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DataONEorg/d1_python | gmn/src/d1_gmn/app/middleware/response_handler.py | ResponseHandler._debug_mode_responses | def _debug_mode_responses(self, request, response):
"""Extra functionality available in debug mode.
- If pretty printed output was requested, force the content type to text. This
causes the browser to not try to format the output in any way.
- If SQL profiling is turned on, return a page with SQL query timing
information instead of the actual response.
"""
if django.conf.settings.DEBUG_GMN:
if 'pretty' in request.GET:
response['Content-Type'] = d1_common.const.CONTENT_TYPE_TEXT
if (
'HTTP_VENDOR_PROFILE_SQL' in request.META
or django.conf.settings.DEBUG_PROFILE_SQL
):
response_list = []
for query in django.db.connection.queries:
response_list.append('{}\n{}'.format(query['time'], query['sql']))
return django.http.HttpResponse(
'\n\n'.join(response_list), d1_common.const.CONTENT_TYPE_TEXT
)
return response | python | def _debug_mode_responses(self, request, response):
"""Extra functionality available in debug mode.
- If pretty printed output was requested, force the content type to text. This
causes the browser to not try to format the output in any way.
- If SQL profiling is turned on, return a page with SQL query timing
information instead of the actual response.
"""
if django.conf.settings.DEBUG_GMN:
if 'pretty' in request.GET:
response['Content-Type'] = d1_common.const.CONTENT_TYPE_TEXT
if (
'HTTP_VENDOR_PROFILE_SQL' in request.META
or django.conf.settings.DEBUG_PROFILE_SQL
):
response_list = []
for query in django.db.connection.queries:
response_list.append('{}\n{}'.format(query['time'], query['sql']))
return django.http.HttpResponse(
'\n\n'.join(response_list), d1_common.const.CONTENT_TYPE_TEXT
)
return response | [
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genialis/resolwe | resolwe/elastic/builder.py | BuildArgumentsCache._get_cache_key | def _get_cache_key(self, obj):
"""Derive cache key for given object."""
if obj is not None:
# Make sure that key is REALLY unique.
return '{}-{}'.format(id(self), obj.pk)
return "{}-None".format(id(self)) | python | def _get_cache_key(self, obj):
"""Derive cache key for given object."""
if obj is not None:
# Make sure that key is REALLY unique.
return '{}-{}'.format(id(self), obj.pk)
return "{}-None".format(id(self)) | [
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genialis/resolwe | resolwe/elastic/builder.py | BuildArgumentsCache.set | def set(self, obj, build_kwargs):
"""Set cached value."""
if build_kwargs is None:
build_kwargs = {}
cached = {}
if 'queryset' in build_kwargs:
cached = {
'model': build_kwargs['queryset'].model,
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}
elif 'obj' in build_kwargs:
cached = {
'obj': build_kwargs['obj'],
}
if not hasattr(self._thread_local, 'cache'):
self._thread_local.cache = {}
self._thread_local.cache[self._get_cache_key(obj)] = cached | python | def set(self, obj, build_kwargs):
"""Set cached value."""
if build_kwargs is None:
build_kwargs = {}
cached = {}
if 'queryset' in build_kwargs:
cached = {
'model': build_kwargs['queryset'].model,
'pks': list(build_kwargs['queryset'].values_list('pk', flat=True)),
}
elif 'obj' in build_kwargs:
cached = {
'obj': build_kwargs['obj'],
}
if not hasattr(self._thread_local, 'cache'):
self._thread_local.cache = {}
self._thread_local.cache[self._get_cache_key(obj)] = cached | [
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genialis/resolwe | resolwe/elastic/builder.py | BuildArgumentsCache.take | def take(self, obj):
"""Get cached value and clean cache."""
cached = self._thread_local.cache[self._get_cache_key(obj)]
build_kwargs = {}
if 'model' in cached and 'pks' in cached:
build_kwargs['queryset'] = cached['model'].objects.filter(pk__in=cached['pks'])
elif 'obj' in cached:
if cached['obj'].__class__.objects.filter(pk=cached['obj'].pk).exists():
build_kwargs['obj'] = cached['obj']
else:
# Object was deleted in the meantime.
build_kwargs['queryset'] = cached['obj'].__class__.objects.none()
self._clean_cache(obj)
return build_kwargs | python | def take(self, obj):
"""Get cached value and clean cache."""
cached = self._thread_local.cache[self._get_cache_key(obj)]
build_kwargs = {}
if 'model' in cached and 'pks' in cached:
build_kwargs['queryset'] = cached['model'].objects.filter(pk__in=cached['pks'])
elif 'obj' in cached:
if cached['obj'].__class__.objects.filter(pk=cached['obj'].pk).exists():
build_kwargs['obj'] = cached['obj']
else:
# Object was deleted in the meantime.
build_kwargs['queryset'] = cached['obj'].__class__.objects.none()
self._clean_cache(obj)
return build_kwargs | [
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genialis/resolwe | resolwe/elastic/builder.py | ElasticSignal.connect | def connect(self, signal, **kwargs):
"""Connect a specific signal type to this receiver."""
signal.connect(self, **kwargs)
self.connections.append((signal, kwargs)) | python | def connect(self, signal, **kwargs):
"""Connect a specific signal type to this receiver."""
signal.connect(self, **kwargs)
self.connections.append((signal, kwargs)) | [
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genialis/resolwe | resolwe/elastic/builder.py | ElasticSignal.disconnect | def disconnect(self):
"""Disconnect all connected signal types from this receiver."""
for signal, kwargs in self.connections:
signal.disconnect(self, **kwargs) | python | def disconnect(self):
"""Disconnect all connected signal types from this receiver."""
for signal, kwargs in self.connections:
signal.disconnect(self, **kwargs) | [
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genialis/resolwe | resolwe/elastic/builder.py | ManyToManyDependency._filter | def _filter(self, objects, **kwargs):
"""Determine if dependent object should be processed."""
for obj in objects:
if self.filter(obj, **kwargs) is False:
return False
return True | python | def _filter(self, objects, **kwargs):
"""Determine if dependent object should be processed."""
for obj in objects:
if self.filter(obj, **kwargs) is False:
return False
return True | [
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genialis/resolwe | resolwe/elastic/builder.py | ManyToManyDependency._get_build_kwargs | def _get_build_kwargs(self, obj, pk_set=None, action=None, update_fields=None, reverse=None, **kwargs):
"""Prepare arguments for rebuilding indices."""
if action is None:
# Check filter before rebuilding index.
if not self._filter([obj], update_fields=update_fields):
return
queryset = getattr(obj, self.accessor).all()
# Special handling for relations to self.
if self.field.rel.model == self.field.rel.related_model:
queryset = queryset.union(getattr(obj, self.field.rel.get_accessor_name()).all())
return {'queryset': queryset}
else:
# Update to relation itself, only update the object in question.
if self.field.rel.model == self.field.rel.related_model:
# Special case, self-reference, update both ends of the relation.
pks = set()
if self._filter(self.model.objects.filter(pk__in=pk_set)):
pks.add(obj.pk)
if self._filter(self.model.objects.filter(pk__in=[obj.pk])):
pks.update(pk_set)
return {'queryset': self.index.object_type.objects.filter(pk__in=pks)}
elif isinstance(obj, self.model):
# Need to switch the role of object and pk_set.
result = {'queryset': self.index.object_type.objects.filter(pk__in=pk_set)}
pk_set = {obj.pk}
else:
result = {'obj': obj}
if action != 'post_clear':
# Check filter before rebuilding index.
if not self._filter(self.model.objects.filter(pk__in=pk_set)):
return
return result | python | def _get_build_kwargs(self, obj, pk_set=None, action=None, update_fields=None, reverse=None, **kwargs):
"""Prepare arguments for rebuilding indices."""
if action is None:
# Check filter before rebuilding index.
if not self._filter([obj], update_fields=update_fields):
return
queryset = getattr(obj, self.accessor).all()
# Special handling for relations to self.
if self.field.rel.model == self.field.rel.related_model:
queryset = queryset.union(getattr(obj, self.field.rel.get_accessor_name()).all())
return {'queryset': queryset}
else:
# Update to relation itself, only update the object in question.
if self.field.rel.model == self.field.rel.related_model:
# Special case, self-reference, update both ends of the relation.
pks = set()
if self._filter(self.model.objects.filter(pk__in=pk_set)):
pks.add(obj.pk)
if self._filter(self.model.objects.filter(pk__in=[obj.pk])):
pks.update(pk_set)
return {'queryset': self.index.object_type.objects.filter(pk__in=pks)}
elif isinstance(obj, self.model):
# Need to switch the role of object and pk_set.
result = {'queryset': self.index.object_type.objects.filter(pk__in=pk_set)}
pk_set = {obj.pk}
else:
result = {'obj': obj}
if action != 'post_clear':
# Check filter before rebuilding index.
if not self._filter(self.model.objects.filter(pk__in=pk_set)):
return
return result | [
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genialis/resolwe | resolwe/elastic/builder.py | ManyToManyDependency.process_predelete | def process_predelete(self, obj, pk_set=None, action=None, update_fields=None, **kwargs):
"""Render the queryset of influenced objects and cache it."""
build_kwargs = self._get_build_kwargs(obj, pk_set, action, update_fields, **kwargs)
self.delete_cache.set(obj, build_kwargs) | python | def process_predelete(self, obj, pk_set=None, action=None, update_fields=None, **kwargs):
"""Render the queryset of influenced objects and cache it."""
build_kwargs = self._get_build_kwargs(obj, pk_set, action, update_fields, **kwargs)
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genialis/resolwe | resolwe/elastic/builder.py | ManyToManyDependency.process_delete | def process_delete(self, obj, pk_set=None, action=None, update_fields=None, **kwargs):
"""Recreate queryset from the index and rebuild the index."""
build_kwargs = self.delete_cache.take(obj)
if build_kwargs:
self.index.build(**build_kwargs) | python | def process_delete(self, obj, pk_set=None, action=None, update_fields=None, **kwargs):
"""Recreate queryset from the index and rebuild the index."""
build_kwargs = self.delete_cache.take(obj)
if build_kwargs:
self.index.build(**build_kwargs) | [
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genialis/resolwe | resolwe/elastic/builder.py | ManyToManyDependency._process_m2m_through | def _process_m2m_through(self, obj, action):
"""Process custom M2M through model actions."""
source = getattr(obj, self.field.rel.field.m2m_field_name())
target = getattr(obj, self.field.rel.field.m2m_reverse_field_name())
pk_set = set()
if target:
pk_set.add(target.pk)
self.process_m2m(source, pk_set, action=action, reverse=False, cache_key=obj) | python | def _process_m2m_through(self, obj, action):
"""Process custom M2M through model actions."""
source = getattr(obj, self.field.rel.field.m2m_field_name())
target = getattr(obj, self.field.rel.field.m2m_reverse_field_name())
pk_set = set()
if target:
pk_set.add(target.pk)
self.process_m2m(source, pk_set, action=action, reverse=False, cache_key=obj) | [
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genialis/resolwe | resolwe/elastic/builder.py | ManyToManyDependency.process_m2m_through_save | def process_m2m_through_save(self, obj, created=False, **kwargs):
"""Process M2M post save for custom through model."""
# We are only interested in signals that establish relations.
if not created:
return
self._process_m2m_through(obj, 'post_add') | python | def process_m2m_through_save(self, obj, created=False, **kwargs):
"""Process M2M post save for custom through model."""
# We are only interested in signals that establish relations.
if not created:
return
self._process_m2m_through(obj, 'post_add') | [
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genialis/resolwe | resolwe/elastic/builder.py | IndexBuilder._connect_signal | def _connect_signal(self, index):
"""Create signals for building indexes."""
post_save_signal = ElasticSignal(index, 'build')
post_save_signal.connect(post_save, sender=index.object_type)
self.signals.append(post_save_signal)
post_delete_signal = ElasticSignal(index, 'remove_object')
post_delete_signal.connect(post_delete, sender=index.object_type)
self.signals.append(post_delete_signal)
# Connect signals for all dependencies.
for dependency in index.get_dependencies():
# Automatically convert m2m fields to dependencies.
if isinstance(dependency, (models.ManyToManyField, ManyToManyDescriptor)):
dependency = ManyToManyDependency(dependency)
elif not isinstance(dependency, Dependency):
raise TypeError("Unsupported dependency type: {}".format(repr(dependency)))
signal = dependency.connect(index)
self.signals.extend(signal) | python | def _connect_signal(self, index):
"""Create signals for building indexes."""
post_save_signal = ElasticSignal(index, 'build')
post_save_signal.connect(post_save, sender=index.object_type)
self.signals.append(post_save_signal)
post_delete_signal = ElasticSignal(index, 'remove_object')
post_delete_signal.connect(post_delete, sender=index.object_type)
self.signals.append(post_delete_signal)
# Connect signals for all dependencies.
for dependency in index.get_dependencies():
# Automatically convert m2m fields to dependencies.
if isinstance(dependency, (models.ManyToManyField, ManyToManyDescriptor)):
dependency = ManyToManyDependency(dependency)
elif not isinstance(dependency, Dependency):
raise TypeError("Unsupported dependency type: {}".format(repr(dependency)))
signal = dependency.connect(index)
self.signals.extend(signal) | [
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genialis/resolwe | resolwe/elastic/builder.py | IndexBuilder.register_signals | def register_signals(self):
"""Register signals for all indexes."""
for index in self.indexes:
if index.object_type:
self._connect_signal(index) | python | def register_signals(self):
"""Register signals for all indexes."""
for index in self.indexes:
if index.object_type:
self._connect_signal(index) | [
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genialis/resolwe | resolwe/elastic/builder.py | IndexBuilder.discover_indexes | def discover_indexes(self):
"""Save list of index builders into ``_index_builders``."""
self.indexes = []
for app_config in apps.get_app_configs():
indexes_path = '{}.elastic_indexes'.format(app_config.name)
try:
indexes_module = import_module(indexes_path)
for attr_name in dir(indexes_module):
attr = getattr(indexes_module, attr_name)
if inspect.isclass(attr) and issubclass(attr, BaseIndex) and attr is not BaseIndex:
# Make sure that parallel tests have different indices.
if is_testing():
index = attr.document_class._index._name # pylint: disable=protected-access
testing_postfix = '_test_{}_{}'.format(TESTING_UUID, os.getpid())
if not index.endswith(testing_postfix):
# Replace current postfix with the new one.
if attr.testing_postfix:
index = index[:-len(attr.testing_postfix)]
index = index + testing_postfix
attr.testing_postfix = testing_postfix
attr.document_class._index._name = index # pylint: disable=protected-access
index = attr()
# Apply any extensions defined for the given index. Currently index extensions are
# limited to extending "mappings".
for extension in composer.get_extensions(attr):
mapping = getattr(extension, 'mapping', {})
index.mapping.update(mapping)
self.indexes.append(index)
except ImportError as ex:
if not re.match('No module named .*elastic_indexes.*', str(ex)):
raise | python | def discover_indexes(self):
"""Save list of index builders into ``_index_builders``."""
self.indexes = []
for app_config in apps.get_app_configs():
indexes_path = '{}.elastic_indexes'.format(app_config.name)
try:
indexes_module = import_module(indexes_path)
for attr_name in dir(indexes_module):
attr = getattr(indexes_module, attr_name)
if inspect.isclass(attr) and issubclass(attr, BaseIndex) and attr is not BaseIndex:
# Make sure that parallel tests have different indices.
if is_testing():
index = attr.document_class._index._name # pylint: disable=protected-access
testing_postfix = '_test_{}_{}'.format(TESTING_UUID, os.getpid())
if not index.endswith(testing_postfix):
# Replace current postfix with the new one.
if attr.testing_postfix:
index = index[:-len(attr.testing_postfix)]
index = index + testing_postfix
attr.testing_postfix = testing_postfix
attr.document_class._index._name = index # pylint: disable=protected-access
index = attr()
# Apply any extensions defined for the given index. Currently index extensions are
# limited to extending "mappings".
for extension in composer.get_extensions(attr):
mapping = getattr(extension, 'mapping', {})
index.mapping.update(mapping)
self.indexes.append(index)
except ImportError as ex:
if not re.match('No module named .*elastic_indexes.*', str(ex)):
raise | [
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genialis/resolwe | resolwe/elastic/builder.py | IndexBuilder.build | def build(self, obj=None, queryset=None, push=True):
"""Trigger building of the indexes.
Support passing ``obj`` parameter to the indexes, so we can
trigger build only for one object.
"""
for index in self.indexes:
index.build(obj, queryset, push) | python | def build(self, obj=None, queryset=None, push=True):
"""Trigger building of the indexes.
Support passing ``obj`` parameter to the indexes, so we can
trigger build only for one object.
"""
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genialis/resolwe | resolwe/elastic/builder.py | IndexBuilder.delete | def delete(self, skip_mapping=False):
"""Delete all entries from ElasticSearch."""
for index in self.indexes:
index.destroy()
if not skip_mapping:
index.create_mapping() | python | def delete(self, skip_mapping=False):
"""Delete all entries from ElasticSearch."""
for index in self.indexes:
index.destroy()
if not skip_mapping:
index.create_mapping() | [
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genialis/resolwe | resolwe/elastic/builder.py | IndexBuilder.destroy | def destroy(self):
"""Delete all indexes from Elasticsearch and index builder."""
self.unregister_signals()
for index in self.indexes:
index.destroy()
self.indexes = [] | python | def destroy(self):
"""Delete all indexes from Elasticsearch and index builder."""
self.unregister_signals()
for index in self.indexes:
index.destroy()
self.indexes = [] | [
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wilson-eft/wilson | wilson/run/smeft/classes.py | SMEFT._set_initial | def _set_initial(self, C_in, scale_in):
r"""Set the initial values for parameters and Wilson coefficients at
the scale `scale_in`."""
self.C_in = C_in
self.scale_in = scale_in | python | def _set_initial(self, C_in, scale_in):
r"""Set the initial values for parameters and Wilson coefficients at
the scale `scale_in`."""
self.C_in = C_in
self.scale_in = scale_in | [
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wilson-eft/wilson | wilson/run/smeft/classes.py | SMEFT._rgevolve_leadinglog | def _rgevolve_leadinglog(self, scale_out):
"""Compute the leading logarithmic approximation to the solution
of the SMEFT RGEs from the initial scale to `scale_out`.
Returns a dictionary with parameters and Wilson coefficients.
Much faster but less precise that `rgevolve`.
"""
self._check_initial()
return rge.smeft_evolve_leadinglog(C_in=self.C_in,
scale_in=self.scale_in,
scale_out=scale_out) | python | def _rgevolve_leadinglog(self, scale_out):
"""Compute the leading logarithmic approximation to the solution
of the SMEFT RGEs from the initial scale to `scale_out`.
Returns a dictionary with parameters and Wilson coefficients.
Much faster but less precise that `rgevolve`.
"""
self._check_initial()
return rge.smeft_evolve_leadinglog(C_in=self.C_in,
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wilson-eft/wilson | wilson/run/smeft/classes.py | SMEFT.get_smpar | def get_smpar(self, accuracy='integrate', scale_sm=91.1876):
"""Compute the SM MS-bar parameters at the electroweak scale.
This method can be used to validate the accuracy of the iterative
extraction of SM parameters. If successful, the values returned by this
method should agree with the values in the dictionary
`wilson.run.smeft.smpar.p`."""
if accuracy == 'integrate':
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C_out = self._rgevolve_leadinglog(scale_sm)
else:
raise ValueError("'{}' is not a valid value of 'accuracy' (must be either 'integrate' or 'leadinglog').".format(accuracy))
return smpar.smpar(C_out) | python | def get_smpar(self, accuracy='integrate', scale_sm=91.1876):
"""Compute the SM MS-bar parameters at the electroweak scale.
This method can be used to validate the accuracy of the iterative
extraction of SM parameters. If successful, the values returned by this
method should agree with the values in the dictionary
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if accuracy == 'integrate':
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else:
raise ValueError("'{}' is not a valid value of 'accuracy' (must be either 'integrate' or 'leadinglog').".format(accuracy))
return smpar.smpar(C_out) | [
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wilson-eft/wilson | wilson/run/smeft/classes.py | SMEFT.run_continuous | def run_continuous(self, scale):
"""Return a continuous solution to the RGE as `RGsolution` instance."""
if scale == self.scale_in:
raise ValueError("The scale must be different from the input scale")
elif scale < self.scale_in:
scale_min = scale
scale_max = self.scale_in
elif scale > self.scale_in:
scale_max = scale
scale_min = self.scale_in
fun = rge.smeft_evolve_continuous(C_in=self.C_in,
scale_in=self.scale_in,
scale_out=scale)
return wilson.classes.RGsolution(fun, scale_min, scale_max) | python | def run_continuous(self, scale):
"""Return a continuous solution to the RGE as `RGsolution` instance."""
if scale == self.scale_in:
raise ValueError("The scale must be different from the input scale")
elif scale < self.scale_in:
scale_min = scale
scale_max = self.scale_in
elif scale > self.scale_in:
scale_max = scale
scale_min = self.scale_in
fun = rge.smeft_evolve_continuous(C_in=self.C_in,
scale_in=self.scale_in,
scale_out=scale)
return wilson.classes.RGsolution(fun, scale_min, scale_max) | [
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genialis/resolwe | resolwe/flow/models/fields.py | ResolweSlugField.deconstruct | def deconstruct(self):
"""Deconstruct method."""
name, path, args, kwargs = super().deconstruct()
if self.populate_from is not None:
kwargs['populate_from'] = self.populate_from
if self.unique_with != ():
kwargs['unique_with'] = self.unique_with
kwargs.pop('unique', None)
return name, path, args, kwargs | python | def deconstruct(self):
"""Deconstruct method."""
name, path, args, kwargs = super().deconstruct()
if self.populate_from is not None:
kwargs['populate_from'] = self.populate_from
if self.unique_with != ():
kwargs['unique_with'] = self.unique_with
kwargs.pop('unique', None)
return name, path, args, kwargs | [
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genialis/resolwe | resolwe/flow/models/fields.py | ResolweSlugField._get_unique_constraints | def _get_unique_constraints(self, instance):
"""Return SQL filter for filtering by fields in ``unique_with`` attribute.
Filter is returned as tuple of two elements where first one is
placeholder which is safe to insert into SQL query and second
one may include potentially dangerous values and must be passed
to SQL query in ``params`` attribute to make sure it is properly
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"""
constraints_expression = []
constraints_values = {}
for field_name in self.unique_with:
if constants.LOOKUP_SEP in field_name:
raise NotImplementedError(
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)
field = instance._meta.get_field(field_name) # pylint: disable=protected-access
field_value = getattr(instance, field_name)
# Convert value to the database representation.
field_db_value = field.get_prep_value(field_value)
constraint_key = 'unique_' + field_name
constraints_expression.append("{} = %({})s".format(
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constraint_key
))
constraints_values[constraint_key] = field_db_value
if not constraints_expression:
return '', []
constraints_expression = 'AND ' + ' AND '.join(constraints_expression)
return constraints_expression, constraints_values | python | def _get_unique_constraints(self, instance):
"""Return SQL filter for filtering by fields in ``unique_with`` attribute.
Filter is returned as tuple of two elements where first one is
placeholder which is safe to insert into SQL query and second
one may include potentially dangerous values and must be passed
to SQL query in ``params`` attribute to make sure it is properly
escaped.
"""
constraints_expression = []
constraints_values = {}
for field_name in self.unique_with:
if constants.LOOKUP_SEP in field_name:
raise NotImplementedError(
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)
field = instance._meta.get_field(field_name) # pylint: disable=protected-access
field_value = getattr(instance, field_name)
# Convert value to the database representation.
field_db_value = field.get_prep_value(field_value)
constraint_key = 'unique_' + field_name
constraints_expression.append("{} = %({})s".format(
connection.ops.quote_name(field.column),
constraint_key
))
constraints_values[constraint_key] = field_db_value
if not constraints_expression:
return '', []
constraints_expression = 'AND ' + ' AND '.join(constraints_expression)
return constraints_expression, constraints_values | [
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genialis/resolwe | resolwe/flow/models/fields.py | ResolweSlugField._get_populate_from_value | def _get_populate_from_value(self, instance):
"""Get the value from ``populate_from`` attribute."""
if hasattr(self.populate_from, '__call__'):
# ResolweSlugField(populate_from=lambda instance: ...)
return self.populate_from(instance)
else:
# ResolweSlugField(populate_from='foo')
attr = getattr(instance, self.populate_from)
return attr() if callable(attr) else attr | python | def _get_populate_from_value(self, instance):
"""Get the value from ``populate_from`` attribute."""
if hasattr(self.populate_from, '__call__'):
# ResolweSlugField(populate_from=lambda instance: ...)
return self.populate_from(instance)
else:
# ResolweSlugField(populate_from='foo')
attr = getattr(instance, self.populate_from)
return attr() if callable(attr) else attr | [
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] | f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86 | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/flow/models/fields.py#L79-L87 | train | 45,524 |
genialis/resolwe | resolwe/flow/execution_engines/workflow/__init__.py | ExecutionEngine._evaluate_expressions | def _evaluate_expressions(self, expression_engine, step_id, values, context):
"""Recursively evaluate expressions in a dictionary of values."""
if expression_engine is None:
return values
processed = {}
for name, value in values.items():
if isinstance(value, str):
value = value.strip()
try:
expression = expression_engine.get_inline_expression(value)
if expression is not None:
# Inline expression.
value = expression_engine.evaluate_inline(expression, context)
else:
# Block expression.
value = expression_engine.evaluate_block(value, context)
except EvaluationError as error:
raise ExecutionError('Error while evaluating expression for step "{}":\n{}'.format(
step_id, error
))
elif isinstance(value, dict):
value = self._evaluate_expressions(expression_engine, step_id, value, context)
processed[name] = value
return processed | python | def _evaluate_expressions(self, expression_engine, step_id, values, context):
"""Recursively evaluate expressions in a dictionary of values."""
if expression_engine is None:
return values
processed = {}
for name, value in values.items():
if isinstance(value, str):
value = value.strip()
try:
expression = expression_engine.get_inline_expression(value)
if expression is not None:
# Inline expression.
value = expression_engine.evaluate_inline(expression, context)
else:
# Block expression.
value = expression_engine.evaluate_block(value, context)
except EvaluationError as error:
raise ExecutionError('Error while evaluating expression for step "{}":\n{}'.format(
step_id, error
))
elif isinstance(value, dict):
value = self._evaluate_expressions(expression_engine, step_id, value, context)
processed[name] = value
return processed | [
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genialis/resolwe | resolwe/flow/executors/manager_commands.py | init | async def init():
"""Create a connection to the Redis server."""
global redis_conn # pylint: disable=global-statement,invalid-name
conn = await aioredis.create_connection(
'redis://{}:{}'.format(
SETTINGS.get('FLOW_EXECUTOR', {}).get('REDIS_CONNECTION', {}).get('host', 'localhost'),
SETTINGS.get('FLOW_EXECUTOR', {}).get('REDIS_CONNECTION', {}).get('port', 56379)
),
db=int(SETTINGS.get('FLOW_EXECUTOR', {}).get('REDIS_CONNECTION', {}).get('db', 1))
)
redis_conn = aioredis.Redis(conn) | python | async def init():
"""Create a connection to the Redis server."""
global redis_conn # pylint: disable=global-statement,invalid-name
conn = await aioredis.create_connection(
'redis://{}:{}'.format(
SETTINGS.get('FLOW_EXECUTOR', {}).get('REDIS_CONNECTION', {}).get('host', 'localhost'),
SETTINGS.get('FLOW_EXECUTOR', {}).get('REDIS_CONNECTION', {}).get('port', 56379)
),
db=int(SETTINGS.get('FLOW_EXECUTOR', {}).get('REDIS_CONNECTION', {}).get('db', 1))
)
redis_conn = aioredis.Redis(conn) | [
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genialis/resolwe | resolwe/flow/executors/manager_commands.py | send_manager_command | async def send_manager_command(cmd, expect_reply=True, extra_fields={}):
"""Send a properly formatted command to the manager.
:param cmd: The command to send (:class:`str`).
:param expect_reply: If ``True``, wait for the manager to reply
with an acknowledgement packet.
:param extra_fields: A dictionary of extra information that's
merged into the packet body (i.e. not under an extra key).
"""
packet = {
ExecutorProtocol.DATA_ID: DATA['id'],
ExecutorProtocol.COMMAND: cmd,
}
packet.update(extra_fields)
logger.debug("Sending command to listener: {}".format(json.dumps(packet)))
# TODO what happens here if the push fails? we don't have any realistic recourse,
# so just let it explode and stop processing
queue_channel = EXECUTOR_SETTINGS['REDIS_CHANNEL_PAIR'][0]
try:
await redis_conn.rpush(queue_channel, json.dumps(packet))
except Exception:
logger.error("Error sending command to manager:\n\n{}".format(traceback.format_exc()))
raise
if not expect_reply:
return
for _ in range(_REDIS_RETRIES):
response = await redis_conn.blpop(QUEUE_RESPONSE_CHANNEL, timeout=1)
if response:
break
else:
# NOTE: If there's still no response after a few seconds, the system is broken
# enough that it makes sense to give up; we're isolated here, so if the manager
# doesn't respond, we can't really do much more than just crash
raise RuntimeError("No response from the manager after {} retries.".format(_REDIS_RETRIES))
_, item = response
result = json.loads(item.decode('utf-8'))[ExecutorProtocol.RESULT]
assert result in [ExecutorProtocol.RESULT_OK, ExecutorProtocol.RESULT_ERROR]
if result == ExecutorProtocol.RESULT_OK:
return True
return False | python | async def send_manager_command(cmd, expect_reply=True, extra_fields={}):
"""Send a properly formatted command to the manager.
:param cmd: The command to send (:class:`str`).
:param expect_reply: If ``True``, wait for the manager to reply
with an acknowledgement packet.
:param extra_fields: A dictionary of extra information that's
merged into the packet body (i.e. not under an extra key).
"""
packet = {
ExecutorProtocol.DATA_ID: DATA['id'],
ExecutorProtocol.COMMAND: cmd,
}
packet.update(extra_fields)
logger.debug("Sending command to listener: {}".format(json.dumps(packet)))
# TODO what happens here if the push fails? we don't have any realistic recourse,
# so just let it explode and stop processing
queue_channel = EXECUTOR_SETTINGS['REDIS_CHANNEL_PAIR'][0]
try:
await redis_conn.rpush(queue_channel, json.dumps(packet))
except Exception:
logger.error("Error sending command to manager:\n\n{}".format(traceback.format_exc()))
raise
if not expect_reply:
return
for _ in range(_REDIS_RETRIES):
response = await redis_conn.blpop(QUEUE_RESPONSE_CHANNEL, timeout=1)
if response:
break
else:
# NOTE: If there's still no response after a few seconds, the system is broken
# enough that it makes sense to give up; we're isolated here, so if the manager
# doesn't respond, we can't really do much more than just crash
raise RuntimeError("No response from the manager after {} retries.".format(_REDIS_RETRIES))
_, item = response
result = json.loads(item.decode('utf-8'))[ExecutorProtocol.RESULT]
assert result in [ExecutorProtocol.RESULT_OK, ExecutorProtocol.RESULT_ERROR]
if result == ExecutorProtocol.RESULT_OK:
return True
return False | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/sysmeta_extract.py | _annotate_query | def _annotate_query(query, generate_dict):
"""Add annotations to the query to retrieve values required by field value generate
functions."""
annotate_key_list = []
for field_name, annotate_dict in generate_dict.items():
for annotate_name, annotate_func in annotate_dict["annotate_dict"].items():
query = annotate_func(query)
annotate_key_list.append(annotate_name)
return query, annotate_key_list | python | def _annotate_query(query, generate_dict):
"""Add annotations to the query to retrieve values required by field value generate
functions."""
annotate_key_list = []
for field_name, annotate_dict in generate_dict.items():
for annotate_name, annotate_func in annotate_dict["annotate_dict"].items():
query = annotate_func(query)
annotate_key_list.append(annotate_name)
return query, annotate_key_list | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/sysmeta_extract.py | _value_list_to_sciobj_dict | def _value_list_to_sciobj_dict(
sciobj_value_list, lookup_list, lookup_dict, generate_dict
):
"""Create a dict where the keys are the requested field names, from the values
returned by Django."""
sciobj_dict = {}
# for sciobj_value, lookup_str in zip(sciobj_value_list, lookup_list):
lookup_to_value_dict = {k: v for k, v in zip(lookup_list, sciobj_value_list)}
for field_name, r_dict in lookup_dict.items():
if r_dict["lookup_str"] in lookup_to_value_dict.keys():
sciobj_dict[field_name] = lookup_to_value_dict[r_dict["lookup_str"]]
for field_name, annotate_dict in generate_dict.items():
for final_name, generate_func in annotate_dict["generate_dict"].items():
sciobj_dict[field_name] = generate_func(lookup_to_value_dict)
return sciobj_dict | python | def _value_list_to_sciobj_dict(
sciobj_value_list, lookup_list, lookup_dict, generate_dict
):
"""Create a dict where the keys are the requested field names, from the values
returned by Django."""
sciobj_dict = {}
# for sciobj_value, lookup_str in zip(sciobj_value_list, lookup_list):
lookup_to_value_dict = {k: v for k, v in zip(lookup_list, sciobj_value_list)}
for field_name, r_dict in lookup_dict.items():
if r_dict["lookup_str"] in lookup_to_value_dict.keys():
sciobj_dict[field_name] = lookup_to_value_dict[r_dict["lookup_str"]]
for field_name, annotate_dict in generate_dict.items():
for final_name, generate_func in annotate_dict["generate_dict"].items():
sciobj_dict[field_name] = generate_func(lookup_to_value_dict)
return sciobj_dict | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/sysmeta_extract.py | _split_field_list | def _split_field_list(field_list):
"""Split the list of fields for which to extract values into lists by extraction
methods.
- Remove any duplicated field names.
- Raises ValueError with list of any invalid field names in ``field_list``.
"""
lookup_dict = {}
generate_dict = {}
for field_name in field_list or FIELD_NAME_TO_EXTRACT_DICT.keys():
try:
extract_dict = FIELD_NAME_TO_EXTRACT_DICT[field_name]
except KeyError:
assert_invalid_field_list(field_list)
else:
if "lookup_str" in extract_dict:
lookup_dict[field_name] = extract_dict
else:
generate_dict[field_name] = extract_dict
return lookup_dict, generate_dict | python | def _split_field_list(field_list):
"""Split the list of fields for which to extract values into lists by extraction
methods.
- Remove any duplicated field names.
- Raises ValueError with list of any invalid field names in ``field_list``.
"""
lookup_dict = {}
generate_dict = {}
for field_name in field_list or FIELD_NAME_TO_EXTRACT_DICT.keys():
try:
extract_dict = FIELD_NAME_TO_EXTRACT_DICT[field_name]
except KeyError:
assert_invalid_field_list(field_list)
else:
if "lookup_str" in extract_dict:
lookup_dict[field_name] = extract_dict
else:
generate_dict[field_name] = extract_dict
return lookup_dict, generate_dict | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/views/util.py | dataoneTypes | def dataoneTypes(request):
"""Return the PyXB binding to use when handling a request."""
if is_v1_api(request):
return d1_common.types.dataoneTypes_v1_1
elif is_v2_api(request) or is_diag_api(request):
return d1_common.types.dataoneTypes_v2_0
else:
raise d1_common.types.exceptions.ServiceFailure(
0, 'Unknown version designator in URL. url="{}"'.format(request.path)
) | python | def dataoneTypes(request):
"""Return the PyXB binding to use when handling a request."""
if is_v1_api(request):
return d1_common.types.dataoneTypes_v1_1
elif is_v2_api(request) or is_diag_api(request):
return d1_common.types.dataoneTypes_v2_0
else:
raise d1_common.types.exceptions.ServiceFailure(
0, 'Unknown version designator in URL. url="{}"'.format(request.path)
) | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/views/util.py | parse_and_normalize_url_date | def parse_and_normalize_url_date(date_str):
"""Parse a ISO 8601 date-time with optional timezone.
- Return as datetime with timezone adjusted to UTC.
- Return naive date-time set to UTC.
"""
if date_str is None:
return None
try:
return d1_common.date_time.dt_from_iso8601_str(date_str)
except d1_common.date_time.iso8601.ParseError as e:
raise d1_common.types.exceptions.InvalidRequest(
0,
'Invalid date format for URL parameter. date="{}" error="{}"'.format(
date_str, str(e)
),
) | python | def parse_and_normalize_url_date(date_str):
"""Parse a ISO 8601 date-time with optional timezone.
- Return as datetime with timezone adjusted to UTC.
- Return naive date-time set to UTC.
"""
if date_str is None:
return None
try:
return d1_common.date_time.dt_from_iso8601_str(date_str)
except d1_common.date_time.iso8601.ParseError as e:
raise d1_common.types.exceptions.InvalidRequest(
0,
'Invalid date format for URL parameter. date="{}" error="{}"'.format(
date_str, str(e)
),
) | [
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DataONEorg/d1_python | lib_client/src/d1_client/solr_client.py | SolrClient.get | def get(self, doc_id):
"""Retrieve the specified document."""
resp_dict = self._get_query(q='id:{}'.format(doc_id))
if resp_dict['response']['numFound'] > 0:
return resp_dict['response']['docs'][0] | python | def get(self, doc_id):
"""Retrieve the specified document."""
resp_dict = self._get_query(q='id:{}'.format(doc_id))
if resp_dict['response']['numFound'] > 0:
return resp_dict['response']['docs'][0] | [
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DataONEorg/d1_python | lib_client/src/d1_client/solr_client.py | SolrClient.get_ids | def get_ids(self, start=0, rows=1000, **query_dict):
"""Retrieve a list of identifiers for documents matching the query."""
resp_dict = self._get_query(start=start, rows=rows, **query_dict)
return {
'matches': resp_dict['response']['numFound'],
'start': start,
'ids': [d['id'] for d in resp_dict['response']['docs']],
} | python | def get_ids(self, start=0, rows=1000, **query_dict):
"""Retrieve a list of identifiers for documents matching the query."""
resp_dict = self._get_query(start=start, rows=rows, **query_dict)
return {
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DataONEorg/d1_python | lib_client/src/d1_client/solr_client.py | SolrClient.get_field_values | def get_field_values(self, name, maxvalues=-1, sort=True, **query_dict):
"""Retrieve the unique values for a field, along with their usage counts.
:param name: Name of field for which to retrieve values
:type name: string
:param sort: Sort the result
:param maxvalues: Maximum number of values to retrieve. Default is -1,
which causes retrieval of all values.
:type maxvalues: int
:returns: dict of {fieldname: [[value, count], ... ], }
"""
param_dict = query_dict.copy()
param_dict.update(
{
'rows': '0',
'facet': 'true',
'facet.field': name,
'facet.limit': str(maxvalues),
'facet.zeros': 'false',
'facet.sort': str(sort).lower(),
}
)
resp_dict = self._post_query(**param_dict)
result_dict = resp_dict['facet_counts']['facet_fields']
result_dict['numFound'] = resp_dict['response']['numFound']
return result_dict | python | def get_field_values(self, name, maxvalues=-1, sort=True, **query_dict):
"""Retrieve the unique values for a field, along with their usage counts.
:param name: Name of field for which to retrieve values
:type name: string
:param sort: Sort the result
:param maxvalues: Maximum number of values to retrieve. Default is -1,
which causes retrieval of all values.
:type maxvalues: int
:returns: dict of {fieldname: [[value, count], ... ], }
"""
param_dict = query_dict.copy()
param_dict.update(
{
'rows': '0',
'facet': 'true',
'facet.field': name,
'facet.limit': str(maxvalues),
'facet.zeros': 'false',
'facet.sort': str(sort).lower(),
}
)
resp_dict = self._post_query(**param_dict)
result_dict = resp_dict['facet_counts']['facet_fields']
result_dict['numFound'] = resp_dict['response']['numFound']
return result_dict | [
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DataONEorg/d1_python | lib_client/src/d1_client/solr_client.py | SolrClient._get_solr_type | def _get_solr_type(self, field):
"""Returns the Solr type of the specified field name.
Assumes the convention of dynamic fields using an underscore + type character
code for the field name.
"""
field_type = 'string'
try:
field_type = FIELD_TYPE_CONVERSION_MAP[field]
return field_type
except:
pass
fta = field.split('_')
if len(fta) > 1:
ft = fta[len(fta) - 1]
try:
field_type = FIELD_TYPE_CONVERSION_MAP[ft]
# cache the type so it's used next time
FIELD_TYPE_CONVERSION_MAP[field] = field_type
except:
pass
return field_type | python | def _get_solr_type(self, field):
"""Returns the Solr type of the specified field name.
Assumes the convention of dynamic fields using an underscore + type character
code for the field name.
"""
field_type = 'string'
try:
field_type = FIELD_TYPE_CONVERSION_MAP[field]
return field_type
except:
pass
fta = field.split('_')
if len(fta) > 1:
ft = fta[len(fta) - 1]
try:
field_type = FIELD_TYPE_CONVERSION_MAP[ft]
# cache the type so it's used next time
FIELD_TYPE_CONVERSION_MAP[field] = field_type
except:
pass
return field_type | [
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DataONEorg/d1_python | lib_client/src/d1_client/solr_client.py | SolrClient._get_query | def _get_query(self, **query_dict):
"""Perform a GET query against Solr and return the response as a Python dict."""
param_dict = query_dict.copy()
return self._send_query(do_post=False, **param_dict) | python | def _get_query(self, **query_dict):
"""Perform a GET query against Solr and return the response as a Python dict."""
param_dict = query_dict.copy()
return self._send_query(do_post=False, **param_dict) | [
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DataONEorg/d1_python | lib_client/src/d1_client/solr_client.py | SolrClient._post_query | def _post_query(self, **query_dict):
"""Perform a POST query against Solr and return the response as a Python
dict."""
param_dict = query_dict.copy()
return self._send_query(do_post=True, **param_dict) | python | def _post_query(self, **query_dict):
"""Perform a POST query against Solr and return the response as a Python
dict."""
param_dict = query_dict.copy()
return self._send_query(do_post=True, **param_dict) | [
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DataONEorg/d1_python | lib_client/src/d1_client/solr_client.py | SolrClient._send_query | def _send_query(self, do_post=False, **query_dict):
"""Perform a query against Solr and return the response as a Python dict."""
# self._prepare_query_term()
param_dict = query_dict.copy()
param_dict.setdefault('wt', 'json')
param_dict.setdefault('q', '*.*')
param_dict.setdefault('fl', '*')
return self.query('solr', '', do_post=do_post, query=param_dict) | python | def _send_query(self, do_post=False, **query_dict):
"""Perform a query against Solr and return the response as a Python dict."""
# self._prepare_query_term()
param_dict = query_dict.copy()
param_dict.setdefault('wt', 'json')
param_dict.setdefault('q', '*.*')
param_dict.setdefault('fl', '*')
return self.query('solr', '', do_post=do_post, query=param_dict) | [
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DataONEorg/d1_python | lib_client/src/d1_client/solr_client.py | SolrClient._escape_query_term | def _escape_query_term(self, term):
"""Escape a query term for inclusion in a query.
- Also see: prepare_query_term().
"""
term = term.replace('\\', '\\\\')
for c in RESERVED_CHAR_LIST:
term = term.replace(c, r'\{}'.format(c))
return term | python | def _escape_query_term(self, term):
"""Escape a query term for inclusion in a query.
- Also see: prepare_query_term().
"""
term = term.replace('\\', '\\\\')
for c in RESERVED_CHAR_LIST:
term = term.replace(c, r'\{}'.format(c))
return term | [
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genialis/resolwe | resolwe/flow/migrations/0023_process_entity_2.py | migrate_flow_collection | def migrate_flow_collection(apps, schema_editor):
"""Migrate 'flow_collection' field to 'entity_type'."""
Process = apps.get_model('flow', 'Process')
DescriptorSchema = apps.get_model('flow', 'DescriptorSchema')
for process in Process.objects.all():
process.entity_type = process.flow_collection
process.entity_descriptor_schema = process.flow_collection
if (process.entity_descriptor_schema is not None and
not DescriptorSchema.objects.filter(slug=process.entity_descriptor_schema).exists()):
raise LookupError(
"Descriptow schema '{}' referenced in 'entity_descriptor_schema' not "
"found.".format(process.entity_descriptor_schema)
)
process.save() | python | def migrate_flow_collection(apps, schema_editor):
"""Migrate 'flow_collection' field to 'entity_type'."""
Process = apps.get_model('flow', 'Process')
DescriptorSchema = apps.get_model('flow', 'DescriptorSchema')
for process in Process.objects.all():
process.entity_type = process.flow_collection
process.entity_descriptor_schema = process.flow_collection
if (process.entity_descriptor_schema is not None and
not DescriptorSchema.objects.filter(slug=process.entity_descriptor_schema).exists()):
raise LookupError(
"Descriptow schema '{}' referenced in 'entity_descriptor_schema' not "
"found.".format(process.entity_descriptor_schema)
)
process.save() | [
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DataONEorg/d1_python | lib_common/src/d1_common/type_conversions.py | get_pyxb_binding_by_api_version | def get_pyxb_binding_by_api_version(api_major, api_minor=0):
"""Map DataONE API version tag to PyXB binding.
Given a DataONE API major version number, return PyXB binding that can
serialize and deserialize DataONE XML docs of that version.
Args:
api_major, api_minor: str or int
DataONE API major and minor version numbers.
- If ``api_major`` is an integer, it is combined with ``api_minor`` to form an
exact version.
- If ``api_major`` is a string of ``v1`` or ``v2``, ``api_minor`` is ignored
and the latest PyXB bindingavailable for the ``api_major`` version is
returned.
Returns:
PyXB binding: E.g., ``d1_common.types.dataoneTypes_v1_1``.
"""
try:
return VERSION_TO_BINDING_DICT[api_major, api_minor]
except KeyError:
raise ValueError(
'Unknown DataONE API version: {}.{}'.format(api_major, api_minor)
) | python | def get_pyxb_binding_by_api_version(api_major, api_minor=0):
"""Map DataONE API version tag to PyXB binding.
Given a DataONE API major version number, return PyXB binding that can
serialize and deserialize DataONE XML docs of that version.
Args:
api_major, api_minor: str or int
DataONE API major and minor version numbers.
- If ``api_major`` is an integer, it is combined with ``api_minor`` to form an
exact version.
- If ``api_major`` is a string of ``v1`` or ``v2``, ``api_minor`` is ignored
and the latest PyXB bindingavailable for the ``api_major`` version is
returned.
Returns:
PyXB binding: E.g., ``d1_common.types.dataoneTypes_v1_1``.
"""
try:
return VERSION_TO_BINDING_DICT[api_major, api_minor]
except KeyError:
raise ValueError(
'Unknown DataONE API version: {}.{}'.format(api_major, api_minor)
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DataONEorg/d1_python | lib_common/src/d1_common/type_conversions.py | extract_version_tag_from_url | def extract_version_tag_from_url(url):
"""Extract a DataONE API version tag from a MN or CN service endpoint URL.
Args:
url : str
Service endpoint URL. E.g.: ``https://mn.example.org/path/v2/object/pid``.
Returns:
str : Valid version tags are currently ``v1`` or ``v2``.
"""
m = re.match(r'(/|^)(v\d)(/|$)', url)
if not m:
return None
return m.group(2) | python | def extract_version_tag_from_url(url):
"""Extract a DataONE API version tag from a MN or CN service endpoint URL.
Args:
url : str
Service endpoint URL. E.g.: ``https://mn.example.org/path/v2/object/pid``.
Returns:
str : Valid version tags are currently ``v1`` or ``v2``.
"""
m = re.match(r'(/|^)(v\d)(/|$)', url)
if not m:
return None
return m.group(2) | [
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DataONEorg/d1_python | lib_common/src/d1_common/type_conversions.py | str_to_v1_str | def str_to_v1_str(xml_str):
"""Convert a API v2 XML doc to v1 XML doc.
Removes elements that are only valid for v2 and changes namespace to v1.
If doc is already v1, it is returned unchanged.
Args:
xml_str : str
API v2 XML doc. E.g.: ``SystemMetadata v2``.
Returns:
str : API v1 XML doc. E.g.: ``SystemMetadata v1``.
"""
if str_is_v1(xml_str):
return xml_str
etree_obj = str_to_etree(xml_str)
strip_v2_elements(etree_obj)
etree_replace_namespace(etree_obj, d1_common.types.dataoneTypes_v1.Namespace)
return etree_to_str(etree_obj) | python | def str_to_v1_str(xml_str):
"""Convert a API v2 XML doc to v1 XML doc.
Removes elements that are only valid for v2 and changes namespace to v1.
If doc is already v1, it is returned unchanged.
Args:
xml_str : str
API v2 XML doc. E.g.: ``SystemMetadata v2``.
Returns:
str : API v1 XML doc. E.g.: ``SystemMetadata v1``.
"""
if str_is_v1(xml_str):
return xml_str
etree_obj = str_to_etree(xml_str)
strip_v2_elements(etree_obj)
etree_replace_namespace(etree_obj, d1_common.types.dataoneTypes_v1.Namespace)
return etree_to_str(etree_obj) | [
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DataONEorg/d1_python | lib_common/src/d1_common/type_conversions.py | str_to_v2_str | def str_to_v2_str(xml_str):
"""Convert a API v1 XML doc to v2 XML doc.
All v1 elements are valid for v2, so only changes namespace.
Args:
xml_str : str
API v1 XML doc. E.g.: ``SystemMetadata v1``.
Returns:
str : API v2 XML doc. E.g.: ``SystemMetadata v2``.
"""
if str_is_v2(xml_str):
return xml_str
etree_obj = str_to_etree(xml_str)
etree_replace_namespace(etree_obj, d1_common.types.dataoneTypes_v2_0.Namespace)
return etree_to_str(etree_obj) | python | def str_to_v2_str(xml_str):
"""Convert a API v1 XML doc to v2 XML doc.
All v1 elements are valid for v2, so only changes namespace.
Args:
xml_str : str
API v1 XML doc. E.g.: ``SystemMetadata v1``.
Returns:
str : API v2 XML doc. E.g.: ``SystemMetadata v2``.
"""
if str_is_v2(xml_str):
return xml_str
etree_obj = str_to_etree(xml_str)
etree_replace_namespace(etree_obj, d1_common.types.dataoneTypes_v2_0.Namespace)
return etree_to_str(etree_obj) | [
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DataONEorg/d1_python | lib_common/src/d1_common/type_conversions.py | str_to_etree | def str_to_etree(xml_str, encoding='utf-8'):
"""Deserialize API XML doc to an ElementTree.
Args:
xml_str: bytes
DataONE API XML doc
encoding: str
Decoder to use when converting the XML doc ``bytes`` to a Unicode str.
Returns:
ElementTree: Matching the API version of the XML doc.
"""
parser = xml.etree.ElementTree.XMLParser(encoding=encoding)
return xml.etree.ElementTree.fromstring(xml_str, parser=parser) | python | def str_to_etree(xml_str, encoding='utf-8'):
"""Deserialize API XML doc to an ElementTree.
Args:
xml_str: bytes
DataONE API XML doc
encoding: str
Decoder to use when converting the XML doc ``bytes`` to a Unicode str.
Returns:
ElementTree: Matching the API version of the XML doc.
"""
parser = xml.etree.ElementTree.XMLParser(encoding=encoding)
return xml.etree.ElementTree.fromstring(xml_str, parser=parser) | [
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DataONEorg/d1_python | lib_common/src/d1_common/type_conversions.py | etree_replace_namespace | def etree_replace_namespace(etree_obj, ns_str):
"""In-place change the namespace of elements in an ElementTree.
Args:
etree_obj: ElementTree
ns_str : str
The namespace to set. E.g.: ``http://ns.dataone.org/service/types/v1``.
"""
def _replace_recursive(el, n):
el.tag = re.sub(r'{.*\}', '{{{}}}'.format(n), el.tag)
el.text = el.text.strip() if el.text else None
el.tail = el.tail.strip() if el.tail else None
for child_el in el:
_replace_recursive(child_el, n)
_replace_recursive(etree_obj, ns_str) | python | def etree_replace_namespace(etree_obj, ns_str):
"""In-place change the namespace of elements in an ElementTree.
Args:
etree_obj: ElementTree
ns_str : str
The namespace to set. E.g.: ``http://ns.dataone.org/service/types/v1``.
"""
def _replace_recursive(el, n):
el.tag = re.sub(r'{.*\}', '{{{}}}'.format(n), el.tag)
el.text = el.text.strip() if el.text else None
el.tail = el.tail.strip() if el.tail else None
for child_el in el:
_replace_recursive(child_el, n)
_replace_recursive(etree_obj, ns_str) | [
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DataONEorg/d1_python | lib_common/src/d1_common/type_conversions.py | strip_v2_elements | def strip_v2_elements(etree_obj):
"""In-place remove elements and attributes that are only valid in v2 types.
Args: etree_obj: ElementTree ElementTree holding one of the DataONE API types
that changed between v1 and v2.
"""
if etree_obj.tag == v2_0_tag('logEntry'):
strip_logEntry(etree_obj)
elif etree_obj.tag == v2_0_tag('log'):
strip_log(etree_obj)
elif etree_obj.tag == v2_0_tag('node'):
strip_node(etree_obj)
elif etree_obj.tag == v2_0_tag('nodeList'):
strip_node_list(etree_obj)
elif etree_obj.tag == v2_0_tag('systemMetadata'):
strip_system_metadata(etree_obj)
else:
raise ValueError('Unknown root element. tag="{}"'.format(etree_obj.tag)) | python | def strip_v2_elements(etree_obj):
"""In-place remove elements and attributes that are only valid in v2 types.
Args: etree_obj: ElementTree ElementTree holding one of the DataONE API types
that changed between v1 and v2.
"""
if etree_obj.tag == v2_0_tag('logEntry'):
strip_logEntry(etree_obj)
elif etree_obj.tag == v2_0_tag('log'):
strip_log(etree_obj)
elif etree_obj.tag == v2_0_tag('node'):
strip_node(etree_obj)
elif etree_obj.tag == v2_0_tag('nodeList'):
strip_node_list(etree_obj)
elif etree_obj.tag == v2_0_tag('systemMetadata'):
strip_system_metadata(etree_obj)
else:
raise ValueError('Unknown root element. tag="{}"'.format(etree_obj.tag)) | [
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DataONEorg/d1_python | lib_common/src/d1_common/type_conversions.py | strip_system_metadata | def strip_system_metadata(etree_obj):
"""In-place remove elements and attributes that are only valid in v2 types from v1
System Metadata.
Args: etree_obj: ElementTree ElementTree holding a v1 SystemMetadata.
"""
for series_id_el in etree_obj.findall('seriesId'):
etree_obj.remove(series_id_el)
for media_type_el in etree_obj.findall('mediaType'):
etree_obj.remove(media_type_el)
for file_name_el in etree_obj.findall('fileName'):
etree_obj.remove(file_name_el) | python | def strip_system_metadata(etree_obj):
"""In-place remove elements and attributes that are only valid in v2 types from v1
System Metadata.
Args: etree_obj: ElementTree ElementTree holding a v1 SystemMetadata.
"""
for series_id_el in etree_obj.findall('seriesId'):
etree_obj.remove(series_id_el)
for media_type_el in etree_obj.findall('mediaType'):
etree_obj.remove(media_type_el)
for file_name_el in etree_obj.findall('fileName'):
etree_obj.remove(file_name_el) | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/process_replication_queue.py | ReplicationQueueProcessor._create_replica | def _create_replica(self, sysmeta_pyxb, sciobj_bytestream):
"""GMN handles replicas differently from native objects, with the main
differences being related to handling of restrictions related to revision chains
and SIDs.
So this create sequence differs significantly from the regular one that is
accessed through MNStorage.create().
"""
pid = d1_common.xml.get_req_val(sysmeta_pyxb.identifier)
self._assert_is_pid_of_local_unprocessed_replica(pid)
self._check_and_create_replica_revision(sysmeta_pyxb, "obsoletes")
self._check_and_create_replica_revision(sysmeta_pyxb, "obsoletedBy")
sciobj_url = d1_gmn.app.sciobj_store.get_rel_sciobj_file_url_by_pid(pid)
sciobj_model = d1_gmn.app.sysmeta.create_or_update(sysmeta_pyxb, sciobj_url)
self._store_science_object_bytes(pid, sciobj_bytestream)
d1_gmn.app.event_log.create_log_entry(
sciobj_model, "create", "0.0.0.0", "[replica]", "[replica]"
) | python | def _create_replica(self, sysmeta_pyxb, sciobj_bytestream):
"""GMN handles replicas differently from native objects, with the main
differences being related to handling of restrictions related to revision chains
and SIDs.
So this create sequence differs significantly from the regular one that is
accessed through MNStorage.create().
"""
pid = d1_common.xml.get_req_val(sysmeta_pyxb.identifier)
self._assert_is_pid_of_local_unprocessed_replica(pid)
self._check_and_create_replica_revision(sysmeta_pyxb, "obsoletes")
self._check_and_create_replica_revision(sysmeta_pyxb, "obsoletedBy")
sciobj_url = d1_gmn.app.sciobj_store.get_rel_sciobj_file_url_by_pid(pid)
sciobj_model = d1_gmn.app.sysmeta.create_or_update(sysmeta_pyxb, sciobj_url)
self._store_science_object_bytes(pid, sciobj_bytestream)
d1_gmn.app.event_log.create_log_entry(
sciobj_model, "create", "0.0.0.0", "[replica]", "[replica]"
) | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/import.py | Command.restricted_import | async def restricted_import(self, async_client, node_type):
"""Import only the Science Objects specified by a text file.
The file must be UTF-8 encoded and contain one PIDs or SIDs per line.
"""
item_task_name = "Importing objects"
pid_path = self.options['pid_path']
if not os.path.exists(pid_path):
raise ConnectionError('File does not exist: {}'.format(pid_path))
with open(pid_path, encoding='UTF-8') as pid_file:
self.progress_logger.start_task_type(
item_task_name, len(pid_file.readlines())
)
pid_file.seek(0)
for pid in pid_file.readlines():
pid = pid.strip()
self.progress_logger.start_task(item_task_name)
# Ignore any blank lines in the file
if not pid:
continue
await self.import_aggregated(async_client, pid)
self.progress_logger.end_task_type(item_task_name) | python | async def restricted_import(self, async_client, node_type):
"""Import only the Science Objects specified by a text file.
The file must be UTF-8 encoded and contain one PIDs or SIDs per line.
"""
item_task_name = "Importing objects"
pid_path = self.options['pid_path']
if not os.path.exists(pid_path):
raise ConnectionError('File does not exist: {}'.format(pid_path))
with open(pid_path, encoding='UTF-8') as pid_file:
self.progress_logger.start_task_type(
item_task_name, len(pid_file.readlines())
)
pid_file.seek(0)
for pid in pid_file.readlines():
pid = pid.strip()
self.progress_logger.start_task(item_task_name)
# Ignore any blank lines in the file
if not pid:
continue
await self.import_aggregated(async_client, pid)
self.progress_logger.end_task_type(item_task_name) | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/import.py | Command.get_object_proxy_location | async def get_object_proxy_location(self, client, pid):
"""If object is proxied, return the proxy location URL.
If object is local, return None.
"""
try:
return (await client.describe(pid)).get("DataONE-Proxy")
except d1_common.types.exceptions.DataONEException:
# Workaround for older GMNs that return 500 instead of 404 for describe()
pass | python | async def get_object_proxy_location(self, client, pid):
"""If object is proxied, return the proxy location URL.
If object is local, return None.
"""
try:
return (await client.describe(pid)).get("DataONE-Proxy")
except d1_common.types.exceptions.DataONEException:
# Workaround for older GMNs that return 500 instead of 404 for describe()
pass | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/import.py | Command.probe_node_type_major | async def probe_node_type_major(self, client):
"""Determine if import source node is a CN or MN and which major version API to
use."""
try:
node_pyxb = await self.get_node_doc(client)
except d1_common.types.exceptions.DataONEException as e:
raise django.core.management.base.CommandError(
"Could not find a functional CN or MN at the provided BaseURL. "
'base_url="{}" error="{}"'.format(
self.options["baseurl"], e.friendly_format()
)
)
is_cn = d1_common.type_conversions.pyxb_get_type_name(node_pyxb) == "NodeList"
if is_cn:
self.assert_is_known_node_id(
node_pyxb, django.conf.settings.NODE_IDENTIFIER
)
self._logger.info(
"Importing from CN: {}. filtered on MN: {}".format(
d1_common.xml.get_req_val(
self.find_node(node_pyxb, self.options["baseurl"]).identifier
),
django.conf.settings.NODE_IDENTIFIER,
)
)
return "cn", "v2"
else:
self._logger.info(
"Importing from MN: {}".format(
d1_common.xml.get_req_val(node_pyxb.identifier)
)
)
return "mn", self.find_node_api_version(node_pyxb) | python | async def probe_node_type_major(self, client):
"""Determine if import source node is a CN or MN and which major version API to
use."""
try:
node_pyxb = await self.get_node_doc(client)
except d1_common.types.exceptions.DataONEException as e:
raise django.core.management.base.CommandError(
"Could not find a functional CN or MN at the provided BaseURL. "
'base_url="{}" error="{}"'.format(
self.options["baseurl"], e.friendly_format()
)
)
is_cn = d1_common.type_conversions.pyxb_get_type_name(node_pyxb) == "NodeList"
if is_cn:
self.assert_is_known_node_id(
node_pyxb, django.conf.settings.NODE_IDENTIFIER
)
self._logger.info(
"Importing from CN: {}. filtered on MN: {}".format(
d1_common.xml.get_req_val(
self.find_node(node_pyxb, self.options["baseurl"]).identifier
),
django.conf.settings.NODE_IDENTIFIER,
)
)
return "cn", "v2"
else:
self._logger.info(
"Importing from MN: {}".format(
d1_common.xml.get_req_val(node_pyxb.identifier)
)
)
return "mn", self.find_node_api_version(node_pyxb) | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/import.py | Command.assert_is_known_node_id | def assert_is_known_node_id(self, node_list_pyxb, node_id):
"""When importing from a CN, ensure that the NodeID which the ObjectList will be
filtered by is known to the CN."""
node_pyxb = self.find_node_by_id(node_list_pyxb, node_id)
assert node_pyxb is not None, (
"The NodeID of this GMN instance is unknown to the CN at the provided BaseURL. "
'node_id="{}" base_url="{}"'.format(node_id, self.options["baseurl"])
) | python | def assert_is_known_node_id(self, node_list_pyxb, node_id):
"""When importing from a CN, ensure that the NodeID which the ObjectList will be
filtered by is known to the CN."""
node_pyxb = self.find_node_by_id(node_list_pyxb, node_id)
assert node_pyxb is not None, (
"The NodeID of this GMN instance is unknown to the CN at the provided BaseURL. "
'node_id="{}" base_url="{}"'.format(node_id, self.options["baseurl"])
) | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/import.py | Command.find_node_api_version | def find_node_api_version(self, node_pyxb):
"""Find the highest API major version supported by node."""
max_major = 0
for s in node_pyxb.services.service:
max_major = max(max_major, int(s.version[1:]))
return max_major | python | def find_node_api_version(self, node_pyxb):
"""Find the highest API major version supported by node."""
max_major = 0
for s in node_pyxb.services.service:
max_major = max(max_major, int(s.version[1:]))
return max_major | [
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genialis/resolwe | resolwe/flow/tasks.py | celery_run | def celery_run(data_id, runtime_dir, argv):
"""Run process executor.
:param data_id: The id of the :class:`~resolwe.flow.models.Data`
object to be processed.
:param runtime_dir: The directory from which to run the executor.
:param argv: The argument vector used to run the executor.
:param verbosity: The logging verbosity level.
"""
subprocess.Popen(
argv,
cwd=runtime_dir,
stdin=subprocess.DEVNULL
).wait() | python | def celery_run(data_id, runtime_dir, argv):
"""Run process executor.
:param data_id: The id of the :class:`~resolwe.flow.models.Data`
object to be processed.
:param runtime_dir: The directory from which to run the executor.
:param argv: The argument vector used to run the executor.
:param verbosity: The logging verbosity level.
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subprocess.Popen(
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DataONEorg/d1_python | gmn/src/d1_gmn/app/sysmeta.py | archive_sciobj | def archive_sciobj(pid):
"""Set the status of an object to archived.
Preconditions:
- The object with the pid is verified to exist.
- The object is not a replica.
- The object is not archived.
"""
sciobj_model = d1_gmn.app.model_util.get_sci_model(pid)
sciobj_model.is_archived = True
sciobj_model.save()
_update_modified_timestamp(sciobj_model) | python | def archive_sciobj(pid):
"""Set the status of an object to archived.
Preconditions:
- The object with the pid is verified to exist.
- The object is not a replica.
- The object is not archived.
"""
sciobj_model = d1_gmn.app.model_util.get_sci_model(pid)
sciobj_model.is_archived = True
sciobj_model.save()
_update_modified_timestamp(sciobj_model) | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/sysmeta.py | create_or_update | def create_or_update(sysmeta_pyxb, sciobj_url=None):
"""Create or update database representation of a System Metadata object and closely
related internal state.
- If ``sciobj_url`` is not passed on create, storage in the internal sciobj store
is assumed
- If ``sciobj_url`` is passed on create, it can reference a location in the
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See the sciobj_store module for more information
- if ``sciobj_url`` is not passed on update, the sciobj location remains unchanged
- If ``sciobj_url`` is passed on update, the sciobj location is updated
Preconditions:
- All values in ``sysmeta_pyxb`` must be valid for the operation being performed
"""
# TODO: Make sure that old sections are removed if not included in update.
pid = d1_common.xml.get_req_val(sysmeta_pyxb.identifier)
if sciobj_url is None:
sciobj_url = d1_gmn.app.sciobj_store.get_rel_sciobj_file_url_by_pid(pid)
try:
sci_model = d1_gmn.app.model_util.get_sci_model(pid)
except d1_gmn.app.models.ScienceObject.DoesNotExist:
sci_model = d1_gmn.app.models.ScienceObject()
sci_model.pid = d1_gmn.app.did.get_or_create_did(pid)
sci_model.url = sciobj_url
sci_model.serial_version = sysmeta_pyxb.serialVersion
sci_model.uploaded_timestamp = d1_common.date_time.normalize_datetime_to_utc(
sysmeta_pyxb.dateUploaded
)
_base_pyxb_to_model(sci_model, sysmeta_pyxb)
sci_model.save()
if _has_media_type_pyxb(sysmeta_pyxb):
_media_type_pyxb_to_model(sci_model, sysmeta_pyxb)
_access_policy_pyxb_to_model(sci_model, sysmeta_pyxb)
if _has_replication_policy_pyxb(sysmeta_pyxb):
_replication_policy_pyxb_to_model(sci_model, sysmeta_pyxb)
replica_pyxb_to_model(sci_model, sysmeta_pyxb)
revision_pyxb_to_model(sci_model, sysmeta_pyxb, pid)
sci_model.save()
return sci_model | python | def create_or_update(sysmeta_pyxb, sciobj_url=None):
"""Create or update database representation of a System Metadata object and closely
related internal state.
- If ``sciobj_url`` is not passed on create, storage in the internal sciobj store
is assumed
- If ``sciobj_url`` is passed on create, it can reference a location in the
internal sciobj store, or an arbitrary location on disk, or a remote web server.
See the sciobj_store module for more information
- if ``sciobj_url`` is not passed on update, the sciobj location remains unchanged
- If ``sciobj_url`` is passed on update, the sciobj location is updated
Preconditions:
- All values in ``sysmeta_pyxb`` must be valid for the operation being performed
"""
# TODO: Make sure that old sections are removed if not included in update.
pid = d1_common.xml.get_req_val(sysmeta_pyxb.identifier)
if sciobj_url is None:
sciobj_url = d1_gmn.app.sciobj_store.get_rel_sciobj_file_url_by_pid(pid)
try:
sci_model = d1_gmn.app.model_util.get_sci_model(pid)
except d1_gmn.app.models.ScienceObject.DoesNotExist:
sci_model = d1_gmn.app.models.ScienceObject()
sci_model.pid = d1_gmn.app.did.get_or_create_did(pid)
sci_model.url = sciobj_url
sci_model.serial_version = sysmeta_pyxb.serialVersion
sci_model.uploaded_timestamp = d1_common.date_time.normalize_datetime_to_utc(
sysmeta_pyxb.dateUploaded
)
_base_pyxb_to_model(sci_model, sysmeta_pyxb)
sci_model.save()
if _has_media_type_pyxb(sysmeta_pyxb):
_media_type_pyxb_to_model(sci_model, sysmeta_pyxb)
_access_policy_pyxb_to_model(sci_model, sysmeta_pyxb)
if _has_replication_policy_pyxb(sysmeta_pyxb):
_replication_policy_pyxb_to_model(sci_model, sysmeta_pyxb)
replica_pyxb_to_model(sci_model, sysmeta_pyxb)
revision_pyxb_to_model(sci_model, sysmeta_pyxb, pid)
sci_model.save()
return sci_model | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/sysmeta.py | _access_policy_pyxb_to_model | def _access_policy_pyxb_to_model(sci_model, sysmeta_pyxb):
"""Create or update the database representation of the sysmeta_pyxb access policy.
If called without an access policy, any existing permissions on the object
are removed and the access policy for the rights holder is recreated.
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"""
_delete_existing_access_policy(sysmeta_pyxb)
# Add an implicit allow rule with all permissions for the rights holder.
allow_rights_holder = d1_common.types.dataoneTypes.AccessRule()
permission = d1_common.types.dataoneTypes.Permission(
d1_gmn.app.auth.CHANGEPERMISSION_STR
)
allow_rights_holder.permission.append(permission)
allow_rights_holder.subject.append(
d1_common.xml.get_req_val(sysmeta_pyxb.rightsHolder)
)
top_level = _get_highest_level_action_for_rule(allow_rights_holder)
_insert_permission_rows(sci_model, allow_rights_holder, top_level)
# Create db entries for all subjects for which permissions have been granted.
if _has_access_policy_pyxb(sysmeta_pyxb):
for allow_rule in sysmeta_pyxb.accessPolicy.allow:
top_level = _get_highest_level_action_for_rule(allow_rule)
_insert_permission_rows(sci_model, allow_rule, top_level) | python | def _access_policy_pyxb_to_model(sci_model, sysmeta_pyxb):
"""Create or update the database representation of the sysmeta_pyxb access policy.
If called without an access policy, any existing permissions on the object
are removed and the access policy for the rights holder is recreated.
Preconditions:
- Each subject has been verified to a valid DataONE account.
- Subject has changePermission for object.
Postconditions:
- The Permission and related tables contain the new access policy.
Notes:
- There can be multiple rules in a policy and each rule can contain multiple
subjects. So there are two ways that the same subject can be specified multiple
times in a policy. If this happens, multiple, conflicting action levels may be
provided for the subject. This is handled by checking for an existing row for
the subject for this object and updating it if it contains a lower action
level. The end result is that there is one row for each subject, for each
object and this row contains the highest action level.
"""
_delete_existing_access_policy(sysmeta_pyxb)
# Add an implicit allow rule with all permissions for the rights holder.
allow_rights_holder = d1_common.types.dataoneTypes.AccessRule()
permission = d1_common.types.dataoneTypes.Permission(
d1_gmn.app.auth.CHANGEPERMISSION_STR
)
allow_rights_holder.permission.append(permission)
allow_rights_holder.subject.append(
d1_common.xml.get_req_val(sysmeta_pyxb.rightsHolder)
)
top_level = _get_highest_level_action_for_rule(allow_rights_holder)
_insert_permission_rows(sci_model, allow_rights_holder, top_level)
# Create db entries for all subjects for which permissions have been granted.
if _has_access_policy_pyxb(sysmeta_pyxb):
for allow_rule in sysmeta_pyxb.accessPolicy.allow:
top_level = _get_highest_level_action_for_rule(allow_rule)
_insert_permission_rows(sci_model, allow_rule, top_level) | [
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DataONEorg/d1_python | lib_common/src/d1_common/cert/view_subject_info.py | deserialize_subject_info | def deserialize_subject_info(subject_info_xml_path):
"""Deserialize a SubjectInfo XML file to a PyXB object."""
try:
with open(subject_info_xml_path) as f:
return d1_common.xml.deserialize(f.read())
except ValueError as e:
raise d1_common.types.exceptions.InvalidToken(
0,
'Could not deserialize SubjectInfo. subject_info="{}", error="{}"'.format(
subject_info_xml_path, str(e)
),
) | python | def deserialize_subject_info(subject_info_xml_path):
"""Deserialize a SubjectInfo XML file to a PyXB object."""
try:
with open(subject_info_xml_path) as f:
return d1_common.xml.deserialize(f.read())
except ValueError as e:
raise d1_common.types.exceptions.InvalidToken(
0,
'Could not deserialize SubjectInfo. subject_info="{}", error="{}"'.format(
subject_info_xml_path, str(e)
),
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DataONEorg/d1_python | lib_client/src/d1_client/session.py | Session.HEAD | def HEAD(self, rest_path_list, **kwargs):
"""Send a HEAD request. See requests.sessions.request for optional parameters.
:returns: Response object
"""
kwargs.setdefault("allow_redirects", False)
return self._request("HEAD", rest_path_list, **kwargs) | python | def HEAD(self, rest_path_list, **kwargs):
"""Send a HEAD request. See requests.sessions.request for optional parameters.
:returns: Response object
"""
kwargs.setdefault("allow_redirects", False)
return self._request("HEAD", rest_path_list, **kwargs) | [
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DataONEorg/d1_python | lib_client/src/d1_client/session.py | Session.get_curl_command_line | def get_curl_command_line(self, method, url, **kwargs):
"""Get request as cURL command line for debugging."""
if kwargs.get("query"):
url = "{}?{}".format(url, d1_common.url.urlencode(kwargs["query"]))
curl_list = ["curl"]
if method.lower() == "head":
curl_list.append("--head")
else:
curl_list.append("-X {}".format(method))
for k, v in sorted(list(kwargs["headers"].items())):
curl_list.append('-H "{}: {}"'.format(k, v))
curl_list.append("{}".format(url))
return " ".join(curl_list) | python | def get_curl_command_line(self, method, url, **kwargs):
"""Get request as cURL command line for debugging."""
if kwargs.get("query"):
url = "{}?{}".format(url, d1_common.url.urlencode(kwargs["query"]))
curl_list = ["curl"]
if method.lower() == "head":
curl_list.append("--head")
else:
curl_list.append("-X {}".format(method))
for k, v in sorted(list(kwargs["headers"].items())):
curl_list.append('-H "{}: {}"'.format(k, v))
curl_list.append("{}".format(url))
return " ".join(curl_list) | [
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DataONEorg/d1_python | lib_client/src/d1_client/session.py | Session.dump_request_and_response | def dump_request_and_response(self, response):
"""Return a string containing a nicely formatted representation of the request
and response objects for logging and debugging.
- Note: Does not work if the request or response body is a MultipartEncoder
object.
"""
if response.reason is None:
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return d1_client.util.normalize_request_response_dump(
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"""Return a string containing a nicely formatted representation of the request
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- Note: Does not work if the request or response body is a MultipartEncoder
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"""
if response.reason is None:
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DataONEorg/d1_python | lib_client/src/d1_client/session.py | Session._timeout_to_float | def _timeout_to_float(self, timeout):
"""Convert timeout to float.
Return None if timeout is None, 0 or 0.0. timeout=None disables timeouts in
Requests.
"""
if timeout is not None:
try:
timeout_float = float(timeout)
except ValueError:
raise ValueError(
'timeout_sec must be a valid number or None. timeout="{}"'.format(
timeout
)
)
if timeout_float:
return timeout_float | python | def _timeout_to_float(self, timeout):
"""Convert timeout to float.
Return None if timeout is None, 0 or 0.0. timeout=None disables timeouts in
Requests.
"""
if timeout is not None:
try:
timeout_float = float(timeout)
except ValueError:
raise ValueError(
'timeout_sec must be a valid number or None. timeout="{}"'.format(
timeout
)
)
if timeout_float:
return timeout_float | [
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DataONEorg/d1_python | dev_tools/src/d1_dev/src-print-redbaron-tree.py | main | def main():
"""Print the RedBaron syntax tree for a Python module."""
parser = argparse.ArgumentParser(
description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter
)
parser.add_argument("path", help="Python module path")
args = parser.parse_args()
r = d1_dev.util.redbaron_module_path_to_tree(args.path)
print(r.help(True)) | python | def main():
"""Print the RedBaron syntax tree for a Python module."""
parser = argparse.ArgumentParser(
description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter
)
parser.add_argument("path", help="Python module path")
args = parser.parse_args()
r = d1_dev.util.redbaron_module_path_to_tree(args.path)
print(r.help(True)) | [
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DataONEorg/d1_python | lib_common/src/d1_common/utils/filesystem.py | abs_path_from_base | def abs_path_from_base(base_path, rel_path):
"""Join a base and a relative path and return an absolute path to the resulting
location.
Args:
base_path: str
Relative or absolute path to prepend to ``rel_path``.
rel_path: str
Path relative to the location of the module file from which this function is called.
Returns:
str : Absolute path to the location specified by ``rel_path``.
"""
# noinspection PyProtectedMember
return os.path.abspath(
os.path.join(
os.path.dirname(sys._getframe(1).f_code.co_filename), base_path, rel_path
)
) | python | def abs_path_from_base(base_path, rel_path):
"""Join a base and a relative path and return an absolute path to the resulting
location.
Args:
base_path: str
Relative or absolute path to prepend to ``rel_path``.
rel_path: str
Path relative to the location of the module file from which this function is called.
Returns:
str : Absolute path to the location specified by ``rel_path``.
"""
# noinspection PyProtectedMember
return os.path.abspath(
os.path.join(
os.path.dirname(sys._getframe(1).f_code.co_filename), base_path, rel_path
)
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DataONEorg/d1_python | lib_common/src/d1_common/utils/filesystem.py | abs_path | def abs_path(rel_path):
"""Convert a path that is relative to the module from which this function is called,
to an absolute path.
Args:
rel_path: str
Path relative to the location of the module file from which this function is called.
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"""Convert a path that is relative to the module from which this function is called,
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Args:
rel_path: str
Path relative to the location of the module file from which this function is called.
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str : Absolute path to the location specified by ``rel_path``.
"""
# noinspection PyProtectedMember
return os.path.abspath(
os.path.join(os.path.dirname(sys._getframe(1).f_code.co_filename), rel_path)
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DataONEorg/d1_python | lib_common/src/d1_common/wrap/simple_xml.py | SimpleXMLWrapper.get_attr_value | def get_attr_value(self, attr_key, el_idx=0):
"""Return the value of the selected attribute in the selected element.
Args:
attr_key : str
Name of attribute for which to search
el_idx : int
Index of element to use in the event that there are multiple sibling
elements with the same name.
Returns:
str : Value of the selected attribute in the selected element.
"""
return self.get_element_by_attr_key(attr_key, el_idx).attrib[attr_key] | python | def get_attr_value(self, attr_key, el_idx=0):
"""Return the value of the selected attribute in the selected element.
Args:
attr_key : str
Name of attribute for which to search
el_idx : int
Index of element to use in the event that there are multiple sibling
elements with the same name.
Returns:
str : Value of the selected attribute in the selected element.
"""
return self.get_element_by_attr_key(attr_key, el_idx).attrib[attr_key] | [
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DataONEorg/d1_python | lib_common/src/d1_common/wrap/simple_xml.py | SimpleXMLWrapper.set_attr_text | def set_attr_text(self, attr_key, attr_val, el_idx=0):
"""Set the value of the selected attribute of the selected element.
Args:
attr_key : str
Name of attribute for which to search
attr_val : str
Text to set for the attribute.
el_idx : int
Index of element to use in the event that there are multiple sibling
elements with the same name.
"""
self.get_element_by_attr_key(attr_key, el_idx).attrib[attr_key] = attr_val | python | def set_attr_text(self, attr_key, attr_val, el_idx=0):
"""Set the value of the selected attribute of the selected element.
Args:
attr_key : str
Name of attribute for which to search
attr_val : str
Text to set for the attribute.
el_idx : int
Index of element to use in the event that there are multiple sibling
elements with the same name.
"""
self.get_element_by_attr_key(attr_key, el_idx).attrib[attr_key] = attr_val | [
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DataONEorg/d1_python | lib_common/src/d1_common/wrap/simple_xml.py | SimpleXMLWrapper.get_element_dt | def get_element_dt(self, el_name, tz=None, el_idx=0):
"""Return the text of the selected element as a ``datetime.datetime`` object.
The element text must be a ISO8601 formatted datetime
Args:
el_name : str
Name of element to use.
tz : datetime.tzinfo
Timezone in which to return the datetime.
- Without a timezone, other contextual information is required in order to
determine the exact represented time.
- If dt has timezone: The ``tz`` parameter is ignored.
- If dt is naive (without timezone): The timezone is set to ``tz``.
- ``tz=None``: Prevent naive dt from being set to a timezone. Without a
timezone, other contextual information is required in order to determine
the exact represented time.
- ``tz=d1_common.date_time.UTC()``: Set naive dt to UTC.
el_idx : int
Index of element to use in the event that there are multiple sibling
elements with the same name.
Returns:
datetime.datetime
"""
return iso8601.parse_date(self.get_element_by_name(el_name, el_idx).text, tz) | python | def get_element_dt(self, el_name, tz=None, el_idx=0):
"""Return the text of the selected element as a ``datetime.datetime`` object.
The element text must be a ISO8601 formatted datetime
Args:
el_name : str
Name of element to use.
tz : datetime.tzinfo
Timezone in which to return the datetime.
- Without a timezone, other contextual information is required in order to
determine the exact represented time.
- If dt has timezone: The ``tz`` parameter is ignored.
- If dt is naive (without timezone): The timezone is set to ``tz``.
- ``tz=None``: Prevent naive dt from being set to a timezone. Without a
timezone, other contextual information is required in order to determine
the exact represented time.
- ``tz=d1_common.date_time.UTC()``: Set naive dt to UTC.
el_idx : int
Index of element to use in the event that there are multiple sibling
elements with the same name.
Returns:
datetime.datetime
"""
return iso8601.parse_date(self.get_element_by_name(el_name, el_idx).text, tz) | [
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DataONEorg/d1_python | lib_common/src/d1_common/wrap/simple_xml.py | SimpleXMLWrapper.set_element_dt | def set_element_dt(self, el_name, dt, tz=None, el_idx=0):
"""Set the text of the selected element to an ISO8601 formatted datetime.
Args:
el_name : str
Name of element to update.
dt : datetime.datetime
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Index of element to use in the event that there are multiple sibling
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"""
dt = d1_common.date_time.cast_naive_datetime_to_tz(dt, tz)
self.get_element_by_name(el_name, el_idx).text = dt.isoformat() | python | def set_element_dt(self, el_name, dt, tz=None, el_idx=0):
"""Set the text of the selected element to an ISO8601 formatted datetime.
Args:
el_name : str
Name of element to update.
dt : datetime.datetime
Date and time to set
tz : datetime.tzinfo
Timezone to set
- Without a timezone, other contextual information is required in order to
determine the exact represented time.
- If dt has timezone: The ``tz`` parameter is ignored.
- If dt is naive (without timezone): The timezone is set to ``tz``.
- ``tz=None``: Prevent naive dt from being set to a timezone. Without a
timezone, other contextual information is required in order to determine
the exact represented time.
- ``tz=d1_common.date_time.UTC()``: Set naive dt to UTC.
el_idx : int
Index of element to use in the event that there are multiple sibling
elements with the same name.
"""
dt = d1_common.date_time.cast_naive_datetime_to_tz(dt, tz)
self.get_element_by_name(el_name, el_idx).text = dt.isoformat() | [
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genialis/resolwe | resolwe/flow/models/functions.py | JsonGetPath.as_sql | def as_sql(self, compiler, connection): # pylint: disable=arguments-differ
"""Compile SQL for this function."""
sql, params = super().as_sql(compiler, connection)
params.append(self.path)
return sql, params | python | def as_sql(self, compiler, connection): # pylint: disable=arguments-differ
"""Compile SQL for this function."""
sql, params = super().as_sql(compiler, connection)
params.append(self.path)
return sql, params | [
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genialis/resolwe | resolwe/flow/models/storage.py | StorageManager.with_json_path | def with_json_path(self, path, field=None):
"""Annotate Storage objects with a specific JSON path.
:param path: Path to get inside the stored object, which can be
either a list of path components or a comma-separated
string
:param field: Optional output field name
"""
if field is None:
field = '_'.join(['json'] + json_path_components(path))
kwargs = {field: JsonGetPath('json', path)}
return self.defer('json').annotate(**kwargs) | python | def with_json_path(self, path, field=None):
"""Annotate Storage objects with a specific JSON path.
:param path: Path to get inside the stored object, which can be
either a list of path components or a comma-separated
string
:param field: Optional output field name
"""
if field is None:
field = '_'.join(['json'] + json_path_components(path))
kwargs = {field: JsonGetPath('json', path)}
return self.defer('json').annotate(**kwargs) | [
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genialis/resolwe | resolwe/flow/models/storage.py | StorageManager.get_json_path | def get_json_path(self, path):
"""Return only a specific JSON path of Storage objects.
:param path: Path to get inside the stored object, which can be
either a list of path components or a comma-separated
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"""
return self.with_json_path(path, field='result').values_list('result', flat=True) | python | def get_json_path(self, path):
"""Return only a specific JSON path of Storage objects.
:param path: Path to get inside the stored object, which can be
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"""
return self.with_json_path(path, field='result').values_list('result', flat=True) | [
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genialis/resolwe | resolwe/flow/models/storage.py | LazyStorageJSON._get_storage | def _get_storage(self):
"""Load `json` field from `Storage` object."""
if self._json is None:
self._json = Storage.objects.get(**self._kwargs).json | python | def _get_storage(self):
"""Load `json` field from `Storage` object."""
if self._json is None:
self._json = Storage.objects.get(**self._kwargs).json | [
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wilson-eft/wilson | wilson/run/smeft/smpar.py | m2Lambda_to_vMh2 | def m2Lambda_to_vMh2(m2, Lambda, C):
"""Function to numerically determine the physical Higgs VEV and mass
given the parameters of the Higgs potential."""
try:
v = (sqrt(2 * m2 / Lambda) + 3 * m2**(3 / 2) /
(sqrt(2) * Lambda**(5 / 2)) * C['phi'])
except ValueError:
v = 0
Mh2 = 2 * m2 * (1 - m2 / Lambda * (3 * C['phi'] - 4 * Lambda * C['phiBox'] +
Lambda * C['phiD']))
return {'v': v, 'Mh2': Mh2} | python | def m2Lambda_to_vMh2(m2, Lambda, C):
"""Function to numerically determine the physical Higgs VEV and mass
given the parameters of the Higgs potential."""
try:
v = (sqrt(2 * m2 / Lambda) + 3 * m2**(3 / 2) /
(sqrt(2) * Lambda**(5 / 2)) * C['phi'])
except ValueError:
v = 0
Mh2 = 2 * m2 * (1 - m2 / Lambda * (3 * C['phi'] - 4 * Lambda * C['phiBox'] +
Lambda * C['phiD']))
return {'v': v, 'Mh2': Mh2} | [
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wilson-eft/wilson | wilson/run/smeft/smpar.py | smeftpar | def smeftpar(scale, C, basis):
"""Get the running parameters in SMEFT."""
# start with a zero dict and update it with the input values
MW = p['m_W']
# MZ = p['m_Z']
GF = p['GF']
Mh = p['m_h']
vb = sqrt(1 / sqrt(2) / GF)
v = vb # TODO
_d = vMh2_to_m2Lambda(v=v, Mh2=Mh**2, C=C)
m2 = _d['m2'].real
Lambda = _d['Lambda'].real
gsbar = sqrt(4 * pi * p['alpha_s'])
gs = (1 - C['phiG'] * (v**2)) * gsbar
gbar = 2 * MW / v
g = gbar * (1 - C['phiW'] * (v**2))
ebar = sqrt(4 * pi * p['alpha_e'])
gp = get_gpbar(ebar, gbar, v, C)
c = {}
c['m2'] = m2
c['Lambda'] = Lambda
c['g'] = g
c['gp'] = gp
c['gs'] = gs
K = ckmutil.ckm.ckm_tree(p['Vus'], p['Vub'], p['Vcb'], p['delta'])
if basis == 'Warsaw':
Mu = K.conj().T @ np.diag([p['m_u'], p['m_c'], p['m_t']])
Md = np.diag([p['m_d'], p['m_s'], p['m_b']])
elif basis == 'Warsaw up':
Mu = np.diag([p['m_u'], p['m_c'], p['m_t']])
Md = K @ np.diag([p['m_d'], p['m_s'], p['m_b']])
else:
raise ValueError("Basis '{}' not supported".format(basis))
Me = np.diag([p['m_e'], p['m_mu'], p['m_tau']])
c['Gd'] = Md / (v / sqrt(2)) + C['dphi'] * (v**2) / 2
c['Gu'] = Mu / (v / sqrt(2)) + C['uphi'] * (v**2) / 2
c['Ge'] = Me / (v / sqrt(2)) + C['ephi'] * (v**2) / 2
return c | python | def smeftpar(scale, C, basis):
"""Get the running parameters in SMEFT."""
# start with a zero dict and update it with the input values
MW = p['m_W']
# MZ = p['m_Z']
GF = p['GF']
Mh = p['m_h']
vb = sqrt(1 / sqrt(2) / GF)
v = vb # TODO
_d = vMh2_to_m2Lambda(v=v, Mh2=Mh**2, C=C)
m2 = _d['m2'].real
Lambda = _d['Lambda'].real
gsbar = sqrt(4 * pi * p['alpha_s'])
gs = (1 - C['phiG'] * (v**2)) * gsbar
gbar = 2 * MW / v
g = gbar * (1 - C['phiW'] * (v**2))
ebar = sqrt(4 * pi * p['alpha_e'])
gp = get_gpbar(ebar, gbar, v, C)
c = {}
c['m2'] = m2
c['Lambda'] = Lambda
c['g'] = g
c['gp'] = gp
c['gs'] = gs
K = ckmutil.ckm.ckm_tree(p['Vus'], p['Vub'], p['Vcb'], p['delta'])
if basis == 'Warsaw':
Mu = K.conj().T @ np.diag([p['m_u'], p['m_c'], p['m_t']])
Md = np.diag([p['m_d'], p['m_s'], p['m_b']])
elif basis == 'Warsaw up':
Mu = np.diag([p['m_u'], p['m_c'], p['m_t']])
Md = K @ np.diag([p['m_d'], p['m_s'], p['m_b']])
else:
raise ValueError("Basis '{}' not supported".format(basis))
Me = np.diag([p['m_e'], p['m_mu'], p['m_tau']])
c['Gd'] = Md / (v / sqrt(2)) + C['dphi'] * (v**2) / 2
c['Gu'] = Mu / (v / sqrt(2)) + C['uphi'] * (v**2) / 2
c['Ge'] = Me / (v / sqrt(2)) + C['ephi'] * (v**2) / 2
return c | [
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wilson-eft/wilson | wilson/util/smeftutil.py | scale_8 | def scale_8(b):
"""Translations necessary for class-8 coefficients
to go from a basis with only non-redundant WCxf
operators to a basis where the Wilson coefficients are symmetrized like
the operators."""
a = np.array(b, copy=True, dtype=complex)
for i in range(3):
a[0, 0, 1, i] = 1/2 * b[0, 0, 1, i]
a[0, 0, 2, i] = 1/2 * b[0, 0, 2, i]
a[0, 1, 1, i] = 1/2 * b[0, 1, 1, i]
a[0, 1, 2, i] = 2/3 * b[0, 1, 2, i] - 1/6 * b[0, 2, 1, i] - 1/6 * b[1, 0, 2, i] + 1/6 * b[1, 2, 0, i]
a[0, 2, 1, i] = - (1/6) * b[0, 1, 2, i] + 2/3 * b[0, 2, 1, i] + 1/6 * b[1, 0, 2, i] + 1/3 * b[1, 2, 0, i]
a[0, 2, 2, i] = 1/2 * b[0, 2, 2, i]
a[1, 0, 2, i] = - (1/6) * b[0, 1, 2, i] + 1/6 * b[0, 2, 1, i] + 2/3 * b[1, 0, 2, i] - 1/6 * b[1, 2, 0, i]
a[1, 1, 2, i] = 1/2 * b[1, 1, 2, i]
a[1, 2, 0, i] = 1/6 * b[0, 1, 2, i] + 1/3 * b[0, 2, 1, i] - 1/6 * b[1, 0, 2, i] + 2/3 * b[1, 2, 0, i]
a[1, 2, 2, i] = 1/2 * b[1, 2, 2, i]
return a | python | def scale_8(b):
"""Translations necessary for class-8 coefficients
to go from a basis with only non-redundant WCxf
operators to a basis where the Wilson coefficients are symmetrized like
the operators."""
a = np.array(b, copy=True, dtype=complex)
for i in range(3):
a[0, 0, 1, i] = 1/2 * b[0, 0, 1, i]
a[0, 0, 2, i] = 1/2 * b[0, 0, 2, i]
a[0, 1, 1, i] = 1/2 * b[0, 1, 1, i]
a[0, 1, 2, i] = 2/3 * b[0, 1, 2, i] - 1/6 * b[0, 2, 1, i] - 1/6 * b[1, 0, 2, i] + 1/6 * b[1, 2, 0, i]
a[0, 2, 1, i] = - (1/6) * b[0, 1, 2, i] + 2/3 * b[0, 2, 1, i] + 1/6 * b[1, 0, 2, i] + 1/3 * b[1, 2, 0, i]
a[0, 2, 2, i] = 1/2 * b[0, 2, 2, i]
a[1, 0, 2, i] = - (1/6) * b[0, 1, 2, i] + 1/6 * b[0, 2, 1, i] + 2/3 * b[1, 0, 2, i] - 1/6 * b[1, 2, 0, i]
a[1, 1, 2, i] = 1/2 * b[1, 1, 2, i]
a[1, 2, 0, i] = 1/6 * b[0, 1, 2, i] + 1/3 * b[0, 2, 1, i] - 1/6 * b[1, 0, 2, i] + 2/3 * b[1, 2, 0, i]
a[1, 2, 2, i] = 1/2 * b[1, 2, 2, i]
return a | [
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wilson-eft/wilson | wilson/util/smeftutil.py | arrays2wcxf | def arrays2wcxf(C):
"""Convert a dictionary with Wilson coefficient names as keys and
numbers or numpy arrays as values to a dictionary with a Wilson coefficient
name followed by underscore and numeric indices as keys and numbers as
values. This is needed for the output in WCxf format."""
d = {}
for k, v in C.items():
if np.shape(v) == () or np.shape(v) == (1,):
d[k] = v
else:
ind = np.indices(v.shape).reshape(v.ndim, v.size).T
for i in ind:
name = k + '_' + ''.join([str(int(j) + 1) for j in i])
d[name] = v[tuple(i)]
return d | python | def arrays2wcxf(C):
"""Convert a dictionary with Wilson coefficient names as keys and
numbers or numpy arrays as values to a dictionary with a Wilson coefficient
name followed by underscore and numeric indices as keys and numbers as
values. This is needed for the output in WCxf format."""
d = {}
for k, v in C.items():
if np.shape(v) == () or np.shape(v) == (1,):
d[k] = v
else:
ind = np.indices(v.shape).reshape(v.ndim, v.size).T
for i in ind:
name = k + '_' + ''.join([str(int(j) + 1) for j in i])
d[name] = v[tuple(i)]
return d | [
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wilson-eft/wilson | wilson/util/smeftutil.py | wcxf2arrays | def wcxf2arrays(d):
"""Convert a dictionary with a Wilson coefficient
name followed by underscore and numeric indices as keys and numbers as
values to a dictionary with Wilson coefficient names as keys and
numbers or numpy arrays as values. This is needed for the parsing
of input in WCxf format."""
C = {}
for k, v in d.items():
name = k.split('_')[0]
s = C_keys_shape[name]
if s == 1:
C[k] = v
else:
ind = k.split('_')[-1]
if name not in C:
C[name] = np.zeros(s, dtype=complex)
C[name][tuple([int(i) - 1 for i in ind])] = v
return C | python | def wcxf2arrays(d):
"""Convert a dictionary with a Wilson coefficient
name followed by underscore and numeric indices as keys and numbers as
values to a dictionary with Wilson coefficient names as keys and
numbers or numpy arrays as values. This is needed for the parsing
of input in WCxf format."""
C = {}
for k, v in d.items():
name = k.split('_')[0]
s = C_keys_shape[name]
if s == 1:
C[k] = v
else:
ind = k.split('_')[-1]
if name not in C:
C[name] = np.zeros(s, dtype=complex)
C[name][tuple([int(i) - 1 for i in ind])] = v
return C | [
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wilson-eft/wilson | wilson/util/smeftutil.py | add_missing | def add_missing(C):
"""Add arrays with zeros for missing Wilson coefficient keys"""
C_out = C.copy()
for k in (set(WC_keys) - set(C.keys())):
C_out[k] = np.zeros(C_keys_shape[k])
return C_out | python | def add_missing(C):
"""Add arrays with zeros for missing Wilson coefficient keys"""
C_out = C.copy()
for k in (set(WC_keys) - set(C.keys())):
C_out[k] = np.zeros(C_keys_shape[k])
return C_out | [
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wilson-eft/wilson | wilson/util/smeftutil.py | C_array2dict | def C_array2dict(C):
"""Convert a 1D array containing C values to a dictionary."""
d = OrderedDict()
i=0
for k in C_keys:
s = C_keys_shape[k]
if s == 1:
j = i+1
d[k] = C[i]
else:
j = i \
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d[k] = C[i:j].reshape(s)
i = j
return d | python | def C_array2dict(C):
"""Convert a 1D array containing C values to a dictionary."""
d = OrderedDict()
i=0
for k in C_keys:
s = C_keys_shape[k]
if s == 1:
j = i+1
d[k] = C[i]
else:
j = i \
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d[k] = C[i:j].reshape(s)
i = j
return d | [
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wilson-eft/wilson | wilson/util/smeftutil.py | C_dict2array | def C_dict2array(C):
"""Convert an OrderedDict containing C values to a 1D array."""
return np.hstack([np.asarray(C[k]).ravel() for k in C_keys]) | python | def C_dict2array(C):
"""Convert an OrderedDict containing C values to a 1D array."""
return np.hstack([np.asarray(C[k]).ravel() for k in C_keys]) | [
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wilson-eft/wilson | wilson/util/smeftutil.py | unscale_dict | def unscale_dict(C):
"""Undo the scaling applied in `scale_dict`."""
C_out = {k: _scale_dict[k] * v for k, v in C.items()}
for k in C_symm_keys[8]:
C_out['qqql'] = unscale_8(C_out['qqql'])
return C_out | python | def unscale_dict(C):
"""Undo the scaling applied in `scale_dict`."""
C_out = {k: _scale_dict[k] * v for k, v in C.items()}
for k in C_symm_keys[8]:
C_out['qqql'] = unscale_8(C_out['qqql'])
return C_out | [
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wilson-eft/wilson | wilson/util/smeftutil.py | wcxf2arrays_symmetrized | def wcxf2arrays_symmetrized(d):
"""Convert a dictionary with a Wilson coefficient
name followed by underscore and numeric indices as keys and numbers as
values to a dictionary with Wilson coefficient names as keys and
numbers or numpy arrays as values.
In contrast to `wcxf2arrays`, here the numpy arrays fulfill the same
symmetry relations as the operators (i.e. they contain redundant entries)
and they do not contain undefined indices.
Zero arrays are added for missing coefficients."""
C = wcxf2arrays(d)
C = symmetrize_nonred(C)
C = add_missing(C)
return C | python | def wcxf2arrays_symmetrized(d):
"""Convert a dictionary with a Wilson coefficient
name followed by underscore and numeric indices as keys and numbers as
values to a dictionary with Wilson coefficient names as keys and
numbers or numpy arrays as values.
In contrast to `wcxf2arrays`, here the numpy arrays fulfill the same
symmetry relations as the operators (i.e. they contain redundant entries)
and they do not contain undefined indices.
Zero arrays are added for missing coefficients."""
C = wcxf2arrays(d)
C = symmetrize_nonred(C)
C = add_missing(C)
return C | [
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genialis/resolwe | resolwe/flow/signals.py | commit_signal | def commit_signal(data_id):
"""Nudge manager at the end of every Data object save event."""
if not getattr(settings, 'FLOW_MANAGER_DISABLE_AUTO_CALLS', False):
immediate = getattr(settings, 'FLOW_MANAGER_SYNC_AUTO_CALLS', False)
async_to_sync(manager.communicate)(data_id=data_id, save_settings=False, run_sync=immediate) | python | def commit_signal(data_id):
"""Nudge manager at the end of every Data object save event."""
if not getattr(settings, 'FLOW_MANAGER_DISABLE_AUTO_CALLS', False):
immediate = getattr(settings, 'FLOW_MANAGER_SYNC_AUTO_CALLS', False)
async_to_sync(manager.communicate)(data_id=data_id, save_settings=False, run_sync=immediate) | [
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genialis/resolwe | resolwe/flow/signals.py | delete_entity | def delete_entity(sender, instance, **kwargs):
"""Delete Entity when last Data object is deleted."""
# 1 means that the last Data object is going to be deleted.
Entity.objects.annotate(num_data=Count('data')).filter(data=instance, num_data=1).delete() | python | def delete_entity(sender, instance, **kwargs):
"""Delete Entity when last Data object is deleted."""
# 1 means that the last Data object is going to be deleted.
Entity.objects.annotate(num_data=Count('data')).filter(data=instance, num_data=1).delete() | [
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genialis/resolwe | resolwe/flow/signals.py | delete_relation | def delete_relation(sender, instance, **kwargs):
"""Delete the Relation object when the last Entity is removed."""
def process_signal(relation_id):
"""Get the relation and delete it if it has no entities left."""
try:
relation = Relation.objects.get(pk=relation_id)
except Relation.DoesNotExist:
return
if relation.entities.count() == 0:
relation.delete()
# Wait for partitions to be recreated.
transaction.on_commit(lambda: process_signal(instance.relation_id)) | python | def delete_relation(sender, instance, **kwargs):
"""Delete the Relation object when the last Entity is removed."""
def process_signal(relation_id):
"""Get the relation and delete it if it has no entities left."""
try:
relation = Relation.objects.get(pk=relation_id)
except Relation.DoesNotExist:
return
if relation.entities.count() == 0:
relation.delete()
# Wait for partitions to be recreated.
transaction.on_commit(lambda: process_signal(instance.relation_id)) | [
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genialis/resolwe | resolwe/flow/executors/__main__.py | run_executor | async def run_executor():
"""Start the actual execution; instantiate the executor and run."""
parser = argparse.ArgumentParser(description="Run the specified executor.")
parser.add_argument('module', help="The module from which to instantiate the concrete executor.")
args = parser.parse_args()
module_name = '{}.run'.format(args.module)
class_name = 'FlowExecutor'
module = import_module(module_name, __package__)
executor = getattr(module, class_name)()
with open(ExecutorFiles.PROCESS_SCRIPT, 'rt') as script_file:
await executor.run(DATA['id'], script_file.read()) | python | async def run_executor():
"""Start the actual execution; instantiate the executor and run."""
parser = argparse.ArgumentParser(description="Run the specified executor.")
parser.add_argument('module', help="The module from which to instantiate the concrete executor.")
args = parser.parse_args()
module_name = '{}.run'.format(args.module)
class_name = 'FlowExecutor'
module = import_module(module_name, __package__)
executor = getattr(module, class_name)()
with open(ExecutorFiles.PROCESS_SCRIPT, 'rt') as script_file:
await executor.run(DATA['id'], script_file.read()) | [
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genialis/resolwe | resolwe/elastic/apps.py | ElasticConfig.ready | def ready(self):
"""Perform application initialization."""
# Initialize the type extension composer.
from . composer import composer
composer.discover_extensions()
is_migrating = sys.argv[1:2] == ['migrate']
if is_migrating:
# Do not register signals and ES indices when:
# * migrating - model instances used during migrations do
# not contain the full functionality of models and things
# like content types don't work correctly and signals are
# not versioned so they are guaranteed to work only with
# the last version of the model
return
# Connect all signals
from . import signals # pylint: disable=unused-import
# Register ES indices
from . builder import index_builder | python | def ready(self):
"""Perform application initialization."""
# Initialize the type extension composer.
from . composer import composer
composer.discover_extensions()
is_migrating = sys.argv[1:2] == ['migrate']
if is_migrating:
# Do not register signals and ES indices when:
# * migrating - model instances used during migrations do
# not contain the full functionality of models and things
# like content types don't work correctly and signals are
# not versioned so they are guaranteed to work only with
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return
# Connect all signals
from . import signals # pylint: disable=unused-import
# Register ES indices
from . builder import index_builder | [
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genialis/resolwe | resolwe/flow/serializers/fields.py | ResolweSlugRelatedField.to_internal_value | def to_internal_value(self, data):
"""Convert to internal value."""
user = getattr(self.context.get('request'), 'user')
queryset = self.get_queryset()
permission = get_full_perm('view', queryset.model)
try:
return get_objects_for_user(
user,
permission,
queryset.filter(**{self.slug_field: data}),
).latest()
except ObjectDoesNotExist:
self.fail(
'does_not_exist',
slug_name=self.slug_field,
value=smart_text(data),
model_name=queryset.model._meta.model_name, # pylint: disable=protected-access
)
except (TypeError, ValueError):
self.fail('invalid') | python | def to_internal_value(self, data):
"""Convert to internal value."""
user = getattr(self.context.get('request'), 'user')
queryset = self.get_queryset()
permission = get_full_perm('view', queryset.model)
try:
return get_objects_for_user(
user,
permission,
queryset.filter(**{self.slug_field: data}),
).latest()
except ObjectDoesNotExist:
self.fail(
'does_not_exist',
slug_name=self.slug_field,
value=smart_text(data),
model_name=queryset.model._meta.model_name, # pylint: disable=protected-access
)
except (TypeError, ValueError):
self.fail('invalid') | [
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Alonreznik/dynamodb-json | dynamodb_json/json_util.py | object_hook | def object_hook(dct):
""" DynamoDB object hook to return python values """
try:
# First - Try to parse the dct as DynamoDB parsed
if 'BOOL' in dct:
return dct['BOOL']
if 'S' in dct:
val = dct['S']
try:
return datetime.strptime(val, '%Y-%m-%dT%H:%M:%S.%f')
except:
return str(val)
if 'SS' in dct:
return list(dct['SS'])
if 'N' in dct:
if re.match("^-?\d+?\.\d+?$", dct['N']) is not None:
return float(dct['N'])
else:
try:
return int(dct['N'])
except:
return int(dct['N'])
if 'B' in dct:
return str(dct['B'])
if 'NS' in dct:
return set(dct['NS'])
if 'BS' in dct:
return set(dct['BS'])
if 'M' in dct:
return dct['M']
if 'L' in dct:
return dct['L']
if 'NULL' in dct and dct['NULL'] is True:
return None
except:
return dct
# In a Case of returning a regular python dict
for key, val in six.iteritems(dct):
if isinstance(val, six.string_types):
try:
dct[key] = datetime.strptime(val, '%Y-%m-%dT%H:%M:%S.%f')
except:
# This is a regular Basestring object
pass
if isinstance(val, Decimal):
if val % 1 > 0:
dct[key] = float(val)
elif six.PY3:
dct[key] = int(val)
elif val < sys.maxsize:
dct[key] = int(val)
else:
dct[key] = long(val)
return dct | python | def object_hook(dct):
""" DynamoDB object hook to return python values """
try:
# First - Try to parse the dct as DynamoDB parsed
if 'BOOL' in dct:
return dct['BOOL']
if 'S' in dct:
val = dct['S']
try:
return datetime.strptime(val, '%Y-%m-%dT%H:%M:%S.%f')
except:
return str(val)
if 'SS' in dct:
return list(dct['SS'])
if 'N' in dct:
if re.match("^-?\d+?\.\d+?$", dct['N']) is not None:
return float(dct['N'])
else:
try:
return int(dct['N'])
except:
return int(dct['N'])
if 'B' in dct:
return str(dct['B'])
if 'NS' in dct:
return set(dct['NS'])
if 'BS' in dct:
return set(dct['BS'])
if 'M' in dct:
return dct['M']
if 'L' in dct:
return dct['L']
if 'NULL' in dct and dct['NULL'] is True:
return None
except:
return dct
# In a Case of returning a regular python dict
for key, val in six.iteritems(dct):
if isinstance(val, six.string_types):
try:
dct[key] = datetime.strptime(val, '%Y-%m-%dT%H:%M:%S.%f')
except:
# This is a regular Basestring object
pass
if isinstance(val, Decimal):
if val % 1 > 0:
dct[key] = float(val)
elif six.PY3:
dct[key] = int(val)
elif val < sys.maxsize:
dct[key] = int(val)
else:
dct[key] = long(val)
return dct | [
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geoadmin/lib-gatilegrid | gatilegrid/tilegrids.py | _TileGrid.tileAddress | def tileAddress(self, zoom, point):
"Returns a tile address based on a zoom level and \
a point in the tile"
[x, y] = point
assert x <= self.MAXX and x >= self.MINX
assert y <= self.MAXY and y >= self.MINY
assert zoom in range(0, len(self.RESOLUTIONS))
tileS = self.tileSize(zoom)
offsetX = abs(x - self.MINX)
if self.originCorner == 'bottom-left':
offsetY = abs(y - self.MINY)
elif self.originCorner == 'top-left':
offsetY = abs(self.MAXY - y)
col = offsetX / tileS
row = offsetY / tileS
# We are exactly on the edge of a tile and the extent
if x in (self.MINX, self.MAXX) and col.is_integer():
col = max(0, col - 1)
if y in (self.MINY, self.MAXY) and row.is_integer():
row = max(0, row - 1)
return [
int(math.floor(col)),
int(math.floor(row))
] | python | def tileAddress(self, zoom, point):
"Returns a tile address based on a zoom level and \
a point in the tile"
[x, y] = point
assert x <= self.MAXX and x >= self.MINX
assert y <= self.MAXY and y >= self.MINY
assert zoom in range(0, len(self.RESOLUTIONS))
tileS = self.tileSize(zoom)
offsetX = abs(x - self.MINX)
if self.originCorner == 'bottom-left':
offsetY = abs(y - self.MINY)
elif self.originCorner == 'top-left':
offsetY = abs(self.MAXY - y)
col = offsetX / tileS
row = offsetY / tileS
# We are exactly on the edge of a tile and the extent
if x in (self.MINX, self.MAXX) and col.is_integer():
col = max(0, col - 1)
if y in (self.MINY, self.MAXY) and row.is_integer():
row = max(0, row - 1)
return [
int(math.floor(col)),
int(math.floor(row))
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geoadmin/lib-gatilegrid | gatilegrid/tilegrids.py | _TileGrid.intersectsExtent | def intersectsExtent(self, extent):
"Determine if an extent intersects this instance extent"
return \
self.extent[0] <= extent[2] and self.extent[2] >= extent[0] and \
self.extent[1] <= extent[3] and self.extent[3] >= extent[1] | python | def intersectsExtent(self, extent):
"Determine if an extent intersects this instance extent"
return \
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self.extent[1] <= extent[3] and self.extent[3] >= extent[1] | [
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] | 28e39cba22451f6ef0ddcb93cbc0838f06815505 | https://github.com/geoadmin/lib-gatilegrid/blob/28e39cba22451f6ef0ddcb93cbc0838f06815505/gatilegrid/tilegrids.py#L248-L252 | train | 45,594 |
geoadmin/lib-gatilegrid | gatilegrid/tilegrids.py | _TileGrid.iterGrid | def iterGrid(self, minZoom, maxZoom):
"Yields the tileBounds, zoom, tileCol and tileRow"
assert minZoom in range(0, len(self.RESOLUTIONS))
assert maxZoom in range(0, len(self.RESOLUTIONS))
assert minZoom <= maxZoom
for zoom in xrange(minZoom, maxZoom + 1):
[minRow, minCol, maxRow, maxCol] = self.getExtentAddress(zoom)
for row in xrange(minRow, maxRow + 1):
for col in xrange(minCol, maxCol + 1):
tileBounds = self.tileBounds(zoom, col, row)
yield (tileBounds, zoom, col, row) | python | def iterGrid(self, minZoom, maxZoom):
"Yields the tileBounds, zoom, tileCol and tileRow"
assert minZoom in range(0, len(self.RESOLUTIONS))
assert maxZoom in range(0, len(self.RESOLUTIONS))
assert minZoom <= maxZoom
for zoom in xrange(minZoom, maxZoom + 1):
[minRow, minCol, maxRow, maxCol] = self.getExtentAddress(zoom)
for row in xrange(minRow, maxRow + 1):
for col in xrange(minCol, maxCol + 1):
tileBounds = self.tileBounds(zoom, col, row)
yield (tileBounds, zoom, col, row) | [
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geoadmin/lib-gatilegrid | gatilegrid/tilegrids.py | _TileGrid.numberOfXTilesAtZoom | def numberOfXTilesAtZoom(self, zoom):
"Returns the number of tiles over x at a given zoom level"
[minRow, minCol, maxRow, maxCol] = self.getExtentAddress(zoom)
return maxCol - minCol + 1 | python | def numberOfXTilesAtZoom(self, zoom):
"Returns the number of tiles over x at a given zoom level"
[minRow, minCol, maxRow, maxCol] = self.getExtentAddress(zoom)
return maxCol - minCol + 1 | [
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geoadmin/lib-gatilegrid | gatilegrid/tilegrids.py | _TileGrid.numberOfYTilesAtZoom | def numberOfYTilesAtZoom(self, zoom):
"Retruns the number of tiles over y at a given zoom level"
[minRow, minCol, maxRow, maxCol] = self.getExtentAddress(zoom)
return maxRow - minRow + 1 | python | def numberOfYTilesAtZoom(self, zoom):
"Retruns the number of tiles over y at a given zoom level"
[minRow, minCol, maxRow, maxCol] = self.getExtentAddress(zoom)
return maxRow - minRow + 1 | [
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geoadmin/lib-gatilegrid | gatilegrid/tilegrids.py | _TileGrid.numberOfTilesAtZoom | def numberOfTilesAtZoom(self, zoom):
"Returns the total number of tile at a given zoom level"
[minRow, minCol, maxRow, maxCol] = self.getExtentAddress(zoom)
return (maxCol - minCol + 1) * (maxRow - minRow + 1) | python | def numberOfTilesAtZoom(self, zoom):
"Returns the total number of tile at a given zoom level"
[minRow, minCol, maxRow, maxCol] = self.getExtentAddress(zoom)
return (maxCol - minCol + 1) * (maxRow - minRow + 1) | [
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geoadmin/lib-gatilegrid | gatilegrid/tilegrids.py | _TileGrid.totalNumberOfTiles | def totalNumberOfTiles(self, minZoom=None, maxZoom=None):
"Return the total number of tiles for this instance extent"
nbTiles = 0
minZoom = minZoom or 0
if maxZoom:
maxZoom = maxZoom + 1
else:
maxZoom = len(self.RESOLUTIONS)
for zoom in xrange(minZoom, maxZoom):
nbTiles += self.numberOfTilesAtZoom(zoom)
return nbTiles | python | def totalNumberOfTiles(self, minZoom=None, maxZoom=None):
"Return the total number of tiles for this instance extent"
nbTiles = 0
minZoom = minZoom or 0
if maxZoom:
maxZoom = maxZoom + 1
else:
maxZoom = len(self.RESOLUTIONS)
for zoom in xrange(minZoom, maxZoom):
nbTiles += self.numberOfTilesAtZoom(zoom)
return nbTiles | [
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