fix factor IDs for result sets

gemmapy/_processors.py

@@ -119,6 +119,7 @@ def process_dea(d):
             d[i].result_sets[j].experimental_factors = [d[i].result_sets[j].experimental_factors[k] for k in order]
             exp_factors = d[i].result_sets[j].experimental_factors
 
+
             if len(exp_factors) == 1:
                 contrast_id = [x.id for x in exp_factors[0].values]
                 baseline_id = d[i].result_sets[j].baseline_group.id
@@ -128,6 +129,18 @@ def process_dea(d):
                 size = len(contrast_id)
 
                 experimental_factors = [sub.process_FactorValueValueObject(x) for x in non_control_factors]
+
+                factor_ID = d[i].result_sets[j].experimental_factors[0].id
+                factor_category = d[i].result_sets[j].experimental_factors[0].category
+                factor_category_URI = d[i].result_sets[j].experimental_factors[0].category_uri
+
+                def add_missing(x):
+                    x.factor_ID = factor_ID
+                    x.factor_category = factor_category
+                    x.factor_category_URI = factor_category_URI
+                    return x
+
+                experimental_factors = [add_missing(x) for x in experimental_factors]
                 baseline_factors =  sub.process_FactorValueBasicValueObject(d[i].result_sets[j].baseline_group) 
 
             else:
@@ -144,11 +157,17 @@ def process_dea(d):
 
                 relevant_ids = [x for x in ids if not any(sub.list_in_list(x, baseline_ids))]
 
-                fac_vals = [sub.access_field(y,'values') for y in exp_factors]
-                all_factors = pd.concat(
-                    [sub.process_FactorValueValueObject_list(y) for y in fac_vals],
-                    ignore_index = True
-                    )
+                def get_factor_vals(x):
+                    vals = sub.access_field(x,'values')
+                    out = sub.process_FactorValueValueObject_list(vals)
+                    out.factor_ID = x.id
+                    out.factor_category = x.category
+                    out.factor_category_URI = x.category_uri
+                    return out
+
+                all_factors = pd.concat([get_factor_vals(x) for x in exp_factors])
+
+
 
                 baseline_factors = all_factors.loc[all_factors.ID.isin(baseline_ids)]
                 experimental_factors = [

gemmapy/_subprocessors.py

@@ -134,7 +134,7 @@ def process_FactorValueBasicValueObject(d):
             "factor_category":[],
             "factor_category_URI":[]
             })
-    elif not d.measurement is None:
+    elif d.is_measurement:
         return pd.DataFrame({
             'category': [access_field(d,"category")],
             "category_URI": [access_field(d,"category_uri")],

gemmapy/sdk/models/factor_value_basic_value_object.py

@@ -28,6 +28,7 @@ class FactorValueBasicValueObject(object):
                             and the value is json key in definition.
     """
     swagger_types = {
+        'measurement': 'MeasurementValueObject',
         'id': 'int',
         'ontology_id': 'str',
         'experimental_factor_id': 'int',
@@ -40,6 +41,7 @@ class FactorValueBasicValueObject(object):
     }
 
     attribute_map = {
+        'measurement': 'measurement',
         'id': 'id',
         'ontology_id': 'ontologyId',
         'experimental_factor_id': 'experimentalFactorId',
@@ -51,8 +53,9 @@ class FactorValueBasicValueObject(object):
         'is_measurement': 'isMeasurement'
     }
 
-    def __init__(self, id=None, ontology_id=None, experimental_factor_id=None, experimental_factor_category=None, characteristics=None, statements=None, summary=None, value=None, is_measurement=None):  # noqa: E501
+    def __init__(self, measurement=None, id=None, ontology_id=None, experimental_factor_id=None, experimental_factor_category=None, characteristics=None, statements=None, summary=None, value=None, is_measurement=None):  # noqa: E501
         """FactorValueBasicValueObject - a model defined in Swagger"""  # noqa: E501
+        self._measurement = None
         self._id = None
         self._ontology_id = None
         self._experimental_factor_id = None
@@ -63,6 +66,8 @@ def __init__(self, id=None, ontology_id=None, experimental_factor_id=None, exper
         self._value = None
         self._is_measurement = None
         self.discriminator = None
+        if measurement is not None:
+            self.measurement = measurement
         if id is not None:
             self.id = id
         if ontology_id is not None:
@@ -82,6 +87,27 @@ def __init__(self, id=None, ontology_id=None, experimental_factor_id=None, exper
         if is_measurement is not None:
             self.is_measurement = is_measurement
 
+    @property
+    def measurement(self):
+        """Gets the measurement of this FactorValueBasicValueObject.  # noqa: E501
+
+
+        :return: The measurement of this FactorValueBasicValueObject.  # noqa: E501
+        :rtype: MeasurementValueObject
+        """
+        return self._measurement
+
+    @measurement.setter
+    def measurement(self, measurement):
+        """Sets the measurement of this FactorValueBasicValueObject.
+
+
+        :param measurement: The measurement of this FactorValueBasicValueObject.  # noqa: E501
+        :type: MeasurementValueObject
+        """
+
+        self._measurement = measurement
+
     @property
     def id(self):
         """Gets the id of this FactorValueBasicValueObject.  # noqa: E501

sdk-gen/openapi.yaml

@@ -3441,6 +3441,8 @@ components:
     FactorValueBasicValueObject:
       type: object
       properties:
+        measurement:
+          $ref: '#/components/schemas/MeasurementValueObject'
         id:
           type: integer
           format: int64