labfreed 0.2.6a6__py3-none-any.whl → 0.2.7__py3-none-any.whl

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Files changed (9) hide show
  1. labfreed/__init__.py +1 -1
  2. labfreed/pac_id/pac_id.py +1 -1
  3. labfreed/pac_id/url_serializer.py +10 -6
  4. labfreed/pac_id_resolver/cit_v1.py +0 -3
  5. labfreed/pac_id_resolver/resolver.py +0 -1
  6. {labfreed-0.2.6a6.dist-info → labfreed-0.2.7.dist-info}/METADATA +29 -22
  7. {labfreed-0.2.6a6.dist-info → labfreed-0.2.7.dist-info}/RECORD +9 -9
  8. {labfreed-0.2.6a6.dist-info → labfreed-0.2.7.dist-info}/WHEEL +0 -0
  9. {labfreed-0.2.6a6.dist-info → labfreed-0.2.7.dist-info}/licenses/LICENSE +0 -0
labfreed/__init__.py CHANGED
@@ -2,7 +2,7 @@
2
2
  Python implementation of LabFREED building blocks
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3
  '''
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- __version__ = "0.2.6a6"
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+ __version__ = "0.2.7"
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6
 
7
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  from labfreed.pac_id import * # noqa: F403
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  from labfreed.pac_cat import * # noqa: F403
labfreed/pac_id/pac_id.py CHANGED
@@ -45,7 +45,7 @@ class PAC_ID(LabFREED_BaseModel):
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  from labfreed.pac_id.url_parser import PAC_Parser
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  return PAC_Parser.from_url(url, try_pac_cat=try_pac_cat, suppress_validation_errors=suppress_validation_errors, extension_interpreters=extension_interpreters)
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- def to_url(self, use_short_notation=False, uppercase_only=False) -> str:
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+ def to_url(self, use_short_notation:None|bool=None, uppercase_only=False) -> str:
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  from labfreed.pac_id.url_serializer import PACID_Serializer
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  return PACID_Serializer.to_url(self, use_short_notation=use_short_notation, uppercase_only=uppercase_only)
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labfreed/pac_id/url_serializer.py CHANGED
@@ -9,20 +9,23 @@ class PACID_Serializer():
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  '''Represents a PAC-ID including it's extensions'''
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  @classmethod
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- def to_url(cls, pac:PAC_ID, use_short_notation=False, uppercase_only=False) -> str:
12
+ def to_url(cls, pac:PAC_ID, use_short_notation:bool|None=None, uppercase_only=False) -> str:
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  """Serializes the PAC-ID including extensions.
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  Args:
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- use_short_notation (bool, optional): Uses shortening conventions for extensions and categories..
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+ use_short_notation (bool|None, optional): None (default): Preserves the identifier as is. Extensions use short form
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+ True: forces short notation for categories and extensions
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+ False: forces long notation for categories and extensions
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  uppercase_only (bool, optional): Forces all uppercase letters (results in smaller QR)..
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  Returns:
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  str: Something like this HTTPS://PAC.METTORIUS.COM/-MD/BAL500/1234*N$N/ABC*SUM$TREX/A$T.A:ABC
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22
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  """
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- extensions_str = cls._serialize_extensions(pac.extensions, use_short_notation=use_short_notation)
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-
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  identifier_str = cls._serialize_identifier(pac, use_short_notation=use_short_notation)
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+
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+ use_short_notation_for_extensions = True if use_short_notation is None else use_short_notation
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+ extensions_str = cls._serialize_extensions(pac.extensions, use_short_notation=use_short_notation_for_extensions)
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  out = f"HTTPS://PAC.{pac.issuer}{identifier_str}{extensions_str}"
27
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28
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  if uppercase_only:
@@ -30,9 +33,10 @@ class PACID_Serializer():
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  return out
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  @classmethod
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- def _serialize_identifier(cls, pac:PAC_ID|PAC_CAT, use_short_notation=True):
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+ def _serialize_identifier(cls, pac:PAC_ID|PAC_CAT, use_short_notation:None|bool=None):
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  ''' Serializes the PAC-ID'''
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- if isinstance(pac, PAC_CAT):
38
+
39
+ if isinstance(pac, PAC_CAT) and use_short_notation is not None:
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  for c in pac.categories:
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  segments = [IDSegment(value=c.key)]
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  if isinstance(c, PredefinedCategory):
labfreed/pac_id_resolver/cit_v1.py CHANGED
@@ -91,7 +91,6 @@ class CIT_v1(LabFREED_BaseModel):
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  cols = [c.strip() for c in line.split('\t')]
93
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  if len(cols) < 5:
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- logging.error(f'invalid line {line}')
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  msg = ValidationMessage(
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  level=ValidationMsgLevel.ERROR,
97
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  source='CIT line',
@@ -102,7 +101,6 @@ class CIT_v1(LabFREED_BaseModel):
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  errors.append(msg)
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  continue
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  if len(cols) > 5:
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- logging.error(f'invalid line {line}')
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  msg = ValidationMessage(
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105
  level=ValidationMsgLevel.ERROR,
108
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  source='CIT line',
@@ -123,7 +121,6 @@ class CIT_v1(LabFREED_BaseModel):
123
121
  )
124
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  entries.append(entry)
125
123
  except ValueError:
126
- logging.error(f'invalid line {line}')
127
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  msg = ValidationMessage(
128
125
  level=ValidationMsgLevel.ERROR,
129
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  source='CIT line',
labfreed/pac_id_resolver/resolver.py CHANGED
@@ -30,7 +30,6 @@ def cit_from_str(s:str, origin:str='') -> CIT_v1|CIT_v2:
30
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  cit_version = 'v2'
31
31
  except Exception:
32
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  cit2 = None
33
- traceback.print_exc()
34
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  try:
35
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  cit1 = CIT_v1.from_csv(s, origin)
36
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  cit_version = 'v1'
{labfreed-0.2.6a6.dist-info → labfreed-0.2.7.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
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  Name: labfreed
3
- Version: 0.2.6a6
3
+ Version: 0.2.7
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  Summary: Python implementation of LabFREED building blocks
5
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  Author-email: Reto Thürer <thuerer.r@buchi.com>
6
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  Requires-Python: >=3.11
@@ -38,7 +38,7 @@ Provides-Extra: dev
38
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  [![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)
39
39
 
40
40
 
41
- This is a Python implementation of [LabFREED](https://labfreed.wega-it.com) building blocks.
41
+ This is a Python implementation of [LabFREED](https://labfreed.org/) building blocks.
42
42
 
43
43
  ## Supported Building Blocks
44
44
  - PAC-ID
@@ -53,7 +53,7 @@ This is a Python implementation of [LabFREED](https://labfreed.wega-it.com) buil
53
53
  - base36 <> str conversions
54
54
  - PAC-ID Resolver
55
55
  - support for CIT v1
56
- - draft support for CIT v1 (improved version)
56
+ - draft support for CIT v2 (improved version)
57
57
  - combined use of multiple cit in any combination of version
58
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  - Generation of QR codes (PAC-ID with extensions)
59
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@@ -105,24 +105,24 @@ pac.print_validation_messages()
105
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  >> Validation Results
106
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  >> ┌───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
107
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  >> │ **RECOMMENDATION** in id segment value bal500 │
108
- >> │ Characters 'b','l','a' should not be used., Characters SHOULD be limited to upper case letters (A-Z), numbers (0-9), '-' and '+' │
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+ >> │ Characters 'a','l','b' should not be used., Characters SHOULD be limited to upper case letters (A-Z), numbers (0-9), '-' and '+' │
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  >> │ │
110
- >> │ HTTPS://PAC.METTORIUS.COM/-MD/240:👉bal👈500/21:@1234 │
110
+ >> │ HTTPS://PAC.METTORIUS.COM/-MD/👉bal👈500/@1234 │
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  >> ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
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  >> │ **RECOMMENDATION** in id segment value @1234 │
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  >> │ Characters '@' should not be used., Characters SHOULD be limited to upper case letters (A-Z), numbers (0-9), '-' and '+' │
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  >> │ │
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- >> │ HTTPS://PAC.METTORIUS.COM/-MD/240:bal500/21:👉@👈1234 │
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+ >> │ HTTPS://PAC.METTORIUS.COM/-MD/bal500/👉@👈1234 │
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  >> ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
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  >> │ **RECOMMENDATION** in id segment value bal500 │
118
- >> │ Characters 'b','l','a' should not be used., Characters SHOULD be limited to upper case letters (A-Z), numbers (0-9), '-' and '+' │
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+ >> │ Characters 'a','l','b' should not be used., Characters SHOULD be limited to upper case letters (A-Z), numbers (0-9), '-' and '+' │
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  >> │ │
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- >> │ HTTPS://PAC.METTORIUS.COM/-MD/240:👉bal👈500/21:@1234 │
120
+ >> │ HTTPS://PAC.METTORIUS.COM/-MD/👉bal👈500/@1234 │
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  >> ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
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  >> │ **RECOMMENDATION** in id segment value @1234 │
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  >> │ Characters '@' should not be used., Characters SHOULD be limited to upper case letters (A-Z), numbers (0-9), '-' and '+' │
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  >> │ │
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- >> │ HTTPS://PAC.METTORIUS.COM/-MD/240:bal500/21:👉@👈1234 │
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+ >> │ HTTPS://PAC.METTORIUS.COM/-MD/bal500/👉@👈1234 │
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  >> └───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
127
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  ```
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  ### Save as QR Code
@@ -152,8 +152,8 @@ if isinstance(pac, PAC_CAT):
152
152
  ```
153
153
  ```text
154
154
  >> Categories in
155
- >> HTTPS://PAC.METTORIUS.COM/-MD/240:
156
- >> bal500/21:@1234
155
+ >> HTTPS://PAC.METTORIUS.COM/-DR/XQ90
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+ >> 8756/-MD/bal500/@1234
157
157
  >> ┌────────────────────┬───────────┐
158
158
  >> │ Main Category │ │
159
159
  >> │ key () │ -DR │
@@ -248,7 +248,7 @@ trex.print_validation_messages()
248
248
  >> Validation Results
249
249
  >> ┌────────────────────────────────────────────────────────────┐
250
250
  >> │ **ERROR** in TREX table column Date │
251
- >> │ Column header key contains invalid characters: 'e','a','t' │
251
+ >> │ Column header key contains invalid characters: 'a','t','e' │
252
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  >> │ │
253
253
  >> │ STOP$T.D:20240505T1306 │
254
254
  >> │ +TEMP$KEL:10.15 │
@@ -256,9 +256,9 @@ trex.print_validation_messages()
256
256
  >> │ +COMMENT$T.A:FOO │
257
257
  >> │ +COMMENT2$T.T:12G3 │
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  >> │ +TABLE$$DURATION$HUR:D👉ate👈$T.D:OK$T.B:COMMENT$T.A:: │
259
- >> │ 1:20250430T100239.279:T:FOO:: │
260
- >> │ 1.1:20250430T100239.280:T:BAR:: │
261
- >> │ 1.3:20250430T100239.280:F:BLUBB │
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+ >> │ 1:20250513T080159.146:T:FOO:: │
260
+ >> │ 1.1:20250513T080159.146:T:BAR:: │
261
+ >> │ 1.3:20250513T080159.146:F:BLUBB │
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  >> └────────────────────────────────────────────────────────────┘
263
263
  ```
264
264
  #### Combine PAC-ID and TREX and serialize
@@ -270,7 +270,7 @@ pac_str = pac.to_url()
270
270
  print(pac_str)
271
271
  ```
272
272
  ```text
273
- >> HTTPS://PAC.METTORIUS.COM/21:1234*MYTREX$TREX/STOP$T.D:20240505T1306+TEMP$KEL:10.15+OK$T.B:F+COMMENT$T.A:FOO+COMMENT2$T.T:12G3+TABLE$$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
273
+ >> 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
274
274
  ```
275
275
  ## PAC-ID Resolver
276
276
 
@@ -306,12 +306,12 @@ for sg in service_groups:
306
306
  >> ┡━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━┩
307
307
  >> │ CAS Search │ https://pubchem.ncbi.nlm.nih.gov/#query=7732-18-5 │ ACTIVE │
308
308
  >> └──────────────┴───────────────────────────────────────────────────┴───────────┘
309
- >> Services from origin 'MY_COMPANY
310
- >> ┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━┓
311
- >> ┃ Service Name ┃ URL ┃ Reachable ┃
312
- >> ┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━┩
313
- >> │ Chemical Management │ https://chem-manager.com/METTORIUS.COM/-MS/240:X3511/CAS:7732-18-5 │ INACTIVE │
314
- >> └─────────────────────┴────────────────────────────────────────────────────────────────────┴───────────┘
309
+ >> Services from origin 'MY_COMPANY
310
+ >> ┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━┓
311
+ >> ┃ Service Name ┃ URL ┃ Reachable ┃
312
+ >> ┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━┩
313
+ >> │ Chemical Management │ https://chem-manager.com/METTORIUS.COM/-MS/X3511/CAS:7732-18-5 │ INACTIVE │
314
+ >> └─────────────────────┴────────────────────────────────────────────────────────────────┴───────────┘
315
315
  >> Services from origin 'METTORIUS.COM
316
316
  >> ┏━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━┓
317
317
  >> ┃ Service Name ┃ URL ┃ Reachable ┃
@@ -327,6 +327,13 @@ for sg in service_groups:
327
327
 
328
328
  <!-- BEGIN CHANGELOG -->
329
329
  ## Change Log
330
+ ### v0.2.7
331
+ - Improved README. No functional changes
332
+
333
+ ### v0.2.6
334
+ - PAC_ID.to_url() preserves the identifier as is by default but allows to force short or long notation.
335
+ - PAC-ID Resolver does not try to resolve PAC-CAT with CIT v1.
336
+
330
337
  ### v0.2.5
331
338
  - resolvers checks service states by default
332
339
  - improvements and bugfixes in conversion from python types to TREX
{labfreed-0.2.6a6.dist-info → labfreed-0.2.7.dist-info}/RECORD RENAMED
@@ -1,4 +1,4 @@
1
- labfreed/__init__.py,sha256=VzBgiJzKQujiC6y6Ge0JHS7huonkWqJ4725faVGhlvI,338
1
+ labfreed/__init__.py,sha256=cdoNTE10KG03M6MTCkgCbySTOajvy8HehAEgYvLJKmY,336
2
2
  labfreed/labfreed_infrastructure.py,sha256=EPDSCaGxWakAoPpHyc6ltf-pOuKyS5829lj_EG6wa74,10072
3
3
  labfreed/pac_cat/__init__.py,sha256=KNPtQzBD1XVohvG_ucOs7RJj-oi6biUTGB1k-T2o6pk,568
4
4
  labfreed/pac_cat/category_base.py,sha256=lFQNiTUukyhWdaSCAI7CZxLtj6kNtnBCE4UsePwsGqE,1801
@@ -7,14 +7,14 @@ labfreed/pac_cat/predefined_categories.py,sha256=5wnMCj-CrACV2W4lH13w7qynWIwi506
7
7
  labfreed/pac_id/__init__.py,sha256=NGMbzkwQ4txKeT5pxdIZordwHO8J3_q84jzPanjKoHg,675
8
8
  labfreed/pac_id/extension.py,sha256=zuHI8e51otPbpO1r1xDFh32uXTT8L5pCJn74B-aOUpI,1112
9
9
  labfreed/pac_id/id_segment.py,sha256=r5JU1SJuRXhZJJxy5T3xjrb598wIDTLpivSJhIUAzjQ,4526
10
- labfreed/pac_id/pac_id.py,sha256=IWXYlKFjQKB_9U5bINWC5_Lb5pcVbuleocvGs79A28w,5300
10
+ labfreed/pac_id/pac_id.py,sha256=PyOa5y2IVLEcmj7ZkFuURC1lrP3BU0Yj8pzAllhtatw,5309
11
11
  labfreed/pac_id/url_parser.py,sha256=TAQHxFf7Li8GA517mfOivmnJAJgh782oaSDzmOOkyTE,5942
12
- labfreed/pac_id/url_serializer.py,sha256=3D5pwcAP4ZrCQ22BRtxIwqWrFtZuY9913hCLPJNeyPI,2845
12
+ labfreed/pac_id/url_serializer.py,sha256=BgGoU_8W0Lvo153cXH8gX1k8H-FJtGizsEzjRaaEMcg,3270
13
13
  labfreed/pac_id_resolver/__init__.py,sha256=RNBlrDOSR42gmSNH9wJVhK_xwEX45cvTKVgWW2bjh7Q,113
14
14
  labfreed/pac_id_resolver/cit_common.py,sha256=xEkSSumj_IYgnXn3yKvoTBbgExnIfPY7E-RHU-7pcX8,2905
15
- labfreed/pac_id_resolver/cit_v1.py,sha256=1dx0zqJfzFOE4kP8_i8EJSLhvjVovc_i9Bazb53B0fU,9548
15
+ labfreed/pac_id_resolver/cit_v1.py,sha256=W7UCO0Gm0w09FSo_USFB1-V2tl3iErDxoe2OHh4fkvc,9383
16
16
  labfreed/pac_id_resolver/cit_v2.py,sha256=wM1wf8UWbepatWNgkJ3l0l-HNJHqsqqPMql5k8fkVso,12127
17
- labfreed/pac_id_resolver/resolver.py,sha256=qYL0FMsbvOU9Y6pUgialY9dWmBvCd_aSpX7ZQk3pDUM,2848
17
+ labfreed/pac_id_resolver/resolver.py,sha256=UfSxRwTTjSgL4VoHfsQiaGTj3tt8dTDDd2wVcbr2Xvc,2817
18
18
  labfreed/pac_id_resolver/services.py,sha256=TPoH6YlSwa0hmawHpOiMwIpBAinhoRhMSoexop0YscI,2462
19
19
  labfreed/qr/__init__.py,sha256=fdKwP6W2Js--yMbBUdn-g_2uq2VqPpfQJeDLHsMDO-Y,61
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  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
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  labfreed/well_known_keys/unece/UneceUnits.json,sha256=kwfQSp_nTuWbADfBBgqTWrvPl6XtM5SedEVLbMJrM7M,898953
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  labfreed/well_known_keys/unece/__init__.py,sha256=MSP9lmjg9_D9iqG9Yq2_ajYfQSNS9wIT7FXA1c--59M,122
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  labfreed/well_known_keys/unece/unece_units.py,sha256=gNDQk6KGl-nGMf9Ycq_fQ8P2xxKITgLkcQWPd4H49gI,1630
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- labfreed-0.2.6a6.dist-info/licenses/LICENSE,sha256=gHFOv9FRKHxO8cInP3YXyPoJnuNeqrvcHjaE_wPSsQ8,1100
43
- labfreed-0.2.6a6.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
44
- labfreed-0.2.6a6.dist-info/METADATA,sha256=FuVqznBpKwp-zhER_-PH4NILKLXCe7CFX5rm3s3rGUU,18616
45
- labfreed-0.2.6a6.dist-info/RECORD,,
42
+ labfreed-0.2.7.dist-info/licenses/LICENSE,sha256=gHFOv9FRKHxO8cInP3YXyPoJnuNeqrvcHjaE_wPSsQ8,1100
43
+ labfreed-0.2.7.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
44
+ labfreed-0.2.7.dist-info/METADATA,sha256=LgChVG_EYO1fXu-FLEfydV_mZvDgmylj3-hxnREkE9g,18795
45
+ labfreed-0.2.7.dist-info/RECORD,,