labfreed 0.2.6a5__py3-none-any.whl → 0.2.7__py3-none-any.whl

labfreed/__init__.py

@@ -2,7 +2,7 @@
 Python implementation of LabFREED building blocks
 '''
 
-__version__ = "0.2.6a5"
+__version__ = "0.2.7"
 
 from labfreed.pac_id import *  # noqa: F403
 from labfreed.pac_cat import * # noqa: F403

labfreed/pac_id/pac_id.py

@@ -45,7 +45,7 @@ class PAC_ID(LabFREED_BaseModel):
         from labfreed.pac_id.url_parser import PAC_Parser
         return PAC_Parser.from_url(url, try_pac_cat=try_pac_cat, suppress_validation_errors=suppress_validation_errors, extension_interpreters=extension_interpreters)
     
-    def to_url(self, use_short_notation=False, uppercase_only=False) -> str:
+    def to_url(self, use_short_notation:None|bool=None, uppercase_only=False) -> str:
         from labfreed.pac_id.url_serializer import PACID_Serializer
         return PACID_Serializer.to_url(self, use_short_notation=use_short_notation, uppercase_only=uppercase_only)
     

labfreed/pac_id/url_serializer.py

@@ -9,20 +9,23 @@ class PACID_Serializer():
     '''Represents a PAC-ID including it's extensions'''
   
     @classmethod
-    def to_url(cls, pac:PAC_ID, use_short_notation=False, uppercase_only=False) -> str:
+    def to_url(cls, pac:PAC_ID, use_short_notation:bool|None=None, uppercase_only=False) -> str:
         """Serializes the PAC-ID including extensions.
 
         Args:
-            use_short_notation (bool, optional): Uses shortening conventions for extensions and categories..
+            use_short_notation (bool|None, optional): None (default): Preserves the identifier as is. Extensions use short form
+                                                      True: forces short notation for categories and extensions
+                                                      False: forces long notation for categories and extensions
             uppercase_only (bool, optional): Forces all uppercase letters (results in smaller QR)..
 
         Returns:
             str: Something like this HTTPS://PAC.METTORIUS.COM/-MD/BAL500/1234*N$N/ABC*SUM$TREX/A$T.A:ABC
 
         """
-        extensions_str = cls._serialize_extensions(pac.extensions, use_short_notation=use_short_notation)
-            
         identifier_str = cls._serialize_identifier(pac, use_short_notation=use_short_notation)
+        
+        use_short_notation_for_extensions = True if use_short_notation is None else use_short_notation 
+        extensions_str = cls._serialize_extensions(pac.extensions, use_short_notation=use_short_notation_for_extensions)
         out = f"HTTPS://PAC.{pac.issuer}{identifier_str}{extensions_str}"
         
         if uppercase_only:
@@ -30,9 +33,10 @@ class PACID_Serializer():
         return out
     
     @classmethod
-    def _serialize_identifier(cls, pac:PAC_ID|PAC_CAT, use_short_notation=True):
+    def _serialize_identifier(cls, pac:PAC_ID|PAC_CAT, use_short_notation:None|bool=None):
         ''' Serializes the PAC-ID'''
-        if isinstance(pac, PAC_CAT):
+        
+        if isinstance(pac, PAC_CAT) and use_short_notation is not None:
             for c in pac.categories:
                 segments = [IDSegment(value=c.key)]
                 if isinstance(c, PredefinedCategory):

labfreed/pac_id_resolver/cit_v1.py

@@ -91,7 +91,6 @@ class CIT_v1(LabFREED_BaseModel):
             
             cols = [c.strip() for c in line.split('\t')]
             if len(cols) < 5:
-                logging.error(f'invalid line {line}')
                 msg = ValidationMessage(
                     level=ValidationMsgLevel.ERROR,
                     source='CIT line',
@@ -102,7 +101,6 @@ class CIT_v1(LabFREED_BaseModel):
                 errors.append(msg)
                 continue
             if len(cols) > 5:
-                logging.error(f'invalid line {line}')
                 msg = ValidationMessage(
                     level=ValidationMsgLevel.ERROR,
                     source='CIT line',
@@ -123,7 +121,6 @@ class CIT_v1(LabFREED_BaseModel):
                                     )
                 entries.append(entry) 
             except ValueError:
-                logging.error(f'invalid line {line}')
                 msg = ValidationMessage(
                     level=ValidationMsgLevel.ERROR,
                     source='CIT line',

labfreed/pac_id_resolver/cit_v2.py

@@ -130,7 +130,12 @@ class CIT_v2(LabFREED_BaseModel):
     
     @classmethod
     def from_yaml(cls, yml:str) -> Self:
-        return cls.model_validate(yml)
+        try:
+            d = yaml.safe_load(yml)
+        except yaml.YAMLError as e:
+            # not a valid yaml
+            raise ValueError("This is not a valid yaml") from e
+        return cls.model_validate(d)
     
     def __str__(self):
         yml = yaml.dump(self.model_dump()                        )

labfreed/pac_id_resolver/resolver.py

@@ -1,4 +1,6 @@
+from functools import lru_cache
 import logging
+import traceback
 from typing import Self
 import yaml
 from requests import get
@@ -24,8 +26,7 @@ def load_cit(path):
     
 def cit_from_str(s:str, origin:str='') -> CIT_v1|CIT_v2:
     try:
-        cit_yml= yaml.safe_load(s)
-        cit2 = CIT_v2.from_yaml(cit_yml)
+        cit2 = CIT_v2.from_yaml(s)
         cit_version = 'v2'
     except Exception:
         cit2 = None
@@ -38,6 +39,7 @@ def cit_from_str(s:str, origin:str='') -> CIT_v1|CIT_v2:
     cit = cit2 or cit1 or None
     return cit
 
+@lru_cache
 def _get_issuer_cit(issuer:str):
     '''Gets the issuer's cit.'''
     url = 'HTTPS://PAC.' + issuer + '/coupling-information-table'
@@ -64,15 +66,16 @@ class PAC_ID_Resolver():
         self._cits = cits
             
         
-    def resolve(self, pac_url:PAC_ID|str, check_service_status=True) -> list[ServiceGroup]:
+    def resolve(self, pac_url:PAC_ID|str, check_service_status=True, use_issuer_cit=True) -> list[ServiceGroup]:
         '''Resolve a PAC-ID'''
         if isinstance(pac_url, str):
             pac_id = PAC_CAT.from_url(pac_url)
             pac_id_catless = PAC_ID.from_url(pac_url, try_pac_cat=False)
                 
         cits = self._cits.copy()
-        if issuer_cit := _get_issuer_cit(pac_id.issuer):
-            cits.append(issuer_cit)
+        if use_issuer_cit:
+            if issuer_cit := _get_issuer_cit(pac_id.issuer):
+                cits.append(issuer_cit)
          
         matches = []
         for cit in cits:

{labfreed-0.2.6a5.dist-info → labfreed-0.2.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: labfreed
-Version: 0.2.6a5
+Version: 0.2.7
 Summary: Python implementation of LabFREED building blocks
 Author-email: Reto Thürer <thuerer.r@buchi.com>
 Requires-Python: >=3.11
@@ -38,7 +38,7 @@ Provides-Extra: dev
 [![PyPI](https://img.shields.io/pypi/v/labfreed.svg)](https://pypi.org/project/labfreed/) ![Python Version](https://img.shields.io/pypi/pyversions/labfreed) [![Test Labfreed](https://github.com/retothuerer/LabFREED/actions/workflows/run-tests.yml/badge.svg)](https://github.com/retothuerer/LabFREED/actions/workflows/run-tests.yml) [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](LICENSE) 
 
 
-This is a Python implementation of [LabFREED](https://labfreed.wega-it.com) building blocks.
+This is a Python implementation of [LabFREED](https://labfreed.org/) building blocks.
 
 ## Supported Building Blocks
 - PAC-ID
@@ -53,7 +53,7 @@ This is a Python implementation of [LabFREED](https://labfreed.wega-it.com) buil
   - base36 <> str conversions
 - PAC-ID Resolver
   - support for CIT v1
-  - draft support for CIT v1 (improved version)
+  - draft support for CIT v2 (improved version)
   - combined use of multiple cit in any combination of version
 - Generation of QR codes (PAC-ID with extensions)
   
@@ -105,24 +105,24 @@ pac.print_validation_messages()
 >> Validation Results                                                                                                                   
 >> ┌───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
 >> │ **RECOMMENDATION** in id segment value bal500                                                                                     │
->> │ Characters 'b','l','a' should not be used., Characters SHOULD be limited to upper case letters (A-Z), numbers (0-9), '-' and '+'  │
+>> │ Characters 'a','l','b' 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                                                                             │
+>> │ HTTPS://PAC.METTORIUS.COM/-MD/👉bal👈500/@1234                                                                                    │
 >> ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
 >> │ **RECOMMENDATION** in id segment value @1234                                                                                      │
 >> │ Characters '@' should not be used., Characters SHOULD be limited to upper case letters (A-Z), numbers (0-9), '-' and '+'          │
 >> │                                                                                                                                   │
->> │ HTTPS://PAC.METTORIUS.COM/-MD/240:bal500/21:👉@👈1234                                                                             │
+>> │ HTTPS://PAC.METTORIUS.COM/-MD/bal500/👉@👈1234                                                                                    │
 >> ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
 >> │ **RECOMMENDATION** in id segment value bal500                                                                                     │
->> │ Characters 'b','l','a' should not be used., Characters SHOULD be limited to upper case letters (A-Z), numbers (0-9), '-' and '+'  │
+>> │ Characters 'a','l','b' 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                                                                             │
+>> │ HTTPS://PAC.METTORIUS.COM/-MD/👉bal👈500/@1234                                                                                    │
 >> ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
 >> │ **RECOMMENDATION** in id segment value @1234                                                                                      │
 >> │ Characters '@' should not be used., Characters SHOULD be limited to upper case letters (A-Z), numbers (0-9), '-' and '+'          │
 >> │                                                                                                                                   │
->> │ HTTPS://PAC.METTORIUS.COM/-MD/240:bal500/21:👉@👈1234                                                                             │
+>> │ HTTPS://PAC.METTORIUS.COM/-MD/bal500/👉@👈1234                                                                                    │
 >> └───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
 ```
 ### Save as QR Code
@@ -152,8 +152,8 @@ if isinstance(pac, PAC_CAT):
 ```
 ```text
 >> Categories in           
->> HTTPS://PAC.METTORIUS.COM/-MD/240:
->>          bal500/21:@1234          
+>> HTTPS://PAC.METTORIUS.COM/-DR/XQ90
+>>       8756/-MD/bal500/@1234       
 >> ┌────────────────────┬───────────┐
 >> │ Main Category      │           │
 >> │ key ()             │  -DR      │
@@ -248,7 +248,7 @@ trex.print_validation_messages()
 >> Validation Results                                            
 >> ┌────────────────────────────────────────────────────────────┐
 >> │ **ERROR** in TREX table column Date                        │
->> │ Column header key contains invalid characters: 'e','a','t' │
+>> │ Column header key contains invalid characters: 'a','t','e' │
 >> │                                                            │
 >> │ STOP$T.D:20240505T1306                                     │
 >> │ +TEMP$KEL:10.15                                            │
@@ -256,9 +256,9 @@ trex.print_validation_messages()
 >> │ +COMMENT$T.A:FOO                                           │
 >> │ +COMMENT2$T.T:12G3                                         │
 >> │ +TABLE$$DURATION$HUR:D👉ate👈$T.D:OK$T.B:COMMENT$T.A::     │
->> │  1:20250430T100239.279:T:FOO::                             │
->> │  1.1:20250430T100239.280:T:BAR::                           │
->> │  1.3:20250430T100239.280:F:BLUBB                           │
+>> │  1:20250513T080159.146:T:FOO::                             │
+>> │  1.1:20250513T080159.146:T:BAR::                           │
+>> │  1.3:20250513T080159.146:F:BLUBB                           │
 >> └────────────────────────────────────────────────────────────┘
 ```
 #### Combine PAC-ID and TREX and serialize
@@ -270,7 +270,7 @@ pac_str = pac.to_url()
 print(pac_str)
 ```
 ```text
->> HTTPS://PAC.METTORIUS.COM/21:1234*MYTREX$TREX/STOP$T.D:20240505T1306+TEMP$KEL:10.15+OK$T.B:F+COMMENT$T.A:FOO+COMMENT2$T.T:12G3+TABLE$$DURATION$HUR:Date$T.D:OK$T.B:COMMENT$T.A::1:20250430T100239.279:T:FOO::1.1:20250430T100239.280:T:BAR::1.3:20250430T100239.280: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::1:20250513T080159.146:T:FOO::1.1:20250513T080159.146:T:BAR::1.3:20250513T080159.146:F:BLUBB
 ```
 ## PAC-ID Resolver
 
@@ -306,12 +306,12 @@ for sg in service_groups:
 >> ┡━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━┩
 >> │ CAS Search   │ https://pubchem.ncbi.nlm.nih.gov/#query=7732-18-5 │ ACTIVE    │
 >> └──────────────┴───────────────────────────────────────────────────┴───────────┘
->>                                     Services from origin 'MY_COMPANY                                    
->> ┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━┓
->> ┃ Service Name        ┃ URL                                                                ┃ Reachable ┃
->> ┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━┩
->> │ Chemical Management │ https://chem-manager.com/METTORIUS.COM/-MS/240:X3511/CAS:7732-18-5 │ INACTIVE  │
->> └─────────────────────┴────────────────────────────────────────────────────────────────────┴───────────┘
+>>                                   Services from origin 'MY_COMPANY                                  
+>> ┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━┓
+>> ┃ Service Name        ┃ URL                                                            ┃ Reachable ┃
+>> ┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━┩
+>> │ Chemical Management │ https://chem-manager.com/METTORIUS.COM/-MS/X3511/CAS:7732-18-5 │ INACTIVE  │
+>> └─────────────────────┴────────────────────────────────────────────────────────────────┴───────────┘
 >>              Services from origin 'METTORIUS.COM              
 >> ┏━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━┓
 >> ┃ Service Name ┃ URL                             ┃ Reachable ┃
@@ -327,6 +327,13 @@ for sg in service_groups:
 
 <!-- BEGIN CHANGELOG -->
 ## Change Log
+### v0.2.7
+- Improved README. No functional changes
+  
+### v0.2.6
+- PAC_ID.to_url() preserves the identifier as is by default but allows to force short or long notation.
+- PAC-ID Resolver does not try to resolve PAC-CAT with CIT v1.
+  
 ### v0.2.5
 - resolvers checks service states by default
 - improvements and bugfixes in conversion from python types to TREX

{labfreed-0.2.6a5.dist-info → labfreed-0.2.7.dist-info}/RECORD

@@ -1,4 +1,4 @@
-labfreed/__init__.py,sha256=HM--oq6iUUbtBQn6g2KfzcilwUaipYei_vdBhlM_itM,338
+labfreed/__init__.py,sha256=cdoNTE10KG03M6MTCkgCbySTOajvy8HehAEgYvLJKmY,336
 labfreed/labfreed_infrastructure.py,sha256=EPDSCaGxWakAoPpHyc6ltf-pOuKyS5829lj_EG6wa74,10072
 labfreed/pac_cat/__init__.py,sha256=KNPtQzBD1XVohvG_ucOs7RJj-oi6biUTGB1k-T2o6pk,568
 labfreed/pac_cat/category_base.py,sha256=lFQNiTUukyhWdaSCAI7CZxLtj6kNtnBCE4UsePwsGqE,1801
@@ -7,14 +7,14 @@ labfreed/pac_cat/predefined_categories.py,sha256=5wnMCj-CrACV2W4lH13w7qynWIwi506
 labfreed/pac_id/__init__.py,sha256=NGMbzkwQ4txKeT5pxdIZordwHO8J3_q84jzPanjKoHg,675
 labfreed/pac_id/extension.py,sha256=zuHI8e51otPbpO1r1xDFh32uXTT8L5pCJn74B-aOUpI,1112
 labfreed/pac_id/id_segment.py,sha256=r5JU1SJuRXhZJJxy5T3xjrb598wIDTLpivSJhIUAzjQ,4526
-labfreed/pac_id/pac_id.py,sha256=IWXYlKFjQKB_9U5bINWC5_Lb5pcVbuleocvGs79A28w,5300
+labfreed/pac_id/pac_id.py,sha256=PyOa5y2IVLEcmj7ZkFuURC1lrP3BU0Yj8pzAllhtatw,5309
 labfreed/pac_id/url_parser.py,sha256=TAQHxFf7Li8GA517mfOivmnJAJgh782oaSDzmOOkyTE,5942
-labfreed/pac_id/url_serializer.py,sha256=3D5pwcAP4ZrCQ22BRtxIwqWrFtZuY9913hCLPJNeyPI,2845
+labfreed/pac_id/url_serializer.py,sha256=BgGoU_8W0Lvo153cXH8gX1k8H-FJtGizsEzjRaaEMcg,3270
 labfreed/pac_id_resolver/__init__.py,sha256=RNBlrDOSR42gmSNH9wJVhK_xwEX45cvTKVgWW2bjh7Q,113
 labfreed/pac_id_resolver/cit_common.py,sha256=xEkSSumj_IYgnXn3yKvoTBbgExnIfPY7E-RHU-7pcX8,2905
-labfreed/pac_id_resolver/cit_v1.py,sha256=1dx0zqJfzFOE4kP8_i8EJSLhvjVovc_i9Bazb53B0fU,9548
-labfreed/pac_id_resolver/cit_v2.py,sha256=I4Eri6r61O_BFFwCIyHZzwCQCVQJ7Rj9TW8MIOb2Rwg,11944
-labfreed/pac_id_resolver/resolver.py,sha256=SQlATlaUsmS6EZlEMyBQsp00ixpN3r-3V5pMXcvHYCw,2739
+labfreed/pac_id_resolver/cit_v1.py,sha256=W7UCO0Gm0w09FSo_USFB1-V2tl3iErDxoe2OHh4fkvc,9383
+labfreed/pac_id_resolver/cit_v2.py,sha256=wM1wf8UWbepatWNgkJ3l0l-HNJHqsqqPMql5k8fkVso,12127
+labfreed/pac_id_resolver/resolver.py,sha256=UfSxRwTTjSgL4VoHfsQiaGTj3tt8dTDDd2wVcbr2Xvc,2817
 labfreed/pac_id_resolver/services.py,sha256=TPoH6YlSwa0hmawHpOiMwIpBAinhoRhMSoexop0YscI,2462
 labfreed/qr/__init__.py,sha256=fdKwP6W2Js--yMbBUdn-g_2uq2VqPpfQJeDLHsMDO-Y,61
 labfreed/qr/generate_qr.py,sha256=mSt-U872O3ReHB_UdS-MzYu0wRgdlKcAOEfTxg5CLRk,16616
@@ -39,7 +39,7 @@ labfreed/well_known_keys/labfreed/well_known_keys.py,sha256=nqk66kHdSwJTJfMKlP-x
 labfreed/well_known_keys/unece/UneceUnits.json,sha256=kwfQSp_nTuWbADfBBgqTWrvPl6XtM5SedEVLbMJrM7M,898953
 labfreed/well_known_keys/unece/__init__.py,sha256=MSP9lmjg9_D9iqG9Yq2_ajYfQSNS9wIT7FXA1c--59M,122
 labfreed/well_known_keys/unece/unece_units.py,sha256=gNDQk6KGl-nGMf9Ycq_fQ8P2xxKITgLkcQWPd4H49gI,1630
-labfreed-0.2.6a5.dist-info/licenses/LICENSE,sha256=gHFOv9FRKHxO8cInP3YXyPoJnuNeqrvcHjaE_wPSsQ8,1100
-labfreed-0.2.6a5.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
-labfreed-0.2.6a5.dist-info/METADATA,sha256=Vdc6vdvGls5bzknFaZmD7OCMz0yM0FNzd0M6UrFbRoM,18616
-labfreed-0.2.6a5.dist-info/RECORD,,
+labfreed-0.2.7.dist-info/licenses/LICENSE,sha256=gHFOv9FRKHxO8cInP3YXyPoJnuNeqrvcHjaE_wPSsQ8,1100
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