labfreed 1.0.0a12__tar.gz → 1.0.0a14__tar.gz

{labfreed-1.0.0a12 → labfreed-1.0.0a14}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: labfreed
-Version: 1.0.0a12
+Version: 1.0.0a14
 Summary: Python implementation of LabFREED building blocks
 Author-email: Reto Thürer <thuerer.r@buchi.com>
 Requires-Python: >=3.11
@@ -25,6 +25,7 @@ Requires-Dist: jsonpath-ng>=1.7.0
 Requires-Dist: requests>=2.32.3
 Requires-Dist: requests_cache>=1.2.1
 Requires-Dist: cachetools>=6.1.0
+Requires-Dist: deprecated>=1.2.18
 Requires-Dist: pytest>=8.3.5 ; extra == "dev"
 Requires-Dist: pdoc>=15.0.1 ; extra == "dev"
 Requires-Dist: flit>=3.12.0 ; extra == "dev"

{labfreed-1.0.0a12 → labfreed-1.0.0a14}/labfreed/__init__.py

@@ -2,7 +2,7 @@
 Python implementation of LabFREED building blocks
 '''
 
-__version__ = "1.0.0a12"
+__version__ = "1.0.0a14"
 
 from labfreed.pac_id import *  # noqa: F403
 from labfreed.pac_cat import * # noqa: F403

{labfreed-1.0.0a12 → labfreed-1.0.0a14}/labfreed/labfreed_extended/app/app_infrastructure.py

@@ -7,9 +7,6 @@ from labfreed.labfreed_extended.app.pac_info.pac_info import PacInfo
 from labfreed.pac_attributes.client.attribute_cache import MemoryAttributeCache
 from labfreed.pac_attributes.client.client import AttributeClient, http_attribute_request_default_callback_factory
 from labfreed.pac_attributes.pythonic.py_attributes import pyAttributeGroup
-from labfreed.pac_attributes.well_knonw_attribute_keys import MetaAttributeKeys
-from labfreed.well_known_extensions.display_name_extension import DisplayNameExtension
-
 
 from labfreed.pac_id.pac_id import PAC_ID
 from labfreed.pac_id_resolver.resolver import PAC_ID_Resolver, cit_from_str
@@ -35,11 +32,15 @@ class Labfreed_App_Infrastructure():
         self._attribute_client = AttributeClient(http_post_callback=callback, cache_store=MemoryAttributeCache(), always_use_cached_value_for_minutes=1)
 
 
-    def add_cit(self, cit:str):
+    def add_resolver_config(self, cit:str):
         cit = cit_from_str(cit)
         if not cit:
             raise ValueError('the cit could not be parsed. Neither as v1 or v2')
-        self._resolver._cits.append(cit)
+        self._resolver._resolver_configs.add(cit)
+        
+    def remove_resolver_config(self, resolver_config:str):
+        resolver_config = cit_from_str(resolver_config)
+        self._resolver._resolver_configs.discard(resolver_config)
         
         
     def process_pac(self, pac_url, markup=None):
@@ -63,6 +64,15 @@ class Labfreed_App_Infrastructure():
                 sg_user_handovers.append(ServiceGroup(origin=sg.origin, services=user_handovers))
         pac_info.user_handovers = sg_user_handovers
         
+        # Actions
+        sg_actions = []
+        for sg in service_groups:
+            actions = [s  for s in sg.services if s.service_type == 'action-generic']
+            
+            if actions:
+                sg_actions.append(ServiceGroup(origin=sg.origin, services=actions))
+        pac_info.actions = sg_actions
+        
         # Attributes
         attribute_groups = {}
         for sg in service_groups:  

{labfreed-1.0.0a12 → labfreed-1.0.0a14}/labfreed/labfreed_extended/app/pac_info/pac_info.py

@@ -8,8 +8,9 @@ from pydantic import BaseModel, Field
 from labfreed.pac_attributes.pythonic.py_attributes import pyAttribute, pyAttributeGroup, pyAttributes, pyReference, pyResource
 from labfreed.pac_attributes.well_knonw_attribute_keys import MetaAttributeKeys
 from labfreed.pac_cat.pac_cat import PAC_CAT
+from labfreed.pac_cat.predefined_categories import PredefinedCategory
 from labfreed.pac_id.pac_id import PAC_ID
-from labfreed.pac_id_resolver.services import ServiceGroup
+from labfreed.pac_id_resolver.services import ServiceGroup, Service
 from labfreed.labfreed_extended.app.formatted_print import StringIOLineBreak
 from labfreed.trex.pythonic.data_table import DataTable
 from labfreed.trex.pythonic.pyTREX import pyTREX
@@ -19,30 +20,133 @@ from labfreed.well_known_extensions.display_name_extension import DisplayNameExt
 class PacInfo(BaseModel):
     """A convenient collection of information about a PAC-ID"""
     pac_id:PAC_ID
+
     user_handovers: list[ServiceGroup] = Field(default_factory=list)
+    actions: list[ServiceGroup] = Field(default_factory=list)
     attribute_groups:dict[str, pyAttributeGroup] = Field(default_factory=dict)
     
-    @property
+    
+    # info about pac-id
+    
+    @cached_property
+    def is_item_serialized(self) -> bool|None: #indicates if the item is at product level (e.g. BAL500), as opposed to a serialized instance thereof (e.g. BAL500 with SN 1234)
+        if not isinstance(self.pac_id, PAC_CAT):
+            return None
+        cat = self.main_category
+        if not isinstance(cat, PredefinedCategory):
+            return None
+        
+        return cat.is_serialized
+
+    
+    @cached_property
     def pac_url(self):
         return self.pac_id.to_url(include_extensions=False)
     
-    @property
+    @cached_property
     def main_category(self):
         if isinstance(self.pac_id, PAC_CAT):
             return self.pac_id.categories[0]
         else:
             return None
         
-    @property
-    def attached_data(self):
+        
+    
+    # attached data
+        
+    @cached_property
+    def attached_data(self) -> dict[str, pyTREX]:
         return { trex_ext.name: pyTREX.from_trex(trex=trex_ext.trex) for trex_ext in self.pac_id.get_extension_of_type('TREX')}
 
     
-    @property
-    def summary(self):
-        return self.pac_id.get_extension('SUM')
+    @cached_property
+    def summary(self) -> pyTREX:
+        return pyTREX.from_trex(self.pac_id.get_extension('SUM').trex)
+    
+    
+    @cached_property
+    def status(self) -> pyTREX:
+        return pyTREX.from_trex(self.pac_id.get_extension('STATUS').trex)
+
+        
+        
+        
+    # Handovers and Actions
+        
+    def get_user_handovers_by_intent(self, intent:str, partial_match=False) -> list[Service]:
+        services = [s for sg in self.user_handovers for s in sg.services if self._match_intent(intent, s.application_intents, partial_match)]
+        return services
+    
+    def get_user_handover_by_intent(self, intent:str, partial_match=False, mode="first"):
+        handovers = self.get_user_handovers_by_intent(intent=intent, partial_match=partial_match)
+        return self._pick_from_list(handovers, mode)
+        
+    
+    
+    def get_actions_by_intent(self, intent:str, partial_match=False) -> list[Service]:
+        actions = [s for sg in self.actions for s in sg.services if self._match_intent(intent, s.application_intents, partial_match)]
+        return actions
+    
+    def get_action_by_intent(self, intent:str, partial_match=False, mode="first"):
+        actions = self.get_actions_by_intent(intent=intent, partial_match=partial_match)
+        return self._pick_from_list(actions, mode)
+    
+    
+    def _match_intent(self, intent, intents, partial_match):
+            if partial_match:
+                # intent 'document' should match 'document-operation-manual' etc
+                return any([intent in i for i in intents])
+            else:
+                # only exact match
+                return intent in intents
+    
+    
+    @cached_property
+    def important_handovers(self) -> list[Service]:
+        return self.get_user_handovers_by_intent('important')
+    
+    
+    @cached_property
+    def important_actions(self) -> list[Service]:
+        return self.get_actions_by_intent('important')
+        
+        
+        
+        
+        
+        
+     # Attributes   
+        
+    @cached_property
+    def _all_attributes(self) -> dict[str, pyAttribute]:
+        out = {}
+        for ag in self.attribute_groups.values():
+            out.update(ag.attributes)   
+        return out
+    
+        
+    def get_attributes(self, key:str) -> list[pyAttribute]:
+        attributes = [a for k, a in self._all_attributes.items() if key in a.key]
+        return attributes  
     
-    @property
+    def get_attribute(self, key:str, mode="first"):        
+        attributes = self.get_attributes(key)
+        return self._pick_from_list(attributes, mode)
+
+        
+    def _pick_from_list(self, list, mode):
+        if mode not in ['first', 'last']:
+            raise ValueError('mode must be "first or "last" ')
+        
+        if not list:
+            return None
+        if mode == 'first':
+            return list[0]
+        if mode == 'last':
+            return list[-1]
+        
+        
+    @cached_property
     def image_url(self) -> str:
         image_attr = self._all_attributes.get(MetaAttributeKeys.IMAGE.value)
         if isinstance(image_attr.value, pyResource):
@@ -51,7 +155,7 @@ class PacInfo(BaseModel):
             return image_attr.value
         
         
-    @property
+    @cached_property
     def display_name(self) -> str|None:
         display_name = None
         pac = self.pac_id
@@ -63,30 +167,41 @@ class PacInfo(BaseModel):
         if dn_attr := self._all_attributes.get(MetaAttributeKeys.DISPLAYNAME.value): 
             dn = dn_attr.value
             display_name = dn + f' ( aka {display_name} )' if display_name else dn
+            
+        if not display_name and self.main_category:
+            seg_240 = [s for s in self.main_category.segments if s.key=="240"]
+            display_name = seg_240[0].value
+            
         return display_name
     
     
-    @property
+    @cached_property
     def safety_pictograms(self) -> dict[str, pyAttribute]:
         pictogram_attributes = {k: a for k, a in self._all_attributes.items() if "https://labfreed.org/ghs/pictogram/" in a.key}
         return pictogram_attributes    
     
     
-    @property
+    @cached_property
     def qualification_state(self) -> pyAttribute:
         if state := self._all_attributes.get("https://labfreed.org/qualification/status"): 
             return state
+
+    
+         
+
+
         
-        
-    @cached_property
-    def _all_attributes(self) -> dict[str, pyAttribute]:
-        out = {}
-        for ag in self.attribute_groups.values():
-            out.update(ag.attributes)   
-        return out
     
     
     
+    
+    
+    
+    
+    
+########
+    
+    
     def format_for_print(self, markup:str='rich') -> str:
         
         printout = StringIOLineBreak(markup=markup)
@@ -126,37 +241,6 @@ class PacInfo(BaseModel):
     
     
     
-    def render_html(self, hide_attribute_groups:list[str]=[]) -> str:        
-        return PACInfo_HTMLRenderer.render_template('pac_info_main.jinja.html', 
-                               pac_info = self, 
-                               hide_attribute_groups=hide_attribute_groups
-                               )
-        
-    def render_html_card(self) -> str:
-        return PACInfo_HTMLRenderer.render_template('pac_info_card.jinja.html', 
-                               pac_info = self
-                               )
-    
-        
-class PACInfo_HTMLRenderer():
-    TEMPLATES_DIR = Path(__file__).parent / "html_renderer"
-    jinja_env = Environment(
-        loader=FileSystemLoader(str(TEMPLATES_DIR), encoding="utf-8"),
-        autoescape=select_autoescape(enabled_extensions=("html", "jinja", "jinja2", "jinja.html")),
-    )
-    
-    @classmethod
-    def render_template(cls, template_name:str, pac_info:PacInfo, hide_attribute_groups):
-        # --- Jinja env pointing at /html_renderer ---
-        template = cls.jinja_env.get_template("pac_info.jinja.html")
-        html = template.render(
-            pac=pac_info.pac_id,
-            pac_info=pac_info,  # your object
-            hide_attribute_groups=hide_attribute_groups,
-            is_data_table = lambda value: isinstance(value, DataTable),
-            is_url = lambda s: isinstance(s, str) and urlparse(s).scheme in ('http', 'https') and bool(urlparse(s).netloc),
-            is_image = lambda s: isinstance(s, str) and s.lower().startswith('http') and s.lower().endswith(('.jpg','.jpeg','.png','.gif','.bmp','.webp','.svg','.tif','.tiff')),
-            is_reference = lambda s: isinstance(s, pyReference) ,
-        )
-        return html
-        
+
+    
+    

{labfreed-1.0.0a12 → labfreed-1.0.0a14}/labfreed/labfreed_infrastructure.py

@@ -4,6 +4,10 @@ import re
 from pydantic import BaseModel, ConfigDict, Field, PrivateAttr, field_validator
 from typing import Any, List, Set
 
+import warnings
+import functools
+import inspect
+
 from rich import print
 from rich.table import Table
 
@@ -256,3 +260,11 @@ def _filter_warnings(val_msg:list[ValidationMessage]) -> list[ValidationMessage]
 def _quote_texts(texts:list[str]):
     return ','.join([f"'{t}'" for t in texts])
 
+
+
+
+
+
+
+
+

{labfreed-1.0.0a12 → labfreed-1.0.0a14}/labfreed/pac_attributes/api_data_models/response.py

@@ -36,7 +36,7 @@ class AttributeBase(LabFREED_BaseModel, ABC):
     
 class DateTimeAttribute(AttributeBase):
     type: Literal["datetime"] 
-    value: datetime | list[datetime]
+    value: datetime
     
     @field_validator('value', mode='before')
     def set_utc__if_naive(cls, value):
@@ -44,60 +44,113 @@ class DateTimeAttribute(AttributeBase):
             return ensure_utc(value)
         else:
             return value
+        
+class DateTimeListAttribute(AttributeBase):
+    type: Literal["datetime-list"] 
+    value: list[datetime]
+    
+    @field_validator('value', mode='before')
+    def set_utc__if_naive(cls, value):
+        value_out = []
+        for v in value:
+            if isinstance(v, datetime):
+                value_out.append(ensure_utc(v))
+            else:
+                return ValueError(f'{v} is of type {type(v)}. It must be datetime')
+    
+    
     
 class BoolAttribute(AttributeBase):
     type: Literal["bool"] 
-    value: bool | list[bool]
+    value: bool
+    
+class BoolListAttribute(AttributeBase):
+    type: Literal["bool-list"] 
+    value: list[bool]
+
+
+
     
 class TextAttribute(AttributeBase):
     type: Literal["text"] 
-    value: str | list[str]
+    value: str
+    
+    @model_validator(mode='after')
+    def _validate_value(self):
+        _validate_text(self, self.value)
+        return self
+    
+class TextListAttribute(AttributeBase):
+    type: Literal["text-list"] 
+    value: list[str]
     
     @model_validator(mode='after')
     def _validate_value(self):
         l = [self.value] if isinstance(self.value, str) else self.value
         for v in l:
-            if len(v) > 5000: 
-                self._add_validation_message(
-                    source="Text Attribute",
-                    level=ValidationMsgLevel.WARNING,  # noqa: F821
-                    msg=f"Text attribute {v} exceeds 5000 characters. It is recommended to stay below",
-                    highlight_pattern = f'{v}'
-                )
+            _validate_text(self, v)
         return self
+    
+
+def _validate_text(mdl:LabFREED_BaseModel, v):
+    if len(v) > 5000: 
+        mdl._add_validation_message(
+            source="Text Attribute",
+            level=ValidationMsgLevel.WARNING,  # noqa: F821
+            msg=f"Text attribute {v} exceeds 5000 characters. It is recommended to stay below",
+            highlight_pattern = f'{v}'
+        )
             
 
+
 class ReferenceAttribute(AttributeBase):
     type: Literal["reference"]
-    value: str | list[str]
+    value: str 
+    
+class ReferenceListAttribute(AttributeBase):
+    type: Literal["reference-list"]
+    value: list[str]
+    
     
+        
 
 class ResourceAttribute(AttributeBase):
     type: Literal["resource"]
-    value: str | list[str]
+    value: str 
+    
+    @model_validator(mode='after')
+    def _validate_value(self):
+        _validate_resource(self, self.value)
+
+class ResourceListAttribute(AttributeBase):
+    type: Literal["resource-list"]
+    value: list[str]
     
     @model_validator(mode='after')
     def _validate_value(self):
         value_list = self.value if isinstance(self.value, list) else [self.value]
         for v in value_list:
-            r = urlparse(v)
-            if not all([r.scheme, r.netloc]):
-                self._add_validation_message(
-                    source="Resource Attribute",
-                    level=ValidationMsgLevel.ERROR,  # noqa: F821
-                    msg=f"Must be a valid url",
-                    highlight_pattern = f'{v}'
-                )
-            pattern = re.compile(r"\.\w{1,3}$", re.IGNORECASE)
-            if not bool(pattern.search(v)):
-                self._add_validation_message(
-                    source="Resource Attribute",
-                    level=ValidationMsgLevel.WARNING,  # noqa: F821
-                    msg=f"It is RECOMMENDED resource links end with a file extension",
-                    highlight_pattern = f'{v}'
-                )
+            _validate_resource(self, v)
         return self
     
+def _validate_resource(mdl:LabFREED_BaseModel, v):
+    r = urlparse(v)
+    if not all([r.scheme, r.netloc]):
+        mdl._add_validation_message(
+            source="Resource Attribute",
+            level=ValidationMsgLevel.ERROR,  # noqa: F821
+            msg="Must be a valid url",
+            highlight_pattern = f'{v}'
+        )
+    pattern = re.compile(r"\.\w{1,3}$", re.IGNORECASE)
+    if not bool(pattern.search(v)):
+        mdl._add_validation_message(
+            source="Resource Attribute",
+            level=ValidationMsgLevel.WARNING,  # noqa: F821
+            msg="It is RECOMMENDED resource links end with a file extension",
+            highlight_pattern = f'{v}'
+        )
+    
         
         
 class NumericValue(LabFREED_BaseModel):
@@ -151,11 +204,22 @@ class NumericValue(LabFREED_BaseModel):
 
 class NumericAttribute(AttributeBase):
     type: Literal["numeric"] 
-    value: NumericValue | list[NumericValue]
+    value: NumericValue 
+    
+class NumericListAttribute(AttributeBase):
+    type: Literal["numeric-list"] 
+    value: list[NumericValue]
+    
+    
     
 class ObjectAttribute(AttributeBase):
     type: Literal["object"] 
-    value: dict[str, Any] |list[dict[str, Any]]
+    value: dict[str, Any]
+    
+    
+class ObjectListAttribute(AttributeBase):
+    type: Literal["object-list"] 
+    value: list[dict[str, Any]]
            
 
      
@@ -168,7 +232,15 @@ Attribute = Annotated[
         TextAttribute,
         NumericAttribute,
         ResourceAttribute,
-        ObjectAttribute
+        ObjectAttribute,
+        
+        ReferenceListAttribute,
+        DateTimeListAttribute,
+        BoolListAttribute,
+        TextListAttribute,
+        NumericListAttribute,
+        ResourceListAttribute,
+        ObjectListAttribute
     ],
     Field(discriminator="type")
 ]

{labfreed-1.0.0a12 → labfreed-1.0.0a14}/labfreed/pac_attributes/pythonic/attribute_server_factory.py

@@ -11,7 +11,6 @@ except ImportError:
     raise ImportError("Please install labfreed with the [extended] extra: pip install labfreed[extended]")
 
 
-# from fastapi import FastAPI, Request
 
 class Authenticator(Protocol):
     def __call__(self, request) -> bool: ...

{labfreed-1.0.0a12 → labfreed-1.0.0a14}/labfreed/pac_cat/category_base.py

@@ -55,7 +55,7 @@ class Category(LabFREED_BaseModel):
                     k = f"{field_name} ({ field_info.alias})"
                 else:
                     k = f"{field_name}"
-            out.update({k : v } ) 
+                out.update({k : v } ) 
             
         for s in getattr(self, 'additional_segments', []):
             out.update( {s.key or '' : s.value })

{labfreed-1.0.0a12 → labfreed-1.0.0a14}/labfreed/pac_cat/predefined_categories.py

@@ -1,5 +1,5 @@
 ## Materials
-from abc import ABC
+from abc import ABC, abstractproperty
 from pydantic import Field, computed_field, model_validator
 
 from labfreed.labfreed_infrastructure import ValidationMsgLevel
@@ -18,6 +18,10 @@ class PredefinedCategory(Category, ABC):
     def segments(self) -> list[IDSegment]:
         return self._get_segments(use_short_notation=False)
     
+    @abstractproperty
+    def is_serialized(self) -> bool:
+        pass
+    
     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
@@ -65,12 +69,17 @@ class Material_Device(PredefinedCategory):
         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',
+                    level = ValidationMsgLevel.WARNING,
+                    msg=f'Category key {self.key} is missing field Serial Number. Check that you are indeed to a product and not a specific device.',
                     highlight_pattern = f"{self.key}"
             )
         return self
     
+    @property
+    def is_serialized(self) -> bool:
+        return bool(self.serial_number)
+    
+    
 class Material_Substance(PredefinedCategory):
     '''Represents the -MS category'''
     key: str =         Field(default='-MS', frozen=True)
@@ -93,6 +102,11 @@ class Material_Substance(PredefinedCategory):
             )
         return self
     
+    @property
+    def is_serialized(self) -> bool:
+        return bool(self.batch_number or self.container_number or self.aliquot)
+    
+    
 class Material_Consumable(PredefinedCategory):
     '''Represents the -MC category'''
     key: str = Field(default='-MC', frozen=True)
@@ -115,6 +129,11 @@ class Material_Consumable(PredefinedCategory):
             )
         return self
     
+    @property
+    def is_serialized(self) -> bool:
+        return bool(self.batch_number or self.serial_number or self.aliquot)
+    
+    
 class Material_Misc(Material_Consumable):
     '''Represents the -MX category'''
     # same fields as Consumable
@@ -128,6 +147,8 @@ class Material_Misc(Material_Consumable):
     ''' Category segments, which are not defined in the specification'''
     
 
+    
+
 
 ## Data
 class Data_Abstract(PredefinedCategory, ABC):
@@ -147,6 +168,11 @@ class Data_Abstract(PredefinedCategory, ABC):
                     highlight_pattern = f"{self.key}"
             )
         return self
+    
+    @property
+    def is_serialized(self) -> bool:
+        return True
+    
 
 class Data_Result(Data_Abstract):
     '''Represents the -DR category'''
@@ -215,6 +241,11 @@ class Processor_Abstract(PredefinedCategory, ABC):
                     highlight_pattern = f"{self.key}"
             )
         return self
+    
+    @property
+    def is_serialized(self) -> bool:
+        return bool(self.processor_instance)
+    
 
 class Processor_Software(Processor_Abstract):
     '''Represents the -PS category'''
@@ -233,6 +264,31 @@ class Processor_Misc(Processor_Abstract):
     ''' Category segments, which are not defined in the specification'''
     
     
+    
+class Misc(Category, ABC):
+    '''@private'''
+    key: str = Field(default='-X', 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'''
+    
+    @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
+    
+    @property
+    def is_serialized(self) -> bool:
+        return bool(self.id)
+    
+    
+    
 category_key_to_class_map  = {
         '-MD': Material_Device,
         '-MS': Material_Substance,
@@ -245,5 +301,6 @@ category_key_to_class_map  = {
         '-DS': Data_Static,
         '-DX': Data_Misc,
         '-PS': Processor_Software,
-        '-PX': Processor_Misc
+        '-PX': Processor_Misc,
+        '-X':Misc
 }