sdk update

gemmapy/sdk/api/default_api.py

@@ -5370,6 +5370,8 @@ def get_result_set(self, result_set, **kwargs):  # noqa: E501
         :param float threshold:
         :param int offset:
         :param int limit:
+        :param bool include_factor_values_in_contrasts: Include complete factor values in contrasts instead of only populating `factorValueId` and `secondFactorValueId`. In 2.9.0, this will default to false.
+        :param bool include_taxon_in_genes: Include complete taxon in genes instead of only populating `taxonId`. When this is set to true, a `taxa` collection will be included in `DifferentialExpressionAnalysisResultSetValueObject`. In 2.9.0, this will default to false.
         :return: PaginatedResultsResponseDataObjectDifferentialExpressionAnalysisResultSetValueObject
                  If the method is called asynchronously,
                  returns the request thread.
@@ -5407,12 +5409,14 @@ def get_result_set_with_http_info(self, result_set, **kwargs):  # noqa: E501
         :param float threshold:
         :param int offset:
         :param int limit:
+        :param bool include_factor_values_in_contrasts: Include complete factor values in contrasts instead of only populating `factorValueId` and `secondFactorValueId`. In 2.9.0, this will default to false.
+        :param bool include_taxon_in_genes: Include complete taxon in genes instead of only populating `taxonId`. When this is set to true, a `taxa` collection will be included in `DifferentialExpressionAnalysisResultSetValueObject`. In 2.9.0, this will default to false.
         :return: PaginatedResultsResponseDataObjectDifferentialExpressionAnalysisResultSetValueObject
                  If the method is called asynchronously,
                  returns the request thread.
         """
 
-        all_params = ['result_set', 'threshold', 'offset', 'limit']  # noqa: E501
+        all_params = ['result_set', 'threshold', 'offset', 'limit', 'include_factor_values_in_contrasts', 'include_taxon_in_genes']  # noqa: E501
         all_params.append('async_req')
         all_params.append('_return_http_data_only')
         all_params.append('_preload_content')
@@ -5447,6 +5451,10 @@ def get_result_set_with_http_info(self, result_set, **kwargs):  # noqa: E501
             query_params.append(('offset', params['offset']))  # noqa: E501
         if 'limit' in params:
             query_params.append(('limit', params['limit']))  # noqa: E501
+        if 'include_factor_values_in_contrasts' in params:
+            query_params.append(('includeFactorValuesInContrasts', params['include_factor_values_in_contrasts']))  # noqa: E501
+        if 'include_taxon_in_genes' in params:
+            query_params.append(('includeTaxonInGenes', params['include_taxon_in_genes']))  # noqa: E501
 
         header_params = {}
 

gemmapy/sdk/api_client.py

@@ -73,7 +73,7 @@ def __init__(self, configuration=None, header_name=None, header_value=None,
             self.default_headers[header_name] = header_value
         self.cookie = cookie
         # Set default User-Agent.
-        self.user_agent = 'gemmapy/1.0.5'
+        self.user_agent = 'gemmapy/1.0.6'
 
     def __del__(self):
         self.pool.close()

gemmapy/sdk/models/audit_event_value_object.py

@@ -34,8 +34,8 @@ class AuditEventValueObject(object):
         'action': 'str',
         'note': 'str',
         'detail': 'str',
-        'event_type_name': 'str',
-        'action_name': 'str'
+        'action_name': 'str',
+        'event_type_name': 'str'
     }
 
     attribute_map = {
@@ -45,20 +45,20 @@ class AuditEventValueObject(object):
         'action': 'action',
         'note': 'note',
         'detail': 'detail',
-        'event_type_name': 'eventTypeName',
-        'action_name': 'actionName'
+        'action_name': 'actionName',
+        'event_type_name': 'eventTypeName'
     }
 
-    def __init__(self, id=None, performer=None, _date=None, action=None, note=None, detail=None, event_type_name=None, action_name=None):  # noqa: E501
+    def __init__(self, id=None, performer=None, _date=None, action=None, note=None, detail=None, action_name=None, event_type_name=None):  # noqa: E501
         """AuditEventValueObject - a model defined in Swagger"""  # noqa: E501
         self._id = None
         self._performer = None
         self.__date = None
         self._action = None
         self._note = None
         self._detail = None
-        self._event_type_name = None
         self._action_name = None
+        self._event_type_name = None
         self.discriminator = None
         if id is not None:
             self.id = id
@@ -72,10 +72,10 @@ def __init__(self, id=None, performer=None, _date=None, action=None, note=None,
             self.note = note
         if detail is not None:
             self.detail = detail
-        if event_type_name is not None:
-            self.event_type_name = event_type_name
         if action_name is not None:
             self.action_name = action_name
+        if event_type_name is not None:
+            self.event_type_name = event_type_name
 
     @property
     def id(self):
@@ -210,46 +210,46 @@ def detail(self, detail):
         self._detail = detail
 
     @property
-    def event_type_name(self):
-        """Gets the event_type_name of this AuditEventValueObject.  # noqa: E501
+    def action_name(self):
+        """Gets the action_name of this AuditEventValueObject.  # noqa: E501
 
 
-        :return: The event_type_name of this AuditEventValueObject.  # noqa: E501
+        :return: The action_name of this AuditEventValueObject.  # noqa: E501
         :rtype: str
         """
-        return self._event_type_name
+        return self._action_name
 
-    @event_type_name.setter
-    def event_type_name(self, event_type_name):
-        """Sets the event_type_name of this AuditEventValueObject.
+    @action_name.setter
+    def action_name(self, action_name):
+        """Sets the action_name of this AuditEventValueObject.
 
 
-        :param event_type_name: The event_type_name of this AuditEventValueObject.  # noqa: E501
+        :param action_name: The action_name of this AuditEventValueObject.  # noqa: E501
         :type: str
         """
 
-        self._event_type_name = event_type_name
+        self._action_name = action_name
 
     @property
-    def action_name(self):
-        """Gets the action_name of this AuditEventValueObject.  # noqa: E501
+    def event_type_name(self):
+        """Gets the event_type_name of this AuditEventValueObject.  # noqa: E501
 
 
-        :return: The action_name of this AuditEventValueObject.  # noqa: E501
+        :return: The event_type_name of this AuditEventValueObject.  # noqa: E501
         :rtype: str
         """
-        return self._action_name
+        return self._event_type_name
 
-    @action_name.setter
-    def action_name(self, action_name):
-        """Sets the action_name of this AuditEventValueObject.
+    @event_type_name.setter
+    def event_type_name(self, event_type_name):
+        """Sets the event_type_name of this AuditEventValueObject.
 
 
-        :param action_name: The action_name of this AuditEventValueObject.  # noqa: E501
+        :param event_type_name: The event_type_name of this AuditEventValueObject.  # noqa: E501
         :type: str
         """
 
-        self._action_name = action_name
+        self._event_type_name = event_type_name
 
     def to_dict(self):
         """Returns the model properties as a dict"""

gemmapy/sdk/models/contrast_result_value_object.py

@@ -170,6 +170,7 @@ def log_fold_change(self, log_fold_change):
     def factor_value_id(self):
         """Gets the factor_value_id of this ContrastResultValueObject.  # noqa: E501
 
+        This property is mutually exclusive with `factorValue`.  # noqa: E501
 
         :return: The factor_value_id of this ContrastResultValueObject.  # noqa: E501
         :rtype: int
@@ -180,6 +181,7 @@ def factor_value_id(self):
     def factor_value_id(self, factor_value_id):
         """Sets the factor_value_id of this ContrastResultValueObject.
 
+        This property is mutually exclusive with `factorValue`.  # noqa: E501
 
         :param factor_value_id: The factor_value_id of this ContrastResultValueObject.  # noqa: E501
         :type: int
@@ -212,6 +214,7 @@ def factor_value(self, factor_value):
     def second_factor_value_id(self):
         """Gets the second_factor_value_id of this ContrastResultValueObject.  # noqa: E501
 
+        This property is mutually exclusive with `secondFactorValue`.  # noqa: E501
 
         :return: The second_factor_value_id of this ContrastResultValueObject.  # noqa: E501
         :rtype: int
@@ -222,6 +225,7 @@ def second_factor_value_id(self):
     def second_factor_value_id(self, second_factor_value_id):
         """Sets the second_factor_value_id of this ContrastResultValueObject.
 
+        This property is mutually exclusive with `secondFactorValue`.  # noqa: E501
 
         :param second_factor_value_id: The second_factor_value_id of this ContrastResultValueObject.  # noqa: E501
         :type: int

gemmapy/sdk/models/diff_ex_result_set_summary_value_object.py

@@ -38,9 +38,9 @@ class DiffExResultSetSummaryValueObject(object):
         'number_of_diff_expressed_probes': 'int',
         'upregulated_count': 'int',
         'downregulated_count': 'int',
+        'number_of_upregulated_probes': 'int',
         'number_of_downregulated_probes': 'int',
-        'qvalue': 'float',
-        'number_of_upregulated_probes': 'int'
+        'qvalue': 'float'
     }
 
     attribute_map = {
@@ -54,12 +54,12 @@ class DiffExResultSetSummaryValueObject(object):
         'number_of_diff_expressed_probes': 'numberOfDiffExpressedProbes',
         'upregulated_count': 'upregulatedCount',
         'downregulated_count': 'downregulatedCount',
+        'number_of_upregulated_probes': 'numberOfUpregulatedProbes',
         'number_of_downregulated_probes': 'numberOfDownregulatedProbes',
-        'qvalue': 'qvalue',
-        'number_of_upregulated_probes': 'numberOfUpregulatedProbes'
+        'qvalue': 'qvalue'
     }
 
-    def __init__(self, id=None, array_designs_used=None, baseline_group=None, experimental_factors=None, number_of_genes_analyzed=None, number_of_probes_analyzed=None, threshold=None, number_of_diff_expressed_probes=None, upregulated_count=None, downregulated_count=None, number_of_downregulated_probes=None, qvalue=None, number_of_upregulated_probes=None):  # noqa: E501
+    def __init__(self, id=None, array_designs_used=None, baseline_group=None, experimental_factors=None, number_of_genes_analyzed=None, number_of_probes_analyzed=None, threshold=None, number_of_diff_expressed_probes=None, upregulated_count=None, downregulated_count=None, number_of_upregulated_probes=None, number_of_downregulated_probes=None, qvalue=None):  # noqa: E501
         """DiffExResultSetSummaryValueObject - a model defined in Swagger"""  # noqa: E501
         self._id = None
         self._array_designs_used = None
@@ -71,9 +71,9 @@ def __init__(self, id=None, array_designs_used=None, baseline_group=None, experi
         self._number_of_diff_expressed_probes = None
         self._upregulated_count = None
         self._downregulated_count = None
+        self._number_of_upregulated_probes = None
         self._number_of_downregulated_probes = None
         self._qvalue = None
-        self._number_of_upregulated_probes = None
         self.discriminator = None
         if id is not None:
             self.id = id
@@ -95,12 +95,12 @@ def __init__(self, id=None, array_designs_used=None, baseline_group=None, experi
             self.upregulated_count = upregulated_count
         if downregulated_count is not None:
             self.downregulated_count = downregulated_count
+        if number_of_upregulated_probes is not None:
+            self.number_of_upregulated_probes = number_of_upregulated_probes
         if number_of_downregulated_probes is not None:
             self.number_of_downregulated_probes = number_of_downregulated_probes
         if qvalue is not None:
             self.qvalue = qvalue
-        if number_of_upregulated_probes is not None:
-            self.number_of_upregulated_probes = number_of_upregulated_probes
 
     @property
     def id(self):
@@ -312,6 +312,27 @@ def downregulated_count(self, downregulated_count):
 
         self._downregulated_count = downregulated_count
 
+    @property
+    def number_of_upregulated_probes(self):
+        """Gets the number_of_upregulated_probes of this DiffExResultSetSummaryValueObject.  # noqa: E501
+
+
+        :return: The number_of_upregulated_probes of this DiffExResultSetSummaryValueObject.  # noqa: E501
+        :rtype: int
+        """
+        return self._number_of_upregulated_probes
+
+    @number_of_upregulated_probes.setter
+    def number_of_upregulated_probes(self, number_of_upregulated_probes):
+        """Sets the number_of_upregulated_probes of this DiffExResultSetSummaryValueObject.
+
+
+        :param number_of_upregulated_probes: The number_of_upregulated_probes of this DiffExResultSetSummaryValueObject.  # noqa: E501
+        :type: int
+        """
+
+        self._number_of_upregulated_probes = number_of_upregulated_probes
+
     @property
     def number_of_downregulated_probes(self):
         """Gets the number_of_downregulated_probes of this DiffExResultSetSummaryValueObject.  # noqa: E501
@@ -354,27 +375,6 @@ def qvalue(self, qvalue):
 
         self._qvalue = qvalue
 
-    @property
-    def number_of_upregulated_probes(self):
-        """Gets the number_of_upregulated_probes of this DiffExResultSetSummaryValueObject.  # noqa: E501
-
-
-        :return: The number_of_upregulated_probes of this DiffExResultSetSummaryValueObject.  # noqa: E501
-        :rtype: int
-        """
-        return self._number_of_upregulated_probes
-
-    @number_of_upregulated_probes.setter
-    def number_of_upregulated_probes(self, number_of_upregulated_probes):
-        """Sets the number_of_upregulated_probes of this DiffExResultSetSummaryValueObject.
-
-
-        :param number_of_upregulated_probes: The number_of_upregulated_probes of this DiffExResultSetSummaryValueObject.  # noqa: E501
-        :type: int
-        """
-
-        self._number_of_upregulated_probes = number_of_upregulated_probes
-
     def to_dict(self):
         """Returns the model properties as a dict"""
         result = {}

gemmapy/sdk/models/differential_expression_analysis_result_set_value_object.py

@@ -33,6 +33,7 @@ class DifferentialExpressionAnalysisResultSetValueObject(object):
         'experimental_factors': 'list[ExperimentalFactorValueObject]',
         'baseline_group': 'FactorValueBasicValueObject',
         'second_baseline_group': 'FactorValueBasicValueObject',
+        'taxa': 'list[TaxonValueObject]',
         'results': 'list[DifferentialExpressionAnalysisResultValueObject]'
     }
 
@@ -42,16 +43,18 @@ class DifferentialExpressionAnalysisResultSetValueObject(object):
         'experimental_factors': 'experimentalFactors',
         'baseline_group': 'baselineGroup',
         'second_baseline_group': 'secondBaselineGroup',
+        'taxa': 'taxa',
         'results': 'results'
     }
 
-    def __init__(self, id=None, analysis=None, experimental_factors=None, baseline_group=None, second_baseline_group=None, results=None):  # noqa: E501
+    def __init__(self, id=None, analysis=None, experimental_factors=None, baseline_group=None, second_baseline_group=None, taxa=None, results=None):  # noqa: E501
         """DifferentialExpressionAnalysisResultSetValueObject - a model defined in Swagger"""  # noqa: E501
         self._id = None
         self._analysis = None
         self._experimental_factors = None
         self._baseline_group = None
         self._second_baseline_group = None
+        self._taxa = None
         self._results = None
         self.discriminator = None
         if id is not None:
@@ -64,6 +67,8 @@ def __init__(self, id=None, analysis=None, experimental_factors=None, baseline_g
             self.baseline_group = baseline_group
         if second_baseline_group is not None:
             self.second_baseline_group = second_baseline_group
+        if taxa is not None:
+            self.taxa = taxa
         if results is not None:
             self.results = results
 
@@ -172,6 +177,27 @@ def second_baseline_group(self, second_baseline_group):
 
         self._second_baseline_group = second_baseline_group
 
+    @property
+    def taxa(self):
+        """Gets the taxa of this DifferentialExpressionAnalysisResultSetValueObject.  # noqa: E501
+
+
+        :return: The taxa of this DifferentialExpressionAnalysisResultSetValueObject.  # noqa: E501
+        :rtype: list[TaxonValueObject]
+        """
+        return self._taxa
+
+    @taxa.setter
+    def taxa(self, taxa):
+        """Sets the taxa of this DifferentialExpressionAnalysisResultSetValueObject.
+
+
+        :param taxa: The taxa of this DifferentialExpressionAnalysisResultSetValueObject.  # noqa: E501
+        :type: list[TaxonValueObject]
+        """
+
+        self._taxa = taxa
+
     @property
     def results(self):
         """Gets the results of this DifferentialExpressionAnalysisResultSetValueObject.  # noqa: E501

gemmapy/sdk/models/differential_expression_analysis_value_object.py

@@ -300,6 +300,7 @@ def subset_factor_value(self, subset_factor_value):
     def subset_factor_value_id(self):
         """Gets the subset_factor_value_id of this DifferentialExpressionAnalysisValueObject.  # noqa: E501
 
+        This property is mutually exclusive with `subsetFactorValue`.  # noqa: E501
 
         :return: The subset_factor_value_id of this DifferentialExpressionAnalysisValueObject.  # noqa: E501
         :rtype: int
@@ -310,6 +311,7 @@ def subset_factor_value_id(self):
     def subset_factor_value_id(self, subset_factor_value_id):
         """Sets the subset_factor_value_id of this DifferentialExpressionAnalysisValueObject.
 
+        This property is mutually exclusive with `subsetFactorValue`.  # noqa: E501
 
         :param subset_factor_value_id: The subset_factor_value_id of this DifferentialExpressionAnalysisValueObject.  # noqa: E501
         :type: int
@@ -388,6 +390,7 @@ def factor_values_used_by_experimental_factor_id(self, factor_values_used_by_exp
     def is_subset(self):
         """Gets the is_subset of this DifferentialExpressionAnalysisValueObject.  # noqa: E501
 
+        Indicate if this analysis is a subset of another experiment. if this is set, additional fields relevant to the subset will be populated.  # noqa: E501
 
         :return: The is_subset of this DifferentialExpressionAnalysisValueObject.  # noqa: E501
         :rtype: bool
@@ -398,6 +401,7 @@ def is_subset(self):
     def is_subset(self, is_subset):
         """Sets the is_subset of this DifferentialExpressionAnalysisValueObject.
 
+        Indicate if this analysis is a subset of another experiment. if this is set, additional fields relevant to the subset will be populated.  # noqa: E501
 
         :param is_subset: The is_subset of this DifferentialExpressionAnalysisValueObject.  # noqa: E501
         :type: bool