from __future__ import with_statement
#cobra.flux_analysis.essentiality.py
#runs flux variablity analysis on a Model object.
from os import name as __name
from warnings import warn
if __name == 'java':
    warn("moma is not supported on %s"%__name)
    warn("flux_analysis.double_deletion is not supported on %s"%__name)
    def moma(a, **kwargs):
        raise Exception("moma is not supported on %s"%__name)

    def double_deletion(a, **kwargs):
        raise Exception("flux_analysis.double_deletion is not supported on %s"%__name)
else:
    try:
        from cobra.flux_analysis.moma import moma
    except:
        warn("moma does not appear to be functional on your system")
from cobra.manipulation import initialize_growth_medium
def assess_medium_component_essentiality(cobra_model, the_components=None,
                                         the_medium=None, medium_compartment='e', solver='glpk',
                                         the_problem='return',
                                         the_condition=None, method='fba'):
    """Determines which components in an in silico medium are essential for growth in the
    context of the remaining components.

    cobra_model: A Model object.

    the_components: None or a list of external boundary reactions that will be sequentially
    disabled.

    the_medium: Is None, a string, or a dictionary.  If a string then the
    initialize_growth_medium function expects that the_model has an
    attribute dictionary called media_compositions, which is a dictionary of
    dictionaries for various medium compositions.  Where a medium
    composition is a dictionary of external boundary reaction ids for the medium
    components and the external boundary fluxes for each medium component.

    medium_compartment: the compartment in which the boundary reactions supplying the medium
    components exist

    NOTE: that these fluxes must be negative because the convention is backwards means something
    is feed into the system.

    solver: 'glpk', 'gurobi', or 'cplex'

    the_problem: Is None, 'return', or an LP model object for the solver.

    returns:
     essentiality_dict:  A dictionary providing the maximum growth rate accessible when
     the respective component is removed from the medium.

    """
    if method.lower() == 'moma':
        wt_model = cobra_model.copy()
    cobra_model = cobra_model.copy()

    if isinstance(the_medium, str):
        try:
            the_medium = cobra_model.media_compositions[the_medium]
        except:
            raise Exception(the_medium + " is not in cobra_model.media_compositions")
    if the_medium is not None:
        initialize_growth_medium(cobra_model, the_medium, medium_compartment)
        if the_components is None:
            the_components = the_medium.keys()
    if not the_components:
            raise Exception("You need to specify the_components or the_medium")
    essentiality_dict = {}
    for the_component in the_components:
        the_reaction = cobra_model.reactions.get_by_id(the_component)
        original_lower_bound = float(the_reaction.lower_bound)
        the_reaction.lower_bound = 0.
        if method.lower() == 'fba':
            cobra_model.optimize(solver=solver, the_problem=the_problem)
            objective_value = cobra_model.solution.f
        elif method.lower() == 'moma':
           objective_value = moma(wt_model, cobra_model, solver=solver)['objective_value'] 
        essentiality_dict[the_component] = objective_value
        the_reaction.lower_bound = original_lower_bound

    return(essentiality_dict)

def deletion_analysis(cobra_model, the_medium=None, deletion_type='single',
                      work_directory=None, growth_cutoff=0.001,
                      the_problem='return', number_of_processes=6, element_type='gene',
                      solver='glpk', error_reporting=None, method='fba', element_list=None):
    """Performs single and/or double deletion analysis on all the genes in the model.  Provides
    an interface to parallelize the deletion studies.

    """
    raise exception("Deletion analysis has been dropped in favor of the single_deletion and double_deletion modules")
