tricc-oo 1.5.13__py3-none-any.whl → 1.6.8__py3-none-any.whl

tricc_oo/models/ocl.py

@@ -1,59 +1,34 @@
 # https://docs.openconceptlab.org/
 
-from enum import Enum
-from typing import Dict, List, Optional,  Union, Literal, Annotated
-from xml.dom import HIERARCHY_REQUEST_ERR
+from typing import Annotated, Dict, List, Literal, Union
 from xmlrpc.client import Boolean
-from pydantic import BaseModel, constr, AnyHttpUrl, StringConstraints
-from ocldev.oclconstants import OclConstants, OclConstants as OclConstantsBase
-
-OCLId = Annotated[
-    str,
-    StringConstraints(pattern=r"^.+$")
-]
-OCLName = Annotated[
-    str,
-    StringConstraints(pattern=r"^.+$")
-]
-OCLShortName = Annotated[
-    str,
-    StringConstraints(pattern=r"^.+$")
-]
-OCLLocale = Annotated[
-    str,
-    StringConstraints(pattern=r"^[a-zA-Z\-]{2,7}$")
-]
-Uri = Annotated[
-    str,
-    StringConstraints(pattern=r"^.+$")
-]
-OCLMapCode = Annotated[
-    str,
-    StringConstraints(pattern=r"^.+$")
-]
+from pydantic import AnyHttpUrl, BaseModel, StringConstraints
+from ocldev.oclconstants import OclConstants as OclConstantsBase
 
+OCLId = Annotated[str, StringConstraints(pattern=r"^.+$")]
+OCLName = Annotated[str, StringConstraints(pattern=r"^.+$")]
+OCLShortName = Annotated[str, StringConstraints(pattern=r"^.+$")]
+OCLLocale = Annotated[str, StringConstraints(pattern=r"^[a-zA-Z\-]{2,7}$")]
+Uri = Annotated[str, StringConstraints(pattern=r"^.+$")]
+OCLMapCode = Annotated[str, StringConstraints(pattern=r"^.+$")]
 
 
 class OclConstants(OclConstantsBase):
-    #OCL Access type
-    ACCESS_TYPE_VIEW = 'View'
-    ACCESS_TYPE_EDIT = 'Edit'
-    ACCESS_TYPE_NONE = 'None'
-    ACCESS_TYPES = [
-        ACCESS_TYPE_EDIT,
-        ACCESS_TYPE_VIEW,
-        ACCESS_TYPE_NONE
-    ]
-    #https://www.hl7.org/fhir/valueset-codesystem-hierarchy-meaning.html
-    HIERARCHY_MEANING_IS_A = 'is-a' 
-    HIERARCHY_MEANING_GROUP_BY = 'grouped-by'
-    HIERARCHY_MEANING_PART_OF = 'part-of'
-    HIERARCHY_MEANING_CLASSIFIED_WITH = ' classified-with'
+    # OCL Access type
+    ACCESS_TYPE_VIEW = "View"
+    ACCESS_TYPE_EDIT = "Edit"
+    ACCESS_TYPE_NONE = "None"
+    ACCESS_TYPES = [ACCESS_TYPE_EDIT, ACCESS_TYPE_VIEW, ACCESS_TYPE_NONE]
+    # https://www.hl7.org/fhir/valueset-codesystem-hierarchy-meaning.html
+    HIERARCHY_MEANING_IS_A = "is-a"
+    HIERARCHY_MEANING_GROUP_BY = "grouped-by"
+    HIERARCHY_MEANING_PART_OF = "part-of"
+    HIERARCHY_MEANING_CLASSIFIED_WITH = " classified-with"
     HIERARCHY_MEANINGS = [
         HIERARCHY_MEANING_IS_A,
         HIERARCHY_MEANING_GROUP_BY,
         HIERARCHY_MEANING_PART_OF,
-        HIERARCHY_MEANING_CLASSIFIED_WITH
+        HIERARCHY_MEANING_CLASSIFIED_WITH,
     ]
     SOURCE_TYPE_DICTIONARY = "Dictionary"
     SOURCE_TYPE_REFERENCE = "Reference"
@@ -61,7 +36,7 @@ class OclConstants(OclConstantsBase):
     SOURCE_TYPES = [
         SOURCE_TYPE_DICTIONARY,
         SOURCE_TYPE_REFERENCE,
-        SOURCE_TYPE_EXTERNAL_DICTIONARY 
+        SOURCE_TYPE_EXTERNAL_DICTIONARY,
     ]
     # MAP type found for fever/malaria on OCL app
     MAP_TYPE_SAME_AS = "SAME-AS"
@@ -86,7 +61,7 @@ class OclConstants(OclConstantsBase):
         MAP_TYPE_HAS_ELEMENT,
         MAP_TYPE_MAP_TO,
     ]
-    DATA_TYPE_BOOLEAN = 'Boolean'
+    DATA_TYPE_BOOLEAN = "Boolean"
     DATA_TYPE_COMPLEX = "Complex"
     DATA_TYPE_STRUCTURED_NUMERIC = "Structured-Numeric"
     DATA_TYPE_RULE = "Rule"
@@ -100,7 +75,7 @@ class OclConstants(OclConstantsBase):
     DATA_TYPE_NA = "N/A"
     DATA_TYPE_NUMERIC = "Numeric"
     DATA_TYPE_NONE = "None"
-    DATA_TYPES =[
+    DATA_TYPES = [
         DATA_TYPE_BOOLEAN,
         DATA_TYPE_CODED,
         DATA_TYPE_STRING,
@@ -114,15 +89,11 @@ class OclConstants(OclConstantsBase):
         DATA_TYPE_DATETIME,
         DATA_TYPE_TIME,
         DATA_TYPE_DATE,
-        DATA_TYPE_DOCUMENT
+        DATA_TYPE_DOCUMENT,
     ]
     DESCRIPTION_TYPE_DEFINITION = "Definition"
     DESCRIPTION_TYPE_NONE = "None"
-    DESCRIPTION_TYPES = [
-        DESCRIPTION_TYPE_DEFINITION,
-        DESCRIPTION_TYPE_NONE
-                         
-    ]
+    DESCRIPTION_TYPES = [DESCRIPTION_TYPE_DEFINITION, DESCRIPTION_TYPE_NONE]
     NAME_TYPE_INDEX_TERM = "Index-Term"
     NAME_TYPE_SHORT = "Short"
     NAME_TYPE_FULLY_SPECIFIED = "Fully-Specified"
@@ -131,151 +102,165 @@ class OclConstants(OclConstantsBase):
         NAME_TYPE_INDEX_TERM,
         NAME_TYPE_SHORT,
         NAME_TYPE_FULLY_SPECIFIED,
-        NAME_TYPE_NONE                   
+        NAME_TYPE_NONE,
     ]
-OCLRessourceType= Literal[tuple(OclConstants.RESOURCE_TYPES)]
+
+
+OCLRessourceType = Literal[tuple(OclConstants.RESOURCE_TYPES)]
 
 
 def get_data_type(tricc_type):
-    if tricc_type.lower() in ('integer', 'decimal', 'add', 'count'):
+    if tricc_type.lower() in ("integer", "decimal", "add", "count"):
         return OclConstants.DATA_TYPE_NUMERIC
-    elif tricc_type.lower() in ('activity', 'page'):
+    elif tricc_type.lower() in ("activity", "page"):
         return OclConstants.DATA_TYPE_DOCUMENT
-    elif tricc_type.lower() in ('select_one'):
+    elif tricc_type.lower() in ("select_one"):
         return OclConstants.DATA_TYPE_CODED
-    elif tricc_type.lower() in ('calculate', 'diagnosis', 'proposed_diagnosis'):
+    elif tricc_type.lower() in ("calculate", "diagnosis", "proposed_diagnosis"):
         return OclConstants.DATA_TYPE_BOOLEAN
-    found_type = [ t  for t in OclConstants.DATA_TYPES if t.lower() == tricc_type.lower()]
+    found_type = [t for t in OclConstants.DATA_TYPES if t.lower() == tricc_type.lower()]
     if found_type:
         return found_type[0]
     return OclConstants.DATA_TYPE_NA
- 
+
+
 class OCLBaseModel(BaseModel):
-    type:OCLRessourceType
-    id:OCLId
-    external_id:str = None
-    public_access:Literal[tuple(OclConstants.ACCESS_TYPES)] = OclConstants.ACCESS_TYPE_VIEW
-    extras:Dict[str,Union[str,Dict[str,str]]] = {}
-    url: Union[AnyHttpUrl,Uri] = None
+    type: OCLRessourceType
+    id: OCLId
+    external_id: str = None
+    public_access: Literal[tuple(OclConstants.ACCESS_TYPES)] = OclConstants.ACCESS_TYPE_VIEW
+    extras: Dict[str, Union[str, Dict[str, str]]] = {}
+    url: Union[AnyHttpUrl, Uri] = None
     # enriched data for get
+
+
 class OclGet(BaseModel):
-    created_on:str = None
-    created_by:str = None
-    updated_on:str = None
-    updated_by:str = None
-    
+    created_on: str = None
+    created_by: str = None
+    updated_on: str = None
+    updated_by: str = None
+
+
 class OCLBaseModelBrowsable(OCLBaseModel):
-    name:OCLName
-    description:str = None
-    website:AnyHttpUrl = None
-    
+    name: OCLName
+    description: str = None
+    website: AnyHttpUrl = None
+
 
 class OCLDetailedName(BaseModel):
     name: str
-    external_id:str = None
-    locale:OCLLocale
-    locale_preferred:Boolean = None
-    name_type:Literal[tuple(OclConstants.NAME_TYPES)] = OclConstants.NAME_TYPE_SHORT
+    external_id: str = None
+    locale: OCLLocale
+    locale_preferred: Boolean = None
+    name_type: Literal[tuple(OclConstants.NAME_TYPES)] = OclConstants.NAME_TYPE_SHORT
+
 
 class OCLDetailedDescription(BaseModel):
-    description:str
-    external_id:str = None
-    locale:OCLLocale
-    locale_preferred:Boolean = None
-    description_type:Literal[tuple(OclConstants.DESCRIPTION_TYPES)] = OclConstants.DESCRIPTION_TYPE_DEFINITION
+    description: str
+    external_id: str = None
+    locale: OCLLocale
+    locale_preferred: Boolean = None
+    description_type: Literal[tuple(OclConstants.DESCRIPTION_TYPES)] = OclConstants.DESCRIPTION_TYPE_DEFINITION
+
 
 class OCLConcept(OCLBaseModel):
-    type:OCLRessourceType = OclConstants.RESOURCE_TYPE_CONCEPT
+    type: OCLRessourceType = OclConstants.RESOURCE_TYPE_CONCEPT
     uuid: str = None
     concept_class: str
-    datatype:Literal[tuple(OclConstants.DATA_TYPES)] = OclConstants.DATA_TYPE_NONE
-    names:List[OCLDetailedName]
+    datatype: Literal[tuple(OclConstants.DATA_TYPES)] = OclConstants.DATA_TYPE_NONE
+    names: List[OCLDetailedName]
     descriptions: List[OCLDetailedDescription] = []
-    retired:Boolean = False
+    retired: Boolean = False
     # not for create
-    versions: str = None # TODO version
-    source:OCLId = None
-    owner:OCLId = None
-    owner_type:Literal[tuple(OclConstants.OWNER_TYPE_TO_STEM)] = None    
-    owner_url:Union[AnyHttpUrl,Uri] = None
-    versions_url:Union[AnyHttpUrl,Uri] = None
-    source_url:Union[AnyHttpUrl,Uri] = None
-    owner_url:Union[AnyHttpUrl,Uri] = None
-    mappings_url:Union[AnyHttpUrl,Uri] = None
-    
+    versions: str = None  # TODO version
+    source: OCLId = None
+    owner: OCLId = None
+    owner_type: Literal[tuple(OclConstants.OWNER_TYPE_TO_STEM)] = None
+    owner_url: Union[AnyHttpUrl, Uri] = None
+    versions_url: Union[AnyHttpUrl, Uri] = None
+    source_url: Union[AnyHttpUrl, Uri] = None
+    owner_url: Union[AnyHttpUrl, Uri] = None
+    mappings_url: Union[AnyHttpUrl, Uri] = None
+
+
 class OCLMapping(BaseModel):
-    type:OCLRessourceType = OclConstants.RESOURCE_TYPE_MAPPING
+    type: OCLRessourceType = OclConstants.RESOURCE_TYPE_MAPPING
     uuid: str = None
-    retired:Boolean = False
+    retired: Boolean = False
     map_type: Literal[tuple(OclConstants.MAP_TYPES)]
-    from_concept_url:Union[AnyHttpUrl,Uri]
-    from_source_url:Uri = None
-    from_concept_code:str = None
-    from_concept_name:str = None
-    to_concept_url:Union[AnyHttpUrl,Uri] = None
-    to_source:str = None
-    to_concept_code:str = None
-    to_source_owner:OCLId = None
-    to_source_owner_type:Literal[tuple(OclConstants.OWNER_TYPE_TO_STEM)] = None
-    #for bulk
-    source:OCLId = None
-    owner:OCLId = None
-    owner_type:Literal[tuple(OclConstants.OWNER_TYPE_TO_STEM.values())] = None
+    from_concept_url: Union[AnyHttpUrl, Uri]
+    from_source_url: Uri = None
+    from_concept_code: str = None
+    from_concept_name: str = None
+    to_concept_url: Union[AnyHttpUrl, Uri] = None
+    to_source: str = None
+    to_concept_code: str = None
+    to_source_owner: OCLId = None
+    to_source_owner_type: Literal[tuple(OclConstants.OWNER_TYPE_TO_STEM)] = None
+    # for bulk
+    source: OCLId = None
+    owner: OCLId = None
+    owner_type: Literal[tuple(OclConstants.OWNER_TYPE_TO_STEM.values())] = None
+
 
 class OCLCollection(OCLBaseModelBrowsable):
-    #TODO https://docs.openconceptlab.org/en/latest/oclapi/apireference/collections.html
+    # TODO https://docs.openconceptlab.org/en/latest/oclapi/apireference/collections.html
     pass
 
+
 class OCLUser(OCLBaseModelBrowsable):
-    #TODO https://docs.openconceptlab.org/en/latest/oclapi/apireference/users.html
-    pass 
-    
-class  OCLMappingInternal(OCLMapping):             
-    to_concept_url:Union[AnyHttpUrl,Uri]
+    # TODO https://docs.openconceptlab.org/en/latest/oclapi/apireference/users.html
+    pass
+
+
+class OCLMappingInternal(OCLMapping):
+    to_concept_url: Union[AnyHttpUrl, Uri]
     # when there is not URL
-    
-class  OCLMappingExternal(OCLMapping):   
-    to_source_url:Uri
-    to_concept_code:str
-    to_concept_name:str = None
-        
+
+
+class OCLMappingExternal(OCLMapping):
+    to_source_url: Uri
+    to_concept_code: str
+    to_concept_name: str = None
+
+
 class OCLOrganisation(OCLBaseModelBrowsable):
-    type:OCLRessourceType = OclConstants.RESOURCE_TYPE_ORGANIZATION
-    company:OCLName
-    logo_url:AnyHttpUrl
-    location:OCLName
-    text:str
-    
-    
+    type: OCLRessourceType = OclConstants.RESOURCE_TYPE_ORGANIZATION
+    company: OCLName
+    logo_url: AnyHttpUrl
+    location: OCLName
+    text: str
+
 
 class OCLSource(OCLBaseModelBrowsable):
-    type:OCLRessourceType = OclConstants.RESOURCE_TYPE_SOURCE
-    short_code:OCLShortName
-    full_name:OCLName
-    source_type:Literal[tuple(OclConstants.SOURCE_TYPES)] = OclConstants.SOURCE_TYPE_DICTIONARY
-    default_locale:OCLLocale = 'en'
-    supported_locales:List[OCLLocale] = ['en']
-    custom_validation_schema:str = 'None'
+    type: OCLRessourceType = OclConstants.RESOURCE_TYPE_SOURCE
+    short_code: OCLShortName
+    full_name: OCLName
+    source_type: Literal[tuple(OclConstants.SOURCE_TYPES)] = OclConstants.SOURCE_TYPE_DICTIONARY
+    default_locale: OCLLocale = "en"
+    supported_locales: List[OCLLocale] = ["en"]
+    custom_validation_schema: str = "None"
     # not for create
-    owner:OCLId = None
-    owner_type:Literal[tuple(OclConstants.OWNER_TYPE_TO_STEM)] = None
-    owner_url:Union[AnyHttpUrl,Uri] = None
-    #FHIR
-    hierarchy_meaning:Literal[tuple(OclConstants.HIERARCHY_MEANINGS)] = None
-    hierarchy_root_url:Union[AnyHttpUrl,Uri] = None
-    meta:str = None
-    canonical_url:Union[AnyHttpUrl,Uri] = None
-    internal_reference_id:OCLId = None
-    #collection_reference:Uri
-    versions_url:Union[AnyHttpUrl,Uri] = None
-    concepts_url:Union[AnyHttpUrl,Uri] = None
-    mappings_url:Union[AnyHttpUrl,Uri] = None
-    
-    versions: str = None # TODO version
-    active_concepts:int = 0
-    active_mappings:int = 0
-    
+    owner: OCLId = None
+    owner_type: Literal[tuple(OclConstants.OWNER_TYPE_TO_STEM)] = None
+    owner_url: Union[AnyHttpUrl, Uri] = None
+    # FHIR
+    hierarchy_meaning: Literal[tuple(OclConstants.HIERARCHY_MEANINGS)] = None
+    hierarchy_root_url: Union[AnyHttpUrl, Uri] = None
+    meta: str = None
+    canonical_url: Union[AnyHttpUrl, Uri] = None
+    internal_reference_id: OCLId = None
+    # collection_reference:Uri
+    versions_url: Union[AnyHttpUrl, Uri] = None
+    concepts_url: Union[AnyHttpUrl, Uri] = None
+    mappings_url: Union[AnyHttpUrl, Uri] = None
+
+    versions: str = None  # TODO version
+    active_concepts: int = 0
+    active_mappings: int = 0
+
+
 class OCLSourceVersion(OCLBaseModelBrowsable):
     released: Boolean = None
-    previous_version :str
-    parent_version :str
+    previous_version: str
+    parent_version: str

tricc_oo/models/ordered_set.py

@@ -1,8 +1,9 @@
 from collections import OrderedDict
 from collections.abc import Iterable, Sequence
-from pydantic import BaseModel, GetCoreSchemaHandler
+from pydantic import GetCoreSchemaHandler
 from pydantic_core import CoreSchema
 
+
 class OrderedSet(Sequence):
     def __init__(self, iterable=None):
         self._od = OrderedDict.fromkeys(iterable or [])
@@ -20,14 +21,15 @@ class OrderedSet(Sequence):
         return self._od.popitem(last=False)[0]
 
     def insert_at_top(self, item):
-            # Add item if not already present
+        # Add item if not already present
         self.insert_at_bottom(item)
         # Move item to the top
         self._od.move_to_end(item, last=False)
-        
+
     def insert_at_bottom(self, item):
         if item not in self._od:
             self._od[item] = None
+
     def __contains__(self, item):
         return item in self._od
 
@@ -44,12 +46,13 @@ class OrderedSet(Sequence):
         for item in items:
             if item not in self:
                 self.insert_at_bottom(item)
+
     def __eq__(self, other):
         if not isinstance(other, self.__class__):
             return False
         else:
             return self._od.keys() == other._od.keys()
-    
+
     # Union method (| operator)
     def __or__(self, other):
         if not isinstance(other, Iterable):
@@ -60,32 +63,26 @@ class OrderedSet(Sequence):
 
     def union(self, other):
         return self.__or__(other)
-    def __or__(self, other):
-        if not isinstance(other, Iterable):
-            raise TypeError("Unsupported operand type(s) for |: 'OrderedSet' and '{}'".format(type(other)))
-        new_set = self.copy()
-        new_set._add_items(other)
-        return new_set
-    
+
     def __iadd__(self, other):
         if not isinstance(other, Iterable):
             raise TypeError("Unsupported operand type(s) for +=: 'OrderedSet' and '{}'".format(type(other)))
         self._add_items(other)
         return self
-    
+
     def get(self, index):
         return self.__getitem__(index)
-    
+
     def __getitem__(self, index):
         try:
             return list(self._od.keys())[index]
         except IndexError:
             raise IndexError("Index out of range") from None
-        
+
     def sort(self, key=None, reverse=False):
         sorted_keys = sorted(self._od.keys(), key=key, reverse=reverse)
         self._od = OrderedDict.fromkeys(sorted_keys)
-        
+
     def find_last(self, filter: callable):
         # Iterate over items in reverse order
         for item in reversed(list(self._od.keys())):
@@ -99,24 +96,23 @@ class OrderedSet(Sequence):
                 return item
         return None  # Return None if no matching item is found
 
-
     def find_prev(self, obj, filter: callable):
         # Get the list of keys (items) in the OrderedSet
         keys = list(self._od.keys())
-        
+
         # If the object is not in the OrderedSet, start from the end
         if obj not in self._od:
             start_index = len(keys)
         else:
             # Find the index of the given object
             start_index = keys.index(obj)
-        
+
         # Iterate backward from the start_index
         for i in range(start_index - 1, -1, -1):
             item = keys[i]
             if filter(item):
                 return item
-        
+
         return None  # Return None if no matching item is found before the object
 
     @classmethod