labfreed 0.2.8__py3-none-any.whl → 0.2.9__py3-none-any.whl

labfreed/trex/python_convenience/pyTREX.py

@@ -1,249 +1,249 @@
-
-from datetime import date, datetime, time
-import logging
-import re
-from typing import Self
-
-from pydantic import RootModel
-from labfreed.well_known_keys.unece.unece_units import unece_unit
-from labfreed.trex.python_convenience.data_table import DataTable
-from labfreed.utilities.base36 import from_base36, base36, to_base36
-
-from labfreed.trex.python_convenience.quantity import Quantity, unece_unit_code_from_quantity
-from labfreed.trex.table_segment import ColumnHeader, TableSegment
-from labfreed.trex.trex import TREX
-from labfreed.trex.trex_base_models import AlphanumericValue, BinaryValue, BoolValue, DateValue, ErrorValue, NumericValue, TextValue
-from labfreed.trex.value_segments import BoolSegment, ErrorSegment, TextSegment, NumericSegment, AlphanumericSegment, DateSegment, ValueSegment
-
-
-class pyTREX(RootModel[dict[str, Quantity | datetime | time | date | bool | str | base36 | DataTable]]):
-    ''' A wrapper around dict, which knows how to convert to and from TREX. 
-        It restricts the types allowed as values. Keys must be str.
-    '''
-    model_config = {'arbitrary_types_allowed':True} # needed to allow Quantity and DataTable w/o implementing the pydantic schema
-    '''@private'''
-
-    
-    @classmethod
-    def from_trex(cls, trex:TREX) -> Self:
-        '''Creates a pyTREX from a TREX'''
-        return {seg.key: _trex_segment_to_python_type(seg) for seg in trex.segments}
-             
-             
-    def to_trex(self) -> TREX:
-        '''Creates a TREX'''
-        segments = list()
-        for k, v in self.root.items():
-            if v is None:
-                value = _error_value_from_python_type(v)
-                segments.append(ErrorSegment(key=k, value=value.value))
-            elif isinstance(v, bool):
-                value = _bool_value_from_python_type(v)
-                segments.append(BoolSegment(key=k, value=value.value))
-            elif isinstance(v, Quantity):
-                unece_code = unece_unit_code_from_quantity(v)
-                value = _numeric_value_from_python_type(v.value)
-                segments.append(NumericSegment(key=k, value=value.value, type=unece_code))
-            elif isinstance(v, (int, float)):
-                value = _numeric_value_from_python_type(v)
-                segments.append(NumericSegment(key=k, value=value.value, type='C63'))  # unitless
-            elif isinstance(v, (datetime, time, date)):
-                value = _date_value_from_python_type(v)
-                segments.append(DateSegment(key=k, value=value.value))
-            elif isinstance(v, str):
-                if re.fullmatch(r'[A-Z0-9\-\.]*', v):
-                    value = _alphanumeric_value_from_python_type(v)
-                    segments.append(AlphanumericSegment(key=k, value=value.value))
-                else:
-                    v = to_base36(v)
-                    value = _text_value_from_python_type(v)
-                    segments.append(TextSegment(key=k, value=value.value))
-            elif isinstance(v, base36):
-                value = _text_value_from_python_type(v)
-                segments.append(TextSegment(key=k, value=value.value))
-                
-            elif isinstance(v, DataTable):
-                v:DataTable = v
-                headers = list()
-                for nm, rt in zip(v.col_names, v.row_template):
-                    if isinstance(rt, bool): # must come first otherwise int matches the bool
-                        t = 'T.B'
-                    elif isinstance(rt, Quantity):
-                        unece_code = unece_unit_code_from_quantity(rt)
-                        t = unece_code
-                    elif isinstance(rt, (datetime, time, date)):
-                        t = 'T.D'     
-                    elif isinstance(rt, str):
-                        if re.fullmatch(r'[A-Z0-9\-\.]*', rt):
-                            t = 'T.A'
-                        else:
-                            t = 'T.T'
-                    elif isinstance(rt, base36):
-                        t = 'T.T'
-                    
-                    headers.append(ColumnHeader(key=nm, type=t))
-                data = []
-                for row in v.data:
-                    r = []
-                    for e in row:
-                        if e is None:
-                            r.append(_error_value_from_python_type(e))
-                        elif isinstance(e, bool): # must come first otherwise int matches the bool
-                            r.append(_bool_value_from_python_type(e))
-                        elif isinstance(e, Quantity):
-                            r.append(_numeric_value_from_python_type(e.value))
-                        elif isinstance(e, (int, float)):
-                            r.append(_numeric_value_from_python_type(e))
-                        elif isinstance(e, (datetime, time, date)):
-                            r.append(_date_value_from_python_type(e))
-                        elif isinstance(e, str):
-                            if re.fullmatch(r'[A-Z0-9\-\.]*', e):
-                                r.append(_alphanumeric_value_from_python_type(e))
-                            else:
-                                e = to_base36(e)
-                                r.append(_text_value_from_python_type(e))
-                        elif isinstance(e, base36):
-                            r.append(_text_value_from_python_type(e))
-                    data.append(r)
-                segments.append(TableSegment(key=k, column_headers=headers, data=data))
-        return TREX(segments=segments)
-    
-    # make the usual dict methods available, for convenience
-    def __getitem__(self, key): return self.root[key]
-    def __setitem__(self, key, value): self.root[key] = value
-    def update(self, *args, **kwargs):
-        return self.root.update(*args, **kwargs)
-    def keys(self): return self.root.keys()
-    def values(self): return self.root.values()
-    def items(self): return self.root.items()
-    def __contains__(self, key): return key in self.root
-    def __iter__(self): return iter(self.root)
-    def __len__(self): return len(self.root)
-    
-  
-  
-# Helper functions to convert python types to TREX types    
-
-def _numeric_value_from_python_type(v:int|float):
-    return NumericValue(value = str(v))
-
-
-def _date_value_from_python_type(v:date|time|datetime):    
-    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 DateValue(value = sd + st)
-    
-    
-def _bool_value_from_python_type(v:bool):
-    return BoolValue(value = 'T' if v else 'F')
-
-
-def _alphanumeric_value_from_python_type(v:str):
-    return AlphanumericValue(value = v)
-
-
-def _text_value_from_python_type(v:base36|str):
-    if isinstance(v, str):
-        logging.info('Got str for text value > converting to base36')
-        out =  to_base36(v).root
-    else:
-        out =  v.root
-    return TextValue(value = out)
-        
-        
-def _binary_value_from_python_type(v:base36|str):
-    if isinstance(v, str):
-        out = v
-    else:
-        out = v.root
-    return BinaryValue(value = out)
-    
-
-def _error_value_from_python_type(v:str):
-    if v is None:
-        v = '-'
-    return ErrorValue(value = v)
-    
-
-
-# Helper functions to convert from TREX types to python types
-def _trex_segment_to_python_type(v):
-    '''Converts a TREX segment to a python value. Note the segment key must be handles outside.'''
-    if isinstance(v, NumericSegment):
-        num_val = _trex_value_to_python_type(v)
-        u = unece_unit(v.type)
-        unit = u.get('symbol')
-        return Quantity(value=num_val, unit=unit)
-    
-    # value segments are derived from their respective value type
-    elif isinstance(v, ValueSegment):
-        return _trex_value_to_python_type(v)
-
-    elif isinstance(v, TableSegment):
-        table = DataTable(col_names=[ch.key for ch in v.column_headers])
-        for row in v.data:
-            r = []
-            for e, h in zip(row, v.column_headers):
-                if isinstance(e, NumericValue):
-                    u = unece_unit(h.type)
-                    unit = u.get('symbol')
-                    r.append(Quantity(value=e.value, unit=unit))
-                else:
-                    r.append(_trex_value_to_python_type(e))
-            table.append(r)
-        return table
-        
-
-
-def _trex_value_to_python_type(v):
-    '''Converts a TREX value to the corresponding python type'''
-    if isinstance(v, NumericValue):
-        if '.' not in v.value and 'E' not in v.value: 
-            return int(v.value)
-        else:
-            return float(v.value)  
-        
-    elif isinstance(v,DateValue):
-        d = v._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)
-            
-    elif isinstance(v, BoolValue):
-        if v.value == 'T':
-            return True
-        elif v.value == 'F':
-            return False
-        else:
-            Exception(f'{v} is not valid boolean. That really should not have been possible -- Contact the maintainers of the library')
-                
-    elif isinstance(v, AlphanumericValue):
-        return v.value
-        
-    elif isinstance(v, TextValue):
-        decoded = from_base36(v.value)
-        return decoded
-        
-    elif isinstance(v, BinaryValue):
-        decoded = bytes(from_base36(v.value), encoding='utf-8')
-        return decoded
-        
-    elif isinstance(v, ErrorValue):
-        return v.value
-        
-    else:
-        raise (TypeError(f'Invalid type {type(v)} of segment'))
+
+from datetime import date, datetime, time
+import logging
+import re
+from typing import Self
+
+from pydantic import RootModel
+from labfreed.well_known_keys.unece.unece_units import unece_unit
+from labfreed.trex.python_convenience.data_table import DataTable
+from labfreed.utilities.base36 import from_base36, base36, to_base36
+
+from labfreed.trex.python_convenience.quantity import Quantity, unece_unit_code_from_quantity
+from labfreed.trex.table_segment import ColumnHeader, TableSegment
+from labfreed.trex.trex import TREX
+from labfreed.trex.trex_base_models import AlphanumericValue, BinaryValue, BoolValue, DateValue, ErrorValue, NumericValue, TextValue
+from labfreed.trex.value_segments import BoolSegment, ErrorSegment, TextSegment, NumericSegment, AlphanumericSegment, DateSegment, ValueSegment
+
+
+class pyTREX(RootModel[dict[str, Quantity | datetime | time | date | bool | str | base36 | DataTable]]):
+    ''' A wrapper around dict, which knows how to convert to and from TREX. 
+        It restricts the types allowed as values. Keys must be str.
+    '''
+    model_config = {'arbitrary_types_allowed':True} # needed to allow Quantity and DataTable w/o implementing the pydantic schema
+    '''@private'''
+
+    
+    @classmethod
+    def from_trex(cls, trex:TREX) -> Self:
+        '''Creates a pyTREX from a TREX'''
+        return {seg.key: _trex_segment_to_python_type(seg) for seg in trex.segments}
+             
+             
+    def to_trex(self) -> TREX:
+        '''Creates a TREX'''
+        segments = list()
+        for k, v in self.root.items():
+            if v is None:
+                value = _error_value_from_python_type(v)
+                segments.append(ErrorSegment(key=k, value=value.value))
+            elif isinstance(v, bool):
+                value = _bool_value_from_python_type(v)
+                segments.append(BoolSegment(key=k, value=value.value))
+            elif isinstance(v, Quantity):
+                unece_code = unece_unit_code_from_quantity(v)
+                value = _numeric_value_from_python_type(v.value)
+                segments.append(NumericSegment(key=k, value=value.value, type=unece_code))
+            elif isinstance(v, (int, float)):
+                value = _numeric_value_from_python_type(v)
+                segments.append(NumericSegment(key=k, value=value.value, type='C63'))  # unitless
+            elif isinstance(v, (datetime, time, date)):
+                value = _date_value_from_python_type(v)
+                segments.append(DateSegment(key=k, value=value.value))
+            elif isinstance(v, str):
+                if re.fullmatch(r'[A-Z0-9\-\.]*', v):
+                    value = _alphanumeric_value_from_python_type(v)
+                    segments.append(AlphanumericSegment(key=k, value=value.value))
+                else:
+                    v = to_base36(v)
+                    value = _text_value_from_python_type(v)
+                    segments.append(TextSegment(key=k, value=value.value))
+            elif isinstance(v, base36):
+                value = _text_value_from_python_type(v)
+                segments.append(TextSegment(key=k, value=value.value))
+                
+            elif isinstance(v, DataTable):
+                v:DataTable = v
+                headers = list()
+                for nm, rt in zip(v.col_names, v.row_template):
+                    if isinstance(rt, bool): # must come first otherwise int matches the bool
+                        t = 'T.B'
+                    elif isinstance(rt, Quantity):
+                        unece_code = unece_unit_code_from_quantity(rt)
+                        t = unece_code
+                    elif isinstance(rt, (datetime, time, date)):
+                        t = 'T.D'     
+                    elif isinstance(rt, str):
+                        if re.fullmatch(r'[A-Z0-9\-\.]*', rt):
+                            t = 'T.A'
+                        else:
+                            t = 'T.T'
+                    elif isinstance(rt, base36):
+                        t = 'T.T'
+                    
+                    headers.append(ColumnHeader(key=nm, type=t))
+                data = []
+                for row in v.data:
+                    r = []
+                    for e in row:
+                        if e is None:
+                            r.append(_error_value_from_python_type(e))
+                        elif isinstance(e, bool): # must come first otherwise int matches the bool
+                            r.append(_bool_value_from_python_type(e))
+                        elif isinstance(e, Quantity):
+                            r.append(_numeric_value_from_python_type(e.value))
+                        elif isinstance(e, (int, float)):
+                            r.append(_numeric_value_from_python_type(e))
+                        elif isinstance(e, (datetime, time, date)):
+                            r.append(_date_value_from_python_type(e))
+                        elif isinstance(e, str):
+                            if re.fullmatch(r'[A-Z0-9\-\.]*', e):
+                                r.append(_alphanumeric_value_from_python_type(e))
+                            else:
+                                e = to_base36(e)
+                                r.append(_text_value_from_python_type(e))
+                        elif isinstance(e, base36):
+                            r.append(_text_value_from_python_type(e))
+                    data.append(r)
+                segments.append(TableSegment(key=k, column_headers=headers, data=data))
+        return TREX(segments=segments)
+    
+    # make the usual dict methods available, for convenience
+    def __getitem__(self, key): return self.root[key]
+    def __setitem__(self, key, value): self.root[key] = value
+    def update(self, *args, **kwargs):
+        return self.root.update(*args, **kwargs)
+    def keys(self): return self.root.keys()
+    def values(self): return self.root.values()
+    def items(self): return self.root.items()
+    def __contains__(self, key): return key in self.root
+    def __iter__(self): return iter(self.root)
+    def __len__(self): return len(self.root)
+    
+  
+  
+# Helper functions to convert python types to TREX types    
+
+def _numeric_value_from_python_type(v:int|float):
+    return NumericValue(value = str(v))
+
+
+def _date_value_from_python_type(v:date|time|datetime):    
+    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 DateValue(value = sd + st)
+    
+    
+def _bool_value_from_python_type(v:bool):
+    return BoolValue(value = 'T' if v else 'F')
+
+
+def _alphanumeric_value_from_python_type(v:str):
+    return AlphanumericValue(value = v)
+
+
+def _text_value_from_python_type(v:base36|str):
+    if isinstance(v, str):
+        logging.info('Got str for text value > converting to base36')
+        out =  to_base36(v).root
+    else:
+        out =  v.root
+    return TextValue(value = out)
+        
+        
+def _binary_value_from_python_type(v:base36|str):
+    if isinstance(v, str):
+        out = v
+    else:
+        out = v.root
+    return BinaryValue(value = out)
+    
+
+def _error_value_from_python_type(v:str):
+    if v is None:
+        v = '-'
+    return ErrorValue(value = v)
+    
+
+
+# Helper functions to convert from TREX types to python types
+def _trex_segment_to_python_type(v):
+    '''Converts a TREX segment to a python value. Note the segment key must be handles outside.'''
+    if isinstance(v, NumericSegment):
+        num_val = _trex_value_to_python_type(v)
+        u = unece_unit(v.type)
+        unit = u.get('symbol')
+        return Quantity(value=num_val, unit=unit)
+    
+    # value segments are derived from their respective value type
+    elif isinstance(v, ValueSegment):
+        return _trex_value_to_python_type(v)
+
+    elif isinstance(v, TableSegment):
+        table = DataTable(col_names=[ch.key for ch in v.column_headers])
+        for row in v.data:
+            r = []
+            for e, h in zip(row, v.column_headers):
+                if isinstance(e, NumericValue):
+                    u = unece_unit(h.type)
+                    unit = u.get('symbol')
+                    r.append(Quantity(value=e.value, unit=unit))
+                else:
+                    r.append(_trex_value_to_python_type(e))
+            table.append(r)
+        return table
+        
+
+
+def _trex_value_to_python_type(v):
+    '''Converts a TREX value to the corresponding python type'''
+    if isinstance(v, NumericValue):
+        if '.' not in v.value and 'E' not in v.value: 
+            return int(v.value)
+        else:
+            return float(v.value)  
+        
+    elif isinstance(v,DateValue):
+        d = v._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)
+            
+    elif isinstance(v, BoolValue):
+        if v.value == 'T':
+            return True
+        elif v.value == 'F':
+            return False
+        else:
+            Exception(f'{v} is not valid boolean. That really should not have been possible -- Contact the maintainers of the library')
+                
+    elif isinstance(v, AlphanumericValue):
+        return v.value
+        
+    elif isinstance(v, TextValue):
+        decoded = from_base36(v.value)
+        return decoded
+        
+    elif isinstance(v, BinaryValue):
+        decoded = bytes(from_base36(v.value), encoding='utf-8')
+        return decoded
+        
+    elif isinstance(v, ErrorValue):
+        return v.value
+        
+    else:
+        raise (TypeError(f'Invalid type {type(v)} of segment'))
  

labfreed/trex/python_convenience/quantity.py

@@ -1,66 +1,66 @@
-from pydantic import BaseModel, model_validator
-from labfreed.well_known_keys.unece.unece_units import unece_units
-
-
-class Quantity(BaseModel):
-    ''' Represents a quantity'''
-    value: float|int
-    unit: str | None 
-    '''unit. Use SI symbols. Set to None of the Quantity is dimensionless'''
-    log_least_significant_digit: int|None = None
-    
-    @model_validator(mode='before')
-    @classmethod
-    def transform_inputs(cls, d:dict):
-        if not isinstance(d, dict):
-            return d
-        # decimals_to_log_significant_digits
-        if decimals:= d.pop('decimals', None):
-            d['log_least_significant_digit'] = - decimals
-        
-        #dimensionless_unit
-        unit= d.get('unit')
-        if unit and unit in ['1', '', 'dimensionless']:
-            d['unit'] = None
-        return d
-    
-        
-    @model_validator(mode='after')
-    def significat_digits_for_int(self):
-        if isinstance(self.value, int):
-            self.log_least_significant_digit = 0
-        return self
-        
-    @property
-    def float(self) -> float:
-        ''' for clarity returns the value'''
-        return self.value
-    
-    def __str__(self):
-        unit_symbol = self.unit
-        if self.unit == "dimensionless" or not self.unit:
-            unit_symbol = ""
-        if self.log_least_significant_digit is not None:
-            val = f"{self.value:.{self.log_least_significant_digit}f}"
-        else:
-            val = str(self.value)
-        return f"{val} {unit_symbol}"
-      
-    def __repr__(self):
-        return f'Quantity: {self.__repr__()}'
-    
-    
-    
-    
-def unece_unit_code_from_quantity(q:Quantity):
-        if not q.unit:
-            return 'C62' # dimensionless
-        by_name =   [ u['commonCode'] for u in unece_units() if u.get('name','') == q.unit] 
-        by_symbol = [ u['commonCode'] for u in unece_units() if u.get('symbol','') == q.unit]
-        by_code = [ u['commonCode'] for u in unece_units() if u.get('commonCode','') == q.unit]
-        code = list(set(by_name) | set(by_symbol) | set(by_code))
-        if len(code) != 1:
-            raise ValueError(f'No UNECE unit code found for Quantity {q}' ) 
-        return code[0]
-    
-    
+from pydantic import BaseModel, model_validator
+from labfreed.well_known_keys.unece.unece_units import unece_units
+
+
+class Quantity(BaseModel):
+    ''' Represents a quantity'''
+    value: float|int
+    unit: str | None 
+    '''unit. Use SI symbols. Set to None of the Quantity is dimensionless'''
+    log_least_significant_digit: int|None = None
+    
+    @model_validator(mode='before')
+    @classmethod
+    def transform_inputs(cls, d:dict):
+        if not isinstance(d, dict):
+            return d
+        # decimals_to_log_significant_digits
+        if decimals:= d.pop('decimals', None):
+            d['log_least_significant_digit'] = - decimals
+        
+        #dimensionless_unit
+        unit= d.get('unit')
+        if unit and unit in ['1', '', 'dimensionless']:
+            d['unit'] = None
+        return d
+    
+        
+    @model_validator(mode='after')
+    def significat_digits_for_int(self):
+        if isinstance(self.value, int):
+            self.log_least_significant_digit = 0
+        return self
+        
+    @property
+    def float(self) -> float:
+        ''' for clarity returns the value'''
+        return self.value
+    
+    def __str__(self):
+        unit_symbol = self.unit
+        if self.unit == "dimensionless" or not self.unit:
+            unit_symbol = ""
+        if self.log_least_significant_digit is not None:
+            val = f"{self.value:.{self.log_least_significant_digit}f}"
+        else:
+            val = str(self.value)
+        return f"{val} {unit_symbol}"
+      
+    def __repr__(self):
+        return f'Quantity: {self.__repr__()}'
+    
+    
+    
+    
+def unece_unit_code_from_quantity(q:Quantity):
+        if not q.unit:
+            return 'C62' # dimensionless
+        by_name =   [ u['commonCode'] for u in unece_units() if u.get('name','') == q.unit] 
+        by_symbol = [ u['commonCode'] for u in unece_units() if u.get('symbol','') == q.unit]
+        by_code = [ u['commonCode'] for u in unece_units() if u.get('commonCode','') == q.unit]
+        code = list(set(by_name) | set(by_symbol) | set(by_code))
+        if len(code) != 1:
+            raise ValueError(f'No UNECE unit code found for Quantity {q}' ) 
+        return code[0]
+    
+