labfreed 0.2.6a6__py3-none-any.whl → 0.2.8__py3-none-any.whl

labfreed/pac_cat/predefined_categories.py

@@ -1,201 +1,201 @@
-## Materials
-from abc import ABC
-from pydantic import Field, computed_field, model_validator
-
-from labfreed.labfreed_infrastructure import ValidationMsgLevel
-from labfreed.pac_cat.category_base import Category
-from labfreed.pac_id.id_segment import IDSegment
-
-class PredefinedCategory(Category, ABC):
-    '''@private 
-    Base for Predefined catergories
-    '''
-    additional_segments: list[IDSegment] = Field(default_factory=list, exclude=True)
-    ''' Category segments, which are not defined in the specification'''
-    
-    @computed_field
-    @property
-    def segments(self) -> list[IDSegment]:
-        return self._get_segments(use_short_notation=False)
-    
-    def _get_segments(self, use_short_notation=False) -> list[IDSegment]:
-        segments = []
-        can_omit_keys = use_short_notation # keeps track of whether keys can still be omitted. That is the case when the segment recommendation is followed
-        for field_name, field_info in self.model_fields.items():
-            if field_name in ['key', 'additional_segments']:
-                continue
-            if value := getattr(self, field_name):
-                if can_omit_keys:
-                    key = None
-                else:
-                    key = field_info.alias
-                segments.append(IDSegment(key= key, value= value)  )
-            else:
-                can_omit_keys = False
-        if self.additional_segments:
-            segments.extend(self.additional_segments)
-        return segments
-    
-    model_config = {
-        "populate_by_name": True 
-    }
-    ''' @private Pydantic tweak to allows model fields to be populated using their Python name, even if they have an alias defined. 
-        The alias we need to use the GS1 code in serialization
-    '''
-
-
-
-class Material_Device(PredefinedCategory):
-    '''Represents the -MD category'''
-    key: str =         Field(default='-MD', frozen=True)
-    model_number: str|None =         Field(              alias='240')
-    serial_number: str|None =        Field(              alias='21')
-    additional_segments: list[IDSegment] = Field(default_factory=list, exclude=True)
-    ''' Category segments, which are not defined in the specification'''
-    
-    @model_validator(mode='after')
-    def _validate_mandatory_fields(self):
-        if not self.model_number:
-            self._add_validation_message(
-                    source=f"Category {self.key}",
-                    level = ValidationMsgLevel.ERROR,
-                    msg=f'Category key {self.key} is missing mandatory field Model Number',
-                    highlight_pattern = f"{self.key}"
-            )
-        if not self.serial_number:
-            self._add_validation_message(
-                    source=f"Category {self.key}",
-                    level = ValidationMsgLevel.ERROR,
-                    msg=f'Category key {self.key} is missing mandatory field Serial Number',
-                    highlight_pattern = f"{self.key}"
-            )
-        return self
-    
-class Material_Substance(PredefinedCategory):
-    '''Represents the -MS category'''
-    key: str =         Field(default='-MS', frozen=True)
-    product_number:str|None =    Field(              alias='240')
-    batch_number:str|None =     Field(default=None, alias='10')
-    container_size:str|None =   Field(default=None, alias='20')
-    container_number:str|None = Field(default=None, alias='21')
-    aliquot:str|None =          Field(default=None, alias='250')
-    additional_segments: list[IDSegment] = Field(default_factory=list, exclude=True)
-    ''' Category segments, which are not defined in the specification'''
-    
-    @model_validator(mode='after')
-    def _validate_mandatory_fields(self):
-        if not self.product_number:
-            self._add_validation_message(
-                    source=f"Category {self.key}",
-                    level = ValidationMsgLevel.ERROR,
-                    msg=f'Category key {self.key} is missing mandatory field Product Number',
-                    highlight_pattern = f"{self.key}"
-            )
-        return self
-    
-class Material_Consumable(PredefinedCategory):
-    '''Represents the -MC category'''
-    key: str = Field(default='-MC', frozen=True)
-    product_number:str|None =   Field(              alias='240')
-    batch_number:str|None =     Field(default=None, alias='10')
-    packaging_size:str|None =     Field(default=None, alias='20')
-    serial_number:str|None =    Field(default=None, alias='21')
-    aliquot:str|None =          Field(default=None, alias='250')
-    additional_segments: list[IDSegment] = Field(default_factory=list, exclude=True)
-    ''' Category segments, which are not defined in the specification'''
-    
-    @model_validator(mode='after')
-    def _validate_mandatory_fields(self):
-        if not self.product_number:
-            self._add_validation_message(
-                    source=f"Category {self.key}",
-                    level = ValidationMsgLevel.ERROR,
-                    msg=f"Category key {self.key} is missing mandatory field 'Product Number'",
-                    highlight_pattern = f"{self.key}"
-            )
-        return self
-    
-class Material_Misc(Material_Consumable):
-    '''Represents the -MC category'''
-    # same fields as Consumable
-    key: str = Field(default='-MM', frozen=True)
-    product_number:str|None =   Field(              alias='240')
-    batch_number:str|None =     Field(default=None, alias='10')
-    packaging_size:str|None =     Field(default=None, alias='20')
-    serial_number:str|None =    Field(default=None, alias='21')
-    aliquot:str|None =          Field(default=None, alias='250')
-    additional_segments: list[IDSegment] = Field(default_factory=list, exclude=True)
-    ''' Category segments, which are not defined in the specification'''
-    
-
-
-## Data
-class Data_Abstract(PredefinedCategory, ABC):
-    '''@private'''
-    key: str
-    id:str|None =                    Field(              alias='21')
-    additional_segments: list[IDSegment] = Field(default_factory=list, exclude=True)
-    ''' Category segments, which are not defined in the specification'''
-    
-    @model_validator(mode='after')
-    def _validate_mandatory_fields(self):
-        if not self.id:
-            self._add_validation_message(
-                    source=f"Category {self.key}",
-                    level = ValidationMsgLevel.ERROR,
-                    msg=f"Category key {self.key} is missing mandatory field 'ID'",
-                    highlight_pattern = f"{self.key}"
-            )
-        return self
-
-class Data_Result(Data_Abstract):
-    '''Represents the -DR category'''
-    key: str = Field(default='-DR', frozen=True)
-    id:str|None =                    Field(              alias='21')
-    additional_segments: list[IDSegment] = Field(default_factory=list, exclude=True)
-    ''' Category segments, which are not defined in the specification'''
-    
-    
-class Data_Method(Data_Abstract):
-    '''Represents the -DM category'''
-    key: str = Field(default='-DM', frozen=True)
-    id:str|None =                    Field(              alias='21')
-    additional_segments: list[IDSegment] = Field(default_factory=list, exclude=True)
-    ''' Category segments, which are not defined in the specification'''
-    
-    
-class Data_Calibration(Data_Abstract):
-    '''Represents the -DC category'''
-    key: str = Field(default='-DC', frozen=True)
-    id:str|None =                    Field(              alias='21')
-    additional_segments: list[IDSegment] = Field(default_factory=list, exclude=True)
-    ''' Category segments, which are not defined in the specification'''
-    
-    
-class Data_Progress(Data_Abstract):
-    '''Represents the -DP category'''
-    key: str = Field(default='-DP', frozen=True)
-    id:str|None =                    Field(              alias='21')
-    additional_segments: list[IDSegment] = Field(default_factory=list, exclude=True)
-    ''' Category segments, which are not defined in the specification'''
-    
-    
-class Data_Static(Data_Abstract):
-    '''Represents the -DS category'''
-    key: str = Field(default='-DS', frozen=True)
-    id:str|None =                    Field(              alias='21')
-    additional_segments: list[IDSegment] = Field(default_factory=list, exclude=True)
-    ''' Category segments, which are not defined in the specification'''
-    
-    
-category_key_to_class_map  = {
-        '-MD': Material_Device,
-        '-MS': Material_Substance,
-        '-MC': Material_Consumable,
-        '-MM': Material_Misc,
-        '-DM': Data_Method,
-        '-DR': Data_Result,
-        '-DC': Data_Calibration,
-        '-DP': Data_Progress,
-        '-DS': Data_Static 
+## Materials
+from abc import ABC
+from pydantic import Field, computed_field, model_validator
+
+from labfreed.labfreed_infrastructure import ValidationMsgLevel
+from labfreed.pac_cat.category_base import Category
+from labfreed.pac_id.id_segment import IDSegment
+
+class PredefinedCategory(Category, ABC):
+    '''@private 
+    Base for Predefined catergories
+    '''
+    additional_segments: list[IDSegment] = Field(default_factory=list, exclude=True)
+    ''' Category segments, which are not defined in the specification'''
+    
+    @computed_field
+    @property
+    def segments(self) -> list[IDSegment]:
+        return self._get_segments(use_short_notation=False)
+    
+    def _get_segments(self, use_short_notation=False) -> list[IDSegment]:
+        segments = []
+        can_omit_keys = use_short_notation # keeps track of whether keys can still be omitted. That is the case when the segment recommendation is followed
+        for field_name, field_info in self.model_fields.items():
+            if field_name in ['key', 'additional_segments']:
+                continue
+            if value := getattr(self, field_name):
+                if can_omit_keys:
+                    key = None
+                else:
+                    key = field_info.alias
+                segments.append(IDSegment(key= key, value= value)  )
+            else:
+                can_omit_keys = False
+        if self.additional_segments:
+            segments.extend(self.additional_segments)
+        return segments
+    
+    model_config = {
+        "populate_by_name": True 
+    }
+    ''' @private Pydantic tweak to allows model fields to be populated using their Python name, even if they have an alias defined. 
+        The alias we need to use the GS1 code in serialization
+    '''
+
+
+
+class Material_Device(PredefinedCategory):
+    '''Represents the -MD category'''
+    key: str =         Field(default='-MD', frozen=True)
+    model_number: str|None =         Field(              alias='240')
+    serial_number: str|None =        Field(              alias='21')
+    additional_segments: list[IDSegment] = Field(default_factory=list, exclude=True)
+    ''' Category segments, which are not defined in the specification'''
+    
+    @model_validator(mode='after')
+    def _validate_mandatory_fields(self):
+        if not self.model_number:
+            self._add_validation_message(
+                    source=f"Category {self.key}",
+                    level = ValidationMsgLevel.ERROR,
+                    msg=f'Category key {self.key} is missing mandatory field Model Number',
+                    highlight_pattern = f"{self.key}"
+            )
+        if not self.serial_number:
+            self._add_validation_message(
+                    source=f"Category {self.key}",
+                    level = ValidationMsgLevel.ERROR,
+                    msg=f'Category key {self.key} is missing mandatory field Serial Number',
+                    highlight_pattern = f"{self.key}"
+            )
+        return self
+    
+class Material_Substance(PredefinedCategory):
+    '''Represents the -MS category'''
+    key: str =         Field(default='-MS', frozen=True)
+    product_number:str|None =    Field(              alias='240')
+    batch_number:str|None =     Field(default=None, alias='10')
+    container_size:str|None =   Field(default=None, alias='20')
+    container_number:str|None = Field(default=None, alias='21')
+    aliquot:str|None =          Field(default=None, alias='250')
+    additional_segments: list[IDSegment] = Field(default_factory=list, exclude=True)
+    ''' Category segments, which are not defined in the specification'''
+    
+    @model_validator(mode='after')
+    def _validate_mandatory_fields(self):
+        if not self.product_number:
+            self._add_validation_message(
+                    source=f"Category {self.key}",
+                    level = ValidationMsgLevel.ERROR,
+                    msg=f'Category key {self.key} is missing mandatory field Product Number',
+                    highlight_pattern = f"{self.key}"
+            )
+        return self
+    
+class Material_Consumable(PredefinedCategory):
+    '''Represents the -MC category'''
+    key: str = Field(default='-MC', frozen=True)
+    product_number:str|None =   Field(              alias='240')
+    batch_number:str|None =     Field(default=None, alias='10')
+    packaging_size:str|None =     Field(default=None, alias='20')
+    serial_number:str|None =    Field(default=None, alias='21')
+    aliquot:str|None =          Field(default=None, alias='250')
+    additional_segments: list[IDSegment] = Field(default_factory=list, exclude=True)
+    ''' Category segments, which are not defined in the specification'''
+    
+    @model_validator(mode='after')
+    def _validate_mandatory_fields(self):
+        if not self.product_number:
+            self._add_validation_message(
+                    source=f"Category {self.key}",
+                    level = ValidationMsgLevel.ERROR,
+                    msg=f"Category key {self.key} is missing mandatory field 'Product Number'",
+                    highlight_pattern = f"{self.key}"
+            )
+        return self
+    
+class Material_Misc(Material_Consumable):
+    '''Represents the -MC category'''
+    # same fields as Consumable
+    key: str = Field(default='-MM', frozen=True)
+    product_number:str|None =   Field(              alias='240')
+    batch_number:str|None =     Field(default=None, alias='10')
+    packaging_size:str|None =     Field(default=None, alias='20')
+    serial_number:str|None =    Field(default=None, alias='21')
+    aliquot:str|None =          Field(default=None, alias='250')
+    additional_segments: list[IDSegment] = Field(default_factory=list, exclude=True)
+    ''' Category segments, which are not defined in the specification'''
+    
+
+
+## Data
+class Data_Abstract(PredefinedCategory, ABC):
+    '''@private'''
+    key: str
+    id:str|None =                    Field(              alias='21')
+    additional_segments: list[IDSegment] = Field(default_factory=list, exclude=True)
+    ''' Category segments, which are not defined in the specification'''
+    
+    @model_validator(mode='after')
+    def _validate_mandatory_fields(self):
+        if not self.id:
+            self._add_validation_message(
+                    source=f"Category {self.key}",
+                    level = ValidationMsgLevel.ERROR,
+                    msg=f"Category key {self.key} is missing mandatory field 'ID'",
+                    highlight_pattern = f"{self.key}"
+            )
+        return self
+
+class Data_Result(Data_Abstract):
+    '''Represents the -DR category'''
+    key: str = Field(default='-DR', frozen=True)
+    id:str|None =                    Field(              alias='21')
+    additional_segments: list[IDSegment] = Field(default_factory=list, exclude=True)
+    ''' Category segments, which are not defined in the specification'''
+    
+    
+class Data_Method(Data_Abstract):
+    '''Represents the -DM category'''
+    key: str = Field(default='-DM', frozen=True)
+    id:str|None =                    Field(              alias='21')
+    additional_segments: list[IDSegment] = Field(default_factory=list, exclude=True)
+    ''' Category segments, which are not defined in the specification'''
+    
+    
+class Data_Calibration(Data_Abstract):
+    '''Represents the -DC category'''
+    key: str = Field(default='-DC', frozen=True)
+    id:str|None =                    Field(              alias='21')
+    additional_segments: list[IDSegment] = Field(default_factory=list, exclude=True)
+    ''' Category segments, which are not defined in the specification'''
+    
+    
+class Data_Progress(Data_Abstract):
+    '''Represents the -DP category'''
+    key: str = Field(default='-DP', frozen=True)
+    id:str|None =                    Field(              alias='21')
+    additional_segments: list[IDSegment] = Field(default_factory=list, exclude=True)
+    ''' Category segments, which are not defined in the specification'''
+    
+    
+class Data_Static(Data_Abstract):
+    '''Represents the -DS category'''
+    key: str = Field(default='-DS', frozen=True)
+    id:str|None =                    Field(              alias='21')
+    additional_segments: list[IDSegment] = Field(default_factory=list, exclude=True)
+    ''' Category segments, which are not defined in the specification'''
+    
+    
+category_key_to_class_map  = {
+        '-MD': Material_Device,
+        '-MS': Material_Substance,
+        '-MC': Material_Consumable,
+        '-MM': Material_Misc,
+        '-DM': Data_Method,
+        '-DR': Data_Result,
+        '-DC': Data_Calibration,
+        '-DP': Data_Progress,
+        '-DS': Data_Static 
 }

labfreed/pac_id/__init__.py

@@ -1,19 +1,19 @@
-from .pac_id import PAC_ID
-from .id_segment import IDSegment
-from .extension import Extension
-
-'''@private
-From a SW engineering perspective it would be best to have no dependencies from other modules to pac_id.
-However from a Python users convenience perspective it is better to have one place where a pac url can be parsed and magically the extensions are in a meaningful type (e.g. TREX in TREX aware format) and categories are known of possible.
-
->> We have given priority to convenient usage and therefore chose to have dependencies from pac_id to pac_cat and well_known_extensions
-'''
-
-
-__all__ = [
-    "PAC_ID",
-    "IDSegment",
-    "Extension"
-]
-
-
+from .pac_id import PAC_ID
+from .id_segment import IDSegment
+from .extension import Extension
+
+'''@private
+From a SW engineering perspective it would be best to have no dependencies from other modules to pac_id.
+However from a Python users convenience perspective it is better to have one place where a pac url can be parsed and magically the extensions are in a meaningful type (e.g. TREX in TREX aware format) and categories are known of possible.
+
+>> We have given priority to convenient usage and therefore chose to have dependencies from pac_id to pac_cat and well_known_extensions
+'''
+
+
+__all__ = [
+    "PAC_ID",
+    "IDSegment",
+    "Extension"
+]
+
+

labfreed/pac_id/extension.py

@@ -1,48 +1,48 @@
-
-from abc import ABC, abstractproperty
-
-from pydantic import model_validator
-
-from labfreed.labfreed_infrastructure import LabFREED_BaseModel
-
-    
-class ExtensionBase(ABC):
-    name: str
-    type: str
-
-
-    @abstractproperty
-    def data(self) -> str:
-        raise NotImplementedError("Subclasses must implement 'data'")
-    
-    def __str__(self):
-        return f'{self.name}${self.type}/{self.data}'
-    
-
-
-class Extension(LabFREED_BaseModel,ExtensionBase):
-    '''Implementation of Extension for unknown extension types'''
-    name:str
-    type:str
-    data_:str
-    
-    @property
-    def data(self) -> str:
-        return self.data_
-       
-    @staticmethod
-    def create(*, name, type, data):
-        return Extension(name=name, type=type, data=data)
-    
-    @model_validator(mode='before')
-    @classmethod
-    def move_data_field(cls, values):
-        if "data" in values:
-            values["data_"] = values.pop("data")
-        return values
-    
-    model_config = {
-        "extra": "allow",  # Allow extra keys during pre-validation
-    }
-    
-
+
+from abc import ABC, abstractproperty
+
+from pydantic import model_validator
+
+from labfreed.labfreed_infrastructure import LabFREED_BaseModel
+
+    
+class ExtensionBase(ABC):
+    name: str
+    type: str
+
+
+    @abstractproperty
+    def data(self) -> str:
+        raise NotImplementedError("Subclasses must implement 'data'")
+    
+    def __str__(self):
+        return f'{self.name}${self.type}/{self.data}'
+    
+
+
+class Extension(LabFREED_BaseModel,ExtensionBase):
+    '''Implementation of Extension for unknown extension types'''
+    name:str
+    type:str
+    data_:str
+    
+    @property
+    def data(self) -> str:
+        return self.data_
+       
+    @staticmethod
+    def create(*, name, type, data):
+        return Extension(name=name, type=type, data=data)
+    
+    @model_validator(mode='before')
+    @classmethod
+    def move_data_field(cls, values):
+        if "data" in values:
+            values["data_"] = values.pop("data")
+        return values
+    
+    model_config = {
+        "extra": "allow",  # Allow extra keys during pre-validation
+    }
+    
+