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refactor: adjust interface and tests
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,115 +1,108 @@ | ||
| # -*- coding: utf-8 -*- | ||
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| """Define the group class.""" | ||
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| from __future__ import absolute_import | ||
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| from cobra.core.object import Object | ||
| from six import string_types | ||
| from warnings import warn | ||
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| kind_types = ["collection", "classification", "partonomy"] | ||
| from six import string_types | ||
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| from cobra.core.object import Object | ||
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| KIND_TYPES = ("collection", "classification", "partonomy") | ||
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| class Group(Object): | ||
| """Group is a class for holding information regarding | ||
| a pathways, subsystems, or other custom groupings of objects | ||
| within a cobra.Model object. | ||
| """ | ||
| Manage groups via this implementation of the SBML group specification. | ||
| `Group` is a class for holding information regarding a pathways, subsystems, | ||
| or other custom groupings of objects within a cobra.Model object. | ||
| Parameters | ||
| ---------- | ||
| id : string | ||
| id : str | ||
| The identifier to associate with this group | ||
| name : string | ||
| name : str, optional | ||
| A human readable name for the group | ||
| members : list | ||
| members : iterable, optional | ||
| A list object containing references to cobra.Model-associated objects | ||
| that belong to the group. | ||
| kind : string | ||
| The kind of group, as specified for the Groups feature in the SBML | ||
| level 3 package specification. Can be any of "classification", | ||
| "partonomy", or "collection". Please consult the SBML level 3 package | ||
| specification to ensure you are using the proper value for kind. In | ||
| short, members of a "classification" group should have an "is-a" | ||
| relationship to the group (e.g. member is-a polar compound, or | ||
| kind : {"collection", "classification", "partonomy"}, optional | ||
| The kind of group, as specified for the Groups feature in the SBML level | ||
| 3 package specification. Can be any of "classification", "partonomy", or | ||
| "collection". The default is "collection". Please consult the SBML level | ||
| 3 package specification to ensure you are using the proper value for | ||
| kind. In short, members of a "classification" group should have an | ||
| "is-a" relationship to the group (e.g. member is-a polar compound, or | ||
| member is-a transporter). Members of a "partonomy" group should have a | ||
| "part-of" relationship (e.g. member is part-of glycolysis). Members of | ||
| a "collection" group do not have an implied relationship between the | ||
| "part-of" relationship (e.g. member is part-of glycolysis). Members of a | ||
| "collection" group do not have an implied relationship between the | ||
| members, so use this value for kind when in doubt (e.g. member is a | ||
| gap-filled reaction, or member is involved in a disease phenotype). | ||
| """ | ||
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| def __init__(self, id=None, name='', members=[], kind=''): | ||
| def __init__(self, id, name='', members=None, kind=None): | ||
| Object.__init__(self, id, name) | ||
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| self._members = set(members) | ||
| self._kind = kind | ||
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| self._members = set() if members is None else set(members) | ||
| self._kind = None | ||
| self.kind = "collection" if kind is None else kind | ||
| # self.model is None or refers to the cobra.Model that | ||
| # contains self | ||
| self._model = None | ||
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| # read-only | ||
| @property | ||
| def members(self): | ||
| return getattr(self, "_members", None) | ||
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| @members.setter | ||
| def members(self, members): | ||
| self._members = set(members) | ||
| return self._members | ||
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| @property | ||
| def kind(self): | ||
| return getattr(self, "_kind", '') | ||
| return self._kind | ||
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| @kind.setter | ||
| def kind(self, kind): | ||
| if kind in kind_types: | ||
| if kind in KIND_TYPES: | ||
| self._kind = kind | ||
| else: | ||
| raise ValueError("kind can only by one of: " + str(kind_types)) | ||
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| @property | ||
| def model(self): | ||
| """returns the model the group is a part of""" | ||
| return self._model | ||
| raise ValueError( | ||
| "Kind can only by one of: {}.".format(", ".join(KIND_TYPES))) | ||
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| def add_members(self, members_list): | ||
| """Add objects to the group. | ||
| def add_members(self, new_members): | ||
| """ | ||
| Add objects to the group. | ||
| Parameters | ||
| ---------- | ||
| members_to_add : list | ||
| list of cobrapy objects to add to the group. | ||
| new_members : list | ||
| A list of cobrapy objects to add to the group. | ||
| """ | ||
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| if isinstance(members_list, string_types) or \ | ||
| hasattr(members_list, "id"): | ||
| if isinstance(new_members, string_types) or \ | ||
| hasattr(new_members, "id"): | ||
| warn("need to pass in a list") | ||
| members_list = [members_list] | ||
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| new_members = [] | ||
| _id_to_members = dict([(x.id, x) for x in self._members]) | ||
| new_members = [new_members] | ||
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| # Check for duplicate members in the group | ||
| for member in members_list: | ||
| # we only need to add the member if it ins't already in the group | ||
| if member.id not in _id_to_members: | ||
| new_members.append(member) | ||
| self._members.update(new_members) | ||
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| self._members = self._members.union(set(new_members)) | ||
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| def remove(self, members_list): | ||
| """Remove objects from the group. | ||
| def remove(self, to_remove): | ||
| """ | ||
| Remove objects from the group. | ||
| Parameters | ||
| ---------- | ||
| members_to_remove : list | ||
| list of cobrapy objects to remove from the group | ||
| to_remove : list | ||
| A list of cobrapy objects to remove from the group | ||
| """ | ||
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| if isinstance(members_list, string_types) or \ | ||
| hasattr(members_list, "id"): | ||
| if isinstance(to_remove, string_types) or \ | ||
| hasattr(to_remove, "id"): | ||
| warn("need to pass in a list") | ||
| members_list = [members_list] | ||
| to_remove = [to_remove] | ||
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| for member in members_list: | ||
| self._members.discard(member) | ||
| self._members.difference_update(to_remove) |
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