Merge pull request #136 from sirius-ms/temp_20241021160225067812723

AutoUpdated

client-api_python/generated/.openapi-generator/FILES

@@ -41,6 +41,7 @@ PySirius/models/compound_class_type.py
 PySirius/models/compound_classes.py
 PySirius/models/compound_import.py
 PySirius/models/compound_opt_field.py
+PySirius/models/computed_subtools.py
 PySirius/models/confidence_mode.py
 PySirius/models/connection_check.py
 PySirius/models/connection_error.py
@@ -141,6 +142,7 @@ docs/CompoundClasses.md
 docs/CompoundImport.md
 docs/CompoundOptField.md
 docs/CompoundsApi.md
+docs/ComputedSubtools.md
 docs/ConfidenceMode.md
 docs/ConnectionCheck.md
 docs/ConnectionError.md

client-api_python/generated/PySirius/__init__.py

@@ -14,7 +14,7 @@
 """  # noqa: E501
 
 
-__version__ = "6.0.6"
+__version__ = "6.0.7"
 
 # import apis into sdk package
 from PySirius.api.actuator_api import ActuatorApi
@@ -62,6 +62,7 @@
 from PySirius.models.compound_classes import CompoundClasses
 from PySirius.models.compound_import import CompoundImport
 from PySirius.models.compound_opt_field import CompoundOptField
+from PySirius.models.computed_subtools import ComputedSubtools
 from PySirius.models.confidence_mode import ConfidenceMode
 from PySirius.models.connection_check import ConnectionCheck
 from PySirius.models.connection_error import ConnectionError

client-api_python/generated/PySirius/api/searchable_databases_api.py

@@ -597,6 +597,7 @@ def _create_database_serialize(
     def get_custom_databases(
         self,
         include_stats: Optional[StrictBool] = None,
+        include_with_errors: Optional[StrictBool] = None,
         _request_timeout: Union[
             None,
             Annotated[StrictFloat, Field(gt=0)],
@@ -615,6 +616,8 @@ def get_custom_databases(
 
         :param include_stats:
         :type include_stats: bool
+        :param include_with_errors:
+        :type include_with_errors: bool
         :param _request_timeout: timeout setting for this request. If one
                                  number provided, it will be total request
                                  timeout. It can also be a pair (tuple) of
@@ -639,6 +642,7 @@ def get_custom_databases(
 
         _param = self._get_custom_databases_serialize(
             include_stats=include_stats,
+            include_with_errors=include_with_errors,
             _request_auth=_request_auth,
             _content_type=_content_type,
             _headers=_headers,
@@ -663,6 +667,7 @@ def get_custom_databases(
     def get_custom_databases_with_http_info(
         self,
         include_stats: Optional[StrictBool] = None,
+        include_with_errors: Optional[StrictBool] = None,
         _request_timeout: Union[
             None,
             Annotated[StrictFloat, Field(gt=0)],
@@ -681,6 +686,8 @@ def get_custom_databases_with_http_info(
 
         :param include_stats:
         :type include_stats: bool
+        :param include_with_errors:
+        :type include_with_errors: bool
         :param _request_timeout: timeout setting for this request. If one
                                  number provided, it will be total request
                                  timeout. It can also be a pair (tuple) of
@@ -705,6 +712,7 @@ def get_custom_databases_with_http_info(
 
         _param = self._get_custom_databases_serialize(
             include_stats=include_stats,
+            include_with_errors=include_with_errors,
             _request_auth=_request_auth,
             _content_type=_content_type,
             _headers=_headers,
@@ -729,6 +737,7 @@ def get_custom_databases_with_http_info(
     def get_custom_databases_without_preload_content(
         self,
         include_stats: Optional[StrictBool] = None,
+        include_with_errors: Optional[StrictBool] = None,
         _request_timeout: Union[
             None,
             Annotated[StrictFloat, Field(gt=0)],
@@ -747,6 +756,8 @@ def get_custom_databases_without_preload_content(
 
         :param include_stats:
         :type include_stats: bool
+        :param include_with_errors:
+        :type include_with_errors: bool
         :param _request_timeout: timeout setting for this request. If one
                                  number provided, it will be total request
                                  timeout. It can also be a pair (tuple) of
@@ -771,6 +782,7 @@ def get_custom_databases_without_preload_content(
 
         _param = self._get_custom_databases_serialize(
             include_stats=include_stats,
+            include_with_errors=include_with_errors,
             _request_auth=_request_auth,
             _content_type=_content_type,
             _headers=_headers,
@@ -790,6 +802,7 @@ def get_custom_databases_without_preload_content(
     def _get_custom_databases_serialize(
         self,
         include_stats,
+        include_with_errors,
         _request_auth,
         _content_type,
         _headers,
@@ -814,6 +827,10 @@ def _get_custom_databases_serialize(
 
             _query_params.append(('includeStats', include_stats))
 
+        if include_with_errors is not None:
+
+            _query_params.append(('includeWithErrors', include_with_errors))
+
         # process the header parameters
         # process the form parameters
         # process the body parameter
@@ -1124,6 +1141,7 @@ def _get_database_serialize(
     def get_databases(
         self,
         include_stats: Optional[StrictBool] = None,
+        include_with_errors: Optional[StrictBool] = None,
         _request_timeout: Union[
             None,
             Annotated[StrictFloat, Field(gt=0)],
@@ -1142,6 +1160,8 @@ def get_databases(
 
         :param include_stats:
         :type include_stats: bool
+        :param include_with_errors:
+        :type include_with_errors: bool
         :param _request_timeout: timeout setting for this request. If one
                                  number provided, it will be total request
                                  timeout. It can also be a pair (tuple) of
@@ -1166,6 +1186,7 @@ def get_databases(
 
         _param = self._get_databases_serialize(
             include_stats=include_stats,
+            include_with_errors=include_with_errors,
             _request_auth=_request_auth,
             _content_type=_content_type,
             _headers=_headers,
@@ -1190,6 +1211,7 @@ def get_databases(
     def get_databases_with_http_info(
         self,
         include_stats: Optional[StrictBool] = None,
+        include_with_errors: Optional[StrictBool] = None,
         _request_timeout: Union[
             None,
             Annotated[StrictFloat, Field(gt=0)],
@@ -1208,6 +1230,8 @@ def get_databases_with_http_info(
 
         :param include_stats:
         :type include_stats: bool
+        :param include_with_errors:
+        :type include_with_errors: bool
         :param _request_timeout: timeout setting for this request. If one
                                  number provided, it will be total request
                                  timeout. It can also be a pair (tuple) of
@@ -1232,6 +1256,7 @@ def get_databases_with_http_info(
 
         _param = self._get_databases_serialize(
             include_stats=include_stats,
+            include_with_errors=include_with_errors,
             _request_auth=_request_auth,
             _content_type=_content_type,
             _headers=_headers,
@@ -1256,6 +1281,7 @@ def get_databases_with_http_info(
     def get_databases_without_preload_content(
         self,
         include_stats: Optional[StrictBool] = None,
+        include_with_errors: Optional[StrictBool] = None,
         _request_timeout: Union[
             None,
             Annotated[StrictFloat, Field(gt=0)],
@@ -1274,6 +1300,8 @@ def get_databases_without_preload_content(
 
         :param include_stats:
         :type include_stats: bool
+        :param include_with_errors:
+        :type include_with_errors: bool
         :param _request_timeout: timeout setting for this request. If one
                                  number provided, it will be total request
                                  timeout. It can also be a pair (tuple) of
@@ -1298,6 +1326,7 @@ def get_databases_without_preload_content(
 
         _param = self._get_databases_serialize(
             include_stats=include_stats,
+            include_with_errors=include_with_errors,
             _request_auth=_request_auth,
             _content_type=_content_type,
             _headers=_headers,
@@ -1317,6 +1346,7 @@ def get_databases_without_preload_content(
     def _get_databases_serialize(
         self,
         include_stats,
+        include_with_errors,
         _request_auth,
         _content_type,
         _headers,
@@ -1341,6 +1371,10 @@ def _get_databases_serialize(
 
             _query_params.append(('includeStats', include_stats))
 
+        if include_with_errors is not None:
+
+            _query_params.append(('includeWithErrors', include_with_errors))
+
         # process the header parameters
         # process the form parameters
         # process the body parameter

client-api_python/generated/PySirius/api_client.py

@@ -88,7 +88,7 @@ def __init__(
             self.default_headers[header_name] = header_value
         self.cookie = cookie
         # Set default User-Agent.
-        self.user_agent = 'OpenAPI-Generator/6.0.6/python'
+        self.user_agent = 'OpenAPI-Generator/6.0.7/python'
         self.client_side_validation = configuration.client_side_validation
 
     def __enter__(self):

client-api_python/generated/PySirius/configuration.py

@@ -370,7 +370,7 @@ def to_debug_report(self):
                "OS: {env}\n"\
                "Python Version: {pyversion}\n"\
                "Version of the API: 2.1\n"\
-               "SDK Package Version: 6.0.6".\
+               "SDK Package Version: 6.0.7".\
                format(env=sys.platform, pyversion=sys.version)
 
     def get_host_settings(self):

client-api_python/generated/PySirius/models/__init__.py

@@ -36,6 +36,7 @@
 from PySirius.models.compound_classes import CompoundClasses
 from PySirius.models.compound_import import CompoundImport
 from PySirius.models.compound_opt_field import CompoundOptField
+from PySirius.models.computed_subtools import ComputedSubtools
 from PySirius.models.confidence_mode import ConfidenceMode
 from PySirius.models.connection_check import ConnectionCheck
 from PySirius.models.connection_error import ConnectionError

client-api_python/generated/PySirius/models/aligned_feature.py

@@ -19,6 +19,7 @@
 
 from pydantic import BaseModel, ConfigDict, Field, StrictBool, StrictInt, StrictStr
 from typing import Any, ClassVar, Dict, List, Optional
+from PySirius.models.computed_subtools import ComputedSubtools
 from PySirius.models.data_quality import DataQuality
 from PySirius.models.feature_annotations import FeatureAnnotations
 from PySirius.models.ms_data import MsData
@@ -46,7 +47,8 @@ class AlignedFeature(BaseModel):
     top_annotations: Optional[FeatureAnnotations] = Field(default=None, alias="topAnnotations")
     top_annotations_de_novo: Optional[FeatureAnnotations] = Field(default=None, alias="topAnnotationsDeNovo")
     computing: Optional[StrictBool] = Field(default=None, description="Write lock for this feature. If the feature is locked no write operations are possible.  True if any computation is modifying this feature or its results")
-    __properties: ClassVar[List[str]] = ["alignedFeatureId", "compoundId", "name", "externalFeatureId", "ionMass", "charge", "detectedAdducts", "rtStartSeconds", "rtEndSeconds", "rtApexSeconds", "quality", "hasMs1", "hasMsMs", "msData", "topAnnotations", "topAnnotationsDeNovo", "computing"]
+    computed_tools: Optional[ComputedSubtools] = Field(default=None, alias="computedTools")
+    __properties: ClassVar[List[str]] = ["alignedFeatureId", "compoundId", "name", "externalFeatureId", "ionMass", "charge", "detectedAdducts", "rtStartSeconds", "rtEndSeconds", "rtApexSeconds", "quality", "hasMs1", "hasMsMs", "msData", "topAnnotations", "topAnnotationsDeNovo", "computing", "computedTools"]
 
     model_config = ConfigDict(
         populate_by_name=True,
@@ -96,6 +98,9 @@ def to_dict(self) -> Dict[str, Any]:
         # override the default output from pydantic by calling `to_dict()` of top_annotations_de_novo
         if self.top_annotations_de_novo:
             _dict['topAnnotationsDeNovo'] = self.top_annotations_de_novo.to_dict()
+        # override the default output from pydantic by calling `to_dict()` of computed_tools
+        if self.computed_tools:
+            _dict['computedTools'] = self.computed_tools.to_dict()
         # set to None if rt_start_seconds (nullable) is None
         # and model_fields_set contains the field
         if self.rt_start_seconds is None and "rt_start_seconds" in self.model_fields_set:
@@ -131,6 +136,11 @@ def to_dict(self) -> Dict[str, Any]:
         if self.top_annotations_de_novo is None and "top_annotations_de_novo" in self.model_fields_set:
             _dict['topAnnotationsDeNovo'] = None
 
+        # set to None if computed_tools (nullable) is None
+        # and model_fields_set contains the field
+        if self.computed_tools is None and "computed_tools" in self.model_fields_set:
+            _dict['computedTools'] = None
+
         return _dict
 
     @classmethod
@@ -159,7 +169,8 @@ def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]:
             "msData": MsData.from_dict(obj["msData"]) if obj.get("msData") is not None else None,
             "topAnnotations": FeatureAnnotations.from_dict(obj["topAnnotations"]) if obj.get("topAnnotations") is not None else None,
             "topAnnotationsDeNovo": FeatureAnnotations.from_dict(obj["topAnnotationsDeNovo"]) if obj.get("topAnnotationsDeNovo") is not None else None,
-            "computing": obj.get("computing")
+            "computing": obj.get("computing"),
+            "computedTools": ComputedSubtools.from_dict(obj["computedTools"]) if obj.get("computedTools") is not None else None
         })
         return _obj
 

client-api_python/generated/PySirius/models/aligned_feature_opt_field.py

@@ -30,6 +30,7 @@ class AlignedFeatureOptField(str, Enum):
     MSDATA = 'msData'
     TOPANNOTATIONS = 'topAnnotations'
     TOPANNOTATIONSDENOVO = 'topAnnotationsDeNovo'
+    COMPUTEDTOOLS = 'computedTools'
 
     @classmethod
     def from_json(cls, json_str: str) -> Self: