labfreed 0.2.1__tar.gz → 0.2.3__tar.gz

{labfreed-0.2.1 → labfreed-0.2.3}/.github/workflows/pypi-publish.yml

@@ -24,7 +24,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Install dependencies
         run: |

{labfreed-0.2.1 → labfreed-0.2.3}/CHANGELOG.md

@@ -1,4 +1,11 @@
 ## Change Log
+### v0.2.3
+- improvements in formatting of validation messages
+- bugfix in DisplayNameExtension
+  
+### v0.2.2
+- minor changes for better access of subfunctions. No change in existing API
+  
 ### v0.2.1
 - improved docu. no code changes
 
@@ -22,11 +29,5 @@
 - QR generation 
 - ok-ish test coverage
 
-# Attributions
-The following tools were used:
-- [pdoc](https://pdoc.dev/) was a great help with generating documentation
-- [Pydantic](https://docs.pydantic.dev/latest/)
-- json with UNECE units from (https://github.com/quadient/unece-units/blob/main/python/src/unece_excel_parser/parsedUneceUnits.json)
-- json with GS1 codes from (https://ref.gs1.org/ai/GS1_Application_Identifiers.jsonld)
 
 

{labfreed-0.2.1 → labfreed-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: labfreed
-Version: 0.2.1
+Version: 0.2.3
 Summary: Python implementation of LabFREED building blocks
 Author-email: Reto Thürer <thuerer.r@buchi.com>
 Requires-Python: >=3.11
@@ -98,30 +98,28 @@ There is a nice function to highlight problems
 pac.print_validation_messages()
 ```
 ```text
->> 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  │
->> │ '+'                                                                                                                           │
->> │                                                                                                                               │
->> │ HTTPS://PAC.METTORIUS.COM/-MD/240:👉bal👈500/21:@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                                                                         │
->> ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
->> │ 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  │
->> │ '+'                                                                                                                           │
->> │                                                                                                                               │
->> │ HTTPS://PAC.METTORIUS.COM/-MD/240:👉bal👈500/21:@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                                                                         │
->> └───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
+>> 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 '+'  │
+>> │                                                                                                                                   │
+>> │ HTTPS://PAC.METTORIUS.COM/-MD/240:👉bal👈500/21:@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                                                                             │
+>> ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
+>> │ **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 '+'  │
+>> │                                                                                                                                   │
+>> │ HTTPS://PAC.METTORIUS.COM/-MD/240:👉bal👈500/21:@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                                                                             │
+>> └───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
 ```
 ### Save as QR Code
 
@@ -141,7 +139,7 @@ PAC-CAT defines a (optional) way how the identifier is structured.
 PAC_ID.from_url() automatically converts to PAC-CAT if possible.
 
 ```python
-from labfreed.pac_cat import PAC_CAT  
+from labfreed import PAC_CAT  
 pac_str = 'HTTPS://PAC.METTORIUS.COM/-DR/XQ908756/-MD/bal500/@1234'
 pac = PAC_ID.from_url(pac_str)
 if isinstance(pac, PAC_CAT):
@@ -197,7 +195,7 @@ print(f'WEIGHT = {v.value}')
 #### Create PAC-ID
 
 ```python
-from labfreed.pac_id import PAC_ID, IDSegment  
+from labfreed import PAC_ID, IDSegment  
 from labfreed.well_known_keys.labfreed.well_known_keys import WellKnownKeys  
 
 pac = PAC_ID(issuer='METTORIUS.COM', identifier=[IDSegment(key=WellKnownKeys.SERIAL, value='1234')])
@@ -213,9 +211,9 @@ Note that utility types for Quantity (number with unit) and table are needed
 
 ```python
 from datetime import datetime  
-from labfreed.trex.python_convenience.pyTREX import pyTREX  
-from labfreed.trex.python_convenience.data_table import DataTable  
-from labfreed.trex.python_convenience.quantity import Quantity  
+from labfreed.trex.python_convenience import pyTREX  
+from labfreed.trex.python_convenience import DataTable  
+from labfreed.trex.python_convenience import Quantity  
 
 # Value segments of different type
 segments = {
@@ -245,18 +243,18 @@ trex.print_validation_messages()
 ```text
 >> Validation Results                                            
 >> ┌────────────────────────────────────────────────────────────┐
->> │ ERROR  in TREX table column Date                           │
->> │ Column header key contains invalid characters: 'a','e','t' │
+>> │ **ERROR** in TREX table column Date                        │
+>> │ Column header key contains invalid characters: 'a','t','e' │
 >> │                                                            │
 >> │ STOP$T.D:20240505T1306                                     │
 >> │ +TEMP$KEL:10.15                                            │
 >> │ +OK$T.B:F                                                  │
 >> │ +COMMENT$T.A:FOO                                           │
->> │ +COMMENT2$T.T:QMDTNXIKU                                    │
+>> │ +COMMENT2$T.T:12G3                                         │
 >> │ +TABLE$$DURATION$HUR:D👉ate👈$T.D:OK$T.B:COMMENT$T.A::     │
->> │  1:20250424T161739.312:T:FOO::                             │
->> │  1.1:20250424T161739.312:T:BAR::                           │
->> │  1.3:20250424T161739.312:F:BLUBB                           │
+>> │  1:20250425T081731.192:T:FOO::                             │
+>> │  1.1:20250425T081731.192:T:BAR::                           │
+>> │  1.3:20250425T081731.192:F:BLUBB                           │
 >> └────────────────────────────────────────────────────────────┘
 ```
 #### Combine PAC-ID and TREX and serialize
@@ -268,12 +266,12 @@ pac_str = pac.to_url()
 print(pac_str)
 ```
 ```text
->> HTTPS://PAC.METTORIUS.COM/21:1234*MYTREX$TREX/STOP$T.D:20240505T1306+TEMP$KEL:10.15+OK$T.B:F+COMMENT$T.A:FOO+COMMENT2$T.T:QMDTNXIKU+TABLE$$DURATION$HUR:Date$T.D:OK$T.B:COMMENT$T.A::1:20250424T161739.312:T:FOO::1.1:20250424T161739.312:T:BAR::1.3:20250424T161739.312: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::1:20250425T081731.192:T:FOO::1.1:20250425T081731.192:T:BAR::1.3:20250425T081731.192:F:BLUBB
 ```
 ## PAC-ID Resolver
 
 ```python
-from labfreed.pac_id_resolver import PAC_ID_Resolver, load_cit  
+from labfreed import PAC_ID_Resolver, load_cit  
 # Get a CIT
 dir = os.path.join(os.getcwd(), 'examples')
 p = os.path.join(dir, 'cit_mine.yaml')       
@@ -299,7 +297,26 @@ for sg in service_groups:
     
 ```
 ```text
->> [Error during execution: No Internet Connection]
+>> Services from origin 'PERSONAL                         
+>> ┏━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━┓
+>> ┃ Service Name ┃ URL                                               ┃ Reachable ┃
+>> ┡━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━┩
+>> │ 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 'METTORIUS.COM              
+>> ┏━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━┓
+>> ┃ Service Name ┃ URL                             ┃ Reachable ┃
+>> ┡━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━┩
+>> │ CoA          │ https://mettorius.com/CoA.pdf   │ ACTIVE    │
+>> │ MSDS         │ https://mettorius.com/MSDS.pdf  │ ACTIVE    │
+>> │ Shop         │ https://mettorius.com/shop.html │ ACTIVE    │
+>> └──────────────┴─────────────────────────────────┴───────────┘
 ```
 <!-- END EXAMPLES -->
 
@@ -307,6 +324,13 @@ for sg in service_groups:
 
 <!-- BEGIN CHANGELOG -->
 ## Change Log
+### v0.2.3
+- improvements in formatting of validation messages
+- bugfix in DisplayNameExtension
+  
+### v0.2.2
+- minor changes for better access of subfunctions. No change in existing API
+  
 ### v0.2.1
 - improved docu. no code changes
 
@@ -329,6 +353,7 @@ for sg in service_groups:
 - supports PAC-ID, PAC-CAT, TREX and DisplayName
 - QR generation 
 - ok-ish test coverage
+<!-- END CHANGELOG -->
 
 # Attributions
 The following tools were used:
@@ -336,4 +361,4 @@ The following tools were used:
 - [Pydantic](https://docs.pydantic.dev/latest/)
 - json with UNECE units from (https://github.com/quadient/unece-units/blob/main/python/src/unece_excel_parser/parsedUneceUnits.json)
 - json with GS1 codes from (https://ref.gs1.org/ai/GS1_Application_Identifiers.jsonld)
-<!-- END CHANGELOG -->
+

{labfreed-0.2.1 → labfreed-0.2.3}/README.md

@@ -67,30 +67,28 @@ There is a nice function to highlight problems
 pac.print_validation_messages()
 ```
 ```text
->> 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  │
->> │ '+'                                                                                                                           │
->> │                                                                                                                               │
->> │ HTTPS://PAC.METTORIUS.COM/-MD/240:👉bal👈500/21:@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                                                                         │
->> ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
->> │ 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  │
->> │ '+'                                                                                                                           │
->> │                                                                                                                               │
->> │ HTTPS://PAC.METTORIUS.COM/-MD/240:👉bal👈500/21:@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                                                                         │
->> └───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
+>> 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 '+'  │
+>> │                                                                                                                                   │
+>> │ HTTPS://PAC.METTORIUS.COM/-MD/240:👉bal👈500/21:@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                                                                             │
+>> ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
+>> │ **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 '+'  │
+>> │                                                                                                                                   │
+>> │ HTTPS://PAC.METTORIUS.COM/-MD/240:👉bal👈500/21:@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                                                                             │
+>> └───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
 ```
 ### Save as QR Code
 
@@ -110,7 +108,7 @@ PAC-CAT defines a (optional) way how the identifier is structured.
 PAC_ID.from_url() automatically converts to PAC-CAT if possible.
 
 ```python
-from labfreed.pac_cat import PAC_CAT  
+from labfreed import PAC_CAT  
 pac_str = 'HTTPS://PAC.METTORIUS.COM/-DR/XQ908756/-MD/bal500/@1234'
 pac = PAC_ID.from_url(pac_str)
 if isinstance(pac, PAC_CAT):
@@ -166,7 +164,7 @@ print(f'WEIGHT = {v.value}')
 #### Create PAC-ID
 
 ```python
-from labfreed.pac_id import PAC_ID, IDSegment  
+from labfreed import PAC_ID, IDSegment  
 from labfreed.well_known_keys.labfreed.well_known_keys import WellKnownKeys  
 
 pac = PAC_ID(issuer='METTORIUS.COM', identifier=[IDSegment(key=WellKnownKeys.SERIAL, value='1234')])
@@ -182,9 +180,9 @@ Note that utility types for Quantity (number with unit) and table are needed
 
 ```python
 from datetime import datetime  
-from labfreed.trex.python_convenience.pyTREX import pyTREX  
-from labfreed.trex.python_convenience.data_table import DataTable  
-from labfreed.trex.python_convenience.quantity import Quantity  
+from labfreed.trex.python_convenience import pyTREX  
+from labfreed.trex.python_convenience import DataTable  
+from labfreed.trex.python_convenience import Quantity  
 
 # Value segments of different type
 segments = {
@@ -214,18 +212,18 @@ trex.print_validation_messages()
 ```text
 >> Validation Results                                            
 >> ┌────────────────────────────────────────────────────────────┐
->> │ ERROR  in TREX table column Date                           │
->> │ Column header key contains invalid characters: 'a','e','t' │
+>> │ **ERROR** in TREX table column Date                        │
+>> │ Column header key contains invalid characters: 'a','t','e' │
 >> │                                                            │
 >> │ STOP$T.D:20240505T1306                                     │
 >> │ +TEMP$KEL:10.15                                            │
 >> │ +OK$T.B:F                                                  │
 >> │ +COMMENT$T.A:FOO                                           │
->> │ +COMMENT2$T.T:QMDTNXIKU                                    │
+>> │ +COMMENT2$T.T:12G3                                         │
 >> │ +TABLE$$DURATION$HUR:D👉ate👈$T.D:OK$T.B:COMMENT$T.A::     │
->> │  1:20250424T161739.312:T:FOO::                             │
->> │  1.1:20250424T161739.312:T:BAR::                           │
->> │  1.3:20250424T161739.312:F:BLUBB                           │
+>> │  1:20250425T081731.192:T:FOO::                             │
+>> │  1.1:20250425T081731.192:T:BAR::                           │
+>> │  1.3:20250425T081731.192:F:BLUBB                           │
 >> └────────────────────────────────────────────────────────────┘
 ```
 #### Combine PAC-ID and TREX and serialize
@@ -237,12 +235,12 @@ pac_str = pac.to_url()
 print(pac_str)
 ```
 ```text
->> HTTPS://PAC.METTORIUS.COM/21:1234*MYTREX$TREX/STOP$T.D:20240505T1306+TEMP$KEL:10.15+OK$T.B:F+COMMENT$T.A:FOO+COMMENT2$T.T:QMDTNXIKU+TABLE$$DURATION$HUR:Date$T.D:OK$T.B:COMMENT$T.A::1:20250424T161739.312:T:FOO::1.1:20250424T161739.312:T:BAR::1.3:20250424T161739.312: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::1:20250425T081731.192:T:FOO::1.1:20250425T081731.192:T:BAR::1.3:20250425T081731.192:F:BLUBB
 ```
 ## PAC-ID Resolver
 
 ```python
-from labfreed.pac_id_resolver import PAC_ID_Resolver, load_cit  
+from labfreed import PAC_ID_Resolver, load_cit  
 # Get a CIT
 dir = os.path.join(os.getcwd(), 'examples')
 p = os.path.join(dir, 'cit_mine.yaml')       
@@ -268,7 +266,26 @@ for sg in service_groups:
     
 ```
 ```text
->> [Error during execution: No Internet Connection]
+>> Services from origin 'PERSONAL                         
+>> ┏━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━┓
+>> ┃ Service Name ┃ URL                                               ┃ Reachable ┃
+>> ┡━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━┩
+>> │ 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 'METTORIUS.COM              
+>> ┏━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━┓
+>> ┃ Service Name ┃ URL                             ┃ Reachable ┃
+>> ┡━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━┩
+>> │ CoA          │ https://mettorius.com/CoA.pdf   │ ACTIVE    │
+>> │ MSDS         │ https://mettorius.com/MSDS.pdf  │ ACTIVE    │
+>> │ Shop         │ https://mettorius.com/shop.html │ ACTIVE    │
+>> └──────────────┴─────────────────────────────────┴───────────┘
 ```
 <!-- END EXAMPLES -->
 
@@ -276,6 +293,13 @@ for sg in service_groups:
 
 <!-- BEGIN CHANGELOG -->
 ## Change Log
+### v0.2.3
+- improvements in formatting of validation messages
+- bugfix in DisplayNameExtension
+  
+### v0.2.2
+- minor changes for better access of subfunctions. No change in existing API
+  
 ### v0.2.1
 - improved docu. no code changes
 
@@ -298,6 +322,7 @@ for sg in service_groups:
 - supports PAC-ID, PAC-CAT, TREX and DisplayName
 - QR generation 
 - ok-ish test coverage
+<!-- END CHANGELOG -->
 
 # Attributions
 The following tools were used:
@@ -305,4 +330,3 @@ The following tools were used:
 - [Pydantic](https://docs.pydantic.dev/latest/)
 - json with UNECE units from (https://github.com/quadient/unece-units/blob/main/python/src/unece_excel_parser/parsedUneceUnits.json)
 - json with GS1 codes from (https://ref.gs1.org/ai/GS1_Application_Identifiers.jsonld)
-<!-- END CHANGELOG -->

labfreed-0.2.3/labfreed/__init__.py

@@ -0,0 +1,11 @@
+''' 
+Python implementation of LabFREED building blocks
+'''
+
+__version__ = "0.2.3"
+
+from labfreed.pac_id import *  # noqa: F403
+from labfreed.pac_cat import * # noqa: F403
+from labfreed.pac_id_resolver import * # noqa: F403
+from labfreed.trex import * # noqa: F403
+from labfreed.labfreed_infrastructure import *  # noqa: F403

{labfreed-0.2.1 → labfreed-0.2.3}/labfreed/labfreed_infrastructure.py

@@ -159,25 +159,9 @@ class LabFREED_BaseModel(PDOC_Workaround_Base):
         return warnings_list
         
 
-        
-    def _emphasize_in(self, validation_msg, validation_node_str:str, fmt, color='black'):
-        if validation_msg.highlight_sub_patterns:
-            replacements = validation_msg.highlight_sub_patterns
-        else:
-            replacements = [validation_msg.highlight]
-        # Sort patterns by length descending to avoid subpattern clobbering
-        sorted_patterns = sorted(replacements, key=len, reverse=True)
-        # Escape the patterns for regex safety
-        escaped_patterns = [re.escape(p) for p in sorted_patterns]
-        # Create one regex pattern with alternation (longest first)
-        pattern = re.compile("|".join(escaped_patterns))
-        
-        out = pattern.sub(lambda m: fmt(m.group(0)), validation_node_str)
-        return out
-    
     
     def print_validation_messages(self, target='console'):
-        msgs = self._get_nested_validation_messages()
+        msgs = self.format_validation_messages(target=target)
         
         table = Table(title="Validation Results", show_header=False, title_justify='left')
 
@@ -185,12 +169,29 @@ class LabFREED_BaseModel(PDOC_Workaround_Base):
             return table.add_column(s, vertical='top')
         col("-")
         
-             
         if not msgs:
             table.add_row('All clear!', end_section=True)
             return
 
         for m in msgs:
+            table.add_row(m)
+            table.add_section()
+
+        logging.info(table)
+        print(table)
+        
+        
+    def format_validation_messages(self, target='console') -> list[str]:
+        """Format validation messages
+
+        Args:
+            target (str, optional): Target format: 'markdown', 'console', 'html', 'html_styled'.
+
+        Returns:
+            list[str]: formated messages
+        """
+        formatted_msg = list()
+        for m in self.validation_messages():
             if m.level == ValidationMsgLevel.ERROR:
                 color = 'red'
             else:
@@ -199,70 +200,48 @@ class LabFREED_BaseModel(PDOC_Workaround_Base):
             match target:
                 case 'markdown':
                     fmt = lambda s: f'👉{s}👈'  # noqa: E731
+                    fmt_title = lambda s: f'**{s}**'  # noqa: E731
+                    br = '\n'
                 case 'console':     
                     fmt = lambda s: f'[{color} bold]{s}[/{color} bold]'  # noqa: E731
+                    fmt_title = fmt
+                    br = '\n'
                 case 'html':
-                    fmt = lambda s: f'<span class="val_{color}">{s}</span>'  # noqa: E731
+                    fmt = lambda s: f'<span class="validation-{m.level.name.lower()}">{s}</span>'  # noqa: E731
+                    fmt_title = lambda s: f'<span class="validation-title">{s}</span>'  # noqa: E731
+                    br = '<br>'
                 case 'html_styled':
-                    fmt = lambda s: f'<b style="color:{color}>{s}</b>'  # noqa: E731
+                    fmt = lambda s: f'<b style="color:{color}">{s}</b>'  # noqa: E731
+                    fmt_title = fmt
+                    br = '<br>'
                 
             serialized = str(self)
-            emphazised_highlight = self._emphasize_in(m, serialized, fmt=fmt, color=color)
+            emphazised_highlight = self._emphasize_in(m, serialized, fmt=fmt)
             emphazised_highlight = emphazised_highlight.replace('👈👉','') # removes two consecutive markers, to make it cleaner
             
-            txt =       f'[bold {color}]{m.level.name} [/bold {color}] in {m.source}'
-            txt += '\n' + f'{m.msg}'
-            txt += '\n\n' + emphazised_highlight
-
-            table.add_row( txt)
-            table.add_section()
-
-        logging.info(table)
-        print(table)
+            txt =   f'{fmt_title(m.level.name)} in {m.source}'
+            txt += br + f'{m.msg}'
+            txt += br+br + emphazised_highlight
             
-
-        
-    
+            formatted_msg.append(txt)
+        return formatted_msg
     
-    # def print_validation_messages_(self, str_to_highlight_in=None, target='console'):
-    #     if not str_to_highlight_in:
-    #         str_to_highlight_in = str(self)
-    #     msgs = self.get_nested_validation_messages()
-    #     print('\n'.join(['\n',
-    #                      '=======================================',
-    #                      'Validation Results',
-    #                      '---------------------------------------'
-    #                     ]
-    #                     )
-    #     )
-        
-    #     if not msgs:
-    #         print('All clear!')
-    #         return
-
-    #     for m in msgs:
-    #         if m.level.casefold() == "error":
-    #             color = 'red'
-    #         else:
-    #             color = 'yellow'
-                
-    #         text = Text.from_markup(f'\n [bold {color}]{m.level} [/bold {color}] in \t {m.source}' )
-    #         print(text)
-    #         match target:
-    #             case 'markdown':
-    #                 formatted_highlight = m.emphazised_highlight.replace('emph', f'🔸').replace('[/', '').replace('[', '').replace(']', '')
-    #             case 'console':     
-    #                 formatted_highlight = m.emphazised_highlight.replace('emph', f'bold {color}')
-    #             case 'html':
-    #                 formatted_highlight = m.emphazised_highlight.replace('emph', f'b').replace('[', '<').replace(']', '>')
-    #         fmtd = str_to_highlight_in.replace(m.highlight, formatted_highlight)
-    #         fmtd = Text.from_markup(fmtd)
-    #         print(fmtd)
-    #         print(Text.from_markup(f'{m.problem_msg}'))
+    def _emphasize_in(self, validation_msg, validation_node_str:str, fmt):
+        if validation_msg.highlight_sub_patterns:
+            replacements = validation_msg.highlight_sub_patterns
+        else:
+            replacements = [validation_msg.highlight]
+        # Sort patterns by length descending to avoid subpattern clobbering
+        sorted_patterns = sorted(replacements, key=len, reverse=True)
+        # Escape the patterns for regex safety
+        escaped_patterns = [re.escape(p) for p in sorted_patterns]
+        # Create one regex pattern with alternation (longest first)
+        pattern = re.compile("|".join(escaped_patterns))
         
-    
-    
-    
+        out = pattern.sub(lambda m: fmt(m.group(0)), validation_node_str)
+        return out
+            
+
     
 def _filter_errors(val_msg:list[ValidationMessage]) -> list[ValidationMessage]:
     return [ m for m in val_msg if m.level == ValidationMsgLevel.ERROR ]

{labfreed-0.2.1 → labfreed-0.2.3}/labfreed/pac_cat/__init__.py

@@ -1,6 +1,9 @@
 from .pac_cat import PAC_CAT
 from .category_base import Category
-from .predefined_categories import Material_Device, Material_Substance, Material_Consumable, Material_Misc, Data_Method, Data_Result, Data_Progress, Data_Calibration, Data_Abstract
+from .predefined_categories import (
+    Material_Device, Material_Substance, Material_Consumable, Material_Misc, Data_Method, Data_Result, Data_Progress, 
+    Data_Calibration, Data_Abstract, category_key_to_class_map
+    )
 
 __all__ = [
     "PAC_CAT",

{labfreed-0.2.1 → labfreed-0.2.3}/labfreed/pac_cat/pac_cat.py

@@ -10,7 +10,7 @@ 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 Data_Calibration, Data_Method, Data_Progress, Data_Result, Material_Consumable, Material_Device, Material_Misc, Material_Substance, Data_Static
+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
 
@@ -68,18 +68,7 @@ class PAC_CAT(PAC_ID):
         category_key = segments[0].value         
         segments.pop(0)
         
-        mapping  = {
-                '-MD': Material_Device,
-                '-MS': Material_Substance,
-                '-MC': Material_Consumable,
-                '-MM': Material_Misc,
-                '-DM': Data_Method,
-                '-DR': Data_Result,
-                '-DC': Data_Calibration,
-                '-DP': Data_Progress,
-                '-DS': Data_Static 
-        }
-        known_cat = mapping.get(category_key)
+        known_cat = category_key_to_class_map.get(category_key)
         
         if not known_cat:
             return Category(key=category_key, segments=segments)
@@ -157,3 +146,5 @@ class PAC_CAT(PAC_ID):
             table.add_section()        
         print(table)
         
+
+        

{labfreed-0.2.1 → labfreed-0.2.3}/labfreed/pac_cat/predefined_categories.py

@@ -188,3 +188,14 @@ class Data_Static(Data_Abstract):
     ''' Category segments, which are not defined in the specification'''
     
     
+category_key_to_class_map  = {
+        '-MD': Material_Device,
+        '-MS': Material_Substance,
+        '-MC': Material_Consumable,
+        '-MM': Material_Misc,
+        '-DM': Data_Method,
+        '-DR': Data_Result,
+        '-DC': Data_Calibration,
+        '-DP': Data_Progress,
+        '-DS': Data_Static 
+}

{labfreed-0.2.1 → labfreed-0.2.3}/labfreed/pac_id/extension.py

@@ -15,6 +15,8 @@ class ExtensionBase(ABC):
     def data(self) -> str:
         raise NotImplementedError("Subclasses must implement 'data'")
     
+    def __str__(self):
+        return f'{self.name}${self.type}/{self.data}'
     
 
 
@@ -43,6 +45,4 @@ class Extension(LabFREED_BaseModel,ExtensionBase):
         "extra": "allow",  # Allow extra keys during pre-validation
     }
     
-    def __str__(self):
-        return f'{self.name}${self.type}/{self.data}'
-    
+

{labfreed-0.2.1 → labfreed-0.2.3}/labfreed/trex/table_segment.py

@@ -8,7 +8,7 @@ from pydantic import RootModel, model_validator
 from labfreed.trex.trex_base_models import Value
 from labfreed.well_known_keys.unece.unece_units import unece_unit_codes
 from labfreed.labfreed_infrastructure import LabFREED_BaseModel, ValidationMsgLevel, _quote_texts
-from labfreed.trex.trex_base_models import AlphanumericValue, BinaryValue, BoolValue, DateValue, ErrorValue, NumericValue, TREX_Segment, TextValue, str_to_value_type
+from labfreed.trex.trex_base_models import AlphanumericValue, BinaryValue, BoolValue, DateValue, ErrorValue, NumericValue, TREX_Segment, TextValue
 
 
 class ColumnHeader(LabFREED_BaseModel):
@@ -217,11 +217,28 @@ def _deserialize_table_segment_from_trex_segment_str(trex_segment_str) -> TableS
          headers.append(ColumnHeader(key=col_key, type=col_type))
     
     data = [row.split(':') for row in body.split('::') ]
-    col_types = [h.type for h in headers]
     # convert to correct value types
-    data_with_types = [[str_to_value_type(c,t) for c, t in zip(r, col_types)] for r in data]
+    data_with_types = [[_str_to_value_type(h.type, cv) for cv, h in zip(r, headers)] for r in data]
     data = [ TableRow(r) for r in data_with_types]
              
-    out = TableSegment(column_headers=headers, data=data_with_types, key=name)
+    out = TableSegment(column_headers=headers, data=data, key=name)
+    return out
+
+def _str_to_value_type(type_, s):
+    match type_:
+        case 'T.D':
+            out = DateValue(value=s)
+        case 'T.B':
+            out = BoolValue(value=s)
+        case 'T.A':
+            out = AlphanumericValue(value=s)
+        case 'T.T':
+            out = TextValue(value=s)
+        case 'T.X':
+            out = BinaryValue(value=s)
+        case 'E':
+            out = ErrorValue(value=s)
+        case _:
+            out = NumericValue(value=s)
     return out
         

{labfreed-0.2.1 → labfreed-0.2.3}/labfreed/trex/trex_base_models.py

@@ -4,11 +4,10 @@ import re
 
 
 
-from pydantic import PrivateAttr,  field_validator, model_validator
+from pydantic import PrivateAttr, model_validator
 from labfreed.labfreed_infrastructure import LabFREED_BaseModel, ValidationMsgLevel, _quote_texts
-from abc import ABC, abstractclassmethod,  abstractmethod
+from abc import ABC, abstractmethod
 
-from labfreed.utilities.base36 import base36, to_base36, from_base36
 
 
 ''' Configure pdoc'''
@@ -32,22 +31,9 @@ class Value(LabFREED_BaseModel, ABC):
     def serialize(self):
         return self.value
         
-    @abstractclassmethod
-    def _from_python_type(cls, v):
-        ...
-        
-    @abstractmethod
-    def _value_to_python_type(self):
-        ...
         
         
 class NumericValue(Value):
-    @field_validator('value', mode='before')
-    @classmethod
-    def _from_python_type(cls, v:str| int|float):
-        if isinstance(v, str):
-            return v
-        return str(v)
         
     @model_validator(mode='after')
     def _validate(self):
@@ -56,7 +42,7 @@ class NumericValue(Value):
             self._add_validation_message(
                 source=f"TREX numeric value {value}",
                 level=ValidationMsgLevel.ERROR,
-                msg=f"Characters {_quote_texts(not_allowed_chars)} are not allowed in quantity segment. Base36 encoding only allows A-Z0-9",
+                msg=f"Characters {_quote_texts(not_allowed_chars)} are not allowed in quantity segment. Must be a number.",
                 highlight_pattern = f'{value}',
                 highlight_sub=not_allowed_chars
             )
@@ -68,36 +54,9 @@ class NumericValue(Value):
                 highlight_pattern = f'{value}'               
             )
         return self
-    
-    def _value_to_python_type(self) -> str:
-        v = float(self.value)  
-        if '.' not in self.value and 'E' not in self.value: 
-            return int(v)
-        else:
-            return v
-
 
 class DateValue(Value):
     _date_time_dict:dict|None = PrivateAttr(default=None)
-    @field_validator('value', mode='before')
-    @classmethod
-    def _from_python_type(cls, v:str| date|time|datetime):
-        if isinstance(v, str):
-            return v
-        
-        sd = ""
-        st = ""
-        if isinstance(v, date) or isinstance(v, datetime):
-            sd = v.strftime('%Y%m%d')
-        if isinstance(v, time) or isinstance(v, datetime):
-            if v.microsecond:
-                st = v.strftime("T%H%M%S.") + f"{v.microsecond // 1000:03d}"
-            elif v.second:
-                st = v.strftime("T%H%M%S")
-            else:
-                st = v.strftime("T%H%M")
-                         
-        return sd + st
     
     @model_validator(mode='after')
     def _validate(self):
@@ -134,24 +93,8 @@ class DateValue(Value):
         self._date_time_dict = d
         return self
     
-    def _value_to_python_type(self) -> str:
-        d = self._date_time_dict
-        if d.get('year') and d.get('hour'): # input is only a time
-            return datetime(**d)
-        elif d.get('year'):
-            return date(**d)
-        else:
-            return time(**d)
-    
-   
+
 class BoolValue(Value):
-    @field_validator('value', mode='before')
-    @classmethod
-    def _from_python_type(cls, v:str| bool):
-        if isinstance(v, str):
-            return v
-        
-        return 'T' if v else 'F'
 
     @model_validator(mode='after')
     def _validate(self):
@@ -164,21 +107,9 @@ class BoolValue(Value):
                 highlight_sub=[c for c in self.value]
             )
         return self
-    
-    def _value_to_python_type(self) -> str:
-        if self.value == 'T':
-            return True
-        elif self.value == 'F':
-            return False
-        else:
-            Exception(f'{self} is not valid boolean. That really should not have been possible -- Contact the maintainers of the library')
-                    
+                  
                     
 class AlphanumericValue(Value):
-    @field_validator('value', mode='before')
-    @classmethod
-    def _from_python_type(cls, v:str):
-        return v
         
     @model_validator(mode='after')
     def _validate(self):
@@ -199,20 +130,9 @@ class AlphanumericValue(Value):
                     highlight_sub=not_allowed_chars
             )
         return self
-           
-    def _value_to_python_type(self) -> str:
-        return self.value
-    
+             
     
 class TextValue(Value):
-    @field_validator('value', mode='before')
-    @classmethod
-    def _from_python_type(cls, v:base36|str):
-        if isinstance(v, str):
-            logging.info('Got str for text value > converting to base36')
-            return to_base36(v).root
-        else:
-            return v.root
         
     @model_validator(mode='after')
     def _validate(self):
@@ -225,20 +145,9 @@ class TextValue(Value):
                     highlight_sub=not_allowed_chars
             )
         return self
-              
-    def _value_to_python_type(self) -> str:
-        decoded = from_base36(self.value)
-        return decoded
-    
+                
     
 class BinaryValue(Value):
-    @field_validator('value', mode='before')
-    @classmethod
-    def _from_python_type(cls, v:base36|str):
-        if isinstance(v, str):
-            return v
-        else:
-            return v.root
         
     @model_validator(mode='after')
     def _validate(self):
@@ -251,17 +160,9 @@ class BinaryValue(Value):
                     highlight_sub=not_allowed_chars
             )
         return self
-              
-    def _value_to_python_type(self) -> bytes:
-        decoded = bytes(from_base36(self))
-        return decoded
-    
+                 
     
 class ErrorValue(Value):
-    @field_validator('value', mode='before')
-    @classmethod
-    def _from_python_type(cls, v:str):
-        return v
     
     @model_validator(mode='after')
     def _validate(self):
@@ -274,10 +175,6 @@ class ErrorValue(Value):
                     highlight_sub=not_allowed_chars
             )
         return self
-       
-    
-    def _value_to_python_type(self) -> str:
-        return self.value
 
 
 class TREX_Segment(LabFREED_BaseModel, ABC):
@@ -305,31 +202,8 @@ class TREX_Segment(LabFREED_BaseModel, ABC):
     
 
         
-      
- 
-def str_to_value_type(s:str, t:str):
-    match t:
-        case 'T.D': 
-            v = DateValue(value=s)
-        case 'T.B': 
-            v = BoolValue(value=s)
-        case 'T.A': 
-            v = AlphanumericValue(value=s)
-        case 'T.T': 
-            try:
-                value = base36(s)
-            except ValueError:
-                logging.error('String given as T.T contains characters which base36 should not')
-                value = s
-            v = TextValue(value=value)
-        case 'T.X': 
-            v = BinaryValue(value=s)
-        case 'E'  : 
-            v = ErrorValue(value=s)
-        case _    : 
-            v = NumericValue(value=s)         
-    return v   
-    
+
+
 
     
 

{labfreed-0.2.1 → labfreed-0.2.3}/labfreed/trex/value_segments.py

@@ -89,19 +89,9 @@ def _deserialize_value_segment_from_trex_segment_str(trex_segment_str) -> ValueS
         case 'T.A':
             out = AlphanumericSegment(key=key, value=value, type=type_)
         case 'T.T':
-            try:
-                value = base36(value)
-            except ValueError:
-                logging.error('String given as T.T contains characters which base36 should not')
-                value = value
-            out = TextSegment(key=key, value=value, type=type_)  # prevent repeated conversion from str to base36 and make explict that when parsing we assume the string tpo be base36 already
+            out = TextSegment(key=key, value=value, type=type_)  
         case 'T.X':
-            try:
-                value = base36(value)
-            except ValueError:
-                logging.error('String given as T.X contains characters which base36 should not')
-                value = value
-            out = BinarySegment(key=key, value=value, type=type_) # prevent repeated conversion from str to base36 and make explict that when parsing we assume the string tpo be base36 already
+            out = BinarySegment(key=key, value=value, type=type_) 
         case 'E':
             out = ErrorSegment(key=key, value=value, type=type_)
         case _:

{labfreed-0.2.1 → labfreed-0.2.3}/labfreed/well_known_extensions/display_name_extension.py

@@ -15,7 +15,7 @@ class DisplayNameExtension(ExtensionBase, LabFREED_BaseModel):
     @property
     def data(self)->str:
         # return '/'.join([to_base36(dn) for dn in self.display_name])
-        return to_base36(self.display_name) 
+        return to_base36(self.display_name).root
     
     @staticmethod
     def from_extension(ext:ExtensionBase) -> Self:

labfreed-0.2.1/labfreed/__init__.py

@@ -1,8 +0,0 @@
-''' 
-Python implementation of LabFREED building blocks
-'''
-
-__version__ = "0.2.1"
-
-from labfreed.pac_id import PAC_ID  # noqa: F401
-from labfreed.labfreed_infrastructure import LabFREED_ValidationError  # noqa: F401