Auto-Updated OpenAPI Clients

client-api_python/generated/PySirius/__init__.py

@@ -14,7 +14,7 @@
 """  # noqa: E501
 
 
-__version__ = "6.0.5"
+__version__ = "6.0.6"
 
 # import apis into sdk package
 from PySirius.api.actuator_api import ActuatorApi

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

@@ -16,7 +16,7 @@
 from typing import Any, Dict, List, Optional, Tuple, Union
 from typing_extensions import Annotated
 
-from pydantic import Field, StrictInt, StrictStr, field_validator
+from pydantic import Field, StrictBool, StrictInt, StrictStr, field_validator
 from typing import List, Optional
 from typing_extensions import Annotated
 from PySirius.models.aligned_feature import AlignedFeature
@@ -6643,9 +6643,9 @@ def _get_ms_data_serialize(
     @validate_call
     def get_quantification(
         self,
-        project_id: StrictStr,
-        aligned_feature_id: StrictStr,
-        type: Optional[StrictStr] = None,
+        project_id: Annotated[StrictStr, Field(description="project-space to read from.")],
+        aligned_feature_id: Annotated[StrictStr, Field(description="feature which intensities should be read out")],
+        type: Annotated[Optional[StrictStr], Field(description="quantification type. Currently, only APEX_HEIGHT is supported, which is the intensity of the feature at its apex.")] = None,
         _request_timeout: Union[
             None,
             Annotated[StrictFloat, Field(gt=0)],
@@ -6659,14 +6659,15 @@ def get_quantification(
         _headers: Optional[Dict[StrictStr, Any]] = None,
         _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
     ) -> QuantificationTable:
-        """get_quantification
+        """Returns a single quantification table row for the given feature.
 
+        Returns a single quantification table row for the given feature. The quantification table contains the intensity of the feature within all  samples it is contained in.
 
-        :param project_id: (required)
+        :param project_id: project-space to read from. (required)
         :type project_id: str
-        :param aligned_feature_id: (required)
+        :param aligned_feature_id: feature which intensities should be read out (required)
         :type aligned_feature_id: str
-        :param type:
+        :param type: quantification type. Currently, only APEX_HEIGHT is supported, which is the intensity of the feature at its apex.
         :type type: str
         :param _request_timeout: timeout setting for this request. If one
                                  number provided, it will be total request
@@ -6717,9 +6718,9 @@ def get_quantification(
     @validate_call
     def get_quantification_with_http_info(
         self,
-        project_id: StrictStr,
-        aligned_feature_id: StrictStr,
-        type: Optional[StrictStr] = None,
+        project_id: Annotated[StrictStr, Field(description="project-space to read from.")],
+        aligned_feature_id: Annotated[StrictStr, Field(description="feature which intensities should be read out")],
+        type: Annotated[Optional[StrictStr], Field(description="quantification type. Currently, only APEX_HEIGHT is supported, which is the intensity of the feature at its apex.")] = None,
         _request_timeout: Union[
             None,
             Annotated[StrictFloat, Field(gt=0)],
@@ -6733,14 +6734,15 @@ def get_quantification_with_http_info(
         _headers: Optional[Dict[StrictStr, Any]] = None,
         _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
     ) -> ApiResponse[QuantificationTable]:
-        """get_quantification
+        """Returns a single quantification table row for the given feature.
 
+        Returns a single quantification table row for the given feature. The quantification table contains the intensity of the feature within all  samples it is contained in.
 
-        :param project_id: (required)
+        :param project_id: project-space to read from. (required)
         :type project_id: str
-        :param aligned_feature_id: (required)
+        :param aligned_feature_id: feature which intensities should be read out (required)
         :type aligned_feature_id: str
-        :param type:
+        :param type: quantification type. Currently, only APEX_HEIGHT is supported, which is the intensity of the feature at its apex.
         :type type: str
         :param _request_timeout: timeout setting for this request. If one
                                  number provided, it will be total request
@@ -6791,9 +6793,9 @@ def get_quantification_with_http_info(
     @validate_call
     def get_quantification_without_preload_content(
         self,
-        project_id: StrictStr,
-        aligned_feature_id: StrictStr,
-        type: Optional[StrictStr] = None,
+        project_id: Annotated[StrictStr, Field(description="project-space to read from.")],
+        aligned_feature_id: Annotated[StrictStr, Field(description="feature which intensities should be read out")],
+        type: Annotated[Optional[StrictStr], Field(description="quantification type. Currently, only APEX_HEIGHT is supported, which is the intensity of the feature at its apex.")] = None,
         _request_timeout: Union[
             None,
             Annotated[StrictFloat, Field(gt=0)],
@@ -6807,14 +6809,15 @@ def get_quantification_without_preload_content(
         _headers: Optional[Dict[StrictStr, Any]] = None,
         _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
     ) -> RESTResponseType:
-        """get_quantification
+        """Returns a single quantification table row for the given feature.
 
+        Returns a single quantification table row for the given feature. The quantification table contains the intensity of the feature within all  samples it is contained in.
 
-        :param project_id: (required)
+        :param project_id: project-space to read from. (required)
         :type project_id: str
-        :param aligned_feature_id: (required)
+        :param aligned_feature_id: feature which intensities should be read out (required)
         :type aligned_feature_id: str
-        :param type:
+        :param type: quantification type. Currently, only APEX_HEIGHT is supported, which is the intensity of the feature at its apex.
         :type type: str
         :param _request_timeout: timeout setting for this request. If one
                                  number provided, it will be total request
@@ -10204,10 +10207,11 @@ def _get_structure_candidates_paged_serialize(
 
 
     @validate_call
-    def get_traces1(
+    def get_traces(
         self,
-        project_id: StrictStr,
-        aligned_feature_id: StrictStr,
+        project_id: Annotated[StrictStr, Field(description="project-space to read from.")],
+        aligned_feature_id: Annotated[StrictStr, Field(description="feature which intensities should be read out")],
+        include_all: Annotated[Optional[StrictBool], Field(description="when true, return all samples that belong to the same merged trace. when false, only return samples which contain the aligned feature.")] = None,
         _request_timeout: Union[
             None,
             Annotated[StrictFloat, Field(gt=0)],
@@ -10221,13 +10225,16 @@ def get_traces1(
         _headers: Optional[Dict[StrictStr, Any]] = None,
         _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
     ) -> TraceSet:
-        """get_traces1
+        """Returns the traces of the given feature.
 
+        Returns the traces of the given feature. A trace consists of m/z and intensity values over the retention  time axis. All the returned traces are 'projected', which means they refer not to the original retention time axis,  but to a recalibrated axis. This means the data points in the trace are not exactly the same as in the raw data.  However, this also means that all traces can be directly compared against each other, as they all lie in the same  retention time axis.  By default, this method only returns traces of samples the aligned feature appears in. When includeAll is set,  it also includes samples in which the same trace appears in.
 
-        :param project_id: (required)
+        :param project_id: project-space to read from. (required)
         :type project_id: str
-        :param aligned_feature_id: (required)
+        :param aligned_feature_id: feature which intensities should be read out (required)
         :type aligned_feature_id: str
+        :param include_all: when true, return all samples that belong to the same merged trace. when false, only return samples which contain the aligned feature.
+        :type include_all: 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
@@ -10250,9 +10257,10 @@ def get_traces1(
         :return: Returns the result object.
         """ # noqa: E501
 
-        _param = self._get_traces1_serialize(
+        _param = self._get_traces_serialize(
             project_id=project_id,
             aligned_feature_id=aligned_feature_id,
+            include_all=include_all,
             _request_auth=_request_auth,
             _content_type=_content_type,
             _headers=_headers,
@@ -10274,10 +10282,11 @@ def get_traces1(
 
 
     @validate_call
-    def get_traces1_with_http_info(
+    def get_traces_with_http_info(
         self,
-        project_id: StrictStr,
-        aligned_feature_id: StrictStr,
+        project_id: Annotated[StrictStr, Field(description="project-space to read from.")],
+        aligned_feature_id: Annotated[StrictStr, Field(description="feature which intensities should be read out")],
+        include_all: Annotated[Optional[StrictBool], Field(description="when true, return all samples that belong to the same merged trace. when false, only return samples which contain the aligned feature.")] = None,
         _request_timeout: Union[
             None,
             Annotated[StrictFloat, Field(gt=0)],
@@ -10291,13 +10300,16 @@ def get_traces1_with_http_info(
         _headers: Optional[Dict[StrictStr, Any]] = None,
         _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
     ) -> ApiResponse[TraceSet]:
-        """get_traces1
+        """Returns the traces of the given feature.
 
+        Returns the traces of the given feature. A trace consists of m/z and intensity values over the retention  time axis. All the returned traces are 'projected', which means they refer not to the original retention time axis,  but to a recalibrated axis. This means the data points in the trace are not exactly the same as in the raw data.  However, this also means that all traces can be directly compared against each other, as they all lie in the same  retention time axis.  By default, this method only returns traces of samples the aligned feature appears in. When includeAll is set,  it also includes samples in which the same trace appears in.
 
-        :param project_id: (required)
+        :param project_id: project-space to read from. (required)
         :type project_id: str
-        :param aligned_feature_id: (required)
+        :param aligned_feature_id: feature which intensities should be read out (required)
         :type aligned_feature_id: str
+        :param include_all: when true, return all samples that belong to the same merged trace. when false, only return samples which contain the aligned feature.
+        :type include_all: 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
@@ -10320,9 +10332,10 @@ def get_traces1_with_http_info(
         :return: Returns the result object.
         """ # noqa: E501
 
-        _param = self._get_traces1_serialize(
+        _param = self._get_traces_serialize(
             project_id=project_id,
             aligned_feature_id=aligned_feature_id,
+            include_all=include_all,
             _request_auth=_request_auth,
             _content_type=_content_type,
             _headers=_headers,
@@ -10344,10 +10357,11 @@ def get_traces1_with_http_info(
 
 
     @validate_call
-    def get_traces1_without_preload_content(
+    def get_traces_without_preload_content(
         self,
-        project_id: StrictStr,
-        aligned_feature_id: StrictStr,
+        project_id: Annotated[StrictStr, Field(description="project-space to read from.")],
+        aligned_feature_id: Annotated[StrictStr, Field(description="feature which intensities should be read out")],
+        include_all: Annotated[Optional[StrictBool], Field(description="when true, return all samples that belong to the same merged trace. when false, only return samples which contain the aligned feature.")] = None,
         _request_timeout: Union[
             None,
             Annotated[StrictFloat, Field(gt=0)],
@@ -10361,13 +10375,16 @@ def get_traces1_without_preload_content(
         _headers: Optional[Dict[StrictStr, Any]] = None,
         _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
     ) -> RESTResponseType:
-        """get_traces1
+        """Returns the traces of the given feature.
 
+        Returns the traces of the given feature. A trace consists of m/z and intensity values over the retention  time axis. All the returned traces are 'projected', which means they refer not to the original retention time axis,  but to a recalibrated axis. This means the data points in the trace are not exactly the same as in the raw data.  However, this also means that all traces can be directly compared against each other, as they all lie in the same  retention time axis.  By default, this method only returns traces of samples the aligned feature appears in. When includeAll is set,  it also includes samples in which the same trace appears in.
 
-        :param project_id: (required)
+        :param project_id: project-space to read from. (required)
         :type project_id: str
-        :param aligned_feature_id: (required)
+        :param aligned_feature_id: feature which intensities should be read out (required)
         :type aligned_feature_id: str
+        :param include_all: when true, return all samples that belong to the same merged trace. when false, only return samples which contain the aligned feature.
+        :type include_all: 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
@@ -10390,9 +10407,10 @@ def get_traces1_without_preload_content(
         :return: Returns the result object.
         """ # noqa: E501
 
-        _param = self._get_traces1_serialize(
+        _param = self._get_traces_serialize(
             project_id=project_id,
             aligned_feature_id=aligned_feature_id,
+            include_all=include_all,
             _request_auth=_request_auth,
             _content_type=_content_type,
             _headers=_headers,
@@ -10409,10 +10427,11 @@ def get_traces1_without_preload_content(
         return response_data.response
 
 
-    def _get_traces1_serialize(
+    def _get_traces_serialize(
         self,
         project_id,
         aligned_feature_id,
+        include_all,
         _request_auth,
         _content_type,
         _headers,
@@ -10437,6 +10456,10 @@ def _get_traces1_serialize(
         if aligned_feature_id is not None:
             _path_params['alignedFeatureId'] = aligned_feature_id
         # process the query parameters
+        if include_all is not None:
+
+            _query_params.append(('includeAll', include_all))
+
         # 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/6.0.5/python'
+        self.user_agent = 'OpenAPI-Generator/6.0.6/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: 6.0.5".\
+               "SDK Package Version: 6.0.6".\
                format(env=sys.platform, pyversion=sys.version)
 
     def get_host_settings(self):

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

@@ -20,6 +20,7 @@
 from pydantic import BaseModel, ConfigDict, Field, StrictInt, StrictStr
 from typing import Any, ClassVar, Dict, List, Optional
 from PySirius.models.basic_spectrum import BasicSpectrum
+from PySirius.models.data_quality import DataQuality
 from typing import Optional, Set
 from typing_extensions import Self
 
@@ -34,10 +35,12 @@ class FeatureImport(BaseModel):
     detected_adducts: Optional[List[Optional[StrictStr]]] = Field(default=None, description="Detected adducts of this feature. Can be NULL or empty if no adducts are known.", alias="detectedAdducts")
     rt_start_seconds: Optional[float] = Field(default=None, alias="rtStartSeconds")
     rt_end_seconds: Optional[float] = Field(default=None, alias="rtEndSeconds")
+    rt_apex_seconds: Optional[float] = Field(default=None, alias="rtApexSeconds")
+    data_quality: Optional[DataQuality] = Field(default=None, alias="dataQuality")
     merged_ms1: Optional[BasicSpectrum] = Field(default=None, alias="mergedMs1")
     ms1_spectra: Optional[List[Optional[BasicSpectrum]]] = Field(default=None, description="List of MS1Spectra belonging to this feature. These spectra will be merged an only a representative  mergedMs1 spectrum will be stored in SIRIUS. At least one of these spectra should contain the  isotope pattern of the precursor ion.  Note: Will be ignored if 'mergedMs1' is given.", alias="ms1Spectra")
     ms2_spectra: Optional[List[Optional[BasicSpectrum]]] = Field(default=None, description="List of MS/MS spectra that belong to this feature.", alias="ms2Spectra")
-    __properties: ClassVar[List[str]] = ["name", "externalFeatureId", "ionMass", "charge", "detectedAdducts", "rtStartSeconds", "rtEndSeconds", "mergedMs1", "ms1Spectra", "ms2Spectra"]
+    __properties: ClassVar[List[str]] = ["name", "externalFeatureId", "ionMass", "charge", "detectedAdducts", "rtStartSeconds", "rtEndSeconds", "rtApexSeconds", "dataQuality", "mergedMs1", "ms1Spectra", "ms2Spectra"]
 
     model_config = ConfigDict(
         populate_by_name=True,
@@ -120,6 +123,16 @@ def to_dict(self) -> Dict[str, Any]:
         if self.rt_end_seconds is None and "rt_end_seconds" in self.model_fields_set:
             _dict['rtEndSeconds'] = None
 
+        # set to None if rt_apex_seconds (nullable) is None
+        # and model_fields_set contains the field
+        if self.rt_apex_seconds is None and "rt_apex_seconds" in self.model_fields_set:
+            _dict['rtApexSeconds'] = None
+
+        # set to None if data_quality (nullable) is None
+        # and model_fields_set contains the field
+        if self.data_quality is None and "data_quality" in self.model_fields_set:
+            _dict['dataQuality'] = None
+
         # set to None if merged_ms1 (nullable) is None
         # and model_fields_set contains the field
         if self.merged_ms1 is None and "merged_ms1" in self.model_fields_set:
@@ -154,6 +167,8 @@ def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]:
             "detectedAdducts": obj.get("detectedAdducts"),
             "rtStartSeconds": obj.get("rtStartSeconds"),
             "rtEndSeconds": obj.get("rtEndSeconds"),
+            "rtApexSeconds": obj.get("rtApexSeconds"),
+            "dataQuality": obj.get("dataQuality"),
             "mergedMs1": BasicSpectrum.from_dict(obj["mergedMs1"]) if obj.get("mergedMs1") is not None else None,
             "ms1Spectra": [BasicSpectrum.from_dict(_item) for _item in obj["ms1Spectra"]] if obj.get("ms1Spectra") is not None else None,
             "ms2Spectra": [BasicSpectrum.from_dict(_item) for _item in obj["ms2Spectra"]] if obj.get("ms2Spectra") is not None else None