labfreed 0.0.15__tar.gz → 0.0.17__tar.gz

{labfreed-0.0.15 → labfreed-0.0.17}/PKG-INFO

@@ -1,11 +1,15 @@
 Metadata-Version: 2.4
 Name: labfreed
-Version: 0.0.15
+Version: 0.0.17
 Summary: Python implementation of LabFREED building blocks
 Author-email: Reto Thürer <thuerer.r@buchi.com>
 Description-Content-Type: text/markdown
 License-Expression: MIT
 License-File: LICENSE
+Requires-Dist: numpy>=2.2.4
+Requires-Dist: pydantic>=2.11.3
+Requires-Dist: segno>=1.6.6
+Requires-Dist: typer>=0.15.2
 
 # LabFREED for Python
 
@@ -32,13 +36,9 @@ pip install labfreed
 
 
 ## Usage Examples
+> ⚠️ **Note:** These examples are building on each other. Imports and parsing are not repeated in each example.
 <!-- BEGIN EXAMPLES -->
-```python
-
-```
-
-### Parse a simple PAC-ID 
-The
+### Parse a simple PAC-ID
 
 ```python
 from labfreed.parse_pac import PAC_Parser
@@ -50,34 +50,33 @@ pac_id = PAC_Parser().parse(pac_str).pac_id
 # Check validity of this PAC-ID
 pac_id = PAC_Parser().parse(pac_str).pac_id
 is_valid = pac_id.is_valid()
-print('PAC-ID is valid: {is_valid}')
-# >> PAC-ID is valid: {is_valid}
+print(f'PAC-ID is valid: {is_valid}')
 ```
-
-Show recommendations:
-Note that the PAC-ID, while valid uses characters, which are not recommended (results in larger QR code).
+```text
+>> [Error during execution: No module named 'quantities']
+```
+### Show recommendations:
+Note that the PAC-ID -- while valid -- uses characters which are not recommended (results in larger QR code).
 There is a nice function to highlight problems
 
 ```python
 pac_id.print_validation_messages()
-# >>
-#   =======================================
-#   Validation Results
-#   ---------------------------------------
-
-#   Recommendation  in      id segment value bal500
-#   HTTPS://PAC.METTORIUS.COM/-MD/bal500/@1234
-#   Characters a b l should not be used.
-
-#   Recommendation  in      id segment value @1234
-#   HTTPS://PAC.METTORIUS.COM/-MD/bal500/@1234
-#   Characters @ should not be used.
-
-#   Warning  in     Category -MD
-#   HTTPS://PAC.METTORIUS.COM/-MD/bal500/@1234
-#   Category key -MD is not a well known key. It is recommended to use well known keys only
 ```
+```text
+>> [Error during execution: name 'pac_id' is not defined]
+```
+### PAC-CAT
 
+```python
+from labfreed.PAC_CAT.data_model import PAC_CAT
+pac_str = 'HTTPS://PAC.METTORIUS.COM/-DR/XQ908756/-MD/bal500/@1234'
+pac_id = PAC_Parser().parse(pac_str).pac_id
+if isinstance(pac_id, PAC_CAT):
+    pac_id.print_categories()
+```
+```text
+>> [Error during execution: name 'PAC_Parser' is not defined]
+```
 ### Parse a PAC-ID with extensions
 PAC-ID can have extensions. Here we parse a PAC-ID with attached display names and summary.
 
@@ -87,17 +86,21 @@ pac_id = PAC_Parser().parse(pac_str)
 
 # Display Name
 display_names = pac_id.get_extension('N') # display name has name 'N'
-print(f'\n {display_names}')
-# >> Display names: My Balance ❤️
-
+print(display_names)
+```
+```text
+>> [Error during execution: name 'PAC_Parser' is not defined]
+```
+```python
 # TREX
 trexes = pac_id.get_extension_of_type('TREX')
 trex = trexes[0] # there could be multiple trexes. In this example there is only one, though
 v = trex.get_segment('WEIGHT').to_python_type() 
 print(f'WEIGHT = {v}')
-# >> WEIGHT = 67.89 g
 ```
-
+```text
+>> [Error during execution: name 'pac_id' is not defined]
+```
 ### Create a PAC-ID with Extensions
 
 #### Create PAC-ID
@@ -108,10 +111,11 @@ from labfreed.utilities.well_known_keys import WellKnownKeys
 
 pac_id = PACID(issuer='METTORIUS:COM', identifier=[IDSegment(key=WellKnownKeys.SERIAL, value='1234')])
 pac_str = pac_id.serialize()
-pac_str = pac_id.serialize()
 print(pac_str)
 ```
-
+```text
+>> HTTPS://PAC.METTORIUS:COM/21:1234
+```
 #### Create a TREX 
 TREX can conveniently be created from a python dictionary.
 Note that utility types for Quantity (number with unit) and table are needed
@@ -149,7 +153,9 @@ if trex.get_nested_validation_messages():
 # Side Note: The TREX can be turned back into a dict
 d = trex.dict()
 ```
-
+```text
+>> [Error during execution: No module named 'quantities']
+```
 #### Combine PAC-ID and TREX and serialize
 
 ```python
@@ -159,13 +165,18 @@ pac_with_trex = PACID_With_Extensions(pac_id=pac_id, extensions=[trex])
 pac_str = pac_with_trex.serialize()
 print(pac_str)
 ```
-
+```text
+>> [Error during execution: No module named 'quantities']
+```
 <!-- END EXAMPLES -->
 
 
 
 ## Change Log
 
-### v0.0.9
+### v0.0.17
+- dependencies are installed automatically
+
+### v0.0.16
 - supports PAC-ID, PAC-CAT, TREX and DisplayName
 - ok-ish test coverage

{labfreed-0.0.15 → labfreed-0.0.17}/README.md

@@ -23,13 +23,9 @@ pip install labfreed
 
 
 ## Usage Examples
+> ⚠️ **Note:** These examples are building on each other. Imports and parsing are not repeated in each example.
 <!-- BEGIN EXAMPLES -->
-```python
-
-```
-
-### Parse a simple PAC-ID 
-The
+### Parse a simple PAC-ID
 
 ```python
 from labfreed.parse_pac import PAC_Parser
@@ -41,34 +37,33 @@ pac_id = PAC_Parser().parse(pac_str).pac_id
 # Check validity of this PAC-ID
 pac_id = PAC_Parser().parse(pac_str).pac_id
 is_valid = pac_id.is_valid()
-print('PAC-ID is valid: {is_valid}')
-# >> PAC-ID is valid: {is_valid}
+print(f'PAC-ID is valid: {is_valid}')
 ```
-
-Show recommendations:
-Note that the PAC-ID, while valid uses characters, which are not recommended (results in larger QR code).
+```text
+>> [Error during execution: No module named 'quantities']
+```
+### Show recommendations:
+Note that the PAC-ID -- while valid -- uses characters which are not recommended (results in larger QR code).
 There is a nice function to highlight problems
 
 ```python
 pac_id.print_validation_messages()
-# >>
-#   =======================================
-#   Validation Results
-#   ---------------------------------------
-
-#   Recommendation  in      id segment value bal500
-#   HTTPS://PAC.METTORIUS.COM/-MD/bal500/@1234
-#   Characters a b l should not be used.
-
-#   Recommendation  in      id segment value @1234
-#   HTTPS://PAC.METTORIUS.COM/-MD/bal500/@1234
-#   Characters @ should not be used.
-
-#   Warning  in     Category -MD
-#   HTTPS://PAC.METTORIUS.COM/-MD/bal500/@1234
-#   Category key -MD is not a well known key. It is recommended to use well known keys only
 ```
+```text
+>> [Error during execution: name 'pac_id' is not defined]
+```
+### PAC-CAT
 
+```python
+from labfreed.PAC_CAT.data_model import PAC_CAT
+pac_str = 'HTTPS://PAC.METTORIUS.COM/-DR/XQ908756/-MD/bal500/@1234'
+pac_id = PAC_Parser().parse(pac_str).pac_id
+if isinstance(pac_id, PAC_CAT):
+    pac_id.print_categories()
+```
+```text
+>> [Error during execution: name 'PAC_Parser' is not defined]
+```
 ### Parse a PAC-ID with extensions
 PAC-ID can have extensions. Here we parse a PAC-ID with attached display names and summary.
 
@@ -78,17 +73,21 @@ pac_id = PAC_Parser().parse(pac_str)
 
 # Display Name
 display_names = pac_id.get_extension('N') # display name has name 'N'
-print(f'\n {display_names}')
-# >> Display names: My Balance ❤️
-
+print(display_names)
+```
+```text
+>> [Error during execution: name 'PAC_Parser' is not defined]
+```
+```python
 # TREX
 trexes = pac_id.get_extension_of_type('TREX')
 trex = trexes[0] # there could be multiple trexes. In this example there is only one, though
 v = trex.get_segment('WEIGHT').to_python_type() 
 print(f'WEIGHT = {v}')
-# >> WEIGHT = 67.89 g
 ```
-
+```text
+>> [Error during execution: name 'pac_id' is not defined]
+```
 ### Create a PAC-ID with Extensions
 
 #### Create PAC-ID
@@ -99,10 +98,11 @@ from labfreed.utilities.well_known_keys import WellKnownKeys
 
 pac_id = PACID(issuer='METTORIUS:COM', identifier=[IDSegment(key=WellKnownKeys.SERIAL, value='1234')])
 pac_str = pac_id.serialize()
-pac_str = pac_id.serialize()
 print(pac_str)
 ```
-
+```text
+>> HTTPS://PAC.METTORIUS:COM/21:1234
+```
 #### Create a TREX 
 TREX can conveniently be created from a python dictionary.
 Note that utility types for Quantity (number with unit) and table are needed
@@ -140,7 +140,9 @@ if trex.get_nested_validation_messages():
 # Side Note: The TREX can be turned back into a dict
 d = trex.dict()
 ```
-
+```text
+>> [Error during execution: No module named 'quantities']
+```
 #### Combine PAC-ID and TREX and serialize
 
 ```python
@@ -150,13 +152,18 @@ pac_with_trex = PACID_With_Extensions(pac_id=pac_id, extensions=[trex])
 pac_str = pac_with_trex.serialize()
 print(pac_str)
 ```
-
+```text
+>> [Error during execution: No module named 'quantities']
+```
 <!-- END EXAMPLES -->
 
 
 
 ## Change Log
 
-### v0.0.9
+### v0.0.17
+- dependencies are installed automatically
+
+### v0.0.16
 - supports PAC-ID, PAC-CAT, TREX and DisplayName
 - ok-ish test coverage

{labfreed-0.0.15 → labfreed-0.0.17}/examples.py

@@ -1,6 +1,5 @@
 ''' 
 ### Parse a simple PAC-ID 
-The 
 '''
 from labfreed.parse_pac import PAC_Parser
 
@@ -11,31 +10,26 @@ pac_id = PAC_Parser().parse(pac_str).pac_id
 # Check validity of this PAC-ID
 pac_id = PAC_Parser().parse(pac_str).pac_id
 is_valid = pac_id.is_valid()
-print('PAC-ID is valid: {is_valid}')
-# >> PAC-ID is valid: {is_valid}
+print(f'PAC-ID is valid: {is_valid}')
 
 ''' 
-Show recommendations:
-Note that the PAC-ID, while valid uses characters, which are not recommended (results in larger QR code).
+### Show recommendations:
+Note that the PAC-ID -- while valid -- uses characters which are not recommended (results in larger QR code).
 There is a nice function to highlight problems
 '''
 pac_id.print_validation_messages()
-# >>
-#   =======================================
-#   Validation Results
-#   ---------------------------------------
 
-#   Recommendation  in      id segment value bal500
-#   HTTPS://PAC.METTORIUS.COM/-MD/bal500/@1234
-#   Characters a b l should not be used.
 
-#   Recommendation  in      id segment value @1234
-#   HTTPS://PAC.METTORIUS.COM/-MD/bal500/@1234
-#   Characters @ should not be used.
+'''
+### PAC-CAT
+'''
+from labfreed.PAC_CAT.data_model import PAC_CAT
+pac_str = 'HTTPS://PAC.METTORIUS.COM/-DR/XQ908756/-MD/bal500/@1234'
+pac_id = PAC_Parser().parse(pac_str).pac_id
+if isinstance(pac_id, PAC_CAT):
+    pac_id.print_categories()
+
 
-#   Warning  in     Category -MD
-#   HTTPS://PAC.METTORIUS.COM/-MD/bal500/@1234
-#   Category key -MD is not a well known key. It is recommended to use well known keys only
 
 
 
@@ -48,15 +42,14 @@ pac_id = PAC_Parser().parse(pac_str)
 
 # Display Name
 display_names = pac_id.get_extension('N') # display name has name 'N'
-print(f'\n {display_names}')
-# >> Display names: My Balance ❤️
+print(display_names)
 
+''''''
 # TREX
 trexes = pac_id.get_extension_of_type('TREX')
 trex = trexes[0] # there could be multiple trexes. In this example there is only one, though
 v = trex.get_segment('WEIGHT').to_python_type() 
 print(f'WEIGHT = {v}')
-# >> WEIGHT = 67.89 g
 
 
 
@@ -70,7 +63,6 @@ from labfreed.utilities.well_known_keys import WellKnownKeys
 
 pac_id = PACID(issuer='METTORIUS:COM', identifier=[IDSegment(key=WellKnownKeys.SERIAL, value='1234')])
 pac_str = pac_id.serialize()
-pac_str = pac_id.serialize()
 print(pac_str)
 
 

{labfreed-0.0.15 → labfreed-0.0.17}/labfreed/PAC_CAT/data_model.py

@@ -138,6 +138,19 @@ class PAC_CAT(PACID):
                     )
             return self
         
+    def print_categories(self):
+        s = ''
+        for i, c in enumerate(self.categories):
+            if i == 0:
+                title = 'Main Category\n----------'
+            else:
+                title = 'Category\n------ '
+            
+            s += f'{title}\n'
+            s += str(c)
+            s += '\n'
+        print(s)
+        
         
     # @classmethod
     # def from_categories(cls, issuer:str, categories:list[Category]):
@@ -198,6 +211,11 @@ class Category(BaseModelWithValidationMessages):
         return self
     
     
+    def __str__(self):
+        s = '\n'.join( [f'{field_name} \t ({field_info.alias or ''}): \t {getattr(self, field_name)}' for  field_name, field_info in self.model_fields.items() if getattr(self, field_name)]) 
+        return s
+    
+    
     # def to_identifier_category(self, use_short_notation=False):
     #     '''Creates a Category with the correct segments. 
     #        Segments are in order of the Pydantic model fields. 
@@ -261,14 +279,14 @@ class Material_Device(Category):
             self.add_validation_message(
                     source=f"Category {self.key}",
                     type="Error",
-                    msg=f'Category key {self.key} is missing mandatory field Model NUmber',
+                    msg=f'Category key {self.key} is missing mandatory field Model Number',
                     highlight_pattern = f"{self.key}"
             )
         if not self.serial_number:
             self.add_validation_message(
                     source=f"Category {self.key}",
                     type="Error",
-                    msg=f'Category key {self.key} is missing mandatory field Serial NUmber',
+                    msg=f'Category key {self.key} is missing mandatory field Serial Number',
                     highlight_pattern = f"{self.key}"
             )
     
@@ -286,7 +304,7 @@ class Material_Substance(Category):
             self.add_validation_message(
                     source=f"Category {self.key}",
                     type="Error",
-                    msg=f'Category key {self.key} is missing mandatory field Product NUmber',
+                    msg=f'Category key {self.key} is missing mandatory field Product Number',
                     highlight_pattern = f"{self.key}"
             )
     
@@ -328,19 +346,19 @@ class Data_Abstract(Category, ABC):
                     highlight_pattern = f"{self.key}"
             )
 
-class Data_Result(Category):
+class Data_Result(Data_Abstract):
     key: str = Field(default='-DR', frozen=True)
     
-class Data_Method(Category):
+class Data_Method(Data_Abstract):
     key: str = Field(default='-DM', frozen=True)
     
-class Data_Calibration(Category):
+class Data_Calibration(Data_Abstract):
     key: str = Field(default='-DC', frozen=True)
     
-class Data_Progress(Category):
+class Data_Progress(Data_Abstract):
     key: str = Field(default='-DP', frozen=True)
     
-class Data_Static(Category):
+class Data_Static(Data_Abstract):
     key: str = Field(default='-DS', frozen=True)