gemmapy 2.0.1__tar.gz → 2.0.3__tar.gz

{gemmapy-2.0.1 → gemmapy-2.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gemmapy
-Version: 2.0.1
+Version: 2.0.3
 Summary: a Python Wrapper for the Gemma API
 Keywords: gemma,bioinformatics
 Requires-Python: >3.10

{gemmapy-2.0.1 → 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-2.0.1 → 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,
@@ -186,7 +185,7 @@ 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 +207,7 @@ 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 --------
@@ -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-2.0.1 → 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-2.0.1 → 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
 """
@@ -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'
@@ -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-2.0.1 → 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/2.0.0'
+        self.user_agent = 'gemmapy/2.0.3'
 
     def __del__(self):
         self.pool.close()

{gemmapy-2.0.1 → 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-2.0.1 → 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-2.0.1 → 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-2.0.1 → 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
 """
@@ -195,7 +195,7 @@ class AnnotationValueObject(object):
         :param evidence_code: The evidence_code of this AnnotationValueObject.  # 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-2.0.1 → 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
 """
@@ -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-2.0.1 → 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-2.0.1 → 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
 """

{gemmapy-2.0.1 → 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-2.0.1 → 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-2.0.1 → 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
 """