Update spec to 2.7.6

gemmapy/sdk/__init__.py

@@ -7,7 +7,7 @@
 
     This website documents the usage of the [Gemma RESTful API](https://gemma.msl.ubc.ca/rest/v2/). Here you can find example script usage of the API, as well as graphical interface for each endpoint, with description of its parameters and the endpoint URL.  Use of this webpage and the Gemma Web services, including the REST API, is subject to [these terms and conditions](https://pavlidislab.github.io/Gemma/terms.html). Please read these in full before continuing to use this webpage or any other part of the Gemma system.  You can [consult the CHANGELOG.md file](https://gemma.msl.ubc.ca/resources/restapidocs/CHANGELOG.md) to view  release notes and recent changes to the Gemma RESTful API.   # noqa: E501
 
-    OpenAPI spec version: 2.7.5
+    OpenAPI spec version: 2.7.6
     Contact: [email protected]
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """
@@ -32,6 +32,7 @@
 from gemmapy.sdk.models.bio_assay_value_object import BioAssayValueObject
 from gemmapy.sdk.models.bio_material_value_object import BioMaterialValueObject
 from gemmapy.sdk.models.bio_sequence_value_object import BioSequenceValueObject
+from gemmapy.sdk.models.build_info_value_object import BuildInfoValueObject
 from gemmapy.sdk.models.category_with_usage_statistics_value_object import CategoryWithUsageStatisticsValueObject
 from gemmapy.sdk.models.characteristic_value_object import CharacteristicValueObject
 from gemmapy.sdk.models.citation_value_object import CitationValueObject
@@ -43,6 +44,7 @@
 from gemmapy.sdk.models.dataset import Dataset
 from gemmapy.sdk.models.dataset1 import Dataset1
 from gemmapy.sdk.models.dataset10 import Dataset10
+from gemmapy.sdk.models.dataset11 import Dataset11
 from gemmapy.sdk.models.dataset2 import Dataset2
 from gemmapy.sdk.models.dataset3 import Dataset3
 from gemmapy.sdk.models.dataset4 import Dataset4

gemmapy/sdk/api/default_api.py

@@ -5,7 +5,7 @@
 
     This website documents the usage of the [Gemma RESTful API](https://gemma.msl.ubc.ca/rest/v2/). Here you can find example script usage of the API, as well as graphical interface for each endpoint, with description of its parameters and the endpoint URL.  Use of this webpage and the Gemma Web services, including the REST API, is subject to [these terms and conditions](https://pavlidislab.github.io/Gemma/terms.html). Please read these in full before continuing to use this webpage or any other part of the Gemma system.  You can [consult the CHANGELOG.md file](https://gemma.msl.ubc.ca/resources/restapidocs/CHANGELOG.md) to view  release notes and recent changes to the Gemma RESTful API.   # noqa: E501
 
-    OpenAPI spec version: 2.7.5
+    OpenAPI spec version: 2.7.6
     Contact: [email protected]
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """
@@ -142,6 +142,127 @@ def get_api_info_with_http_info(self, **kwargs):  # noqa: E501
             _request_timeout=params.get('_request_timeout'),
             collection_formats=collection_formats)
 
+    def get_dataset(self, dataset, **kwargs):  # noqa: E501
+        """Retrieve a refreshed dataset  # noqa: E501
+
+        This method makes a synchronous HTTP request by default. To make an
+        asynchronous HTTP request, please pass async_req=True
+        >>> thread = api.get_dataset(dataset, async_req=True)
+        >>> result = thread.get()
+
+        :param async_req bool
+        :param Dataset dataset: (required)
+        :param bool refresh_vectors: Refresh raw and processed data vectors.
+        :param bool refresh_reports: Refresh experiment reports which include differential expression analyses and batch effects.
+        :return: None
+                 If the method is called asynchronously,
+                 returns the request thread.
+        """
+        kwargs['_return_http_data_only'] = True
+
+
+        attempts = 0
+
+        while True:
+            try:
+                if kwargs.get('async_req'):
+                    return self.get_dataset_with_http_info(dataset, **kwargs)  # noqa: E501
+                else:
+                    (data) = self.get_dataset_with_http_info(dataset, **kwargs)  # noqa: E501
+                    return data
+            except ApiException as err:
+                if err.status in [429,500] and attempts < 2:
+                    attempts += 1
+                    time.sleep(3)
+                else: 
+                    raise err
+
+    def get_dataset_with_http_info(self, dataset, **kwargs):  # noqa: E501
+        """Retrieve a refreshed dataset  # noqa: E501
+
+        This method makes a synchronous HTTP request by default. To make an
+        asynchronous HTTP request, please pass async_req=True
+        >>> thread = api.get_dataset_with_http_info(dataset, async_req=True)
+        >>> result = thread.get()
+
+        :param async_req bool
+        :param Dataset dataset: (required)
+        :param bool refresh_vectors: Refresh raw and processed data vectors.
+        :param bool refresh_reports: Refresh experiment reports which include differential expression analyses and batch effects.
+        :return: None
+                 If the method is called asynchronously,
+                 returns the request thread.
+        """
+
+        all_params = ['dataset', 'refresh_vectors', 'refresh_reports']  # noqa: E501
+        all_params.append('async_req')
+        all_params.append('_return_http_data_only')
+        all_params.append('_preload_content')
+        all_params.append('_request_timeout')
+        all_params.append('_force_table')
+
+
+        params = locals()
+        for key, val in six.iteritems(params['kwargs']):
+            if key not in all_params:
+                raise TypeError(
+                    "Got an unexpected keyword argument '%s'"
+                    " to method get_dataset" % key
+                )
+            params[key] = val
+        del params['kwargs']
+        # verify the required parameter 'dataset' is set
+        if ('dataset' not in params or
+                params['dataset'] is None):
+            raise ValueError("Missing the required parameter `dataset` when calling `get_dataset`")  # noqa: E501
+
+        collection_formats = {}
+
+        path_params = {}
+        if 'dataset' in params:
+            path_params['dataset'] = params['dataset']  # noqa: E501
+
+        query_params = []
+        if 'refresh_vectors' in params:
+            query_params.append(('refreshVectors', params['refresh_vectors']))  # noqa: E501
+        if 'refresh_reports' in params:
+            query_params.append(('refreshReports', params['refresh_reports']))  # noqa: E501
+
+        header_params = {}
+
+        form_params = []
+        local_var_files = {}
+
+        body_params = None
+        # HTTP header `Accept`
+        if not kwargs.get('_force_table'):
+            header_params['Accept'] = self.api_client.select_header_accept(
+                ['application/json'])  # noqa: E501
+            response_type = None # noqa: E501
+        else:
+            header_params['Accept'] = 'text/tab-separated-values; charset=UTF-8'
+            response_type = 'str'
+
+
+        # Authentication setting
+        auth_settings = ['basicAuth', 'cookieAuth']  # noqa: E501
+
+        return self.api_client.call_api(
+            '/datasets/{dataset}/refresh', 'GET',
+            path_params,
+            query_params,
+            header_params,
+            body=body_params,
+            post_params=form_params,
+            files=local_var_files,
+            response_type=response_type,
+            auth_settings=auth_settings,
+            async_req=params.get('async_req'),
+            _return_http_data_only=params.get('_return_http_data_only'),
+            _preload_content=params.get('_preload_content', True),
+            _request_timeout=params.get('_request_timeout'),
+            collection_formats=collection_formats)
+
     def get_dataset_annotations(self, dataset, **kwargs):  # noqa: E501
         """Retrieve the annotations of a dataset  # noqa: E501
 
@@ -151,7 +272,7 @@ def get_dataset_annotations(self, dataset, **kwargs):  # noqa: E501
         >>> result = thread.get()
 
         :param async_req bool
-        :param Dataset dataset: (required)
+        :param Dataset1 dataset: (required)
         :return: ResponseDataObjectSetAnnotationValueObject
                  If the method is called asynchronously,
                  returns the request thread.
@@ -184,7 +305,7 @@ def get_dataset_annotations_with_http_info(self, dataset, **kwargs):  # noqa: E5
         >>> result = thread.get()
 
         :param async_req bool
-        :param Dataset dataset: (required)
+        :param Dataset1 dataset: (required)
         :return: ResponseDataObjectSetAnnotationValueObject
                  If the method is called asynchronously,
                  returns the request thread.
@@ -264,7 +385,7 @@ def get_dataset_design(self, dataset, **kwargs):  # noqa: E501
         >>> result = thread.get()
 
         :param async_req bool
-        :param Dataset1 dataset: (required)
+        :param Dataset2 dataset: (required)
         :return: str
                  If the method is called asynchronously,
                  returns the request thread.
@@ -297,7 +418,7 @@ def get_dataset_design_with_http_info(self, dataset, **kwargs):  # noqa: E501
         >>> result = thread.get()
 
         :param async_req bool
-        :param Dataset1 dataset: (required)
+        :param Dataset2 dataset: (required)
         :return: str
                  If the method is called asynchronously,
                  returns the request thread.
@@ -511,7 +632,7 @@ def get_dataset_differential_expression_analyses(self, dataset, **kwargs):  # no
         >>> result = thread.get()
 
         :param async_req bool
-        :param Dataset2 dataset: (required)
+        :param Dataset3 dataset: (required)
         :param int offset:
         :param int limit:
         :return: ResponseDataObjectListDifferentialExpressionAnalysisValueObject
@@ -546,7 +667,7 @@ def get_dataset_differential_expression_analyses_with_http_info(self, dataset, *
         >>> result = thread.get()
 
         :param async_req bool
-        :param Dataset2 dataset: (required)
+        :param Dataset3 dataset: (required)
         :param int offset:
         :param int limit:
         :return: ResponseDataObjectListDifferentialExpressionAnalysisValueObject
@@ -632,7 +753,7 @@ def get_dataset_differential_expression_analyses_result_sets(self, dataset, **kw
         >>> result = thread.get()
 
         :param async_req bool
-        :param Dataset3 dataset: (required)
+        :param Dataset4 dataset: (required)
         :return: None
                  If the method is called asynchronously,
                  returns the request thread.
@@ -665,7 +786,7 @@ def get_dataset_differential_expression_analyses_result_sets_with_http_info(self
         >>> result = thread.get()
 
         :param async_req bool
-        :param Dataset3 dataset: (required)
+        :param Dataset4 dataset: (required)
         :return: None
                  If the method is called asynchronously,
                  returns the request thread.
@@ -746,7 +867,7 @@ def get_dataset_expression(self, dataset, **kwargs):  # noqa: E501
         >>> result = thread.get()
 
         :param async_req bool
-        :param Dataset4 dataset: (required)
+        :param Dataset5 dataset: (required)
         :param bool filter:
         :return: None
                  If the method is called asynchronously,
@@ -781,7 +902,7 @@ def get_dataset_expression_with_http_info(self, dataset, **kwargs):  # noqa: E50
         >>> result = thread.get()
 
         :param async_req bool
-        :param Dataset4 dataset: (required)
+        :param Dataset5 dataset: (required)
         :param bool filter:
         :return: None
                  If the method is called asynchronously,
@@ -1264,7 +1385,7 @@ def get_dataset_platforms(self, dataset, **kwargs):  # noqa: E501
         >>> result = thread.get()
 
         :param async_req bool
-        :param Dataset5 dataset: (required)
+        :param Dataset6 dataset: (required)
         :return: ResponseDataObjectListArrayDesignValueObject
                  If the method is called asynchronously,
                  returns the request thread.
@@ -1297,7 +1418,7 @@ def get_dataset_platforms_with_http_info(self, dataset, **kwargs):  # noqa: E501
         >>> result = thread.get()
 
         :param async_req bool
-        :param Dataset5 dataset: (required)
+        :param Dataset6 dataset: (required)
         :return: ResponseDataObjectListArrayDesignValueObject
                  If the method is called asynchronously,
                  returns the request thread.
@@ -1377,7 +1498,7 @@ def get_dataset_processed_expression(self, dataset, **kwargs):  # noqa: E501
         >>> result = thread.get()
 
         :param async_req bool
-        :param Dataset6 dataset: (required)
+        :param Dataset7 dataset: (required)
         :return: str
                  If the method is called asynchronously,
                  returns the request thread.
@@ -1410,7 +1531,7 @@ def get_dataset_processed_expression_with_http_info(self, dataset, **kwargs):  #
         >>> result = thread.get()
 
         :param async_req bool
-        :param Dataset6 dataset: (required)
+        :param Dataset7 dataset: (required)
         :return: str
                  If the method is called asynchronously,
                  returns the request thread.
@@ -1490,7 +1611,7 @@ def get_dataset_quantitation_types(self, dataset, **kwargs):  # noqa: E501
         >>> result = thread.get()
 
         :param async_req bool
-        :param Dataset7 dataset: (required)
+        :param Dataset8 dataset: (required)
         :return: ResponseDataObjectSetQuantitationTypeValueObject
                  If the method is called asynchronously,
                  returns the request thread.
@@ -1523,7 +1644,7 @@ def get_dataset_quantitation_types_with_http_info(self, dataset, **kwargs):  # n
         >>> result = thread.get()
 
         :param async_req bool
-        :param Dataset7 dataset: (required)
+        :param Dataset8 dataset: (required)
         :return: ResponseDataObjectSetQuantitationTypeValueObject
                  If the method is called asynchronously,
                  returns the request thread.
@@ -1603,7 +1724,7 @@ def get_dataset_raw_expression(self, dataset, **kwargs):  # noqa: E501
         >>> result = thread.get()
 
         :param async_req bool
-        :param Dataset8 dataset: (required)
+        :param Dataset9 dataset: (required)
         :param QuantitationType quantitation_type:
         :return: str
                  If the method is called asynchronously,
@@ -1637,7 +1758,7 @@ def get_dataset_raw_expression_with_http_info(self, dataset, **kwargs):  # noqa:
         >>> result = thread.get()
 
         :param async_req bool
-        :param Dataset8 dataset: (required)
+        :param Dataset9 dataset: (required)
         :param QuantitationType quantitation_type:
         :return: str
                  If the method is called asynchronously,
@@ -1720,7 +1841,7 @@ def get_dataset_samples(self, dataset, **kwargs):  # noqa: E501
         >>> result = thread.get()
 
         :param async_req bool
-        :param Dataset9 dataset: (required)
+        :param Dataset10 dataset: (required)
         :return: ResponseDataObjectListBioAssayValueObject
                  If the method is called asynchronously,
                  returns the request thread.
@@ -1753,7 +1874,7 @@ def get_dataset_samples_with_http_info(self, dataset, **kwargs):  # noqa: E501
         >>> result = thread.get()
 
         :param async_req bool
-        :param Dataset9 dataset: (required)
+        :param Dataset10 dataset: (required)
         :return: ResponseDataObjectListBioAssayValueObject
                  If the method is called asynchronously,
                  returns the request thread.
@@ -1833,7 +1954,7 @@ def get_dataset_svd(self, dataset, **kwargs):  # noqa: E501
         >>> result = thread.get()
 
         :param async_req bool
-        :param Dataset10 dataset: (required)
+        :param Dataset11 dataset: (required)
         :return: ResponseDataObjectSimpleSVDValueObject
                  If the method is called asynchronously,
                  returns the request thread.
@@ -1866,7 +1987,7 @@ def get_dataset_svd_with_http_info(self, dataset, **kwargs):  # noqa: E501
         >>> result = thread.get()
 
         :param async_req bool
-        :param Dataset10 dataset: (required)
+        :param Dataset11 dataset: (required)
         :return: ResponseDataObjectSimpleSVDValueObject
                  If the method is called asynchronously,
                  returns the request thread.

gemmapy/sdk/api_client.py

@@ -4,7 +4,7 @@
 
     This website documents the usage of the [Gemma RESTful API](https://gemma.msl.ubc.ca/rest/v2/). Here you can find example script usage of the API, as well as graphical interface for each endpoint, with description of its parameters and the endpoint URL.  Use of this webpage and the Gemma Web services, including the REST API, is subject to [these terms and conditions](https://pavlidislab.github.io/Gemma/terms.html). Please read these in full before continuing to use this webpage or any other part of the Gemma system.  You can [consult the CHANGELOG.md file](https://gemma.msl.ubc.ca/resources/restapidocs/CHANGELOG.md) to view  release notes and recent changes to the Gemma RESTful API.   # noqa: E501
 
-    OpenAPI spec version: 2.7.5
+    OpenAPI spec version: 2.7.6
     Contact: [email protected]
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """

gemmapy/sdk/configuration.py

@@ -5,7 +5,7 @@
 
     This website documents the usage of the [Gemma RESTful API](https://gemma.msl.ubc.ca/rest/v2/). Here you can find example script usage of the API, as well as graphical interface for each endpoint, with description of its parameters and the endpoint URL.  Use of this webpage and the Gemma Web services, including the REST API, is subject to [these terms and conditions](https://pavlidislab.github.io/Gemma/terms.html). Please read these in full before continuing to use this webpage or any other part of the Gemma system.  You can [consult the CHANGELOG.md file](https://gemma.msl.ubc.ca/resources/restapidocs/CHANGELOG.md) to view  release notes and recent changes to the Gemma RESTful API.   # noqa: E501
 
-    OpenAPI spec version: 2.7.5
+    OpenAPI spec version: 2.7.6
     Contact: [email protected]
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """
@@ -256,6 +256,6 @@ def to_debug_report(self):
         return "Python SDK Debug Report:\n"\
                "OS: {env}\n"\
                "Python Version: {pyversion}\n"\
-               "Version of the API: 2.7.5\n"\
+               "Version of the API: 2.7.6\n"\
                "SDK Package Version: 1.0.0".\
                format(env=sys.platform, pyversion=sys.version)