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Update spec to 2.7.6
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@arteymix
arteymix committed Jun 24, 2024
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4 changes: 3 additions & 1 deletion gemmapy/sdk/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
"""
Expand All @@ -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
Expand All @@ -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
Expand Down
167 changes: 144 additions & 23 deletions gemmapy/sdk/api/default_api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
"""
Expand Down Expand Up @@ -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
Expand All @@ -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.
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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.
Expand Down
2 changes: 1 addition & 1 deletion gemmapy/sdk/api_client.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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
"""
Expand Down
4 changes: 2 additions & 2 deletions gemmapy/sdk/configuration.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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
"""
Expand Down Expand Up @@ -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)
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