Source code for disbi.experiment_filter

Functions for filtering the experiments based on conditions.
# standard library
from copy import deepcopy

# Django
from django.conf import settings

from disbi.utils import clean_set

[docs]def lookup_format(dic): """ Return a dictionary readily useable for filter kwargs. Args: dic (dict): The dictionary to be formatted. Returns: dict: The same dictionary with the keys concatenated with '__in' """ return dict((k + '__in', v) for k, v in dic.items())
[docs]def combine_on_sep(items, separator): """ Combine each item with each other item on a `separator`. Args: items (list): A list or iterable that remembers order. separator (str): The SEPARATOR the items will be combined on. Returns: list: A list with all the combined items as strings. """ combined_items = [] # Combine items only if there is more than 1 items. if len(items) > 1: # Convert the empty string back to minus. items = [i if i!='' else '-' for i in items] for i, item in enumerate(items): reduced_items = items[:i] + items[i+1:] combined_with_item = [separator.join((item, r)) for r in reduced_items] combined_items += combined_with_item # Else simply return the given list. else: combined_items = items return combined_items
[docs]def combine_conditions(conditions, combinable_conditions): """ Apply :func:`combine_on_sep` to each value in a dictionary. Args: conditions (dict): Dictionary with a list of condition values. Returns: dict: A dictionary with the same keys and lists of combined values. """ combined_conditions = {} for k, values in conditions.items(): if k in combinable_conditions: combined_conditions[k] = combine_on_sep(values, settings.DISBI['SEPARATOR']) else: combined_conditions[k] = values return combined_conditions
[docs]def get_experiments_by_condition(conditions, experiment_model): """ Return a set of experiments that match the conditions. Args: conditions (dict): A dictionary with conditions as keys and a list of values. Returns: set: A set of experiments that match the conditions. """ # If nothing was chosen conditions is an empty dict and # evaluates to false. if not conditions: return set() query_conditions = lookup_format(conditions) # Experiments from parameters. exps_by_condition = set(experiment_model.objects.filter(**query_conditions)) # Experimental parameters that can be combined in a microarray experiment. combinable_conditions = [ for field in experiment_model._meta.get_fields() if getattr(field, 'di_combinable', False)] combined_conditions = combine_conditions(conditions, combinable_conditions) combined_query_conditions = lookup_format(combined_conditions) # Experiments from all combinable conditions combined. exps_by_combined_condtion = set(experiment_model.objects.filter(**combined_query_conditions) or ()) # Experiments from a single combinable condition, combined each. for combinable_condition in combinable_conditions: if combinable_condition in conditions.keys(): c_conditions = deepcopy(conditions) c_conditions[combinable_condition] = combine_on_sep(conditions[combinable_condition], settings.DISBI['SEPARATOR']) c_combined_query_conditons = lookup_format(c_conditions) exps_by_combined_condtion |= set(experiment_model.objects.filter( **c_combined_query_conditons) or ()) return exps_by_condition | exps_by_combined_condtion
[docs]def get_requested_experiments(formset_list, experiment_model): """ Return all experiments that match the request from the form. Args: formset_list (list): Formsets containing POST data. Returns: set: The union of the set of the directly requested experiments and those that matched the requested conditons. """ # Formsets with these prefixes return model instances, # thus no further query is needed. no_query = ['experiment'] conditions = {} for formset in formset_list: if formset.prefix not in no_query: conditions.update(clean_set(formset.cleaned_data)) elif formset.prefix == 'experiment': # Directly requested experiments. directly_req_exps = (set( clean_set(formset.cleaned_data).get('experiment') or ()) ) exps_from_conditions = get_experiments_by_condition(conditions, experiment_model) return directly_req_exps | exps_from_conditions