Source code for disbi.models

# standard library
from collections import OrderedDict

# Django
from django.apps import apps
from django.db import models

import disbi.disbimodels as dmodels

[docs]class MetaModel(models.Model): """ Baseclass for clustering the entities with meta information. Meta informations are considered here as entities that can not be measured in an experiment. """
[docs] class Meta: abstract = True
[docs]class BiologicalModel(models.Model): """ Baseclass for clustering the biological entities. """ pass
[docs] class Meta: abstract = True
[docs]class MeasurementModel(models.Model): """Base class for clustering the measurement models.""" experiment = dmodels.ForeignKey('Experiment', on_delete=models.CASCADE)
[docs] class Meta: abstract = True
[docs]class DisbiExperiment(): """ Mixin for managing experiments. """
[docs] def view(self): """ Construct an OrderedDict based on a tuple of column names. Each column name is either expected to be a method or an attribute of the object. For the keys of the dict, the `short_description` is preferred. For attributes `verbose_name` is preferred over `name`. Args: cols (tuple): The column names. Returns: OrderedDict: The external representation or view of the experiment object. """ cols = [ for field in self.__class__._meta.get_fields() if field.concrete and getattr(field, 'di_show', False) ] # Use the string representation as first field. cols.insert(0, '__str__') view = OrderedDict() for col in cols: # Will throw an error if the given col is no attribute. attr = self.__getattribute__(col) if callable(attr): if hasattr(attr, 'short_description'): header = attr.short_description elif col == '__str__': header = self.__class__.__name__ else: header = col view[header] = attr() else: try: field = self.__class__._meta.get_field(col) header = field.verbose_name\ if field.verbose_name !='_', ' ')\ else field.verbose_name.capitalize() except: header = col if isinstance(attr, models.Model): attr = attr.__str__() view[header] = attr return view
[docs] def result_view(self): """ Creates a row with information that should be displayed in the data view. Override in your app, if you need specific information in the table. Returns: OrderedDict: Contains the information for one row of the result table. """ return self.view()
[docs]class DisbiExperimentMetaInfo(): """ Mixin for Experiment proxy model, that fetches additionaly information about the experiment when instantiated. """
[docs] class Meta: proxy = True
def __init__(self, *args, **kwargs): """ Get the related MeasurementModel and the biological model for the experiment. The found classes are attached as attributes to the instance. """ super().__init__(*args, **kwargs) app_models = apps.get_app_config(self._meta.app_label).get_models() # Iterate throw all models and check whether they are a MeasurementModel and no proxy. # If the key of the experiment exists in the model table, that is the # right model. self.measurementmodel = None for model in app_models: if issubclass(model, MeasurementModel) and not model._meta.proxy: related_data = model.objects.filter( if related_data.exists(): self.measurementmodel = model if self.measurementmodel is not None: for field in self.measurementmodel._meta.get_fields(): # Assuming that each MeasurementModel maps to one type in the biological # level, the first that is of that type is the right one. if field.rel: if issubclass(field.related_model, BiologicalModel): self.biofield = field self.biomodel = field.related_model else: self.biofield = None self.biomodel = None
[docs]class Checksum(models.Model): """ Model for storing the checksums of other tables for checking whether data has changed. """ table_name = models.CharField(max_length=512) checksum = models.CharField(max_length=1024, null=True)