labfreed 0.2.5a21__py3-none-any.whl → 0.2.6__py3-none-any.whl

labfreed/pac_cat/category_base.py

@@ -1,51 +1,51 @@
-               
-from typing import Any
-from pydantic import PrivateAttr, computed_field, model_validator
-from labfreed.labfreed_infrastructure import LabFREED_BaseModel, ValidationMsgLevel
-from labfreed.pac_id.id_segment import IDSegment
-
-
-class Category(LabFREED_BaseModel):
-    '''
-    Represents a category. \n
-    This is the base class for categories. If possible a more specific category should be used.
-    '''    
-    key:str
-    '''The category key, e.g. "-MD"'''
-    _segments: list[IDSegment] = PrivateAttr(default_factory=list)
-    
-        
-    @computed_field
-    @property
-    def segments(self) -> list[IDSegment]:
-        return self._segments
-    
-    def __init__(self, **data: Any):
-        '''@private'''
-        # Pop the user-provided value for computed segments
-        input_segments = data.pop("segments", None)
-        super().__init__(**data)
-        self._segments = input_segments
-    
-    @model_validator(mode='after')
-    def _warn_unusual_category_key(self):
-        ''' this base class is instantiated only if the key is not a known category key'''
-        if type(self) is Category:
-            self._add_validation_message(
-                        source=f"Category {self.key}",
-                        level = ValidationMsgLevel.RECOMMENDATION,
-                        msg=f'Category key {self.key} is not a well known key. It is recommended to use well known keys only',
-                        highlight_pattern = f"{self.key}"
-            )
-        return self
-    
-    
-    def __str__(self):
-        s = '\n'.join( [f"{field_name} \t ({field_info.alias or ''}): \t {getattr(self, field_name)}" for  field_name, field_info in self.model_fields.items() if getattr(self, field_name)]) 
-        return s 
-
-
-
-
-
-
+               
+from typing import Any
+from pydantic import PrivateAttr, computed_field, model_validator
+from labfreed.labfreed_infrastructure import LabFREED_BaseModel, ValidationMsgLevel
+from labfreed.pac_id.id_segment import IDSegment
+
+
+class Category(LabFREED_BaseModel):
+    '''
+    Represents a category. \n
+    This is the base class for categories. If possible a more specific category should be used.
+    '''    
+    key:str
+    '''The category key, e.g. "-MD"'''
+    _segments: list[IDSegment] = PrivateAttr(default_factory=list)
+    
+        
+    @computed_field
+    @property
+    def segments(self) -> list[IDSegment]:
+        return self._segments
+    
+    def __init__(self, **data: Any):
+        '''@private'''
+        # Pop the user-provided value for computed segments
+        input_segments = data.pop("segments", None)
+        super().__init__(**data)
+        self._segments = input_segments
+    
+    @model_validator(mode='after')
+    def _warn_unusual_category_key(self):
+        ''' this base class is instantiated only if the key is not a known category key'''
+        if type(self) is Category:
+            self._add_validation_message(
+                        source=f"Category {self.key}",
+                        level = ValidationMsgLevel.RECOMMENDATION,
+                        msg=f'Category key {self.key} is not a well known key. It is recommended to use well known keys only',
+                        highlight_pattern = f"{self.key}"
+            )
+        return self
+    
+    
+    def __str__(self):
+        s = '\n'.join( [f"{field_name} \t ({field_info.alias or ''}): \t {getattr(self, field_name)}" for  field_name, field_info in self.model_fields.items() if getattr(self, field_name)]) 
+        return s 
+
+
+
+
+
+

labfreed/pac_cat/pac_cat.py

@@ -1,150 +1,150 @@
-from __future__ import annotations  # optional in 3.11, but recommended for consistency
-
-from typing import Self
-from pydantic import computed_field, model_validator
-
-from rich import print
-from rich.text import Text
-from rich.table import Table
-
-from labfreed.labfreed_infrastructure import ValidationMsgLevel
-
-from labfreed.pac_cat.category_base import Category
-from labfreed.pac_cat.predefined_categories import category_key_to_class_map
-from labfreed.pac_id.id_segment import IDSegment
-from labfreed.pac_id.pac_id import PAC_ID
-
-''' Configure pdoc'''
-
-    
-class PAC_CAT(PAC_ID):
-    ''' 
-    Extends a PAC-ID with interpretation of the identifier as categories
-    '''
-    @computed_field
-    @property
-    def categories(self) -> list[Category]: 
-        '''The categories present in the PAC-ID's identifier'''
-        category_segments = self._split_segments_by_category(self.identifier)
-        categories = list()
-        for c in category_segments:
-            categories.append(self._cat_from_cat_segments(c))
-        return categories
-    
-    
-
-    def get_category(self, key) -> Category:
-        """Helper to get a category by key
-        """ 
-        tmp = [c for c in self.categories if c.key == key]
-        if not tmp:
-            return None
-        return tmp[0]
-    
-    
-    @classmethod
-    def from_categories(cls, issuer:str, categories:list[Category]) -> PAC_CAT:
-        identifier = list()
-        for category in categories:
-            identifier.append(IDSegment(value=category.key))
-            identifier.extend(category.segments)
-        return PAC_CAT(issuer=issuer, identifier=identifier)
-    
-    
-    @classmethod
-    def from_pac_id(cls, pac_id:PAC_ID) -> Self:
-        '''Constructs a PAC-CAT from a PAC-ID'''
-        return PAC_CAT(issuer=pac_id.issuer, identifier=pac_id.identifier)
-    
-
-    
-    def to_pac_id(self) -> PAC_ID:
-        return PAC_ID(issuer=self.issuer, identifier=self.identifier)
-        
-            
-    @classmethod
-    def _cat_from_cat_segments(cls, segments:list[IDSegment]) -> Category:
-        segments = segments.copy()
-        category_key = segments[0].value         
-        segments.pop(0)
-        
-        known_cat = category_key_to_class_map.get(category_key)
-        
-        if not known_cat:
-            return Category(key=category_key, segments=segments)
-
-        # implicit segment keys
-        model_dict = {v.alias: None for k, v in known_cat.model_fields.items() if v.alias and k not in ['key','additional_segments']}
-        for k, seg in zip(model_dict.keys(), segments.copy()):
-            if seg.key:
-                break
-            model_dict[k] = seg.value
-            segments.pop(0)
-            
-        # try to fill model keys if not already set
-        for s in segments.copy():
-            if s.key in model_dict.keys() and not model_dict.get(s.key):
-                model_dict[s.key] = s.value
-                segments.remove(s)
-            
-        model_dict['additional_segments'] = segments
-        model_dict['key'] = category_key
-        cat= known_cat(**model_dict)
-        return cat
-    
-    @staticmethod
-    def _split_segments_by_category(segments:list[IDSegment]) -> list[list[IDSegment]]:
-        category_segments = list()
-        c = list()
-        for s in segments:
-            # new category starts with "-"
-            if s.value[0] == '-':
-                c = [s]
-                category_segments.append(c)
-            else:
-                c.append(s)
-                
-        # first cat can be empty > remove
-        category_segments = [c for c in category_segments if len(c) > 0]
-                            
-        return category_segments
-    
-    
-    @model_validator(mode='after')
-    def _check_keys_are_unique_in_each_category(self) -> Self:
-        for c in self.categories:
-            keys = [s.key for s in c.segments if s.key]
-            duplicate_keys = [k for k in set(keys) if keys.count(k) > 1]
-            if duplicate_keys:
-                for k in duplicate_keys:
-                    self._add_validation_message(
-                        source=f"identifier {k}",
-                        level = ValidationMsgLevel.ERROR,
-                        msg=f"Duplicate key {k} in category {c.key}",
-                        highlight_pattern = k
-                    )
-            return self
-        
-    def print_categories(self):
-        table = Table(title=f'Categories in {str(self)}', show_header=False)
-        table.add_column('0')
-        table.add_column('1')
-        for i, c in enumerate(self.categories):
-            if i == 0:
-                title = Text('Main Category', style='bold')
-            else:
-                title = Text('Category', style='bold')
-            
-            table.add_row(title)
-            
-            for field_name, field_info in c.model_fields.items():
-                if not getattr(c, field_name):
-                    continue
-                table.add_row(f"{field_name} ({field_info.alias or ''})",
-                              f" {getattr(c, field_name)}"
-                              )      
-            table.add_section()        
-        print(table)
-        
-
-        
+from __future__ import annotations  # optional in 3.11, but recommended for consistency
+
+from typing import Self
+from pydantic import computed_field, model_validator
+
+from rich import print
+from rich.text import Text
+from rich.table import Table
+
+from labfreed.labfreed_infrastructure import ValidationMsgLevel
+
+from labfreed.pac_cat.category_base import Category
+from labfreed.pac_cat.predefined_categories import category_key_to_class_map
+from labfreed.pac_id.id_segment import IDSegment
+from labfreed.pac_id.pac_id import PAC_ID
+
+''' Configure pdoc'''
+
+    
+class PAC_CAT(PAC_ID):
+    ''' 
+    Extends a PAC-ID with interpretation of the identifier as categories
+    '''
+    @computed_field
+    @property
+    def categories(self) -> list[Category]: 
+        '''The categories present in the PAC-ID's identifier'''
+        category_segments = self._split_segments_by_category(self.identifier)
+        categories = list()
+        for c in category_segments:
+            categories.append(self._cat_from_cat_segments(c))
+        return categories
+    
+    
+
+    def get_category(self, key) -> Category:
+        """Helper to get a category by key
+        """ 
+        tmp = [c for c in self.categories if c.key == key]
+        if not tmp:
+            return None
+        return tmp[0]
+    
+    
+    @classmethod
+    def from_categories(cls, issuer:str, categories:list[Category]) -> PAC_CAT:
+        identifier = list()
+        for category in categories:
+            identifier.append(IDSegment(value=category.key))
+            identifier.extend(category.segments)
+        return PAC_CAT(issuer=issuer, identifier=identifier)
+    
+    
+    @classmethod
+    def from_pac_id(cls, pac_id:PAC_ID) -> Self:
+        '''Constructs a PAC-CAT from a PAC-ID'''
+        return PAC_CAT(issuer=pac_id.issuer, identifier=pac_id.identifier)
+    
+
+    
+    def to_pac_id(self) -> PAC_ID:
+        return PAC_ID(issuer=self.issuer, identifier=self.identifier)
+        
+            
+    @classmethod
+    def _cat_from_cat_segments(cls, segments:list[IDSegment]) -> Category:
+        segments = segments.copy()
+        category_key = segments[0].value         
+        segments.pop(0)
+        
+        known_cat = category_key_to_class_map.get(category_key)
+        
+        if not known_cat:
+            return Category(key=category_key, segments=segments)
+
+        # implicit segment keys
+        model_dict = {v.alias: None for k, v in known_cat.model_fields.items() if v.alias and k not in ['key','additional_segments']}
+        for k, seg in zip(model_dict.keys(), segments.copy()):
+            if seg.key:
+                break
+            model_dict[k] = seg.value
+            segments.pop(0)
+            
+        # try to fill model keys if not already set
+        for s in segments.copy():
+            if s.key in model_dict.keys() and not model_dict.get(s.key):
+                model_dict[s.key] = s.value
+                segments.remove(s)
+            
+        model_dict['additional_segments'] = segments
+        model_dict['key'] = category_key
+        cat= known_cat(**model_dict)
+        return cat
+    
+    @staticmethod
+    def _split_segments_by_category(segments:list[IDSegment]) -> list[list[IDSegment]]:
+        category_segments = list()
+        c = list()
+        for s in segments:
+            # new category starts with "-"
+            if s.value[0] == '-':
+                c = [s]
+                category_segments.append(c)
+            else:
+                c.append(s)
+                
+        # first cat can be empty > remove
+        category_segments = [c for c in category_segments if len(c) > 0]
+                            
+        return category_segments
+    
+    
+    @model_validator(mode='after')
+    def _check_keys_are_unique_in_each_category(self) -> Self:
+        for c in self.categories:
+            keys = [s.key for s in c.segments if s.key]
+            duplicate_keys = [k for k in set(keys) if keys.count(k) > 1]
+            if duplicate_keys:
+                for k in duplicate_keys:
+                    self._add_validation_message(
+                        source=f"identifier {k}",
+                        level = ValidationMsgLevel.ERROR,
+                        msg=f"Duplicate key {k} in category {c.key}",
+                        highlight_pattern = k
+                    )
+            return self
+        
+    def print_categories(self):
+        table = Table(title=f'Categories in {str(self)}', show_header=False)
+        table.add_column('0')
+        table.add_column('1')
+        for i, c in enumerate(self.categories):
+            if i == 0:
+                title = Text('Main Category', style='bold')
+            else:
+                title = Text('Category', style='bold')
+            
+            table.add_row(title)
+            
+            for field_name, field_info in c.model_fields.items():
+                if not getattr(c, field_name):
+                    continue
+                table.add_row(f"{field_name} ({field_info.alias or ''})",
+                              f" {getattr(c, field_name)}"
+                              )      
+            table.add_section()        
+        print(table)
+        
+
+