBioinformatics/loom
|
client/loomengine/playbooks/gce.py
|
GceInventory.group_instances
|
def group_instances(self, zones=None):
'''Group all instances'''
groups = {}
meta = {}
meta["hostvars"] = {}
for node in self.list_nodes():
# This check filters on the desired instance states defined in the
# config file with the instance_states config option.
#
# If the instance_states list is _empty_ then _ALL_ states are returned.
#
# If the instance_states list is _populated_ then check the current
# state against the instance_states list
if self.instance_states and not node.extra['status'] in self.instance_states:
continue
name = node.name
meta["hostvars"][name] = self.node_to_dict(node)
zone = node.extra['zone'].name
# To avoid making multiple requests per zone
# we list all nodes and then filter the results
if zones and zone not in zones:
continue
if zone in groups: groups[zone].append(name)
else: groups[zone] = [name]
tags = node.extra['tags']
for t in tags:
if t.startswith('group-'):
tag = t[6:]
else:
tag = 'tag_%s' % t
if tag in groups: groups[tag].append(name)
else: groups[tag] = [name]
net = node.extra['networkInterfaces'][0]['network'].split('/')[-1]
net = 'network_%s' % net
if net in groups: groups[net].append(name)
else: groups[net] = [name]
machine_type = node.size
if machine_type in groups: groups[machine_type].append(name)
else: groups[machine_type] = [name]
image = node.image and node.image or 'persistent_disk'
if image in groups: groups[image].append(name)
else: groups[image] = [name]
status = node.extra['status']
stat = 'status_%s' % status.lower()
if stat in groups: groups[stat].append(name)
else: groups[stat] = [name]
groups["_meta"] = meta
return groups
|
python
|
def group_instances(self, zones=None):
'''Group all instances'''
groups = {}
meta = {}
meta["hostvars"] = {}
for node in self.list_nodes():
# This check filters on the desired instance states defined in the
# config file with the instance_states config option.
#
# If the instance_states list is _empty_ then _ALL_ states are returned.
#
# If the instance_states list is _populated_ then check the current
# state against the instance_states list
if self.instance_states and not node.extra['status'] in self.instance_states:
continue
name = node.name
meta["hostvars"][name] = self.node_to_dict(node)
zone = node.extra['zone'].name
# To avoid making multiple requests per zone
# we list all nodes and then filter the results
if zones and zone not in zones:
continue
if zone in groups: groups[zone].append(name)
else: groups[zone] = [name]
tags = node.extra['tags']
for t in tags:
if t.startswith('group-'):
tag = t[6:]
else:
tag = 'tag_%s' % t
if tag in groups: groups[tag].append(name)
else: groups[tag] = [name]
net = node.extra['networkInterfaces'][0]['network'].split('/')[-1]
net = 'network_%s' % net
if net in groups: groups[net].append(name)
else: groups[net] = [name]
machine_type = node.size
if machine_type in groups: groups[machine_type].append(name)
else: groups[machine_type] = [name]
image = node.image and node.image or 'persistent_disk'
if image in groups: groups[image].append(name)
else: groups[image] = [name]
status = node.extra['status']
stat = 'status_%s' % status.lower()
if stat in groups: groups[stat].append(name)
else: groups[stat] = [name]
groups["_meta"] = meta
return groups
|
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"return",
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] |
Group all instances
|
[
"Group",
"all",
"instances"
] |
train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/client/loomengine/playbooks/gce.py#L402-L463
|
StanfordBioinformatics/loom
|
client/loomengine/playbooks/gce.py
|
GceInventory.json_format_dict
|
def json_format_dict(self, data, pretty=False):
''' Converts a dict to a JSON object and dumps it as a formatted
string '''
if pretty:
return json.dumps(data, sort_keys=True, indent=2)
else:
return json.dumps(data)
|
python
|
def json_format_dict(self, data, pretty=False):
''' Converts a dict to a JSON object and dumps it as a formatted
string '''
if pretty:
return json.dumps(data, sort_keys=True, indent=2)
else:
return json.dumps(data)
|
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Converts a dict to a JSON object and dumps it as a formatted
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|
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/client/loomengine/playbooks/gce.py#L465-L472
|
StanfordBioinformatics/loom
|
worker/loomengine_worker/task_monitor.py
|
TaskMonitor._stream_docker_logs
|
def _stream_docker_logs(self):
"""Stream stdout and stderr from the task container to this
process's stdout and stderr, respectively.
"""
thread = threading.Thread(target=self._stderr_stream_worker)
thread.start()
for line in self.docker_client.logs(self.container, stdout=True,
stderr=False, stream=True):
sys.stdout.write(line)
thread.join()
|
python
|
def _stream_docker_logs(self):
"""Stream stdout and stderr from the task container to this
process's stdout and stderr, respectively.
"""
thread = threading.Thread(target=self._stderr_stream_worker)
thread.start()
for line in self.docker_client.logs(self.container, stdout=True,
stderr=False, stream=True):
sys.stdout.write(line)
thread.join()
|
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Stream stdout and stderr from the task container to this
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[
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train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/worker/loomengine_worker/task_monitor.py#L286-L295
|
StanfordBioinformatics/loom
|
server/loomengine_server/api/serializers/templates.py
|
TemplateSerializer.to_internal_value
|
def to_internal_value(self, data):
"""Because we allow template ID string values, where
serializers normally expect a dict
"""
converted_data = _convert_template_id_to_dict(data)
return super(TemplateSerializer, self)\
.to_internal_value(converted_data)
|
python
|
def to_internal_value(self, data):
"""Because we allow template ID string values, where
serializers normally expect a dict
"""
converted_data = _convert_template_id_to_dict(data)
return super(TemplateSerializer, self)\
.to_internal_value(converted_data)
|
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Because we allow template ID string values, where
serializers normally expect a dict
|
[
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"where",
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"normally",
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] |
train
|
https://github.com/StanfordBioinformatics/loom/blob/db2031a1a87124fee1aeb7414a668c03d774a698/server/loomengine_server/api/serializers/templates.py#L105-L111
|
rbarrois/python-semanticversion
|
semantic_version/base.py
|
identifier_cmp
|
def identifier_cmp(a, b):
"""Compare two identifier (for pre-release/build components)."""
a_cmp, a_is_int = _to_int(a)
b_cmp, b_is_int = _to_int(b)
if a_is_int and b_is_int:
# Numeric identifiers are compared as integers
return base_cmp(a_cmp, b_cmp)
elif a_is_int:
# Numeric identifiers have lower precedence
return -1
elif b_is_int:
return 1
else:
# Non-numeric identifiers are compared lexicographically
return base_cmp(a_cmp, b_cmp)
|
python
|
def identifier_cmp(a, b):
"""Compare two identifier (for pre-release/build components)."""
a_cmp, a_is_int = _to_int(a)
b_cmp, b_is_int = _to_int(b)
if a_is_int and b_is_int:
# Numeric identifiers are compared as integers
return base_cmp(a_cmp, b_cmp)
elif a_is_int:
# Numeric identifiers have lower precedence
return -1
elif b_is_int:
return 1
else:
# Non-numeric identifiers are compared lexicographically
return base_cmp(a_cmp, b_cmp)
|
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Compare two identifier (for pre-release/build components).
|
[
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"identifier",
"(",
"for",
"pre",
"-",
"release",
"/",
"build",
"components",
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"."
] |
train
|
https://github.com/rbarrois/python-semanticversion/blob/fdef1e9cdae901d095d8e8c9cd6fa6adcfe02074/semantic_version/base.py#L28-L44
|
rbarrois/python-semanticversion
|
semantic_version/base.py
|
identifier_list_cmp
|
def identifier_list_cmp(a, b):
"""Compare two identifier list (pre-release/build components).
The rule is:
- Identifiers are paired between lists
- They are compared from left to right
- If all first identifiers match, the longest list is greater.
>>> identifier_list_cmp(['1', '2'], ['1', '2'])
0
>>> identifier_list_cmp(['1', '2a'], ['1', '2b'])
-1
>>> identifier_list_cmp(['1'], ['1', '2'])
-1
"""
identifier_pairs = zip(a, b)
for id_a, id_b in identifier_pairs:
cmp_res = identifier_cmp(id_a, id_b)
if cmp_res != 0:
return cmp_res
# alpha1.3 < alpha1.3.1
return base_cmp(len(a), len(b))
|
python
|
def identifier_list_cmp(a, b):
"""Compare two identifier list (pre-release/build components).
The rule is:
- Identifiers are paired between lists
- They are compared from left to right
- If all first identifiers match, the longest list is greater.
>>> identifier_list_cmp(['1', '2'], ['1', '2'])
0
>>> identifier_list_cmp(['1', '2a'], ['1', '2b'])
-1
>>> identifier_list_cmp(['1'], ['1', '2'])
-1
"""
identifier_pairs = zip(a, b)
for id_a, id_b in identifier_pairs:
cmp_res = identifier_cmp(id_a, id_b)
if cmp_res != 0:
return cmp_res
# alpha1.3 < alpha1.3.1
return base_cmp(len(a), len(b))
|
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Compare two identifier list (pre-release/build components).
The rule is:
- Identifiers are paired between lists
- They are compared from left to right
- If all first identifiers match, the longest list is greater.
>>> identifier_list_cmp(['1', '2'], ['1', '2'])
0
>>> identifier_list_cmp(['1', '2a'], ['1', '2b'])
-1
>>> identifier_list_cmp(['1'], ['1', '2'])
-1
|
[
"Compare",
"two",
"identifier",
"list",
"(",
"pre",
"-",
"release",
"/",
"build",
"components",
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"."
] |
train
|
https://github.com/rbarrois/python-semanticversion/blob/fdef1e9cdae901d095d8e8c9cd6fa6adcfe02074/semantic_version/base.py#L47-L68
|
rbarrois/python-semanticversion
|
semantic_version/base.py
|
Version.coerce
|
def coerce(cls, version_string, partial=False):
"""Coerce an arbitrary version string into a semver-compatible one.
The rule is:
- If not enough components, fill minor/patch with zeroes; unless
partial=True
- If more than 3 dot-separated components, extra components are "build"
data. If some "build" data already appeared, append it to the
extra components
Examples:
>>> Version.coerce('0.1')
Version(0, 1, 0)
>>> Version.coerce('0.1.2.3')
Version(0, 1, 2, (), ('3',))
>>> Version.coerce('0.1.2.3+4')
Version(0, 1, 2, (), ('3', '4'))
>>> Version.coerce('0.1+2-3+4_5')
Version(0, 1, 0, (), ('2-3', '4-5'))
"""
base_re = re.compile(r'^\d+(?:\.\d+(?:\.\d+)?)?')
match = base_re.match(version_string)
if not match:
raise ValueError(
"Version string lacks a numerical component: %r"
% version_string
)
version = version_string[:match.end()]
if not partial:
# We need a not-partial version.
while version.count('.') < 2:
version += '.0'
if match.end() == len(version_string):
return Version(version, partial=partial)
rest = version_string[match.end():]
# Cleanup the 'rest'
rest = re.sub(r'[^a-zA-Z0-9+.-]', '-', rest)
if rest[0] == '+':
# A 'build' component
prerelease = ''
build = rest[1:]
elif rest[0] == '.':
# An extra version component, probably 'build'
prerelease = ''
build = rest[1:]
elif rest[0] == '-':
rest = rest[1:]
if '+' in rest:
prerelease, build = rest.split('+', 1)
else:
prerelease, build = rest, ''
elif '+' in rest:
prerelease, build = rest.split('+', 1)
else:
prerelease, build = rest, ''
build = build.replace('+', '.')
if prerelease:
version = '%s-%s' % (version, prerelease)
if build:
version = '%s+%s' % (version, build)
return cls(version, partial=partial)
|
python
|
def coerce(cls, version_string, partial=False):
"""Coerce an arbitrary version string into a semver-compatible one.
The rule is:
- If not enough components, fill minor/patch with zeroes; unless
partial=True
- If more than 3 dot-separated components, extra components are "build"
data. If some "build" data already appeared, append it to the
extra components
Examples:
>>> Version.coerce('0.1')
Version(0, 1, 0)
>>> Version.coerce('0.1.2.3')
Version(0, 1, 2, (), ('3',))
>>> Version.coerce('0.1.2.3+4')
Version(0, 1, 2, (), ('3', '4'))
>>> Version.coerce('0.1+2-3+4_5')
Version(0, 1, 0, (), ('2-3', '4-5'))
"""
base_re = re.compile(r'^\d+(?:\.\d+(?:\.\d+)?)?')
match = base_re.match(version_string)
if not match:
raise ValueError(
"Version string lacks a numerical component: %r"
% version_string
)
version = version_string[:match.end()]
if not partial:
# We need a not-partial version.
while version.count('.') < 2:
version += '.0'
if match.end() == len(version_string):
return Version(version, partial=partial)
rest = version_string[match.end():]
# Cleanup the 'rest'
rest = re.sub(r'[^a-zA-Z0-9+.-]', '-', rest)
if rest[0] == '+':
# A 'build' component
prerelease = ''
build = rest[1:]
elif rest[0] == '.':
# An extra version component, probably 'build'
prerelease = ''
build = rest[1:]
elif rest[0] == '-':
rest = rest[1:]
if '+' in rest:
prerelease, build = rest.split('+', 1)
else:
prerelease, build = rest, ''
elif '+' in rest:
prerelease, build = rest.split('+', 1)
else:
prerelease, build = rest, ''
build = build.replace('+', '.')
if prerelease:
version = '%s-%s' % (version, prerelease)
if build:
version = '%s+%s' % (version, build)
return cls(version, partial=partial)
|
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Coerce an arbitrary version string into a semver-compatible one.
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partial=True
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data. If some "build" data already appeared, append it to the
extra components
Examples:
>>> Version.coerce('0.1')
Version(0, 1, 0)
>>> Version.coerce('0.1.2.3')
Version(0, 1, 2, (), ('3',))
>>> Version.coerce('0.1.2.3+4')
Version(0, 1, 2, (), ('3', '4'))
>>> Version.coerce('0.1+2-3+4_5')
Version(0, 1, 0, (), ('2-3', '4-5'))
|
[
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"-",
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"one",
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] |
train
|
https://github.com/rbarrois/python-semanticversion/blob/fdef1e9cdae901d095d8e8c9cd6fa6adcfe02074/semantic_version/base.py#L114-L183
|
rbarrois/python-semanticversion
|
semantic_version/base.py
|
Version.parse
|
def parse(cls, version_string, partial=False, coerce=False):
"""Parse a version string into a Version() object.
Args:
version_string (str), the version string to parse
partial (bool), whether to accept incomplete input
coerce (bool), whether to try to map the passed in string into a
valid Version.
"""
if not version_string:
raise ValueError('Invalid empty version string: %r' % version_string)
if partial:
version_re = cls.partial_version_re
else:
version_re = cls.version_re
match = version_re.match(version_string)
if not match:
raise ValueError('Invalid version string: %r' % version_string)
major, minor, patch, prerelease, build = match.groups()
if _has_leading_zero(major):
raise ValueError("Invalid leading zero in major: %r" % version_string)
if _has_leading_zero(minor):
raise ValueError("Invalid leading zero in minor: %r" % version_string)
if _has_leading_zero(patch):
raise ValueError("Invalid leading zero in patch: %r" % version_string)
major = int(major)
minor = cls._coerce(minor, partial)
patch = cls._coerce(patch, partial)
if prerelease is None:
if partial and (build is None):
# No build info, strip here
return (major, minor, patch, None, None)
else:
prerelease = ()
elif prerelease == '':
prerelease = ()
else:
prerelease = tuple(prerelease.split('.'))
cls._validate_identifiers(prerelease, allow_leading_zeroes=False)
if build is None:
if partial:
build = None
else:
build = ()
elif build == '':
build = ()
else:
build = tuple(build.split('.'))
cls._validate_identifiers(build, allow_leading_zeroes=True)
return (major, minor, patch, prerelease, build)
|
python
|
def parse(cls, version_string, partial=False, coerce=False):
"""Parse a version string into a Version() object.
Args:
version_string (str), the version string to parse
partial (bool), whether to accept incomplete input
coerce (bool), whether to try to map the passed in string into a
valid Version.
"""
if not version_string:
raise ValueError('Invalid empty version string: %r' % version_string)
if partial:
version_re = cls.partial_version_re
else:
version_re = cls.version_re
match = version_re.match(version_string)
if not match:
raise ValueError('Invalid version string: %r' % version_string)
major, minor, patch, prerelease, build = match.groups()
if _has_leading_zero(major):
raise ValueError("Invalid leading zero in major: %r" % version_string)
if _has_leading_zero(minor):
raise ValueError("Invalid leading zero in minor: %r" % version_string)
if _has_leading_zero(patch):
raise ValueError("Invalid leading zero in patch: %r" % version_string)
major = int(major)
minor = cls._coerce(minor, partial)
patch = cls._coerce(patch, partial)
if prerelease is None:
if partial and (build is None):
# No build info, strip here
return (major, minor, patch, None, None)
else:
prerelease = ()
elif prerelease == '':
prerelease = ()
else:
prerelease = tuple(prerelease.split('.'))
cls._validate_identifiers(prerelease, allow_leading_zeroes=False)
if build is None:
if partial:
build = None
else:
build = ()
elif build == '':
build = ()
else:
build = tuple(build.split('.'))
cls._validate_identifiers(build, allow_leading_zeroes=True)
return (major, minor, patch, prerelease, build)
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train
|
https://github.com/rbarrois/python-semanticversion/blob/fdef1e9cdae901d095d8e8c9cd6fa6adcfe02074/semantic_version/base.py#L186-L243
|
rbarrois/python-semanticversion
|
semantic_version/base.py
|
Version._comparison_functions
|
def _comparison_functions(cls, partial=False):
"""Retrieve comparison methods to apply on version components.
This is a private API.
Args:
partial (bool): whether to provide 'partial' or 'strict' matching.
Returns:
5-tuple of cmp-like functions.
"""
def prerelease_cmp(a, b):
"""Compare prerelease components.
Special rule: a version without prerelease component has higher
precedence than one with a prerelease component.
"""
if a and b:
return identifier_list_cmp(a, b)
elif a:
# Versions with prerelease field have lower precedence
return -1
elif b:
return 1
else:
return 0
def build_cmp(a, b):
"""Compare build metadata.
Special rule: there is no ordering on build metadata.
"""
if a == b:
return 0
else:
return NotImplemented
def make_optional(orig_cmp_fun):
"""Convert a cmp-like function to consider 'None == *'."""
@functools.wraps(orig_cmp_fun)
def alt_cmp_fun(a, b):
if a is None or b is None:
return 0
return orig_cmp_fun(a, b)
return alt_cmp_fun
if partial:
return [
base_cmp, # Major is still mandatory
make_optional(base_cmp),
make_optional(base_cmp),
make_optional(prerelease_cmp),
make_optional(build_cmp),
]
else:
return [
base_cmp,
base_cmp,
base_cmp,
prerelease_cmp,
build_cmp,
]
|
python
|
def _comparison_functions(cls, partial=False):
"""Retrieve comparison methods to apply on version components.
This is a private API.
Args:
partial (bool): whether to provide 'partial' or 'strict' matching.
Returns:
5-tuple of cmp-like functions.
"""
def prerelease_cmp(a, b):
"""Compare prerelease components.
Special rule: a version without prerelease component has higher
precedence than one with a prerelease component.
"""
if a and b:
return identifier_list_cmp(a, b)
elif a:
# Versions with prerelease field have lower precedence
return -1
elif b:
return 1
else:
return 0
def build_cmp(a, b):
"""Compare build metadata.
Special rule: there is no ordering on build metadata.
"""
if a == b:
return 0
else:
return NotImplemented
def make_optional(orig_cmp_fun):
"""Convert a cmp-like function to consider 'None == *'."""
@functools.wraps(orig_cmp_fun)
def alt_cmp_fun(a, b):
if a is None or b is None:
return 0
return orig_cmp_fun(a, b)
return alt_cmp_fun
if partial:
return [
base_cmp, # Major is still mandatory
make_optional(base_cmp),
make_optional(base_cmp),
make_optional(prerelease_cmp),
make_optional(build_cmp),
]
else:
return [
base_cmp,
base_cmp,
base_cmp,
prerelease_cmp,
build_cmp,
]
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|
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] |
train
|
https://github.com/rbarrois/python-semanticversion/blob/fdef1e9cdae901d095d8e8c9cd6fa6adcfe02074/semantic_version/base.py#L281-L344
|
rbarrois/python-semanticversion
|
semantic_version/base.py
|
Version.__compare_helper
|
def __compare_helper(self, other, condition, notimpl_target):
"""Helper for comparison.
Allows the caller to provide:
- The condition
- The return value if the comparison is meaningless (ie versions with
build metadata).
"""
if not isinstance(other, self.__class__):
return NotImplemented
cmp_res = self.__cmp__(other)
if cmp_res is NotImplemented:
return notimpl_target
return condition(cmp_res)
|
python
|
def __compare_helper(self, other, condition, notimpl_target):
"""Helper for comparison.
Allows the caller to provide:
- The condition
- The return value if the comparison is meaningless (ie versions with
build metadata).
"""
if not isinstance(other, self.__class__):
return NotImplemented
cmp_res = self.__cmp__(other)
if cmp_res is NotImplemented:
return notimpl_target
return condition(cmp_res)
|
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Helper for comparison.
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[
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train
|
https://github.com/rbarrois/python-semanticversion/blob/fdef1e9cdae901d095d8e8c9cd6fa6adcfe02074/semantic_version/base.py#L365-L380
|
rbarrois/python-semanticversion
|
semantic_version/base.py
|
Spec.match
|
def match(self, version):
"""Check whether a Version satisfies the Spec."""
return all(spec.match(version) for spec in self.specs)
|
python
|
def match(self, version):
"""Check whether a Version satisfies the Spec."""
return all(spec.match(version) for spec in self.specs)
|
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Check whether a Version satisfies the Spec.
|
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train
|
https://github.com/rbarrois/python-semanticversion/blob/fdef1e9cdae901d095d8e8c9cd6fa6adcfe02074/semantic_version/base.py#L514-L516
|
rbarrois/python-semanticversion
|
semantic_version/base.py
|
Spec.select
|
def select(self, versions):
"""Select the best compatible version among an iterable of options."""
options = list(self.filter(versions))
if options:
return max(options)
return None
|
python
|
def select(self, versions):
"""Select the best compatible version among an iterable of options."""
options = list(self.filter(versions))
if options:
return max(options)
return None
|
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train
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https://github.com/rbarrois/python-semanticversion/blob/fdef1e9cdae901d095d8e8c9cd6fa6adcfe02074/semantic_version/base.py#L524-L529
|
rbarrois/python-semanticversion
|
semantic_version/django_fields.py
|
VersionField.deconstruct
|
def deconstruct(self):
"""Handle django.db.migrations."""
name, path, args, kwargs = super(VersionField, self).deconstruct()
kwargs['partial'] = self.partial
kwargs['coerce'] = self.coerce
return name, path, args, kwargs
|
python
|
def deconstruct(self):
"""Handle django.db.migrations."""
name, path, args, kwargs = super(VersionField, self).deconstruct()
kwargs['partial'] = self.partial
kwargs['coerce'] = self.coerce
return name, path, args, kwargs
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[
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train
|
https://github.com/rbarrois/python-semanticversion/blob/fdef1e9cdae901d095d8e8c9cd6fa6adcfe02074/semantic_version/django_fields.py#L53-L58
|
rbarrois/python-semanticversion
|
semantic_version/django_fields.py
|
VersionField.to_python
|
def to_python(self, value):
"""Converts any value to a base.Version field."""
if value is None or value == '':
return value
if isinstance(value, base.Version):
return value
if self.coerce:
return base.Version.coerce(value, partial=self.partial)
else:
return base.Version(value, partial=self.partial)
|
python
|
def to_python(self, value):
"""Converts any value to a base.Version field."""
if value is None or value == '':
return value
if isinstance(value, base.Version):
return value
if self.coerce:
return base.Version.coerce(value, partial=self.partial)
else:
return base.Version(value, partial=self.partial)
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train
|
https://github.com/rbarrois/python-semanticversion/blob/fdef1e9cdae901d095d8e8c9cd6fa6adcfe02074/semantic_version/django_fields.py#L60-L69
|
rbarrois/python-semanticversion
|
semantic_version/django_fields.py
|
SpecField.to_python
|
def to_python(self, value):
"""Converts any value to a base.Spec field."""
if value is None or value == '':
return value
if isinstance(value, base.Spec):
return value
return base.Spec(value)
|
python
|
def to_python(self, value):
"""Converts any value to a base.Spec field."""
if value is None or value == '':
return value
if isinstance(value, base.Spec):
return value
return base.Spec(value)
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|
[
"Converts",
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train
|
https://github.com/rbarrois/python-semanticversion/blob/fdef1e9cdae901d095d8e8c9cd6fa6adcfe02074/semantic_version/django_fields.py#L78-L84
|
fkmclane/python-ardrone
|
ardrone/drone.py
|
ARDrone.move_left
|
def move_left(self):
"""Make the drone move left."""
self.at(ardrone.at.pcmd, True, -self.speed, 0, 0, 0)
|
python
|
def move_left(self):
"""Make the drone move left."""
self.at(ardrone.at.pcmd, True, -self.speed, 0, 0, 0)
|
[
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Make the drone move left.
|
[
"Make",
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"."
] |
train
|
https://github.com/fkmclane/python-ardrone/blob/def437148a114f66d1ca30bf2398a017002b2cd6/ardrone/drone.py#L55-L57
|
fkmclane/python-ardrone
|
ardrone/drone.py
|
ARDrone.move_right
|
def move_right(self):
"""Make the drone move right."""
self.at(ardrone.at.pcmd, True, self.speed, 0, 0, 0)
|
python
|
def move_right(self):
"""Make the drone move right."""
self.at(ardrone.at.pcmd, True, self.speed, 0, 0, 0)
|
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"speed",
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")"
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Make the drone move right.
|
[
"Make",
"the",
"drone",
"move",
"right",
"."
] |
train
|
https://github.com/fkmclane/python-ardrone/blob/def437148a114f66d1ca30bf2398a017002b2cd6/ardrone/drone.py#L59-L61
|
fkmclane/python-ardrone
|
ardrone/drone.py
|
ARDrone.move_up
|
def move_up(self):
"""Make the drone rise upwards."""
self.at(ardrone.at.pcmd, True, 0, 0, self.speed, 0)
|
python
|
def move_up(self):
"""Make the drone rise upwards."""
self.at(ardrone.at.pcmd, True, 0, 0, self.speed, 0)
|
[
"def",
"move_up",
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Make the drone rise upwards.
|
[
"Make",
"the",
"drone",
"rise",
"upwards",
"."
] |
train
|
https://github.com/fkmclane/python-ardrone/blob/def437148a114f66d1ca30bf2398a017002b2cd6/ardrone/drone.py#L63-L65
|
fkmclane/python-ardrone
|
ardrone/drone.py
|
ARDrone.move_down
|
def move_down(self):
"""Make the drone decent downwards."""
self.at(ardrone.at.pcmd, True, 0, 0, -self.speed, 0)
|
python
|
def move_down(self):
"""Make the drone decent downwards."""
self.at(ardrone.at.pcmd, True, 0, 0, -self.speed, 0)
|
[
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Make the drone decent downwards.
|
[
"Make",
"the",
"drone",
"decent",
"downwards",
"."
] |
train
|
https://github.com/fkmclane/python-ardrone/blob/def437148a114f66d1ca30bf2398a017002b2cd6/ardrone/drone.py#L67-L69
|
fkmclane/python-ardrone
|
ardrone/drone.py
|
ARDrone.move_forward
|
def move_forward(self):
"""Make the drone move forward."""
self.at(ardrone.at.pcmd, True, 0, -self.speed, 0, 0)
|
python
|
def move_forward(self):
"""Make the drone move forward."""
self.at(ardrone.at.pcmd, True, 0, -self.speed, 0, 0)
|
[
"def",
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"-",
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"speed",
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")"
] |
Make the drone move forward.
|
[
"Make",
"the",
"drone",
"move",
"forward",
"."
] |
train
|
https://github.com/fkmclane/python-ardrone/blob/def437148a114f66d1ca30bf2398a017002b2cd6/ardrone/drone.py#L71-L73
|
fkmclane/python-ardrone
|
ardrone/drone.py
|
ARDrone.move_backward
|
def move_backward(self):
"""Make the drone move backwards."""
self.at(ardrone.at.pcmd, True, 0, self.speed, 0, 0)
|
python
|
def move_backward(self):
"""Make the drone move backwards."""
self.at(ardrone.at.pcmd, True, 0, self.speed, 0, 0)
|
[
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",",
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")"
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Make the drone move backwards.
|
[
"Make",
"the",
"drone",
"move",
"backwards",
"."
] |
train
|
https://github.com/fkmclane/python-ardrone/blob/def437148a114f66d1ca30bf2398a017002b2cd6/ardrone/drone.py#L75-L77
|
fkmclane/python-ardrone
|
ardrone/drone.py
|
ARDrone.turn_left
|
def turn_left(self):
"""Make the drone rotate left."""
self.at(ardrone.at.pcmd, True, 0, 0, 0, -self.speed)
|
python
|
def turn_left(self):
"""Make the drone rotate left."""
self.at(ardrone.at.pcmd, True, 0, 0, 0, -self.speed)
|
[
"def",
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",",
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"-",
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Make the drone rotate left.
|
[
"Make",
"the",
"drone",
"rotate",
"left",
"."
] |
train
|
https://github.com/fkmclane/python-ardrone/blob/def437148a114f66d1ca30bf2398a017002b2cd6/ardrone/drone.py#L79-L81
|
fkmclane/python-ardrone
|
ardrone/drone.py
|
ARDrone.turn_right
|
def turn_right(self):
"""Make the drone rotate right."""
self.at(ardrone.at.pcmd, True, 0, 0, 0, self.speed)
|
python
|
def turn_right(self):
"""Make the drone rotate right."""
self.at(ardrone.at.pcmd, True, 0, 0, 0, self.speed)
|
[
"def",
"turn_right",
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"True",
",",
"0",
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"0",
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"speed",
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Make the drone rotate right.
|
[
"Make",
"the",
"drone",
"rotate",
"right",
"."
] |
train
|
https://github.com/fkmclane/python-ardrone/blob/def437148a114f66d1ca30bf2398a017002b2cd6/ardrone/drone.py#L83-L85
|
fkmclane/python-ardrone
|
ardrone/drone.py
|
ARDrone.reset
|
def reset(self):
"""Toggle the drone's emergency state."""
self.at(ardrone.at.ref, False, True)
time.sleep(0.1)
self.at(ardrone.at.ref, False, False)
|
python
|
def reset(self):
"""Toggle the drone's emergency state."""
self.at(ardrone.at.ref, False, True)
time.sleep(0.1)
self.at(ardrone.at.ref, False, False)
|
[
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Toggle the drone's emergency state.
|
[
"Toggle",
"the",
"drone",
"s",
"emergency",
"state",
"."
] |
train
|
https://github.com/fkmclane/python-ardrone/blob/def437148a114f66d1ca30bf2398a017002b2cd6/ardrone/drone.py#L87-L91
|
fkmclane/python-ardrone
|
ardrone/drone.py
|
ARDrone.at
|
def at(self, cmd, *args, **kwargs):
"""Wrapper for the low level at commands.
This method takes care that the sequence number is increased after each
at command and the watchdog timer is started to make sure the drone
receives a command at least every second.
"""
with self.lock:
self.com_watchdog_timer.cancel()
cmd(self.host, self.sequence, *args, **kwargs)
self.sequence += 1
self.com_watchdog_timer = threading.Timer(self.timer, self.commwdg)
self.com_watchdog_timer.start()
|
python
|
def at(self, cmd, *args, **kwargs):
"""Wrapper for the low level at commands.
This method takes care that the sequence number is increased after each
at command and the watchdog timer is started to make sure the drone
receives a command at least every second.
"""
with self.lock:
self.com_watchdog_timer.cancel()
cmd(self.host, self.sequence, *args, **kwargs)
self.sequence += 1
self.com_watchdog_timer = threading.Timer(self.timer, self.commwdg)
self.com_watchdog_timer.start()
|
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Wrapper for the low level at commands.
This method takes care that the sequence number is increased after each
at command and the watchdog timer is started to make sure the drone
receives a command at least every second.
|
[
"Wrapper",
"for",
"the",
"low",
"level",
"at",
"commands",
"."
] |
train
|
https://github.com/fkmclane/python-ardrone/blob/def437148a114f66d1ca30bf2398a017002b2cd6/ardrone/drone.py#L111-L123
|
fkmclane/python-ardrone
|
ardrone/drone.py
|
ARDrone.halt
|
def halt(self):
"""Shutdown the drone.
This method does not land or halt the actual drone, but the
communication with the drone. You should call it at the end of your
application to close all sockets, pipes, processes and threads related
with this object.
"""
with self.lock:
self.com_watchdog_timer.cancel()
self.ipc_thread.stop()
self.ipc_thread.join()
self.network_process.terminate()
self.network_process.join()
|
python
|
def halt(self):
"""Shutdown the drone.
This method does not land or halt the actual drone, but the
communication with the drone. You should call it at the end of your
application to close all sockets, pipes, processes and threads related
with this object.
"""
with self.lock:
self.com_watchdog_timer.cancel()
self.ipc_thread.stop()
self.ipc_thread.join()
self.network_process.terminate()
self.network_process.join()
|
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".",
"terminate",
"(",
")",
"self",
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"network_process",
".",
"join",
"(",
")"
] |
Shutdown the drone.
This method does not land or halt the actual drone, but the
communication with the drone. You should call it at the end of your
application to close all sockets, pipes, processes and threads related
with this object.
|
[
"Shutdown",
"the",
"drone",
"."
] |
train
|
https://github.com/fkmclane/python-ardrone/blob/def437148a114f66d1ca30bf2398a017002b2cd6/ardrone/drone.py#L133-L146
|
fkmclane/python-ardrone
|
ardrone/drone.py
|
ARDrone.move
|
def move(self, lr, fb, vv, va):
"""Makes the drone move (translate/rotate).
Parameters:
lr -- left-right tilt: float [-1..1] negative: left, positive: right
fb -- front-back tilt: float [-1..1] negative: forwards, positive:
backwards
vv -- vertical speed: float [-1..1] negative: go down, positive: rise
va -- angular speed: float [-1..1] negative: spin left, positive: spin
right"""
self.at(ardrone.at.pcmd, True, lr, fb, vv, va)
|
python
|
def move(self, lr, fb, vv, va):
"""Makes the drone move (translate/rotate).
Parameters:
lr -- left-right tilt: float [-1..1] negative: left, positive: right
fb -- front-back tilt: float [-1..1] negative: forwards, positive:
backwards
vv -- vertical speed: float [-1..1] negative: go down, positive: rise
va -- angular speed: float [-1..1] negative: spin left, positive: spin
right"""
self.at(ardrone.at.pcmd, True, lr, fb, vv, va)
|
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Makes the drone move (translate/rotate).
Parameters:
lr -- left-right tilt: float [-1..1] negative: left, positive: right
fb -- front-back tilt: float [-1..1] negative: forwards, positive:
backwards
vv -- vertical speed: float [-1..1] negative: go down, positive: rise
va -- angular speed: float [-1..1] negative: spin left, positive: spin
right
|
[
"Makes",
"the",
"drone",
"move",
"(",
"translate",
"/",
"rotate",
")",
"."
] |
train
|
https://github.com/fkmclane/python-ardrone/blob/def437148a114f66d1ca30bf2398a017002b2cd6/ardrone/drone.py#L148-L158
|
fkmclane/python-ardrone
|
ardrone/at.py
|
ref
|
def ref(host, seq, takeoff, emergency=False):
"""
Basic behaviour of the drone: take-off/landing, emergency stop/reset)
Parameters:
seq -- sequence number
takeoff -- True: Takeoff / False: Land
emergency -- True: Turn off the engines
"""
p = 0b10001010101000000000000000000
if takeoff:
p |= 0b1000000000
if emergency:
p |= 0b100000000
at(host, 'REF', seq, [p])
|
python
|
def ref(host, seq, takeoff, emergency=False):
"""
Basic behaviour of the drone: take-off/landing, emergency stop/reset)
Parameters:
seq -- sequence number
takeoff -- True: Takeoff / False: Land
emergency -- True: Turn off the engines
"""
p = 0b10001010101000000000000000000
if takeoff:
p |= 0b1000000000
if emergency:
p |= 0b100000000
at(host, 'REF', seq, [p])
|
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Basic behaviour of the drone: take-off/landing, emergency stop/reset)
Parameters:
seq -- sequence number
takeoff -- True: Takeoff / False: Land
emergency -- True: Turn off the engines
|
[
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"landing",
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"/",
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train
|
https://github.com/fkmclane/python-ardrone/blob/def437148a114f66d1ca30bf2398a017002b2cd6/ardrone/at.py#L16-L30
|
fkmclane/python-ardrone
|
ardrone/at.py
|
pcmd
|
def pcmd(host, seq, progressive, lr, fb, vv, va):
"""
Makes the drone move (translate/rotate).
Parameters:
seq -- sequence number
progressive -- True: enable progressive commands, False: disable (i.e.
enable hovering mode)
lr -- left-right tilt: float [-1..1] negative: left, positive: right
rb -- front-back tilt: float [-1..1] negative: forwards, positive:
backwards
vv -- vertical speed: float [-1..1] negative: go down, positive: rise
va -- angular speed: float [-1..1] negative: spin left, positive: spin
right
The above float values are a percentage of the maximum speed.
"""
p = 1 if progressive else 0
at(host, 'PCMD', seq, [p, float(lr), float(fb), float(vv), float(va)])
|
python
|
def pcmd(host, seq, progressive, lr, fb, vv, va):
"""
Makes the drone move (translate/rotate).
Parameters:
seq -- sequence number
progressive -- True: enable progressive commands, False: disable (i.e.
enable hovering mode)
lr -- left-right tilt: float [-1..1] negative: left, positive: right
rb -- front-back tilt: float [-1..1] negative: forwards, positive:
backwards
vv -- vertical speed: float [-1..1] negative: go down, positive: rise
va -- angular speed: float [-1..1] negative: spin left, positive: spin
right
The above float values are a percentage of the maximum speed.
"""
p = 1 if progressive else 0
at(host, 'PCMD', seq, [p, float(lr), float(fb), float(vv), float(va)])
|
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Makes the drone move (translate/rotate).
Parameters:
seq -- sequence number
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enable hovering mode)
lr -- left-right tilt: float [-1..1] negative: left, positive: right
rb -- front-back tilt: float [-1..1] negative: forwards, positive:
backwards
vv -- vertical speed: float [-1..1] negative: go down, positive: rise
va -- angular speed: float [-1..1] negative: spin left, positive: spin
right
The above float values are a percentage of the maximum speed.
|
[
"Makes",
"the",
"drone",
"move",
"(",
"translate",
"/",
"rotate",
")",
"."
] |
train
|
https://github.com/fkmclane/python-ardrone/blob/def437148a114f66d1ca30bf2398a017002b2cd6/ardrone/at.py#L33-L51
|
fkmclane/python-ardrone
|
ardrone/at.py
|
config
|
def config(host, seq, option, value):
"""Set configuration parameters of the drone."""
at(host, 'CONFIG', seq, [str(option), str(value)])
|
python
|
def config(host, seq, option, value):
"""Set configuration parameters of the drone."""
at(host, 'CONFIG', seq, [str(option), str(value)])
|
[
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Set configuration parameters of the drone.
|
[
"Set",
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"of",
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"drone",
"."
] |
train
|
https://github.com/fkmclane/python-ardrone/blob/def437148a114f66d1ca30bf2398a017002b2cd6/ardrone/at.py#L76-L78
|
fkmclane/python-ardrone
|
ardrone/at.py
|
pwm
|
def pwm(host, seq, m1, m2, m3, m4):
"""
Sends control values directly to the engines, overriding control loops.
Parameters:
seq -- sequence number
m1 -- Integer: front left command
m2 -- Integer: front right command
m3 -- Integer: back right command
m4 -- Integer: back left command
"""
at(host, 'PWM', seq, [m1, m2, m3, m4])
|
python
|
def pwm(host, seq, m1, m2, m3, m4):
"""
Sends control values directly to the engines, overriding control loops.
Parameters:
seq -- sequence number
m1 -- Integer: front left command
m2 -- Integer: front right command
m3 -- Integer: back right command
m4 -- Integer: back left command
"""
at(host, 'PWM', seq, [m1, m2, m3, m4])
|
[
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Sends control values directly to the engines, overriding control loops.
Parameters:
seq -- sequence number
m1 -- Integer: front left command
m2 -- Integer: front right command
m3 -- Integer: back right command
m4 -- Integer: back left command
|
[
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"the",
"engines",
"overriding",
"control",
"loops",
"."
] |
train
|
https://github.com/fkmclane/python-ardrone/blob/def437148a114f66d1ca30bf2398a017002b2cd6/ardrone/at.py#L100-L111
|
fkmclane/python-ardrone
|
ardrone/at.py
|
led
|
def led(host, seq, anim, f, d):
"""
Control the drones LED.
Parameters:
seq -- sequence number
anim -- Integer: animation to play
f -- Float: frequency in HZ of the animation
d -- Integer: total duration in seconds of the animation
"""
at(host, 'LED', seq, [anim, float(f), d])
|
python
|
def led(host, seq, anim, f, d):
"""
Control the drones LED.
Parameters:
seq -- sequence number
anim -- Integer: animation to play
f -- Float: frequency in HZ of the animation
d -- Integer: total duration in seconds of the animation
"""
at(host, 'LED', seq, [anim, float(f), d])
|
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Control the drones LED.
Parameters:
seq -- sequence number
anim -- Integer: animation to play
f -- Float: frequency in HZ of the animation
d -- Integer: total duration in seconds of the animation
|
[
"Control",
"the",
"drones",
"LED",
"."
] |
train
|
https://github.com/fkmclane/python-ardrone/blob/def437148a114f66d1ca30bf2398a017002b2cd6/ardrone/at.py#L114-L124
|
fkmclane/python-ardrone
|
ardrone/at.py
|
anim
|
def anim(host, seq, anim, d):
"""
Makes the drone execute a predefined movement (animation).
Parameters:
seq -- sequcence number
anim -- Integer: animation to play
d -- Integer: total duration in seconds of the animation
"""
at(host, 'ANIM', seq, [anim, d])
|
python
|
def anim(host, seq, anim, d):
"""
Makes the drone execute a predefined movement (animation).
Parameters:
seq -- sequcence number
anim -- Integer: animation to play
d -- Integer: total duration in seconds of the animation
"""
at(host, 'ANIM', seq, [anim, d])
|
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"'ANIM'",
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"seq",
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Makes the drone execute a predefined movement (animation).
Parameters:
seq -- sequcence number
anim -- Integer: animation to play
d -- Integer: total duration in seconds of the animation
|
[
"Makes",
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")",
"."
] |
train
|
https://github.com/fkmclane/python-ardrone/blob/def437148a114f66d1ca30bf2398a017002b2cd6/ardrone/at.py#L127-L136
|
fkmclane/python-ardrone
|
ardrone/at.py
|
at
|
def at(host, command, seq, params):
"""
Parameters:
command -- the command
seq -- the sequence number
params -- a list of elements which can be either int, float or string
"""
params_str = []
for p in params:
if type(p) == int:
params_str.append('{:d}'.format(p))
elif type(p) == float:
params_str.append('{:d}'.format(f2i(p)))
elif type(p) == str:
params_str.append('"{:s}"'.format(p))
msg = 'AT*{:s}={:d},{:s}\r'.format(command, seq, ','.join(params_str))
sock = socket.socket(socket.AF_INET, socket.SOCK_DGRAM)
sock.sendto(msg.encode(), (host, ardrone.constant.COMMAND_PORT))
|
python
|
def at(host, command, seq, params):
"""
Parameters:
command -- the command
seq -- the sequence number
params -- a list of elements which can be either int, float or string
"""
params_str = []
for p in params:
if type(p) == int:
params_str.append('{:d}'.format(p))
elif type(p) == float:
params_str.append('{:d}'.format(f2i(p)))
elif type(p) == str:
params_str.append('"{:s}"'.format(p))
msg = 'AT*{:s}={:d},{:s}\r'.format(command, seq, ','.join(params_str))
sock = socket.socket(socket.AF_INET, socket.SOCK_DGRAM)
sock.sendto(msg.encode(), (host, ardrone.constant.COMMAND_PORT))
|
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|
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] |
train
|
https://github.com/fkmclane/python-ardrone/blob/def437148a114f66d1ca30bf2398a017002b2cd6/ardrone/at.py#L138-L155
|
fkmclane/python-ardrone
|
ardrone/navdata.py
|
decode
|
def decode(packet):
"""Decode a navdata packet."""
offset = 0
_ = struct.unpack_from('IIII', packet, offset)
s = _[1]
state = dict()
state['fly'] = s & 1 # FLY MASK : (0) ardrone is landed, (1) ardrone is flying
state['video'] = s >> 1 & 1 # VIDEO MASK : (0) video disable, (1) video enable
state['vision'] = s >> 2 & 1 # VISION MASK : (0) vision disable, (1) vision enable
state['control'] = s >> 3 & 1 # CONTROL ALGO (0) euler angles control, (1) angular speed control
state['altitude'] = s >> 4 & 1 # ALTITUDE CONTROL ALGO : (0) altitude control inactive (1) altitude control active
state['user_feedback_start'] = s >> 5 & 1 # USER feedback : Start button state
state['command'] = s >> 6 & 1 # Control command ACK : (0) None, (1) one received
state['fw_file'] = s >> 7 & 1 # Firmware file is good (1)
state['fw_ver'] = s >> 8 & 1 # Firmware update is newer (1)
state['fw_upd'] = s >> 9 & 1 # Firmware update is ongoing (1)
state['navdata_demo'] = s >> 10 & 1 # Navdata demo : (0) All navdata, (1) only navdata demo
state['navdata_bootstrap'] = s >> 11 & 1 # Navdata bootstrap : (0) options sent in all or demo mode, (1) no navdata options sent
state['motors'] = s >> 12 & 1 # Motor status : (0) Ok, (1) Motors problem
state['com_lost'] = s >> 13 & 1 # Communication lost : (1) com problem, (0) Com is ok
state['vbat_low'] = s >> 15 & 1 # VBat low : (1) too low, (0) Ok
state['user_el'] = s >> 16 & 1 # User Emergency Landing : (1) User EL is ON, (0) User EL is OFF
state['timer_elapsed'] = s >> 17 & 1 # Timer elapsed : (1) elapsed, (0) not elapsed
state['angles_out_of_range'] = s >> 19 & 1 # Angles : (0) Ok, (1) out of range
state['ultrasound'] = s >> 21 & 1 # Ultrasonic sensor : (0) Ok, (1) deaf
state['cutout'] = s >> 22 & 1 # Cutout system detection : (0) Not detected, (1) detected
state['pic_version'] = s >> 23 & 1 # PIC Version number OK : (0) a bad version number, (1) version number is OK
state['atcodec_thread_on'] = s >> 24 & 1 # ATCodec thread ON : (0) thread OFF (1) thread ON
state['navdata_thread_on'] = s >> 25 & 1 # Navdata thread ON : (0) thread OFF (1) thread ON
state['video_thread_on'] = s >> 26 & 1 # Video thread ON : (0) thread OFF (1) thread ON
state['acq_thread_on'] = s >> 27 & 1 # Acquisition thread ON : (0) thread OFF (1) thread ON
state['ctrl_watchdog'] = s >> 28 & 1 # CTRL watchdog : (1) delay in control execution (> 5ms), (0) control is well scheduled
state['adc_watchdog'] = s >> 29 & 1 # ADC Watchdog : (1) delay in uart2 dsr (> 5ms), (0) uart2 is good
state['com_watchdog'] = s >> 30 & 1 # Communication Watchdog : (1) com problem, (0) Com is ok
state['emergency'] = s >> 31 & 1 # Emergency landing : (0) no emergency, (1) emergency
data = dict()
data['state'] = state
data['header'] = _[0]
data['sequence'] = _[2]
data['vision'] = _[3]
offset += struct.calcsize('IIII')
demo_fields = [
'ctrl_state',
'battery',
'theta',
'phi',
'psi',
'altitude',
'vx',
'vy',
'vz',
'num_frames'
]
angles = ['theta', 'phi', 'psi']
while True:
try:
id_nr, size = struct.unpack_from('HH', packet, offset)
offset += struct.calcsize('HH')
except struct.error:
break
values = []
for i in range(size - struct.calcsize('HH')):
values.append(struct.unpack_from('c', packet, offset)[0])
offset += struct.calcsize('c')
if id_nr == 0:
values = struct.unpack_from('IIfffIfffI', b''.join(values))
demo = dict(zip(demo_fields, values))
for a in angles:
demo[a] = int(demo[a] / 1000)
data['demo'] = demo
return data
|
python
|
def decode(packet):
"""Decode a navdata packet."""
offset = 0
_ = struct.unpack_from('IIII', packet, offset)
s = _[1]
state = dict()
state['fly'] = s & 1 # FLY MASK : (0) ardrone is landed, (1) ardrone is flying
state['video'] = s >> 1 & 1 # VIDEO MASK : (0) video disable, (1) video enable
state['vision'] = s >> 2 & 1 # VISION MASK : (0) vision disable, (1) vision enable
state['control'] = s >> 3 & 1 # CONTROL ALGO (0) euler angles control, (1) angular speed control
state['altitude'] = s >> 4 & 1 # ALTITUDE CONTROL ALGO : (0) altitude control inactive (1) altitude control active
state['user_feedback_start'] = s >> 5 & 1 # USER feedback : Start button state
state['command'] = s >> 6 & 1 # Control command ACK : (0) None, (1) one received
state['fw_file'] = s >> 7 & 1 # Firmware file is good (1)
state['fw_ver'] = s >> 8 & 1 # Firmware update is newer (1)
state['fw_upd'] = s >> 9 & 1 # Firmware update is ongoing (1)
state['navdata_demo'] = s >> 10 & 1 # Navdata demo : (0) All navdata, (1) only navdata demo
state['navdata_bootstrap'] = s >> 11 & 1 # Navdata bootstrap : (0) options sent in all or demo mode, (1) no navdata options sent
state['motors'] = s >> 12 & 1 # Motor status : (0) Ok, (1) Motors problem
state['com_lost'] = s >> 13 & 1 # Communication lost : (1) com problem, (0) Com is ok
state['vbat_low'] = s >> 15 & 1 # VBat low : (1) too low, (0) Ok
state['user_el'] = s >> 16 & 1 # User Emergency Landing : (1) User EL is ON, (0) User EL is OFF
state['timer_elapsed'] = s >> 17 & 1 # Timer elapsed : (1) elapsed, (0) not elapsed
state['angles_out_of_range'] = s >> 19 & 1 # Angles : (0) Ok, (1) out of range
state['ultrasound'] = s >> 21 & 1 # Ultrasonic sensor : (0) Ok, (1) deaf
state['cutout'] = s >> 22 & 1 # Cutout system detection : (0) Not detected, (1) detected
state['pic_version'] = s >> 23 & 1 # PIC Version number OK : (0) a bad version number, (1) version number is OK
state['atcodec_thread_on'] = s >> 24 & 1 # ATCodec thread ON : (0) thread OFF (1) thread ON
state['navdata_thread_on'] = s >> 25 & 1 # Navdata thread ON : (0) thread OFF (1) thread ON
state['video_thread_on'] = s >> 26 & 1 # Video thread ON : (0) thread OFF (1) thread ON
state['acq_thread_on'] = s >> 27 & 1 # Acquisition thread ON : (0) thread OFF (1) thread ON
state['ctrl_watchdog'] = s >> 28 & 1 # CTRL watchdog : (1) delay in control execution (> 5ms), (0) control is well scheduled
state['adc_watchdog'] = s >> 29 & 1 # ADC Watchdog : (1) delay in uart2 dsr (> 5ms), (0) uart2 is good
state['com_watchdog'] = s >> 30 & 1 # Communication Watchdog : (1) com problem, (0) Com is ok
state['emergency'] = s >> 31 & 1 # Emergency landing : (0) no emergency, (1) emergency
data = dict()
data['state'] = state
data['header'] = _[0]
data['sequence'] = _[2]
data['vision'] = _[3]
offset += struct.calcsize('IIII')
demo_fields = [
'ctrl_state',
'battery',
'theta',
'phi',
'psi',
'altitude',
'vx',
'vy',
'vz',
'num_frames'
]
angles = ['theta', 'phi', 'psi']
while True:
try:
id_nr, size = struct.unpack_from('HH', packet, offset)
offset += struct.calcsize('HH')
except struct.error:
break
values = []
for i in range(size - struct.calcsize('HH')):
values.append(struct.unpack_from('c', packet, offset)[0])
offset += struct.calcsize('c')
if id_nr == 0:
values = struct.unpack_from('IIfffIfffI', b''.join(values))
demo = dict(zip(demo_fields, values))
for a in angles:
demo[a] = int(demo[a] / 1000)
data['demo'] = demo
return data
|
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"[",
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"]",
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"return",
"data"
] |
Decode a navdata packet.
|
[
"Decode",
"a",
"navdata",
"packet",
"."
] |
train
|
https://github.com/fkmclane/python-ardrone/blob/def437148a114f66d1ca30bf2398a017002b2cd6/ardrone/navdata.py#L4-L82
|
pearu/pyvtk
|
pyvtk/__init__.py
|
VtkData.tofile
|
def tofile(self, filename, format = 'ascii'):
"""Save VTK data to file.
"""
if not common.is_string(filename):
raise TypeError('argument filename must be string but got %s'%(type(filename)))
if format not in ['ascii','binary']:
raise TypeError('argument format must be ascii | binary')
filename = filename.strip()
if not filename:
raise ValueError('filename must be non-empty string')
if filename[-4:]!='.vtk':
filename += '.vtk'
f = open(filename,'wb')
f.write(self.to_string(format))
f.close()
|
python
|
def tofile(self, filename, format = 'ascii'):
"""Save VTK data to file.
"""
if not common.is_string(filename):
raise TypeError('argument filename must be string but got %s'%(type(filename)))
if format not in ['ascii','binary']:
raise TypeError('argument format must be ascii | binary')
filename = filename.strip()
if not filename:
raise ValueError('filename must be non-empty string')
if filename[-4:]!='.vtk':
filename += '.vtk'
f = open(filename,'wb')
f.write(self.to_string(format))
f.close()
|
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Save VTK data to file.
|
[
"Save",
"VTK",
"data",
"to",
"file",
"."
] |
train
|
https://github.com/pearu/pyvtk/blob/b004ec3c03299a2d75338a4be93dd29f076b70ab/pyvtk/__init__.py#L190-L204
|
GoodCloud/django-zebra
|
zebra/mixins.py
|
_get_attr_value
|
def _get_attr_value(instance, attr, default=None):
"""
Simple helper to get the value of an instance's attribute if it exists.
If the instance attribute is callable it will be called and the result will
be returned.
Optionally accepts a default value to return if the attribute is missing.
Defaults to `None`
>>> class Foo(object):
... bar = 'baz'
... def hi(self):
... return 'hi'
>>> f = Foo()
>>> _get_attr_value(f, 'bar')
'baz'
>>> _get_attr_value(f, 'xyz')
>>> _get_attr_value(f, 'xyz', False)
False
>>> _get_attr_value(f, 'hi')
'hi'
"""
value = default
if hasattr(instance, attr):
value = getattr(instance, attr)
if callable(value):
value = value()
return value
|
python
|
def _get_attr_value(instance, attr, default=None):
"""
Simple helper to get the value of an instance's attribute if it exists.
If the instance attribute is callable it will be called and the result will
be returned.
Optionally accepts a default value to return if the attribute is missing.
Defaults to `None`
>>> class Foo(object):
... bar = 'baz'
... def hi(self):
... return 'hi'
>>> f = Foo()
>>> _get_attr_value(f, 'bar')
'baz'
>>> _get_attr_value(f, 'xyz')
>>> _get_attr_value(f, 'xyz', False)
False
>>> _get_attr_value(f, 'hi')
'hi'
"""
value = default
if hasattr(instance, attr):
value = getattr(instance, attr)
if callable(value):
value = value()
return value
|
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Simple helper to get the value of an instance's attribute if it exists.
If the instance attribute is callable it will be called and the result will
be returned.
Optionally accepts a default value to return if the attribute is missing.
Defaults to `None`
>>> class Foo(object):
... bar = 'baz'
... def hi(self):
... return 'hi'
>>> f = Foo()
>>> _get_attr_value(f, 'bar')
'baz'
>>> _get_attr_value(f, 'xyz')
>>> _get_attr_value(f, 'xyz', False)
False
>>> _get_attr_value(f, 'hi')
'hi'
|
[
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"an",
"instance",
"s",
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"."
] |
train
|
https://github.com/GoodCloud/django-zebra/blob/fdb2f2eb9eddb83eebb339359e629c88f4f6ba17/zebra/mixins.py#L6-L35
|
GoodCloud/django-zebra
|
zebra/utils.py
|
audit_customer_subscription
|
def audit_customer_subscription(customer, unknown=True):
"""
Audits the provided customer's subscription against stripe and returns a pair
that contains a boolean and a result type.
Default result types can be found in zebra.conf.defaults and can be
overridden in your project's settings.
"""
if (hasattr(customer, 'suspended') and customer.suspended):
result = AUDIT_RESULTS['suspended']
else:
if hasattr(customer, 'subscription'):
try:
result = AUDIT_RESULTS[customer.subscription.status]
except KeyError, err:
# TODO should this be a more specific exception class?
raise Exception("Unable to locate a result set for \
subscription status %s in ZEBRA_AUDIT_RESULTS") % str(err)
else:
result = AUDIT_RESULTS['no_subscription']
return result
|
python
|
def audit_customer_subscription(customer, unknown=True):
"""
Audits the provided customer's subscription against stripe and returns a pair
that contains a boolean and a result type.
Default result types can be found in zebra.conf.defaults and can be
overridden in your project's settings.
"""
if (hasattr(customer, 'suspended') and customer.suspended):
result = AUDIT_RESULTS['suspended']
else:
if hasattr(customer, 'subscription'):
try:
result = AUDIT_RESULTS[customer.subscription.status]
except KeyError, err:
# TODO should this be a more specific exception class?
raise Exception("Unable to locate a result set for \
subscription status %s in ZEBRA_AUDIT_RESULTS") % str(err)
else:
result = AUDIT_RESULTS['no_subscription']
return result
|
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Audits the provided customer's subscription against stripe and returns a pair
that contains a boolean and a result type.
Default result types can be found in zebra.conf.defaults and can be
overridden in your project's settings.
|
[
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"."
] |
train
|
https://github.com/GoodCloud/django-zebra/blob/fdb2f2eb9eddb83eebb339359e629c88f4f6ba17/zebra/utils.py#L6-L26
|
pearu/pyvtk
|
pyvtk/PolyData.py
|
polydata_fromfile
|
def polydata_fromfile(f, self):
"""Use VtkData(<filename>)."""
points = []
data = dict(vertices=[], lines=[], polygons=[], triangle_strips=[])
l = common._getline(f).decode('ascii')
k,n,datatype = [s.strip().lower() for s in l.split(' ')]
if k!='points':
raise ValueError('expected points but got %s'%(repr(k)))
n = int(n)
assert datatype in ['bit','unsigned_char','char','unsigned_short','short','unsigned_int','int','unsigned_long','long','float','double'],repr(datatype)
log.debug('\tgetting %s points'%n)
while len(points) < 3*n:
l = common._getline(f).decode('ascii')
points += map(eval,l.split(' '))
assert len(points)==3*n
while 1:
l = common._getline(f)
if l is None:
break
l = l.decode('ascii')
sl = l.split(' ')
k = sl[0].strip().lower()
if k not in ['vertices','lines','polygons','triangle_strips']:
break
assert len(sl)==3
n = int(sl[1])
size = int(sl[2])
lst = []
while len(lst) < size:
l = common._getline(f).decode('ascii')
lst += map(eval, l.split(' '))
assert len(lst)==size
lst2 = []
j = 0
for i in range(n):
lst2.append(lst[j+1:j+lst[j]+1])
j += lst[j]+1
data[k] = lst2
return PolyData(points,data['vertices'], data['lines'], data['polygons'], data['triangle_strips']), l.encode()
|
python
|
def polydata_fromfile(f, self):
"""Use VtkData(<filename>)."""
points = []
data = dict(vertices=[], lines=[], polygons=[], triangle_strips=[])
l = common._getline(f).decode('ascii')
k,n,datatype = [s.strip().lower() for s in l.split(' ')]
if k!='points':
raise ValueError('expected points but got %s'%(repr(k)))
n = int(n)
assert datatype in ['bit','unsigned_char','char','unsigned_short','short','unsigned_int','int','unsigned_long','long','float','double'],repr(datatype)
log.debug('\tgetting %s points'%n)
while len(points) < 3*n:
l = common._getline(f).decode('ascii')
points += map(eval,l.split(' '))
assert len(points)==3*n
while 1:
l = common._getline(f)
if l is None:
break
l = l.decode('ascii')
sl = l.split(' ')
k = sl[0].strip().lower()
if k not in ['vertices','lines','polygons','triangle_strips']:
break
assert len(sl)==3
n = int(sl[1])
size = int(sl[2])
lst = []
while len(lst) < size:
l = common._getline(f).decode('ascii')
lst += map(eval, l.split(' '))
assert len(lst)==size
lst2 = []
j = 0
for i in range(n):
lst2.append(lst[j+1:j+lst[j]+1])
j += lst[j]+1
data[k] = lst2
return PolyData(points,data['vertices'], data['lines'], data['polygons'], data['triangle_strips']), l.encode()
|
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Use VtkData(<filename>).
|
[
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"(",
"<filename",
">",
")",
"."
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train
|
https://github.com/pearu/pyvtk/blob/b004ec3c03299a2d75338a4be93dd29f076b70ab/pyvtk/PolyData.py#L73-L113
|
GoodCloud/django-zebra
|
zebra/views.py
|
webhooks
|
def webhooks(request):
"""
Handles all known webhooks from stripe, and calls signals.
Plug in as you need.
"""
if request.method != "POST":
return HttpResponse("Invalid Request.", status=400)
json = simplejson.loads(request.POST["json"])
if json["event"] == "recurring_payment_failed":
zebra_webhook_recurring_payment_failed.send(sender=None, customer=_try_to_get_customer_from_customer_id(json["customer"]), full_json=json)
elif json["event"] == "invoice_ready":
zebra_webhook_invoice_ready.send(sender=None, customer=_try_to_get_customer_from_customer_id(json["customer"]), full_json=json)
elif json["event"] == "recurring_payment_succeeded":
zebra_webhook_recurring_payment_succeeded.send(sender=None, customer=_try_to_get_customer_from_customer_id(json["customer"]), full_json=json)
elif json["event"] == "subscription_trial_ending":
zebra_webhook_subscription_trial_ending.send(sender=None, customer=_try_to_get_customer_from_customer_id(json["customer"]), full_json=json)
elif json["event"] == "subscription_final_payment_attempt_failed":
zebra_webhook_subscription_final_payment_attempt_failed.send(sender=None, customer=_try_to_get_customer_from_customer_id(json["customer"]), full_json=json)
elif json["event"] == "ping":
zebra_webhook_subscription_ping_sent.send(sender=None)
else:
return HttpResponse(status=400)
return HttpResponse(status=200)
|
python
|
def webhooks(request):
"""
Handles all known webhooks from stripe, and calls signals.
Plug in as you need.
"""
if request.method != "POST":
return HttpResponse("Invalid Request.", status=400)
json = simplejson.loads(request.POST["json"])
if json["event"] == "recurring_payment_failed":
zebra_webhook_recurring_payment_failed.send(sender=None, customer=_try_to_get_customer_from_customer_id(json["customer"]), full_json=json)
elif json["event"] == "invoice_ready":
zebra_webhook_invoice_ready.send(sender=None, customer=_try_to_get_customer_from_customer_id(json["customer"]), full_json=json)
elif json["event"] == "recurring_payment_succeeded":
zebra_webhook_recurring_payment_succeeded.send(sender=None, customer=_try_to_get_customer_from_customer_id(json["customer"]), full_json=json)
elif json["event"] == "subscription_trial_ending":
zebra_webhook_subscription_trial_ending.send(sender=None, customer=_try_to_get_customer_from_customer_id(json["customer"]), full_json=json)
elif json["event"] == "subscription_final_payment_attempt_failed":
zebra_webhook_subscription_final_payment_attempt_failed.send(sender=None, customer=_try_to_get_customer_from_customer_id(json["customer"]), full_json=json)
elif json["event"] == "ping":
zebra_webhook_subscription_ping_sent.send(sender=None)
else:
return HttpResponse(status=400)
return HttpResponse(status=200)
|
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"return",
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] |
Handles all known webhooks from stripe, and calls signals.
Plug in as you need.
|
[
"Handles",
"all",
"known",
"webhooks",
"from",
"stripe",
"and",
"calls",
"signals",
".",
"Plug",
"in",
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"you",
"need",
"."
] |
train
|
https://github.com/GoodCloud/django-zebra/blob/fdb2f2eb9eddb83eebb339359e629c88f4f6ba17/zebra/views.py#L28-L60
|
GoodCloud/django-zebra
|
zebra/views.py
|
webhooks_v2
|
def webhooks_v2(request):
"""
Handles all known webhooks from stripe, and calls signals.
Plug in as you need.
"""
if request.method != "POST":
return HttpResponse("Invalid Request.", status=400)
try:
event_json = simplejson.loads(request.body)
except AttributeError:
# Backwords compatibility
# Prior to Django 1.4, request.body was named request.raw_post_data
event_json = simplejson.loads(request.raw_post_data)
event_key = event_json['type'].replace('.', '_')
if event_key in WEBHOOK_MAP:
WEBHOOK_MAP[event_key].send(sender=None, full_json=event_json)
return HttpResponse(status=200)
|
python
|
def webhooks_v2(request):
"""
Handles all known webhooks from stripe, and calls signals.
Plug in as you need.
"""
if request.method != "POST":
return HttpResponse("Invalid Request.", status=400)
try:
event_json = simplejson.loads(request.body)
except AttributeError:
# Backwords compatibility
# Prior to Django 1.4, request.body was named request.raw_post_data
event_json = simplejson.loads(request.raw_post_data)
event_key = event_json['type'].replace('.', '_')
if event_key in WEBHOOK_MAP:
WEBHOOK_MAP[event_key].send(sender=None, full_json=event_json)
return HttpResponse(status=200)
|
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Handles all known webhooks from stripe, and calls signals.
Plug in as you need.
|
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"need",
"."
] |
train
|
https://github.com/GoodCloud/django-zebra/blob/fdb2f2eb9eddb83eebb339359e629c88f4f6ba17/zebra/views.py#L63-L82
|
pearu/pyvtk
|
pyvtk/common.py
|
is_number
|
def is_number(obj):
"""Check if obj is number."""
return isinstance(obj, (int, float, np.int_, np.float_))
|
python
|
def is_number(obj):
"""Check if obj is number."""
return isinstance(obj, (int, float, np.int_, np.float_))
|
[
"def",
"is_number",
"(",
"obj",
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"int",
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"float",
",",
"np",
".",
"int_",
",",
"np",
".",
"float_",
")",
")"
] |
Check if obj is number.
|
[
"Check",
"if",
"obj",
"is",
"number",
"."
] |
train
|
https://github.com/pearu/pyvtk/blob/b004ec3c03299a2d75338a4be93dd29f076b70ab/pyvtk/common.py#L34-L36
|
pearu/pyvtk
|
pyvtk/common.py
|
Common.get_seq
|
def get_seq(self,obj,default=None):
"""Return sequence."""
if is_sequence(obj):
return obj
if is_number(obj): return [obj]
if obj is None and default is not None:
log.warning('using default value (%s)'%(default))
return self.get_seq(default)
raise ValueError('expected sequence|number but got %s'%(type(obj)))
|
python
|
def get_seq(self,obj,default=None):
"""Return sequence."""
if is_sequence(obj):
return obj
if is_number(obj): return [obj]
if obj is None and default is not None:
log.warning('using default value (%s)'%(default))
return self.get_seq(default)
raise ValueError('expected sequence|number but got %s'%(type(obj)))
|
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"'expected sequence|number but got %s'",
"%",
"(",
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"(",
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")",
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")"
] |
Return sequence.
|
[
"Return",
"sequence",
"."
] |
train
|
https://github.com/pearu/pyvtk/blob/b004ec3c03299a2d75338a4be93dd29f076b70ab/pyvtk/common.py#L130-L138
|
pearu/pyvtk
|
pyvtk/common.py
|
Common.get_seq_seq
|
def get_seq_seq(self,obj,default=None):
"""Return sequence of sequences."""
if is_sequence2(obj):
return [self.get_seq(o,default) for o in obj]
else:
return [self.get_seq(obj,default)]
|
python
|
def get_seq_seq(self,obj,default=None):
"""Return sequence of sequences."""
if is_sequence2(obj):
return [self.get_seq(o,default) for o in obj]
else:
return [self.get_seq(obj,default)]
|
[
"def",
"get_seq_seq",
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"obj",
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"None",
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"get_seq",
"(",
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"default",
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"in",
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"else",
":",
"return",
"[",
"self",
".",
"get_seq",
"(",
"obj",
",",
"default",
")",
"]"
] |
Return sequence of sequences.
|
[
"Return",
"sequence",
"of",
"sequences",
"."
] |
train
|
https://github.com/pearu/pyvtk/blob/b004ec3c03299a2d75338a4be93dd29f076b70ab/pyvtk/common.py#L139-L144
|
pearu/pyvtk
|
pyvtk/common.py
|
Common.get_3_tuple
|
def get_3_tuple(self,obj,default=None):
"""Return 3-tuple from
number -> (obj,default[1],default[2])
0-sequence|None -> default
1-sequence -> (obj[0],default[1],default[2])
2-sequence -> (obj[0],obj[1],default[2])
(3 or more)-sequence -> (obj[0],obj[1],obj[2])
"""
if not (default is not None \
and type(default) is tuple \
and len(default)==3):
raise ValueError('argument default must be 3-tuple|None but got %s'%(default))
if is_sequence(obj):
n = len(obj)
if n>3:
log.warning('expected 3-sequence but got %s-%s'%(n,type(obj)))
if n>=3:
return tuple(obj)
log.warning('filling with default value (%s) to obtain size=3'%(default[0]))
if default is not None:
if n==0:
return default
elif n==1:
return (obj[0],default[1],default[2])
elif n==2:
return (obj[0],obj[1],default[2])
elif is_number(obj) and default is not None:
log.warning('filling with default value (%s) to obtain size=3'%(default[0]))
return (obj,default[1],default[2])
elif obj is None and default is not None:
log.warning('filling with default value (%s) to obtain size=3'%(default[0]))
return default
raise ValueError('failed to construct 3-tuple from %s-%s'%(n,type(obj)))
|
python
|
def get_3_tuple(self,obj,default=None):
"""Return 3-tuple from
number -> (obj,default[1],default[2])
0-sequence|None -> default
1-sequence -> (obj[0],default[1],default[2])
2-sequence -> (obj[0],obj[1],default[2])
(3 or more)-sequence -> (obj[0],obj[1],obj[2])
"""
if not (default is not None \
and type(default) is tuple \
and len(default)==3):
raise ValueError('argument default must be 3-tuple|None but got %s'%(default))
if is_sequence(obj):
n = len(obj)
if n>3:
log.warning('expected 3-sequence but got %s-%s'%(n,type(obj)))
if n>=3:
return tuple(obj)
log.warning('filling with default value (%s) to obtain size=3'%(default[0]))
if default is not None:
if n==0:
return default
elif n==1:
return (obj[0],default[1],default[2])
elif n==2:
return (obj[0],obj[1],default[2])
elif is_number(obj) and default is not None:
log.warning('filling with default value (%s) to obtain size=3'%(default[0]))
return (obj,default[1],default[2])
elif obj is None and default is not None:
log.warning('filling with default value (%s) to obtain size=3'%(default[0]))
return default
raise ValueError('failed to construct 3-tuple from %s-%s'%(n,type(obj)))
|
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"%",
"(",
"n",
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")",
")",
")"
] |
Return 3-tuple from
number -> (obj,default[1],default[2])
0-sequence|None -> default
1-sequence -> (obj[0],default[1],default[2])
2-sequence -> (obj[0],obj[1],default[2])
(3 or more)-sequence -> (obj[0],obj[1],obj[2])
|
[
"Return",
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"-",
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"(",
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"[",
"1",
"]",
"obj",
"[",
"2",
"]",
")"
] |
train
|
https://github.com/pearu/pyvtk/blob/b004ec3c03299a2d75338a4be93dd29f076b70ab/pyvtk/common.py#L163-L195
|
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