labfreed 0.2.3__py3-none-any.whl → 0.2.5__py3-none-any.whl

labfreed/utilities/base36.py

@@ -1,82 +1,82 @@
-import re
-import string
-
-from pydantic import field_validator, RootModel
-
-class base36(RootModel[str]):
-    @field_validator('root')
-    @classmethod
-    def validate_format(cls, v: str) -> str:
-        if not re.fullmatch(r'[A-Z0-9]*', v):
-            raise ValueError("Value must only contain uppercase letters and digits (A-Z, 0-9)")
-        return v
-    
-
-def to_base36(s:str) -> base36:
-    """Takes a string, encodes it in UTF-8 and then as base36 string."""
-    utf8_encoded = s.encode('utf-8')
-    num = int.from_bytes(utf8_encoded, byteorder='big', signed=False)
-    
-    # note: this cannot be arbitrarily chosen. The choice here corresponds to what pythons int(s:str, base:int=10) function used.
-    base36_chars = _alphabet(base=36)
-    if num == 0:
-        return base36_chars[0]
-    base_36 = []
-    _num = num
-    while _num:
-        _num, i = divmod(_num, 36)
-        base_36.append(base36_chars[i])
-    b36_str = ''.join(reversed(base_36))
-    b36_str = base36(b36_str)
-    return b36_str
-
-
-def from_base36(s36:base36) -> str:
-    """inverse of to_base36"""
-    # this built in function interprets each character as number in a base represented by the standartd alphabet [0-9 (A-Z|a-z)][0:base] it is case INsensitive.
-    num = int(s36, 36)
-    num_bytes = (num.bit_length() + 7) // 8
-    _bytes = num.to_bytes(num_bytes, byteorder='big')
-    s = _bytes.decode('utf-8')
-    return s
-
-
-def _alphabet(base):
-    """ returns an alphabet, which corresponds to what pythons int(s:str, base:int=10) function used.
-    """
-    if base < 2 or base > 36:
-        ValueError('base can only be between 2 and 36')    
-    alphabet = (string.digits + string.ascii_uppercase)[0:base]
-    return alphabet
-
-
-if __name__ == "__main__":
-    ss = ["A",
-      "B-500 B",
-      "B-500 Ba",
-      "B-500 Bal",
-      "B-500 Bala",
-      "B-500 Balanc",
-      "B-500 Balance",
-      "B-500 D",
-      "Mini Spray Dryer S-300", 
-      "w3ApashAt!!£NAGDSAF*ç%&/()",
-      "HELLOWORLD", 
-      "Helloworld",
-      "$£äö!'?^{]<@#¦&¬|¢)&§°😀你好🌍🏯😇🎵🔥你👻🐉😀你好🌍🏯😇🎵🔥你👻🐉😀你好🌍🏯😇🎵🔥你👻🐉😀你好🌍🏯😇🎵🔥你👻🐉😀你好🌍🏯😇🎵🔥你👻🐉😀你好🌍🏯😇🎵🔥你👻🐉😀你好🌍🏯😇🎵🔥你👻🐉",
-      "往跟住！師立甲錯什正再圓身升因月室",
-      "Balance BAL500 @☣️Lab",
-      "BAL500 @☣️Lab",
-      "BAL-CLEAN",
-      "Smørrebrød µ-Nutrients",
-      "Demo Result from R-300",
-      "Rotavapor R-300",
-      "Rotavapor R-250",
-      "Rotavapor R-220",
-      "SyncorePlus"
-      ]
-    for s in ss:
-        s36 = to_base36(s)
-        s_back = from_base36(s36)
-        identical = (s == s_back)
-        print(f'{s} >> {s36} >> {s_back}: match:{identical}')
+import re
+import string
+
+from pydantic import field_validator, RootModel
+
+class base36(RootModel[str]):
+    @field_validator('root')
+    @classmethod
+    def validate_format(cls, v: str) -> str:
+        if not re.fullmatch(r'[A-Z0-9]*', v):
+            raise ValueError("Value must only contain uppercase letters and digits (A-Z, 0-9)")
+        return v
+    
+
+def to_base36(s:str) -> base36:
+    """Takes a string, encodes it in UTF-8 and then as base36 string."""
+    utf8_encoded = s.encode('utf-8')
+    num = int.from_bytes(utf8_encoded, byteorder='big', signed=False)
+    
+    # note: this cannot be arbitrarily chosen. The choice here corresponds to what pythons int(s:str, base:int=10) function used.
+    base36_chars = _alphabet(base=36)
+    if num == 0:
+        return base36_chars[0]
+    base_36 = []
+    _num = num
+    while _num:
+        _num, i = divmod(_num, 36)
+        base_36.append(base36_chars[i])
+    b36_str = ''.join(reversed(base_36))
+    b36_str = base36(b36_str)
+    return b36_str
+
+
+def from_base36(s36:base36) -> str:
+    """inverse of to_base36"""
+    # this built in function interprets each character as number in a base represented by the standartd alphabet [0-9 (A-Z|a-z)][0:base] it is case INsensitive.
+    num = int(s36, 36)
+    num_bytes = (num.bit_length() + 7) // 8
+    _bytes = num.to_bytes(num_bytes, byteorder='big')
+    s = _bytes.decode('utf-8')
+    return s
+
+
+def _alphabet(base):
+    """ returns an alphabet, which corresponds to what pythons int(s:str, base:int=10) function used.
+    """
+    if base < 2 or base > 36:
+        ValueError('base can only be between 2 and 36')    
+    alphabet = (string.digits + string.ascii_uppercase)[0:base]
+    return alphabet
+
+
+if __name__ == "__main__":
+    ss = ["A",
+      "B-500 B",
+      "B-500 Ba",
+      "B-500 Bal",
+      "B-500 Bala",
+      "B-500 Balanc",
+      "B-500 Balance",
+      "B-500 D",
+      "Mini Spray Dryer S-300", 
+      "w3ApashAt!!£NAGDSAF*ç%&/()",
+      "HELLOWORLD", 
+      "Helloworld",
+      "$£äö!'?^{]<@#¦&¬|¢)&§°😀你好🌍🏯😇🎵🔥你👻🐉😀你好🌍🏯😇🎵🔥你👻🐉😀你好🌍🏯😇🎵🔥你👻🐉😀你好🌍🏯😇🎵🔥你👻🐉😀你好🌍🏯😇🎵🔥你👻🐉😀你好🌍🏯😇🎵🔥你👻🐉😀你好🌍🏯😇🎵🔥你👻🐉",
+      "往跟住！師立甲錯什正再圓身升因月室",
+      "Balance BAL500 @☣️Lab",
+      "BAL500 @☣️Lab",
+      "BAL-CLEAN",
+      "Smørrebrød µ-Nutrients",
+      "Demo Result from R-300",
+      "Rotavapor R-300",
+      "Rotavapor R-250",
+      "Rotavapor R-220",
+      "SyncorePlus"
+      ]
+    for s in ss:
+        s36 = to_base36(s)
+        s_back = from_base36(s36)
+        identical = (s == s_back)
+        print(f'{s} >> {s36} >> {s_back}: match:{identical}')

labfreed/well_known_extensions/__init__.py

@@ -1,5 +1,5 @@
-from .display_name_extension import DisplayNameExtension
-from .trex_extension import TREX_Extension
-from .default_extension_interpreters import default_extension_interpreters  # noqa: F401
-
+from .display_name_extension import DisplayNameExtension
+from .trex_extension import TREX_Extension
+from .default_extension_interpreters import default_extension_interpreters  # noqa: F401
+
 __all__ = ["DisplayNameExtension", "TREX_Extension"]

labfreed/well_known_extensions/default_extension_interpreters.py

@@ -1,7 +1,7 @@
-from .display_name_extension import DisplayNameExtension
-from .trex_extension import TREX_Extension
-
-default_extension_interpreters = {
-    'TREX': TREX_Extension,
-    'N': DisplayNameExtension
+from .display_name_extension import DisplayNameExtension
+from .trex_extension import TREX_Extension
+
+default_extension_interpreters = {
+    'TREX': TREX_Extension,
+    'N': DisplayNameExtension
 }

labfreed/well_known_extensions/display_name_extension.py

@@ -1,40 +1,40 @@
-import logging
-from typing import Literal, Self
-from pydantic import computed_field
-from labfreed.labfreed_infrastructure import LabFREED_BaseModel
-from labfreed.pac_id.extension import ExtensionBase
-from labfreed.utilities.base36 import from_base36, to_base36
-
-
-class DisplayNameExtension(ExtensionBase, LabFREED_BaseModel):
-    name:Literal['N'] = 'N'
-    type:Literal['N'] = 'N'
-    display_name: str       
-    
-    @computed_field
-    @property
-    def data(self)->str:
-        # return '/'.join([to_base36(dn) for dn in self.display_name])
-        return to_base36(self.display_name).root
-    
-    @staticmethod
-    def from_extension(ext:ExtensionBase) -> Self:
-        return DisplayNameExtension.create(name=ext.name,
-                                  type=ext.type,
-                                  data=ext.data)
-    
-    @staticmethod
-    def create(*, name, type, data):
-        if name != 'N':
-            logging.warning(f'Name {name} was given, but this extension should only be used with name "N". Will ignore input')
-            
-        if type != 'N':
-            logging.warning(f'Type {name} was given, but this extension should only be used with type "N". Will try to parse data as display names')
-        
-        display_name = from_base36(data)
-         
-        return DisplayNameExtension(display_name=display_name)
-    
-    def __str__(self):
-        return 'Display name: '+ self.display_name
-
+import logging
+from typing import Literal, Self
+from pydantic import computed_field
+from labfreed.labfreed_infrastructure import LabFREED_BaseModel
+from labfreed.pac_id.extension import ExtensionBase
+from labfreed.utilities.base36 import from_base36, to_base36
+
+
+class DisplayNameExtension(ExtensionBase, LabFREED_BaseModel):
+    name:Literal['N'] = 'N'
+    type:Literal['N'] = 'N'
+    display_name: str       
+    
+    @computed_field
+    @property
+    def data(self)->str:
+        # return '/'.join([to_base36(dn) for dn in self.display_name])
+        return to_base36(self.display_name).root
+    
+    @staticmethod
+    def from_extension(ext:ExtensionBase) -> Self:
+        return DisplayNameExtension.create(name=ext.name,
+                                  type=ext.type,
+                                  data=ext.data)
+    
+    @staticmethod
+    def create(*, name, type, data):
+        if name != 'N':
+            logging.warning(f'Name {name} was given, but this extension should only be used with name "N". Will ignore input')
+            
+        if type != 'N':
+            logging.warning(f'Type {name} was given, but this extension should only be used with type "N". Will try to parse data as display names')
+        
+        display_name = from_base36(data)
+         
+        return DisplayNameExtension(display_name=display_name)
+    
+    def __str__(self):
+        return 'Display name: '+ self.display_name
+

labfreed/well_known_extensions/trex_extension.py

@@ -1,31 +1,31 @@
-from typing import Literal, Self
-
-from pydantic import computed_field 
-from labfreed.labfreed_infrastructure import LabFREED_BaseModel
-from labfreed.pac_id.extension import ExtensionBase
-from labfreed.trex.trex import TREX
-
-
-class TREX_Extension(ExtensionBase, LabFREED_BaseModel):
-    name:str
-    type:Literal['TREX'] = 'TREX'
-    trex:TREX
-           
-    @computed_field
-    @property
-    def data(self)->str:
-        trex_str = self.trex.serialize()
-        return trex_str
-        
-    @staticmethod
-    def from_extension(ext:ExtensionBase) -> Self:
-        return TREX_Extension.create(name=ext.name,
-                                    type=ext.type,
-                                    data=ext.data)
-    
-    @staticmethod
-    def create(*, name, data, type='TREX'):
-        trex_extension = TREX_Extension(name= name, trex = TREX.deserialize(data))
-        return trex_extension
-    
+from typing import Literal, Self
+
+from pydantic import computed_field 
+from labfreed.labfreed_infrastructure import LabFREED_BaseModel
+from labfreed.pac_id.extension import ExtensionBase
+from labfreed.trex.trex import TREX
+
+
+class TREX_Extension(ExtensionBase, LabFREED_BaseModel):
+    name:str
+    type:Literal['TREX'] = 'TREX'
+    trex:TREX
+           
+    @computed_field
+    @property
+    def data(self)->str:
+        trex_str = self.trex.serialize()
+        return trex_str
+        
+    @staticmethod
+    def from_extension(ext:ExtensionBase) -> Self:
+        return TREX_Extension.create(name=ext.name,
+                                    type=ext.type,
+                                    data=ext.data)
+    
+    @staticmethod
+    def create(*, name, data, type='TREX'):
+        trex_extension = TREX_Extension(name= name, trex = TREX.deserialize(data))
+        return trex_extension
+    
    

labfreed/well_known_keys/gs1/__init__.py

@@ -1,6 +1,6 @@
-'''
-Data from 
-https://ref.gs1.org/ai/GS1_Application_Identifiers.jsonld
-
-processes by ChatGPT
+'''
+Data from 
+https://ref.gs1.org/ai/GS1_Application_Identifiers.jsonld
+
+processes by ChatGPT
 '''

labfreed/well_known_keys/gs1/gs1.py

@@ -1,4 +1,4 @@
-'''
-Data from 
-https://ref.gs1.org/ai/GS1_Application_Identifiers.jsonld
+'''
+Data from 
+https://ref.gs1.org/ai/GS1_Application_Identifiers.jsonld
 '''

labfreed/well_known_keys/labfreed/well_known_keys.py

@@ -1,16 +1,16 @@
-from enum import Enum
-
-
-class WellKnownKeys(Enum):
-    GTIN = '01'
-    BATCH = '10'
-    SERIAL = '21'
-    ADDITIONAL_IDINTIFIER = '240'
-    RUN_ID_ABSOLUTE = 'RNR'
-    SAMPLE_ID = 'SMP'
-    EXPERIMENT_ID = 'EXP'
-    RESULT_ID = 'RST'
-    METHOD_ID = 'MTD'
-    REPORT_ID = 'RPT'
-    TIMESTAMP = 'TS'
+from enum import Enum
+
+
+class WellKnownKeys(Enum):
+    GTIN = '01'
+    BATCH = '10'
+    SERIAL = '21'
+    ADDITIONAL_IDINTIFIER = '240'
+    RUN_ID_ABSOLUTE = 'RNR'
+    SAMPLE_ID = 'SMP'
+    EXPERIMENT_ID = 'EXP'
+    RESULT_ID = 'RST'
+    METHOD_ID = 'MTD'
+    REPORT_ID = 'RPT'
+    TIMESTAMP = 'TS'
     VERSION = 'V'

labfreed/well_known_keys/unece/__init__.py

@@ -1,4 +1,4 @@
-'''
-Data from
-https://github.com/quadient/unece-units/blob/main/python/src/unece_excel_parser/parsedUneceUnits.json
+'''
+Data from
+https://github.com/quadient/unece-units/blob/main/python/src/unece_excel_parser/parsedUneceUnits.json
 '''

labfreed/well_known_keys/unece/unece_units.py

@@ -1,68 +1,68 @@
-from functools import cache
-import json
-from pathlib import Path
-
-
-
-
-@cache
-def unece_units() -> list[dict]:
-    p = Path(__file__).parent / 'UneceUnits.json'
-    with open(p) as f:
-        l = json.load(f)  # noqa: E741
-    return l
-
-@cache
-def unece_unit_codes():
-    codes= [u.get('commonCode') for u in unece_units() if u.get('state') == 'ACTIVE']
-    return codes
-
-
-def unece_unit(unit_code):
-    unit =  [u for u in unece_units() if u['commonCode'] == unit_code]
-    if len(unit) == 0:
-        return None
-    else:
-        return unit[0]
-    
-def unit_symbol(unit:dict) ->str:
-    return unit.get('symbol')
-
-def unit_name(unit:dict) ->str:
-    return unit.get('name')
-
-
-
-# def check_compatibility_unece_quantities():
-#     unece = unece_units()
-#     print(f'Number of units in file: {len(unece)}')
-    
-#     failed = list()
-#     success = list()
-#     for u in unece:
-#         if u.get('state') ==  'ACTIVE':
-#             try:
-#                 if not u.get('symbol'):
-#                     assert False
-#                 u.get('name')  
-#                 validate_unit(u.get('symbol'))
-#                 success.append(u)
-#             except AssertionError:
-#                 failed.append(u)
-#         else:
-#             pass
-        
-    
-    
-#     print('[blue] FAILED [/blue]')
-#     for u in failed:
-#         print(f'{u.get('commonCode')}: {u.get('name')}')
-    
-#     print('[yellow] SUCCESSFUL [/yellow]')
-#     for u in success:
-#         print(u)
-        
-#     print(f'{len(failed)} / {len(unece)} failed to convert')
-        
-
+from functools import cache
+import json
+from pathlib import Path
+
+
+
+
+@cache
+def unece_units() -> list[dict]:
+    p = Path(__file__).parent / 'UneceUnits.json'
+    with open(p) as f:
+        l = json.load(f)  # noqa: E741
+    return l
+
+@cache
+def unece_unit_codes():
+    codes= [u.get('commonCode') for u in unece_units() if u.get('state') == 'ACTIVE']
+    return codes
+
+
+def unece_unit(unit_code):
+    unit =  [u for u in unece_units() if u['commonCode'] == unit_code]
+    if len(unit) == 0:
+        return None
+    else:
+        return unit[0]
+    
+def unit_symbol(unit:dict) ->str:
+    return unit.get('symbol')
+
+def unit_name(unit:dict) ->str:
+    return unit.get('name')
+
+
+
+# def check_compatibility_unece_quantities():
+#     unece = unece_units()
+#     print(f'Number of units in file: {len(unece)}')
+    
+#     failed = list()
+#     success = list()
+#     for u in unece:
+#         if u.get('state') ==  'ACTIVE':
+#             try:
+#                 if not u.get('symbol'):
+#                     assert False
+#                 u.get('name')  
+#                 validate_unit(u.get('symbol'))
+#                 success.append(u)
+#             except AssertionError:
+#                 failed.append(u)
+#         else:
+#             pass
+        
+    
+    
+#     print('[blue] FAILED [/blue]')
+#     for u in failed:
+#         print(f'{u.get('commonCode')}: {u.get('name')}')
+    
+#     print('[yellow] SUCCESSFUL [/yellow]')
+#     for u in success:
+#         print(u)
+        
+#     print(f'{len(failed)} / {len(unece)} failed to convert')
+        
+
         

{labfreed-0.2.3.dist-info → labfreed-0.2.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: labfreed
-Version: 0.2.3
+Version: 0.2.5
 Summary: Python implementation of LabFREED building blocks
 Author-email: Reto Thürer <thuerer.r@buchi.com>
 Requires-Python: >=3.11
@@ -27,6 +27,10 @@ Requires-Dist: pytest>=8.3.5 ; extra == "dev"
 Requires-Dist: pdoc>=15.0.1 ; extra == "dev"
 Requires-Dist: flit>=3.12.0 ; extra == "dev"
 Requires-Dist: ruff>=0.11.5 ; extra == "dev"
+Project-URL: Documentation, https://github.com/retothuerer/LabFREED?tab=readme-ov-file#readme
+Project-URL: Homepage, https://github.com/retothuerer/LabFREED
+Project-URL: Source, https://github.com/retothuerer/LabFREED
+Project-URL: Tracker, https://github.com/retothuerer/LabFREED/issues
 Provides-Extra: dev
 
 # LabFREED for Python
@@ -101,7 +105,7 @@ pac.print_validation_messages()
 >> Validation Results                                                                                                                   
 >> ┌───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
 >> │ **RECOMMENDATION** in id segment value bal500                                                                                     │
->> │ Characters 'a','l','b' should not be used., Characters SHOULD be limited to upper case letters (A-Z), numbers (0-9), '-' and '+'  │
+>> │ Characters 'b','l','a' should not be used., Characters SHOULD be limited to upper case letters (A-Z), numbers (0-9), '-' and '+'  │
 >> │                                                                                                                                   │
 >> │ HTTPS://PAC.METTORIUS.COM/-MD/240:👉bal👈500/21:@1234                                                                             │
 >> ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
@@ -111,7 +115,7 @@ pac.print_validation_messages()
 >> │ HTTPS://PAC.METTORIUS.COM/-MD/240:bal500/21:👉@👈1234                                                                             │
 >> ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
 >> │ **RECOMMENDATION** in id segment value bal500                                                                                     │
->> │ Characters 'a','l','b' should not be used., Characters SHOULD be limited to upper case letters (A-Z), numbers (0-9), '-' and '+'  │
+>> │ Characters 'b','l','a' should not be used., Characters SHOULD be limited to upper case letters (A-Z), numbers (0-9), '-' and '+'  │
 >> │                                                                                                                                   │
 >> │ HTTPS://PAC.METTORIUS.COM/-MD/240:👉bal👈500/21:@1234                                                                             │
 >> ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
@@ -244,7 +248,7 @@ trex.print_validation_messages()
 >> Validation Results                                            
 >> ┌────────────────────────────────────────────────────────────┐
 >> │ **ERROR** in TREX table column Date                        │
->> │ Column header key contains invalid characters: 'a','t','e' │
+>> │ Column header key contains invalid characters: 'e','a','t' │
 >> │                                                            │
 >> │ STOP$T.D:20240505T1306                                     │
 >> │ +TEMP$KEL:10.15                                            │
@@ -252,9 +256,9 @@ trex.print_validation_messages()
 >> │ +COMMENT$T.A:FOO                                           │
 >> │ +COMMENT2$T.T:12G3                                         │
 >> │ +TABLE$$DURATION$HUR:D👉ate👈$T.D:OK$T.B:COMMENT$T.A::     │
->> │  1:20250425T081731.192:T:FOO::                             │
->> │  1.1:20250425T081731.192:T:BAR::                           │
->> │  1.3:20250425T081731.192:F:BLUBB                           │
+>> │  1:20250430T100239.279:T:FOO::                             │
+>> │  1.1:20250430T100239.280:T:BAR::                           │
+>> │  1.3:20250430T100239.280:F:BLUBB                           │
 >> └────────────────────────────────────────────────────────────┘
 ```
 #### Combine PAC-ID and TREX and serialize
@@ -266,7 +270,7 @@ pac_str = pac.to_url()
 print(pac_str)
 ```
 ```text
->> HTTPS://PAC.METTORIUS.COM/21:1234*MYTREX$TREX/STOP$T.D:20240505T1306+TEMP$KEL:10.15+OK$T.B:F+COMMENT$T.A:FOO+COMMENT2$T.T:12G3+TABLE$$DURATION$HUR:Date$T.D:OK$T.B:COMMENT$T.A::1:20250425T081731.192:T:FOO::1.1:20250425T081731.192:T:BAR::1.3:20250425T081731.192:F:BLUBB
+>> HTTPS://PAC.METTORIUS.COM/21:1234*MYTREX$TREX/STOP$T.D:20240505T1306+TEMP$KEL:10.15+OK$T.B:F+COMMENT$T.A:FOO+COMMENT2$T.T:12G3+TABLE$$DURATION$HUR:Date$T.D:OK$T.B:COMMENT$T.A::1:20250430T100239.279:T:FOO::1.1:20250430T100239.280:T:BAR::1.3:20250430T100239.280:F:BLUBB
 ```
 ## PAC-ID Resolver
 
@@ -292,7 +296,6 @@ cit2.origin = 'MY_COMPANY'
 pac_str = 'HTTPS://PAC.METTORIUS.COM/-MS/X3511/CAS:7732-18-5'
 service_groups = PAC_ID_Resolver(cits=[cit, cit2]).resolve(pac_str)
 for sg in service_groups:
-    sg.update_states()
     sg.print()
     
 ```
@@ -324,6 +327,15 @@ for sg in service_groups:
 
 <!-- BEGIN CHANGELOG -->
 ## Change Log
+### v0.2.5
+- resolvers checks service states by default
+- improvements and bugfixes in conversion from python types to TREX
+- follow better naming conventions in CIT v1 
+  
+### v0.2.4
+- improvements in formatting of validation messages
+- bugfix in DataTable
+ 
 ### v0.2.3
 - improvements in formatting of validation messages
 - bugfix in DisplayNameExtension