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Merge pull request #198 from NeuralEnsemble/feat/better-warnings
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chore: add logger to generatedssupersuper + support addition of `__ANY__`  + external morph fixing tweaks
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@sanjayankur31
sanjayankur31 authored Aug 23, 2024
2 parents 8f60aca + 5e36a9f commit fdb9821
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Showing 5 changed files with 315 additions and 232 deletions.
200 changes: 164 additions & 36 deletions neuroml/nml/generatedssupersuper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,16 +13,16 @@

from .generatedscollector import GdsCollector

logger = logging.getLogger(__name__)
logger.setLevel(logging.INFO)


class GeneratedsSuperSuper(object):
"""Super class for GeneratedsSuper.
Any bits that must go into every libNeuroML class should go here.
"""

logger = logging.getLogger(__name__)
logger.setLevel(logging.INFO)

def add(self, obj=None, hint=None, force=False, validate=True, **kwargs):
"""Generic function to allow easy addition of a new member to a NeuroML object.
Without arguments, when `obj=None`, it simply calls the `info()` method
Expand All @@ -37,7 +37,14 @@ def add(self, obj=None, hint=None, force=False, validate=True, **kwargs):
calling (parent) component type object.
:param obj: member object or class type (neuroml.NeuroMLDocument) or
name of class type ("NeuroMLDocument"), or None
name of class type ("NeuroMLDocument"), a string, or None
If the string that is passed is not the name of a NeuroML
component type, it will be added as a string if the parent
component type allows "any" elements. This does not mean that one
can add anything, since it must still be valid XML/LEMS. The
only usecase for this currently is to add RDF strings to the
Annotation component type.
:type obj: str or type or None
:param hint: member name to add to when there are multiple members that `obj` can be added to
:type hint: string
Expand All @@ -58,20 +65,44 @@ def add(self, obj=None, hint=None, force=False, validate=True, **kwargs):
if type(obj) is type or isinstance(obj, str):
obj = self.component_factory(obj, validate=validate, **kwargs)

# if obj is still a string, it is a general string, but to confirm that
# this is what the user intends, ask them to provide a hint.
if isinstance(obj, str):
# no hint, no pass
if not hint:
e = Exception(
"Received a text object to add. "
+ 'Please pass `hint="__ANY__"` to confirm that this is what you intend. '
+ "I will then try to add this to an __ANY__ member in the object."
)
raise e
# hint confirmed, try to add it below
else:
self.logger.warning("Received a text object to add.")
self.logger.warning(
"Trying to add this to an __ANY__ member in the object."
)

# getattr only returns the value of the provided member but one cannot
# then use this to modify the member. Using `vars` also allows us to
# modify the value
targets = []
all_members = self._get_members()
for member in all_members:
# get_data_type() returns the type as a string, e.g.: 'IncludeType'

# handle "__ANY__"
if isinstance(obj, str) and member.get_data_type() == "__ANY__":
targets.append(member)
break

if member.get_data_type() == type(obj).__name__:
targets.append(member)

if len(targets) == 0:
# no targets found
e = Exception(
"""A member object of {} type could not be found in NeuroML class {}.\n{}
"""A member object of '{}' type could not be found in NeuroML class {}.\n{}
""".format(type(obj).__name__, type(self).__name__, self.info())
)
raise e
Expand All @@ -97,7 +128,14 @@ def add(self, obj=None, hint=None, force=False, validate=True, **kwargs):
if neuroml.build_time_validation.ENABLED and validate:
self.validate()
else:
logger.warning("Build time validation is disabled.")
if not neuroml.build_time_validation.ENABLED:
self.logger.debug(
f"Build time validation is globally disabled: adding new {obj.__class__.__name__}."
)
else:
self.logger.debug(
f"Build time validation is locally disabled: adding new {obj.__class__.__name__}."
)
return obj

@classmethod
Expand Down Expand Up @@ -128,25 +166,45 @@ def component_factory(cls, component_type, validate=True, **kwargs):
Note that when providing the class type, one will need to import it,
e.g.: `import NeuroMLDocument`, to ensure that it is defined, whereas
this will not be required when using the string.
If the value passed for component_type is a general string (with
spaces), it is simply returned
:type component_type: str/type
:param validate: toggle validation (default: True)
:type validate: bool
:param kwargs: named arguments to be passed to ComponentType constructor
:type kwargs: named arguments
:returns: new Component (object) of provided ComponentType
:returns: new Component (object) of provided ComponentType, or
unprocessed string with spaces if given for component_type
:rtype: object
:raises ValueError: if validation/checks fail
"""
module_object = sys.modules[cls.__module__]

if isinstance(component_type, str):
comp_type_class = getattr(module_object, component_type)
# class names do not have spaces, so if we find a space, we treat
# it as a general string and just return it.
if " " in component_type:
cls.logger.warning(
"Component Type appears to be a generic string: nothing to do."
)
return component_type
else:
comp_type_class = getattr(module_object, component_type)
else:
comp_type_class = getattr(module_object, component_type.__name__)

comp = comp_type_class(**kwargs)

# handle component types that support __ANY__
try:
anytypevalue = kwargs["__ANY__"]
# append value to anytypeobjs_ list
comp.anytypeobjs_.append(anytypevalue)
except KeyError:
pass

# additional setups where required
if comp_type_class.__name__ == "Cell":
comp.setup_nml_cell()
Expand All @@ -156,7 +214,14 @@ def component_factory(cls, component_type, validate=True, **kwargs):
if neuroml.build_time_validation.ENABLED and validate:
comp.validate()
else:
logger.warning("Build time validation is disabled.")
if not neuroml.build_time_validation.ENABLED:
cls.logger.debug(
f"Build time validation is globally disabled: creating new {comp_type_class.__name__}."
)
else:
cls.logger.debug(
f"Build time validation is locally disabled: creating new {comp_type_class.__name__}."
)
return comp

def __add(self, obj, member, force=False):
Expand All @@ -170,38 +235,49 @@ def __add(self, obj, member, force=False):
:type force: bool
"""
import warnings

# A single value, not a list:
if member.get_container() == 0:
if force:
vars(self)[member.get_name()] = obj
else:
if vars(self)[member.get_name()]:
warnings.warn(
"""{} has already been assigned. Use `force=True` to overwrite. Hint: you can make changes to the already added object as required without needing to re-add it because only references to the objects are added, not their values.""".format(
member.get_name()
)
# handle __ANY__ which is to be stored in anytypeobjs_
if member.get_name() == "__ANY__":
self.logger.debug("__ANY__ member, appending to anytypeobjs_.")
vars(self)["anytypeobjs_"].append(obj)
else:
# A single value, not a list:
self.logger.debug("Not a container member, assigning.")
if member.get_container() == 0:
if force:
vars(self)[member.get_name()] = obj
self.logger.warning(
"""Overwriting member '{}'.""".format(member.get_name())
)
else:
vars(self)[member.get_name()] = obj
# List
else:
if force:
vars(self)[member.get_name()].append(obj)
else:
# "obj in .." checks by identity and value.
# In XML, two children with same values are identical.
# There is no use case where the same child would be added
# twice to a component.
if obj in vars(self)[member.get_name()]:
warnings.warn(
"""{} already exists in {}. Use `force=True` to force readdition. Hint: you can make changes to the already added object as required without needing to re-add it because only references to the objects are added, not their values.""".format(
obj, member.get_name()
if vars(self)[member.get_name()]:
self.logger.debug(
"""Member '{}' has already been assigned. Use `force=True` to overwrite. Hint: you can make changes to the already added object as required without needing to re-add it because only references to the objects are added, not their values.""".format(
member.get_name()
)
)
else:
vars(self)[member.get_name()] = obj
# List
else:
self.logger.debug("Container member, appending.")
if force:
vars(self)[member.get_name()].append(obj)
self.logger.warning(
"""Force appending to member '{}'""".format(member.get_name())
)
else:
vars(self)[member.get_name()].append(obj)
# "obj in .." checks by identity and value.
# In XML, two children with same values are identical.
# There is no use case where the same child would be added
# twice to a component.
if obj in vars(self)[member.get_name()]:
self.logger.warning(
"""{} already exists in {}. Use `force=True` to force readdition.""".format(
obj, member.get_name()
)
)
else:
vars(self)[member.get_name()].append(obj)

@classmethod
def _get_members(cls):
Expand Down Expand Up @@ -616,3 +692,55 @@ def get_nml2_class_hierarchy(cls):
schema = sys.modules[cls.__module__]
cls.__nml_hier = schema.NeuroMLDocument.get_class_hierarchy()
return cls.__nml_hier

def get_by_id(self, id_):
"""Get a component or attribute by its ID, or type, or attribute name
:param id_: id of component ("biophys"), or its type
("BiophysicalProperties"), or its attribute name
("biophysical_properties")
When the attribute name or type are given, this simply returns the
associated object, which could be a list.
:type id_: str
:returns: component if found, else None
"""
all_ids = []
all_members = self._get_members()
for member in all_members:
# check name: biophysical_properties
if member.get_name() == id_:
return getattr(self, member.get_name())
# check type: BiophysicalProperties
elif member.get_data_type() == id_:
return getattr(self, member.get_name())

# check contents

# not a list
if member.get_container() == 0:
# check contents for id: biophysical_properties.id
contents = getattr(self, member.get_name(), None)
if hasattr(contents, "id"):
if contents.id == id_:
return contents
else:
all_ids.append(member.get_name())
else:
# container: iterate over each item
contents = getattr(self, member.get_name(), [])
for m in contents:
if hasattr(m, "id"):
if m.id == id_:
return m
else:
all_ids.append(m.id)

try:
self.logger.warning(f"Id '{id_}' not found in {self.__name__}")
except AttributeError:
self.logger.warning(f"Id '{id_}' not found in {self.id}")
self.logger.warning(f"All ids: {sorted(all_ids)}")
return None
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