Merge pull request #25 from PavlidisLab/update-gemma-to-2.7.5

Update spec to 2.7.5

Author: oganm

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: 2.7.4
+    OpenAPI spec version: 2.7.5
     Contact: [email protected]
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """
@@ -78,6 +78,7 @@
 from gemmapy.sdk.models.gene2 import Gene2
 from gemmapy.sdk.models.gene3 import Gene3
 from gemmapy.sdk.models.gene4 import Gene4
+from gemmapy.sdk.models.gene5 import Gene5
 from gemmapy.sdk.models.gene_arg import GeneArg
 from gemmapy.sdk.models.gene_element_expressions_value_object import GeneElementExpressionsValueObject
 from gemmapy.sdk.models.gene_ontology_term_value_object import GeneOntologyTermValueObject
@@ -90,6 +91,7 @@
 from gemmapy.sdk.models.ontology_term_value_object import OntologyTermValueObject
 from gemmapy.sdk.models.paginated_response_data_object_composite_sequence_value_object import PaginatedResponseDataObjectCompositeSequenceValueObject
 from gemmapy.sdk.models.paginated_response_data_object_expression_experiment_value_object import PaginatedResponseDataObjectExpressionExperimentValueObject
+from gemmapy.sdk.models.paginated_response_data_object_gene_value_object import PaginatedResponseDataObjectGeneValueObject
 from gemmapy.sdk.models.physical_location_value_object import PhysicalLocationValueObject
 from gemmapy.sdk.models.platform import Platform
 from gemmapy.sdk.models.platform1 import Platform1
@@ -132,16 +134,19 @@
 from gemmapy.sdk.models.sort_arg_array_design import SortArgArrayDesign
 from gemmapy.sdk.models.sort_arg_expression_analysis_result_set import SortArgExpressionAnalysisResultSet
 from gemmapy.sdk.models.sort_arg_expression_experiment import SortArgExpressionExperiment
-from gemmapy.sdk.models.sort_arg_taxon import SortArgTaxon
 from gemmapy.sdk.models.sort_value_object import SortValueObject
 from gemmapy.sdk.models.statement_value_object import StatementValueObject
+from gemmapy.sdk.models.taxa import Taxa
 from gemmapy.sdk.models.taxon import Taxon
 from gemmapy.sdk.models.taxon1 import Taxon1
 from gemmapy.sdk.models.taxon2 import Taxon2
 from gemmapy.sdk.models.taxon3 import Taxon3
 from gemmapy.sdk.models.taxon4 import Taxon4
 from gemmapy.sdk.models.taxon5 import Taxon5
 from gemmapy.sdk.models.taxon6 import Taxon6
+from gemmapy.sdk.models.taxon7 import Taxon7
+from gemmapy.sdk.models.taxon8 import Taxon8
+from gemmapy.sdk.models.taxon9 import Taxon9
 from gemmapy.sdk.models.taxon_arg import TaxonArg
 from gemmapy.sdk.models.taxon_value_object import TaxonValueObject
 from gemmapy.sdk.models.taxon_with_usage_statistics_value_object import TaxonWithUsageStatisticsValueObject

gemmapy/sdk/api/default_api.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: 2.7.4
+    OpenAPI spec version: 2.7.5
     Contact: [email protected]
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """

gemmapy/sdk/api_client.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: 2.7.4
+    OpenAPI spec version: 2.7.5
     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: 2.7.4\n"\
+               "Version of the API: 2.7.5\n"\
                "SDK Package Version: 1.0.0".\
                format(env=sys.platform, pyversion=sys.version)

gemmapy/sdk/configuration.py

@@ -6,7 +6,7 @@
 
     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: 2.7.4
+    OpenAPI spec version: 2.7.5
     Contact: [email protected]
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """
@@ -72,6 +72,7 @@
 from gemmapy.sdk.models.gene2 import Gene2
 from gemmapy.sdk.models.gene3 import Gene3
 from gemmapy.sdk.models.gene4 import Gene4
+from gemmapy.sdk.models.gene5 import Gene5
 from gemmapy.sdk.models.gene_arg import GeneArg
 from gemmapy.sdk.models.gene_element_expressions_value_object import GeneElementExpressionsValueObject
 from gemmapy.sdk.models.gene_ontology_term_value_object import GeneOntologyTermValueObject
@@ -84,6 +85,7 @@
 from gemmapy.sdk.models.ontology_term_value_object import OntologyTermValueObject
 from gemmapy.sdk.models.paginated_response_data_object_composite_sequence_value_object import PaginatedResponseDataObjectCompositeSequenceValueObject
 from gemmapy.sdk.models.paginated_response_data_object_expression_experiment_value_object import PaginatedResponseDataObjectExpressionExperimentValueObject
+from gemmapy.sdk.models.paginated_response_data_object_gene_value_object import PaginatedResponseDataObjectGeneValueObject
 from gemmapy.sdk.models.physical_location_value_object import PhysicalLocationValueObject
 from gemmapy.sdk.models.platform import Platform
 from gemmapy.sdk.models.platform1 import Platform1
@@ -126,16 +128,19 @@
 from gemmapy.sdk.models.sort_arg_array_design import SortArgArrayDesign
 from gemmapy.sdk.models.sort_arg_expression_analysis_result_set import SortArgExpressionAnalysisResultSet
 from gemmapy.sdk.models.sort_arg_expression_experiment import SortArgExpressionExperiment
-from gemmapy.sdk.models.sort_arg_taxon import SortArgTaxon
 from gemmapy.sdk.models.sort_value_object import SortValueObject
 from gemmapy.sdk.models.statement_value_object import StatementValueObject
+from gemmapy.sdk.models.taxa import Taxa
 from gemmapy.sdk.models.taxon import Taxon
 from gemmapy.sdk.models.taxon1 import Taxon1
 from gemmapy.sdk.models.taxon2 import Taxon2
 from gemmapy.sdk.models.taxon3 import Taxon3
 from gemmapy.sdk.models.taxon4 import Taxon4
 from gemmapy.sdk.models.taxon5 import Taxon5
 from gemmapy.sdk.models.taxon6 import Taxon6
+from gemmapy.sdk.models.taxon7 import Taxon7
+from gemmapy.sdk.models.taxon8 import Taxon8
+from gemmapy.sdk.models.taxon9 import Taxon9
 from gemmapy.sdk.models.taxon_arg import TaxonArg
 from gemmapy.sdk.models.taxon_value_object import TaxonValueObject
 from gemmapy.sdk.models.taxon_with_usage_statistics_value_object import TaxonWithUsageStatisticsValueObject

gemmapy/sdk/models/__init__.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: 2.7.4
+    OpenAPI spec version: 2.7.5
     Contact: [email protected]
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """

gemmapy/sdk/models/annotation_search_result_value_object.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: 2.7.4
+    OpenAPI spec version: 2.7.5
     Contact: [email protected]
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """

gemmapy/sdk/models/annotation_value_object.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: 2.7.4
+    OpenAPI spec version: 2.7.5
     Contact: [email protected]
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """

gemmapy/sdk/models/annotation_with_usage_statistics_value_object.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: 2.7.4
+    OpenAPI spec version: 2.7.5
     Contact: [email protected]
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """

gemmapy/sdk/models/api_info_value_object.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: 2.7.4
+    OpenAPI spec version: 2.7.5
     Contact: [email protected]
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """
@@ -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 @@ def __init__(self, id=None, last_updated=None, troubled=None, last_troubled_even
         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 @@ def __init__(self, id=None, last_updated=None, troubled=None, last_troubled_even
             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 @@ def external_references(self, external_references):
         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/sdk/models/array_design_value_object.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: 2.7.4
+    OpenAPI spec version: 2.7.5
     Contact: [email protected]
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """