Merge pull request #461 from matthiaskoenig/develop

Changes for v0.7.0

backend/pkdb_app/_version.py

@@ -1,4 +1,4 @@
 """
 Definition of version string.
 """
-__version__ = "0.6.9"
+__version__ = "0.7.0"

backend/pkdb_app/categorials/behaviours.py

@@ -1,7 +1,19 @@
-from pkdb_app.categorials.models import ureg, MeasurementType
-from pkdb_app.substances.models import Substance
+from pkdb_app.behaviours import Sidable
+from pkdb_app.categorials.managers import AnnotatableManager
 from django.db import models
 from pkdb_app.utils import CHAR_MAX_LENGTH_LONG, CHAR_MAX_LENGTH
+import pint
+
+ureg = pint.UnitRegistry()
+# Units
+ureg.define('cups = count')
+ureg.define('beverages = count')
+ureg.define('none = count')
+ureg.define('yr = year')
+ureg.define('percent = 0.01*count')
+ureg.define('U = 60*10**6*mol/second')
+ureg.define('IU = [activity_amount]')
+ureg.define('NO_UNIT = [no_unit]')
 
 
 def map_field(fields):
@@ -51,13 +63,23 @@ class Meta:
         abstract = True
 
 
+class Annotatable(Sidable):
+    description = models.TextField(blank=True, null=True)
+    name = models.CharField(max_length=CHAR_MAX_LENGTH)
+    annotations = models.ManyToManyField('categorials.Annotation')
+
+    objects = AnnotatableManager()
+
+    class Meta:
+        abstract = True
+
+
 class ExMeasurementTypeable(ValueableNotBlank, ValueableMapNotBlank):
     measurement_type = models.CharField(max_length=CHAR_MAX_LENGTH, null=True)
     measurement_type_map = models.CharField(max_length=CHAR_MAX_LENGTH_LONG, null=True)
 
     choice = models.CharField(max_length=CHAR_MAX_LENGTH_LONG, null=True)
     choice_map = models.CharField(max_length=CHAR_MAX_LENGTH_LONG, null=True)
-    # substance = models.ForeignKey(Substance, null=True, on_delete=models.PROTECT)
     substance = models.CharField(max_length=CHAR_MAX_LENGTH, null=True)
     substance_map = models.CharField(max_length=CHAR_MAX_LENGTH_LONG, null=True)
 
@@ -66,8 +88,8 @@ class Meta:
 
 
 class MeasurementTypeable(ValueableNotBlank):
-    measurement_type = models.ForeignKey(MeasurementType, on_delete=models.CASCADE)
-    substance = models.ForeignKey(Substance, null=True, on_delete=models.PROTECT)
+    measurement_type = models.ForeignKey('categorials.MeasurementType', on_delete=models.CASCADE)
+    substance = models.ForeignKey('substances.Substance', null=True, on_delete=models.PROTECT)
     choice = models.CharField(max_length=CHAR_MAX_LENGTH_LONG, null=True)
 
     class Meta:
@@ -124,7 +146,7 @@ def is_removeable_substance_dimension(self):
         if substance and substance.mass:
             dimension_of_substance = self.measurement_type.p_unit(self.unit).dimensionality.get('[substance]')
             if dimension_of_substance != 0:
-                return (True, dimension_of_substance)
+                return True, dimension_of_substance
 
         return (False, None)
 
@@ -139,9 +161,9 @@ def remove_substance_dimension(self):
             molar_weight = ureg("g/mol") * self.substance.mass
             p_unit = self.measurement_type.p_unit(self.unit)
             this_quantity = p_unit * molar_weight ** dimension
-            return (this_quantity.magnitude, str(this_quantity.units))
+            return this_quantity.magnitude, str(this_quantity.units)
         else:
-            return (1, self.unit)
+            return 1, self.unit
 
     def normalize(self):
         """ Normalizes the units.

backend/pkdb_app/categorials/documents.py

@@ -48,6 +48,13 @@ class MeasurementTypeDocument(Document):
             "label": string_field("label")
         }
     )
+    synonyms = ObjectField(
+        attr="synonyms",
+        multi=True,
+        properties={
+            "name": string_field("name"),
+        }
+    )
     creator = string_field("creator_username")
     description = string_field('description')
 

backend/pkdb_app/categorials/managers.py

@@ -2,10 +2,10 @@
 from pkdb_app.utils import update_or_create_multiple
 
 
-class ChoiceManager(models.Manager):
+class AnnotatableManager(models.Manager):
     def create(self, *args, **kwargs):
         annotations = kwargs.pop('annotations', [])
-        choice = super().create(*args, **kwargs)
-        update_or_create_multiple(choice, annotations, 'annotations', lookup_fields=["term", "relation"])
-        choice.save()
-        return choice
+        instance = super().create(*args, **kwargs)
+        update_or_create_multiple(instance, annotations, 'annotations', lookup_fields=["term", "relation"])
+        instance.save()
+        return instance

backend/pkdb_app/categorials/models.py

@@ -3,31 +3,17 @@
 
 FIXME: Some duplication to pkdb_data/categorials
 """
-import pint
 from pint import UndefinedUnitError
-import numpy as np
-
 from numbers import Number
-
 from django.db import models
-from pkdb_app.categorials.managers import ChoiceManager
-from pkdb_app.users.models import User
-from pkdb_app.utils import CHAR_MAX_LENGTH, create_choices, _validate_requried_key, CHAR_MAX_LENGTH_LONG
 
-ureg = pint.UnitRegistry()
+from pkdb_app.categorials.managers import AnnotatableManager
+from pkdb_app.users.models import User
+from pkdb_app.utils import CHAR_MAX_LENGTH, create_choices, _validate_requried_key
+from pkdb_app.categorials.behaviours import Annotatable, ureg
 
-# Units
-ureg.define('cups = count')
-ureg.define('beverages = count')
-ureg.define('none = count')
-ureg.define('yr = year')
-ureg.define('percent = 0.01*count')
-ureg.define('U = 60*10**6*mol/second')
-ureg.define('IU = [activity_amount]')
-ureg.define('NO_UNIT = [no_unit]')
 
 NO_UNIT = 'NO_UNIT'
-
 NUMERIC_TYPE = "numeric"
 CATEGORIAL_TYPE = "categorial"
 BOOLEAN_TYPE = "boolean"
@@ -57,7 +43,11 @@ def p_unit(self):
         return ureg(self.name).u
 
 
+
+
+
 class Annotation(models.Model):
+    """ Annotation Model """
     term = models.CharField(max_length=CHAR_MAX_LENGTH)
     relation = models.CharField(max_length=CHAR_MAX_LENGTH, )
     collection = models.CharField(max_length=CHAR_MAX_LENGTH, null=True)
@@ -67,49 +57,52 @@ class Annotation(models.Model):
 
 class Choice(models.Model):
     """Choice Model"""
+    description = models.TextField(blank=True, null=True)
     name = models.CharField(max_length=CHAR_MAX_LENGTH)
     annotations = models.ManyToManyField(Annotation)
-    description = models.TextField(blank=True, null=True)
-    objects = ChoiceManager()
+    objects = AnnotatableManager()
 
 
-class Tissue(models.Model):
-    name = models.CharField(max_length=CHAR_MAX_LENGTH, unique=True)
+class Tissue(Annotatable):
+    """ Tissue Model """
+
     creator = models.ForeignKey(User, related_name="tissues", on_delete=models.CASCADE)
     url_slug = models.CharField(max_length=CHAR_MAX_LENGTH, unique=True)
-    description = models.TextField(blank=True, null=True)
 
 
-class Route(models.Model):
-    name = models.CharField(max_length=CHAR_MAX_LENGTH, unique=True)
+class Route(Annotatable):
+    """ Route Model """
+
     creator = models.ForeignKey(User, related_name="routes", on_delete=models.CASCADE)
     url_slug = models.CharField(max_length=CHAR_MAX_LENGTH, unique=True)
-    description = models.TextField(blank=True, null=True)
 
 
-class Application(models.Model):
-    name = models.CharField(max_length=CHAR_MAX_LENGTH, unique=True)
+class Application(Annotatable):
+    """ Application Model """
     creator = models.ForeignKey(User, related_name="applications", on_delete=models.CASCADE)
     url_slug = models.CharField(max_length=CHAR_MAX_LENGTH, unique=True)
-    description = models.TextField(blank=True, null=True)
 
 
-class Form(models.Model):
-    name = models.CharField(max_length=CHAR_MAX_LENGTH, unique=True)
+class Form(Annotatable):
+    """ Form Model """
+
     creator = models.ForeignKey(User, related_name="forms", on_delete=models.CASCADE)
     url_slug = models.CharField(max_length=CHAR_MAX_LENGTH, unique=True)
-    description = models.TextField(blank=True, null=True)
 
 
 class MeasurementType(models.Model):
-    name = models.CharField(max_length=CHAR_MAX_LENGTH, unique=True)
+    """ MeasurementType Model """
+    #fixme: add sid to pkdb_data and use Annotatable
     url_slug = models.CharField(max_length=CHAR_MAX_LENGTH, unique=True)
     units = models.ManyToManyField(Unit, related_name="measurement_types")
     dtype = models.CharField(max_length=CHAR_MAX_LENGTH, choices=DTYPE_CHOICES)
     creator = models.ForeignKey(User, related_name="measurement_types", on_delete=models.CASCADE)
     choices = models.ManyToManyField(Choice, related_name="measurement_types")
+
     description = models.TextField(blank=True, null=True)
+    name = models.CharField(max_length=CHAR_MAX_LENGTH)
     annotations = models.ManyToManyField(Annotation)
+    objects = AnnotatableManager()
 
     def __str__(self):
         return self.name
@@ -143,7 +136,8 @@ def valid_dimensions_str(self):
     def dimension_to_n_unit(self):
         return {str(n_unit_p.dimensionality): n_unit_p for n_unit_p in self.n_p_units}
 
-    def p_unit(self, unit):
+    @staticmethod
+    def p_unit(unit):
         try:
             return ureg(unit)
         except (UndefinedUnitError, AttributeError):
@@ -171,7 +165,8 @@ def is_valid_unit(self, unit):
 
     def validate_unit(self, unit):
         if not self.is_valid_unit(unit):
-            msg = f"For measurement type `{self.name}` the unit [{unit}] with dimension {self.unit_dimension(unit)} is not allowed."
+            msg = f"For measurement type `{self.name}` the unit [{unit}] with dimension {self.unit_dimension(unit)} " \
+                  f"is not allowed."
             raise ValueError(
                 {"unit": msg, "Only units with the following dimensions are allowed:": self.valid_dimensions_str,
                  "Units are allowed which can be converted to the following normalized units:": self.n_units})
@@ -239,7 +234,8 @@ def validate_choice(self, choice):
                       f"For encoding substances use the `substance` field."
                 raise ValueError({"choice": msg})
         elif self.choices.exists():
-            msg = f"{choice}. A choice is required for `{self.name}`. Allowed choices are: `{list(self.choices_list())}`."
+            msg = f"{choice}. A choice is required for `{self.name}`." \
+                  f" Allowed choices are: `{list(self.choices_list())}`."
             raise ValueError({"choice": msg})
 
     @property
@@ -297,3 +293,13 @@ def creator_username(self):
         :return: list of normalized units in the data format of pint
         """
         return self.creator.username
+
+class Synonym(models.Model):
+    """Units Model"""
+    name = models.CharField(max_length=CHAR_MAX_LENGTH, unique=True)
+    substance = models.ForeignKey('substances.Substance', on_delete=models.CASCADE, related_name="synonyms", null=True)
+    tissue = models.ForeignKey(Tissue, on_delete=models.CASCADE, related_name="synonyms", null=True)
+    route = models.ForeignKey(Route, on_delete=models.CASCADE, related_name="synonyms", null=True)
+    form = models.ForeignKey(Form, on_delete=models.CASCADE, related_name="synonyms", null=True)
+    application = models.ForeignKey(Application, on_delete=models.CASCADE, related_name="synonyms", null=True)
+    measurement_type = models.ForeignKey(MeasurementType, on_delete=models.CASCADE, related_name="synonyms", null=True)