add doc strings for step configs

open_icu/__init__.py

@@ -0,0 +1,44 @@
+"""
+OpenICU: A Python package for analysing time series data in the ICU.
+
+This package provides a set of tools for analysing time series data in the ICU.
+It is designed to be modular and extensible, allowing users to easily add new data
+sources, filters, and analyses.
+
+Modules:
+-
+
+Usage:
+```python
+
+```
+
+Author:
+- Paul Brauckmann
+- Christian Porschen
+
+License:
+```
+MIT License
+
+Copyright (c) 2023 AIDH MS
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+```
+"""

open_icu/types/conf/cohort.py

@@ -4,6 +4,23 @@
 
 
 class CohortFilterConfig(BaseModel):
+    """
+    A class representing the cohort filter step configuration.
+
+    Attributes
+    ----------
+    name : str
+        The name of the cohort filter step.
+    description : str
+        The description of the cohort filter step.
+    concepts : list[str]
+        A list of concepts used in the filter.
+    filter : str
+        A python dotter path to the filter class.
+    params : dict[str, Any]
+        A dictionary of parameters that will passed to the filter class.
+    """
+
     name: str
     description: str
     concepts: list[str]

open_icu/types/conf/concept.py

@@ -4,18 +4,63 @@
 
 
 class ConceptLimits(BaseModel):
+    """
+    A class representing the limits of a concept.
+
+    Attributes
+    ----------
+    upper : str
+        The upper limit of the concept.
+    lower : str
+        The lower limit of the concept
+    """
+
     upper: str
     lower: str
 
 
 class ConceptSource(BaseModel):
+    """
+    A class representing the source of a concept.
+
+    Attributes
+    ----------
+    source : str
+        The source of the concept.
+    extractor : str
+        A python dotter path to the extractor class.
+    unit : dict[str, str]
+        A dictionary mapping between values and units used in the source.
+    params : dict[str, Any]
+        A dictionary of parameters that will passed to the extractor class.
+    """
+
     source: str
     extractor: str
     unit: dict[str, str]
     params: dict[str, Any]
 
 
 class ConceptConfig(BaseModel):
+    """
+    A class representing the concept configuration.
+
+    Attributes
+    ----------
+    name : str
+        The name of the concept.
+    description : str
+        The description of the concept.
+    identifiers : dict[str, str]
+        A dictionary of identifiers used in the concept.
+    unit : dict[str, str]
+        A dictionary mapping between values and units used in the concept.
+    limits : ConceptLimits
+        The limits of the concept.
+    sources : list[ConceptSource]
+        A list of sources used in the concept.
+    """
+
     name: str
     description: str
     identifiers: dict[str, str]
@@ -24,6 +69,15 @@ class ConceptConfig(BaseModel):
     sources: list[ConceptSource]
 
     def model_post_init(self, __context: Any) -> None:
+        """
+        The post init method is used to set the open_icu identifier to the name of the concept.
+
+        Parameters
+        ----------
+        __context : Any
+            The context of the model.
+        """
+
         super().model_post_init(__context)
 
         self.identifiers["open_icu"] = self.name

open_icu/types/conf/preprocessing.py

@@ -4,6 +4,23 @@
 
 
 class PreprocessorConfig(BaseModel):
+    """
+    A class representing the preprocessor step configuration.
+
+    Attributes
+    ----------
+    name : str
+        The name of the preprocessor step.
+    description : str
+        The description of the preprocessor step.
+    concepts : list[str]
+        A list of concepts used in the preprocessor.
+    preprocessor : str
+        A python dotter path to the preprocessor class.
+    params : dict[str, Any]
+        A dictionary of parameters that will passed to the preprocessor class.
+    """
+
     name: str
     description: str
     concepts: list[str]

open_icu/types/conf/sink.py

@@ -4,6 +4,21 @@
 
 
 class SinkConfig(BaseModel):
+    """
+    A class representing the sink configuration.
+
+    Attributes
+    ----------
+    name : str
+        The name of the sink.
+    description : str
+        The description of the sink.
+    sink : str
+        A python dotter path to the sink class.
+    params : dict[str, Any]
+        A dictionary of parameters that will passed to the sink class
+    """
+
     name: str
     description: str
     sink: str

open_icu/types/conf/source.py

@@ -2,12 +2,38 @@
 
 
 class SampleConfig(BaseModel):
+    """
+    A class representing the sample configuration.
+
+    Attributes
+    ----------
+    samples : list[str]
+        A list of samples.
+    sampler : str
+        A python dotter path to the sampler class.
+    params : dict[str, str]
+        A dictionary of parameters that will passed to the sampler class.
+    """
+
     samples: list[str] = []
     sampler: str
     params: dict[str, str]
 
 
 class SourceConfig(BaseModel):
+    """
+    A class representing the source configuration.
+
+    Attributes
+    ----------
+    name : str
+        The name of the source.
+    connection_uri : str
+        The connection uri of the source.
+    sample : SampleConfig
+        The sample configuration.
+    """
+
     name: str
     connection_uri: str
     sample: SampleConfig

open_icu/types/conf/unit.py

@@ -4,6 +4,23 @@
 
 
 class UnitConverterConfig(BaseModel):
+    """
+    A class representing the unit converter configuration.
+
+    Attributes
+    ----------
+    name : str
+        The name of the unit converter.
+    description : str
+        The description of the unit converter.
+    unitconverter : str
+        A python dotter path to the unit converter class.
+    base_unit : str
+        The base unit of the unit converter.
+    params : dict[str, Any]
+        A dictionary of parameters that will passed to the unit converter class.
+    """
+
     name: str
     description: str
     unitconverter: str