gemmapy 2.0.2__tar.gz → 2.0.3__tar.gz

{gemmapy-2.0.2 → gemmapy-2.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gemmapy
-Version: 2.0.2
+Version: 2.0.3
 Summary: a Python Wrapper for the Gemma API
 Keywords: gemma,bioinformatics
 Requires-Python: >3.10

{gemmapy-2.0.2 → gemmapy-2.0.3}/gemmapy/_validators.py

@@ -7,7 +7,14 @@ Created on Wed Feb 28 23:09:30 2024
 """
 
 import typing as T
+import base64
+import gzip
 
+def compress_arg(arg:str):
+    if arg is not None:
+        return base64.b64encode(gzip.compress(arg.encode())).decode()
+    else: 
+        return arg
 
 def remove_nones(**kwargs):
     out = kwargs.copy()
@@ -17,7 +24,6 @@ def remove_nones(**kwargs):
     return out
 
 def add_to_filter(filt:T.Optional[str], prop: str, terms: T.List[T.Union[str,int]]):
-    
     if terms is None:
         return filt
     

{gemmapy-2.0.2 → gemmapy-2.0.3}/gemmapy/gemmapy_api.py

@@ -15,7 +15,6 @@ import anndata as ad
 from anndata import AnnData
 from io import StringIO
 import warnings
-import re
 import json
 
 
@@ -149,7 +148,7 @@ class GemmaPy(object):
         """
         
         filter = vs.add_to_filter(filter, 'id', result_sets)
-        
+        filter = vs.compress_arg(filter)
         
         kwargs = vs.remove_nones(
             datasets = datasets,
@@ -229,7 +228,7 @@ class GemmaPy(object):
         :rtype: DataFrame
 
         """
-
+        
         response = self.raw.search_annotations(query=query, **kwargs)
         return ps.process_search_annotations(response.data)
     
@@ -598,7 +597,7 @@ class GemmaPy(object):
         
         filter = vs.add_to_filter(filter, 'allCharacteristics.valueUri', uris)
         filter = vs.add_to_filter(filter, 'taxon.commonName', taxa)
-        
+        filter = vs.compress_arg(filter)
         kwargs = vs.remove_nones(
             query = query,
             filter = filter,
@@ -693,6 +692,7 @@ class GemmaPy(object):
         filter = vs.add_to_filter(filter, 'allCharacteristics.valueUri', uris)
         filter = vs.add_to_filter(filter, 'taxon.commonName', taxa)
         
+        filter = vs.compress_arg(filter)
         
         kwargs = vs.remove_nones(
             filter = filter,
@@ -1140,6 +1140,7 @@ class GemmaPy(object):
 
         """
         filter = vs.add_to_filter(filter,"taxon.commonName",taxa)
+        filter = vs.compress_arg(filter)
         kwargs = vs.remove_nones(filter = filter,
                                  offset = offset,
                                  limit = limit,

{gemmapy-2.0.2 → gemmapy-2.0.3}/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: 2.9.0
+    OpenAPI spec version: 2.9.1
     Contact: pavlab-support@msl.ubc.ca
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """

{gemmapy-2.0.2 → gemmapy-2.0.3}/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: 2.9.0
+    OpenAPI spec version: 2.9.1
     Contact: pavlab-support@msl.ubc.ca
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """
@@ -613,7 +613,8 @@ class DefaultApi(object):
         :param async_req bool
         :param Dataset2 dataset: (required)
         :param QuantitationType1 quantitation_type:
-        :param str cell_type_assignment: The name of of the cell type assignment to retrieve. If left unset, this the preferred one is returned.
+        :param str cell_type_assignment: The name of the cell type assignment to retrieve. If left unset, this the preferred one is returned.
+        :param str protocol: The protocol of the cell type assignment to retrieve. This cannot be used in combination with `cellTypeAssignment`.
         :return: ResponseDataObjectCellTypeAssignmentValueObject
                  If the method is called asynchronously,
                  returns the request thread.
@@ -648,13 +649,14 @@ class DefaultApi(object):
         :param async_req bool
         :param Dataset2 dataset: (required)
         :param QuantitationType1 quantitation_type:
-        :param str cell_type_assignment: The name of of the cell type assignment to retrieve. If left unset, this the preferred one is returned.
+        :param str cell_type_assignment: The name of the cell type assignment to retrieve. If left unset, this the preferred one is returned.
+        :param str protocol: The protocol of the cell type assignment to retrieve. This cannot be used in combination with `cellTypeAssignment`.
         :return: ResponseDataObjectCellTypeAssignmentValueObject
                  If the method is called asynchronously,
                  returns the request thread.
         """
 
-        all_params = ['dataset', 'quantitation_type', 'cell_type_assignment']  # noqa: E501
+        all_params = ['dataset', 'quantitation_type', 'cell_type_assignment', 'protocol']  # noqa: E501
         all_params.append('async_req')
         all_params.append('_return_http_data_only')
         all_params.append('_preload_content')
@@ -687,6 +689,8 @@ class DefaultApi(object):
             query_params.append(('quantitationType', params['quantitation_type']))  # noqa: E501
         if 'cell_type_assignment' in params:
             query_params.append(('cellTypeAssignment', params['cell_type_assignment']))  # noqa: E501
+        if 'protocol' in params:
+            query_params.append(('protocol', params['protocol']))  # noqa: E501
 
         header_params = {}
 

{gemmapy-2.0.2 → gemmapy-2.0.3}/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: 2.9.0
+    OpenAPI spec version: 2.9.1
     Contact: pavlab-support@msl.ubc.ca
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """
@@ -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/2.0.2'
+        self.user_agent = 'gemmapy/2.0.3'
 
     def __del__(self):
         self.pool.close()

{gemmapy-2.0.2 → gemmapy-2.0.3}/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: 2.9.0
+    OpenAPI spec version: 2.9.1
     Contact: pavlab-support@msl.ubc.ca
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """
@@ -256,6 +256,6 @@ class Configuration(six.with_metaclass(TypeWithDefault, object)):
         return "Python SDK Debug Report:\n"\
                "OS: {env}\n"\
                "Python Version: {pyversion}\n"\
-               "Version of the API: 2.9.0\n"\
+               "Version of the API: 2.9.1\n"\
                "SDK Package Version: 1.0.0".\
                format(env=sys.platform, pyversion=sys.version)

{gemmapy-2.0.2 → gemmapy-2.0.3}/gemmapy/sdk/models/__init__.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: 2.9.0
+    OpenAPI spec version: 2.9.1
     Contact: pavlab-support@msl.ubc.ca
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """

{gemmapy-2.0.2 → gemmapy-2.0.3}/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: 2.9.0
+    OpenAPI spec version: 2.9.1
     Contact: pavlab-support@msl.ubc.ca
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """

{gemmapy-2.0.2 → gemmapy-2.0.3}/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: 2.9.0
+    OpenAPI spec version: 2.9.1
     Contact: pavlab-support@msl.ubc.ca
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """

{gemmapy-2.0.2 → gemmapy-2.0.3}/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: 2.9.0
+    OpenAPI spec version: 2.9.1
     Contact: pavlab-support@msl.ubc.ca
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """

{gemmapy-2.0.2 → gemmapy-2.0.3}/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: 2.9.0
+    OpenAPI spec version: 2.9.1
     Contact: pavlab-support@msl.ubc.ca
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """

{gemmapy-2.0.2 → gemmapy-2.0.3}/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: 2.9.0
+    OpenAPI spec version: 2.9.1
     Contact: pavlab-support@msl.ubc.ca
     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]',
-        'number_of_expression_experiments': 'int',
         'taxon_id': 'int',
+        'number_of_expression_experiments': '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',
-        'number_of_expression_experiments': 'numberOfExpressionExperiments',
         'taxon_id': 'taxonID',
+        'number_of_expression_experiments': 'numberOfExpressionExperiments',
         '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, number_of_expression_experiments=None, taxon_id=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, taxon_id=None, number_of_expression_experiments=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._number_of_expression_experiments = None
         self._taxon_id = None
+        self._number_of_expression_experiments = 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 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 number_of_expression_experiments is not None:
+            self.number_of_expression_experiments = number_of_expression_experiments
         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 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 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 trouble_details(self):

{gemmapy-2.0.2 → gemmapy-2.0.3}/gemmapy/sdk/models/array_design_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: 2.9.0
+    OpenAPI spec version: 2.9.1
     Contact: pavlab-support@msl.ubc.ca
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """

{gemmapy-2.0.2 → gemmapy-2.0.3}/gemmapy/sdk/models/audit_event_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: 2.9.0
+    OpenAPI spec version: 2.9.1
     Contact: pavlab-support@msl.ubc.ca
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """

{gemmapy-2.0.2 → gemmapy-2.0.3}/gemmapy/sdk/models/bibliographic_reference_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: 2.9.0
+    OpenAPI spec version: 2.9.1
     Contact: pavlab-support@msl.ubc.ca
     Generated by: https://github.com/swagger-api/swagger-codegen.git
 """