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feat: add yaml round tripping support (#496)
- introduce read/write for yaml, io.yaml - move dict related functions from io.json to io.dict
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| Original file line number | Diff line number | Diff line change |
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| # -*- coding: utf-8 -*- | ||
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| from __future__ import absolute_import | ||
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| from collections import OrderedDict | ||
| from operator import attrgetter | ||
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| from numpy import bool_, float_ | ||
| from six import iteritems, string_types | ||
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| from cobra.core import Gene, Metabolite, Model, Reaction | ||
| from cobra.util.solver import set_objective | ||
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| _REQUIRED_REACTION_ATTRIBUTES = [ | ||
| "id", "name", "metabolites", "lower_bound", "upper_bound", | ||
| "gene_reaction_rule"] | ||
| _ORDERED_OPTIONAL_REACTION_KEYS = [ | ||
| "objective_coefficient", "variable_kind", "subsystem", "notes", | ||
| "annotation"] | ||
| _OPTIONAL_REACTION_ATTRIBUTES = { | ||
| "objective_coefficient": 0, | ||
| "variable_kind": "continuous", | ||
| "subsystem": "", | ||
| "notes": {}, | ||
| "annotation": {}, | ||
| } | ||
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| _REQUIRED_METABOLITE_ATTRIBUTES = ["id", "name", "compartment"] | ||
| _ORDERED_OPTIONAL_METABOLITE_KEYS = [ | ||
| "charge", "formula", "_bound", "_constraint_sense", "notes", "annotation"] | ||
| _OPTIONAL_METABOLITE_ATTRIBUTES = { | ||
| "charge": None, | ||
| "formula": None, | ||
| "_bound": 0, | ||
| "_constraint_sense": "E", | ||
| "notes": {}, | ||
| "annotation": {}, | ||
| } | ||
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| _REQUIRED_GENE_ATTRIBUTES = ["id", "name"] | ||
| _ORDERED_OPTIONAL_GENE_KEYS = ["notes", "annotation"] | ||
| _OPTIONAL_GENE_ATTRIBUTES = { | ||
| "notes": {}, | ||
| "annotation": {}, | ||
| } | ||
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| _ORDERED_OPTIONAL_MODEL_KEYS = ["name", "compartments", "notes", "annotation"] | ||
| _OPTIONAL_MODEL_ATTRIBUTES = { | ||
| "name": None, | ||
| # "description": None, should not actually be included | ||
| "compartments": [], | ||
| "notes": {}, | ||
| "annotation": {}, | ||
| } | ||
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| def _fix_type(value): | ||
| """convert possible types to str, float, and bool""" | ||
| # Because numpy floats can not be pickled to json | ||
| if isinstance(value, string_types): | ||
| return str(value) | ||
| if isinstance(value, float_): | ||
| return float(value) | ||
| if isinstance(value, bool_): | ||
| return bool(value) | ||
| if isinstance(value, set): | ||
| return list(value) | ||
| # handle legacy Formula type | ||
| if value.__class__.__name__ == "Formula": | ||
| return str(value) | ||
| if value is None: | ||
| return "" | ||
| return value | ||
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| def _update_optional(cobra_object, new_dict, optional_attribute_dict, | ||
| ordered_keys): | ||
| """update new_dict with optional attributes from cobra_object""" | ||
| for key in ordered_keys: | ||
| default = optional_attribute_dict[key] | ||
| value = getattr(cobra_object, key) | ||
| if value is None or value == default: | ||
| continue | ||
| new_dict[key] = _fix_type(value) | ||
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| def metabolite_to_dict(metabolite): | ||
| new_met = OrderedDict() | ||
| for key in _REQUIRED_METABOLITE_ATTRIBUTES: | ||
| new_met[key] = _fix_type(getattr(metabolite, key)) | ||
| _update_optional(metabolite, new_met, _OPTIONAL_METABOLITE_ATTRIBUTES, | ||
| _ORDERED_OPTIONAL_METABOLITE_KEYS) | ||
| return new_met | ||
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| def metabolite_from_dict(metabolite): | ||
| new_metabolite = Metabolite() | ||
| for k, v in iteritems(metabolite): | ||
| setattr(new_metabolite, k, v) | ||
| return new_metabolite | ||
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| def gene_to_dict(gene): | ||
| new_gene = OrderedDict() | ||
| for key in _REQUIRED_GENE_ATTRIBUTES: | ||
| new_gene[key] = _fix_type(getattr(gene, key)) | ||
| _update_optional(gene, new_gene, _OPTIONAL_GENE_ATTRIBUTES, | ||
| _ORDERED_OPTIONAL_GENE_KEYS) | ||
| return new_gene | ||
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| def gene_from_dict(gene): | ||
| new_gene = Gene(gene["id"]) | ||
| for k, v in iteritems(gene): | ||
| setattr(new_gene, k, v) | ||
| return new_gene | ||
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| def reaction_to_dict(reaction): | ||
| new_reaction = OrderedDict() | ||
| for key in _REQUIRED_REACTION_ATTRIBUTES: | ||
| if key != "metabolites": | ||
| new_reaction[key] = _fix_type(getattr(reaction, key)) | ||
| continue | ||
| mets = OrderedDict() | ||
| for met in sorted(reaction.metabolites, key=attrgetter("id")): | ||
| mets[str(met)] = reaction.metabolites[met] | ||
| new_reaction["metabolites"] = mets | ||
| _update_optional(reaction, new_reaction, _OPTIONAL_REACTION_ATTRIBUTES, | ||
| _ORDERED_OPTIONAL_REACTION_KEYS) | ||
| return new_reaction | ||
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| def reaction_from_dict(reaction, model): | ||
| new_reaction = Reaction() | ||
| for k, v in iteritems(reaction): | ||
| if k in {'objective_coefficient', 'reversibility', 'reaction'}: | ||
| continue | ||
| elif k == 'metabolites': | ||
| new_reaction.add_metabolites(OrderedDict( | ||
| (model.metabolites.get_by_id(str(met)), coeff) | ||
| for met, coeff in iteritems(v))) | ||
| else: | ||
| setattr(new_reaction, k, v) | ||
| return new_reaction | ||
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| def model_to_dict(model): | ||
| """Convert model to a dict. | ||
| Parameters | ||
| ---------- | ||
| model : cobra.Model | ||
| The model to reformulate as a dict | ||
| Returns | ||
| ------- | ||
| OrderedDict | ||
| A dictionary with elements, 'genes', 'compartments', 'id', | ||
| 'metabolites', 'notes' and 'reactions'; where 'metabolites', 'genes' | ||
| and 'metabolites' are in turn lists with dictionaries holding all | ||
| attributes to form the corresponding object. | ||
| See Also | ||
| -------- | ||
| cobra.io.model_from_dict | ||
| """ | ||
| obj = OrderedDict() | ||
| obj["reactions"] = [reaction_to_dict(reaction) | ||
| for reaction in model.reactions] | ||
| obj["metabolites"] = [metabolite_to_dict(metabolite) | ||
| for metabolite in model.metabolites] | ||
| obj["genes"] = [gene_to_dict(gene) | ||
| for gene in model.genes] | ||
| obj["id"] = model.id | ||
| _update_optional(model, obj, _OPTIONAL_MODEL_ATTRIBUTES, | ||
| _ORDERED_OPTIONAL_MODEL_KEYS) | ||
| return obj | ||
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| def model_from_dict(obj): | ||
| """Build a model from a dict. | ||
| Models stored in json are first formulated as a dict that can be read to | ||
| cobra model using this function. | ||
| Parameters | ||
| ---------- | ||
| obj : dict | ||
| A dictionary with elements, 'genes', 'compartments', 'id', | ||
| 'metabolites', 'notes' and 'reactions'; where 'metabolites', 'genes' | ||
| and 'metabolites' are in turn lists with dictionaries holding all | ||
| attributes to form the corresponding object. | ||
| Returns | ||
| ------- | ||
| cora.core.Model | ||
| The generated model. | ||
| See Also | ||
| -------- | ||
| cobra.io.model_to_dict | ||
| """ | ||
| if 'reactions' not in obj: | ||
| raise ValueError('Object has no reactions attribute. Cannot load.') | ||
| model = Model() | ||
| model.add_metabolites( | ||
| [metabolite_from_dict(metabolite) for metabolite in obj['metabolites']] | ||
| ) | ||
| model.genes.extend([gene_from_dict(gene) for gene in obj['genes']]) | ||
| model.add_reactions( | ||
| [reaction_from_dict(reaction, model) for reaction in obj['reactions']] | ||
| ) | ||
| objective_reactions = [rxn for rxn in obj['reactions'] if | ||
| rxn.get('objective_coefficient', 0) != 0] | ||
| coefficients = { | ||
| model.reactions.get_by_id(rxn['id']): rxn['objective_coefficient'] for | ||
| rxn in objective_reactions} | ||
| set_objective(model, coefficients) | ||
| for k, v in iteritems(obj): | ||
| if k in {'id', 'name', 'notes', 'compartments', 'annotation'}: | ||
| setattr(model, k, v) | ||
| return model |
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