gemmapy 2.0.0__tar.gz → 2.0.2__tar.gz

{gemmapy-2.0.0 → gemmapy-2.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gemmapy
-Version: 2.0.0
+Version: 2.0.2
 Summary: a Python Wrapper for the Gemma API
 Keywords: gemma,bioinformatics
 Requires-Python: >3.10

{gemmapy-2.0.0 → gemmapy-2.0.2}/gemmapy/gemmapy_api.py

@@ -186,7 +186,7 @@ class GemmaPy(object):
         """
         
         response = self.raw.get_annotations_children(uri=uri,**kwargs)
-        df = ps.process_search_annotations(response)
+        df = ps.process_search_annotations(response.data)
         return df
 
     def get_annotation_parents(self,uri:str,**kwargs)->DataFrame:
@@ -208,7 +208,7 @@ class GemmaPy(object):
         """
         
         response = self.raw.get_annotations_parents(uri=uri,**kwargs)
-        df = ps.process_search_annotations(response)
+        df = ps.process_search_annotations(response.data)
         return df
     
     # /annotations/search, search_annotations --------

{gemmapy-2.0.0 → gemmapy-2.0.2}/gemmapy/sdk/api/default_api.py

@@ -47,7 +47,7 @@ class DefaultApi(object):
         :param async_req bool
         :param str uri: Term URI
         :param bool direct: Only include direct parents.
-        :return: list[AnnotationSearchResultValueObject]
+        :return: ResponseDataObjectListAnnotationSearchResultValueObject
                  If the method is called asynchronously,
                  returns the request thread.
         """
@@ -82,7 +82,7 @@ class DefaultApi(object):
         :param async_req bool
         :param str uri: Term URI
         :param bool direct: Only include direct parents.
-        :return: list[AnnotationSearchResultValueObject]
+        :return: ResponseDataObjectListAnnotationSearchResultValueObject
                  If the method is called asynchronously,
                  returns the request thread.
         """
@@ -125,7 +125,7 @@ class DefaultApi(object):
         if not kwargs.get('_force_table'):
             header_params['Accept'] = self.api_client.select_header_accept(
                 ['application/json'])  # noqa: E501
-            response_type = 'list[AnnotationSearchResultValueObject]' # noqa: E501
+            response_type = 'ResponseDataObjectListAnnotationSearchResultValueObject' # noqa: E501
         else:
             header_params['Accept'] = 'text/tab-separated-values; charset=UTF-8'
             response_type = 'str'
@@ -162,7 +162,7 @@ class DefaultApi(object):
         :param async_req bool
         :param str uri: Term URI
         :param bool direct: Only include direct children.
-        :return: list[AnnotationSearchResultValueObject]
+        :return: ResponseDataObjectListAnnotationSearchResultValueObject
                  If the method is called asynchronously,
                  returns the request thread.
         """
@@ -197,7 +197,7 @@ class DefaultApi(object):
         :param async_req bool
         :param str uri: Term URI
         :param bool direct: Only include direct children.
-        :return: list[AnnotationSearchResultValueObject]
+        :return: ResponseDataObjectListAnnotationSearchResultValueObject
                  If the method is called asynchronously,
                  returns the request thread.
         """
@@ -240,7 +240,7 @@ class DefaultApi(object):
         if not kwargs.get('_force_table'):
             header_params['Accept'] = self.api_client.select_header_accept(
                 ['application/json'])  # noqa: E501
-            response_type = 'list[AnnotationSearchResultValueObject]' # noqa: E501
+            response_type = 'ResponseDataObjectListAnnotationSearchResultValueObject' # noqa: E501
         else:
             header_params['Accept'] = 'text/tab-separated-values; charset=UTF-8'
             response_type = 'str'

{gemmapy-2.0.0 → gemmapy-2.0.2}/gemmapy/sdk/api_client.py

@@ -73,7 +73,7 @@ class ApiClient(object):
             self.default_headers[header_name] = header_value
         self.cookie = cookie
         # Set default User-Agent.
-        self.user_agent = 'gemmapy/2.0.0'
+        self.user_agent = 'gemmapy/2.0.2'
 
     def __del__(self):
         self.pool.close()

{gemmapy-2.0.0 → gemmapy-2.0.2}/gemmapy/sdk/models/annotation_with_usage_statistics_value_object.py

@@ -174,7 +174,7 @@ class AnnotationWithUsageStatisticsValueObject(object):
         :param evidence_code: The evidence_code of this AnnotationWithUsageStatisticsValueObject.  # noqa: E501
         :type: str
         """
-        allowed_values = ["", "IC", "IDA", "IEA", "IEP", "IGI", "IMP", "IPI", "ISS", "NAS", "ND", "RCA", "TAS", "NR", "EXP", "ISA", "ISM", "IGC", "ISO", "IIA", "IBA", "IBD", "IKR", "IRD", "IMR", "IED", "IAGP", "IPM", "QTM", "HDA", "HEP", "HGI", "HMP", "HTP", "OTHER"]  # noqa: E501
+        allowed_values = ["IC", "IDA", "IEA", "IEP", "IGI", "IMP", "IPI", "ISS", "NAS", "ND", "RCA", "TAS", "NR", "EXP", "ISA", "ISM", "IGC", "ISO", "IIA", "IBA", "IBD", "IKR", "IRD", "IMR", "IED", "IAGP", "IPM", "QTM", "HDA", "HEP", "HGI", "HMP", "HTP", "OTHER"]  # noqa: E501
         if evidence_code not in allowed_values:
             raise ValueError(
                 "Invalid value for `evidence_code` ({0}), must be one of {1}"  # noqa: E501

{gemmapy-2.0.0 → gemmapy-2.0.2}/gemmapy/sdk/models/array_design_value_object.py

@@ -47,8 +47,8 @@ class ArrayDesignValueObject(object):
         'release_version': 'str',
         'release_url': 'str',
         'external_references': 'list[DatabaseEntryValueObject]',
-        'taxon_id': 'int',
         'number_of_expression_experiments': 'int',
+        'taxon_id': 'int',
         'trouble_details': 'str',
         'number_of_switched_expression_experiments': 'int',
         'taxon': 'TaxonValueObject'
@@ -74,14 +74,14 @@ class ArrayDesignValueObject(object):
         'release_version': 'releaseVersion',
         'release_url': 'releaseUrl',
         'external_references': 'externalReferences',
-        'taxon_id': 'taxonID',
         'number_of_expression_experiments': 'numberOfExpressionExperiments',
+        'taxon_id': 'taxonID',
         'trouble_details': 'troubleDetails',
         'number_of_switched_expression_experiments': 'numberOfSwitchedExpressionExperiments',
         'taxon': 'taxon'
     }
 
-    def __init__(self, id=None, last_updated=None, troubled=None, last_troubled_event=None, needs_attention=None, last_needs_attention_event=None, curation_note=None, last_note_update_event=None, color=None, description=None, expression_experiment_count=None, is_merged=None, is_mergee=None, name=None, short_name=None, technology_type=None, release_version=None, release_url=None, external_references=None, taxon_id=None, number_of_expression_experiments=None, trouble_details=None, number_of_switched_expression_experiments=None, taxon=None):  # noqa: E501
+    def __init__(self, id=None, last_updated=None, troubled=None, last_troubled_event=None, needs_attention=None, last_needs_attention_event=None, curation_note=None, last_note_update_event=None, color=None, description=None, expression_experiment_count=None, is_merged=None, is_mergee=None, name=None, short_name=None, technology_type=None, release_version=None, release_url=None, external_references=None, number_of_expression_experiments=None, taxon_id=None, trouble_details=None, number_of_switched_expression_experiments=None, taxon=None):  # noqa: E501
         """ArrayDesignValueObject - a model defined in Swagger"""  # noqa: E501
         self._id = None
         self._last_updated = None
@@ -102,8 +102,8 @@ class ArrayDesignValueObject(object):
         self._release_version = None
         self._release_url = None
         self._external_references = None
-        self._taxon_id = None
         self._number_of_expression_experiments = None
+        self._taxon_id = None
         self._trouble_details = None
         self._number_of_switched_expression_experiments = None
         self._taxon = None
@@ -146,10 +146,10 @@ class ArrayDesignValueObject(object):
             self.release_url = release_url
         if external_references is not None:
             self.external_references = external_references
-        if taxon_id is not None:
-            self.taxon_id = taxon_id
         if number_of_expression_experiments is not None:
             self.number_of_expression_experiments = number_of_expression_experiments
+        if taxon_id is not None:
+            self.taxon_id = taxon_id
         if trouble_details is not None:
             self.trouble_details = trouble_details
         if number_of_switched_expression_experiments is not None:
@@ -569,46 +569,46 @@ class ArrayDesignValueObject(object):
         self._external_references = external_references
 
     @property
-    def taxon_id(self):
-        """Gets the taxon_id of this ArrayDesignValueObject.  # noqa: E501
+    def number_of_expression_experiments(self):
+        """Gets the number_of_expression_experiments of this ArrayDesignValueObject.  # noqa: E501
 
 
-        :return: The taxon_id of this ArrayDesignValueObject.  # noqa: E501
+        :return: The number_of_expression_experiments of this ArrayDesignValueObject.  # noqa: E501
         :rtype: int
         """
-        return self._taxon_id
+        return self._number_of_expression_experiments
 
-    @taxon_id.setter
-    def taxon_id(self, taxon_id):
-        """Sets the taxon_id of this ArrayDesignValueObject.
+    @number_of_expression_experiments.setter
+    def number_of_expression_experiments(self, number_of_expression_experiments):
+        """Sets the number_of_expression_experiments of this ArrayDesignValueObject.
 
 
-        :param taxon_id: The taxon_id of this ArrayDesignValueObject.  # noqa: E501
+        :param number_of_expression_experiments: The number_of_expression_experiments of this ArrayDesignValueObject.  # noqa: E501
         :type: int
         """
 
-        self._taxon_id = taxon_id
+        self._number_of_expression_experiments = number_of_expression_experiments
 
     @property
-    def number_of_expression_experiments(self):
-        """Gets the number_of_expression_experiments of this ArrayDesignValueObject.  # noqa: E501
+    def taxon_id(self):
+        """Gets the taxon_id of this ArrayDesignValueObject.  # noqa: E501
 
 
-        :return: The number_of_expression_experiments of this ArrayDesignValueObject.  # noqa: E501
+        :return: The taxon_id of this ArrayDesignValueObject.  # noqa: E501
         :rtype: int
         """
-        return self._number_of_expression_experiments
+        return self._taxon_id
 
-    @number_of_expression_experiments.setter
-    def number_of_expression_experiments(self, number_of_expression_experiments):
-        """Sets the number_of_expression_experiments of this ArrayDesignValueObject.
+    @taxon_id.setter
+    def taxon_id(self, taxon_id):
+        """Sets the taxon_id of this ArrayDesignValueObject.
 
 
-        :param number_of_expression_experiments: The number_of_expression_experiments of this ArrayDesignValueObject.  # noqa: E501
+        :param taxon_id: The taxon_id of this ArrayDesignValueObject.  # noqa: E501
         :type: int
         """
 
-        self._number_of_expression_experiments = number_of_expression_experiments
+        self._taxon_id = taxon_id
 
     @property
     def trouble_details(self):

{gemmapy-2.0.0 → gemmapy-2.0.2}/gemmapy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gemmapy
-Version: 2.0.0
+Version: 2.0.2
 Summary: a Python Wrapper for the Gemma API
 Keywords: gemma,bioinformatics
 Requires-Python: >3.10

{gemmapy-2.0.0 → gemmapy-2.0.2}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = gemmapy
-version = 2.0.0
+version = 2.0.2
 description = a Python Wrapper for the Gemma API
 long_description = file: README.rst
 keywords = gemma, bioinformatics

{gemmapy-2.0.0 → gemmapy-2.0.2}/tests/test_basic.py

@@ -55,10 +55,6 @@ def test_get_dataset_annotations():
     assert type(res) is pd.core.frame.DataFrame
     assert res.shape[1] == 5
 
-def test_get_dataset_design():
-    res = api._GemmaPy__get_dataset_design('1')
-    assert type(res) is pd.core.frame.DataFrame
-
 def test_get_dataset_differential_expression_analyses():
     res = api.get_dataset_differential_expression_analyses(200)
     assert type(res) is pd.core.frame.DataFrame
@@ -131,4 +127,4 @@ def test_get_dataset_object():
 # def test_measurements():
 #    dataset = "GSE106"
 #    samples = api.get_dataset_samples(dataset)
-    
+