"""
The database module provides support for reading and writing data types
associated with structured thermodynamic/kinetic data.
"""
from io import StringIO
from tinydb import TinyDB
from tinydb.storages import MemoryStorage
from datetime import datetime
from collections import namedtuple
import os
from pycalphad.variables import Species
from pycalphad.core.cache import fhash
from pycalphad.core.utils import recursive_tuplify
[docs]
class DatabaseExportError(Exception):
"""Raised when a database cannot be written."""
pass
[docs]
class Phase(object): #pylint: disable=R0903
"""
Phase in the database.
Attributes
----------
name : string
System-local name of the phase.
constituents : tuple of frozenset
Possible sublattice constituents (elements and/or species).
sublattices : list
Site ratios of sublattices.
model_hints : dict
Structured "hints" for a Model trying to read this phase.
Hints for major constituents and typedefs (Thermo-Calc) go here.
"""
def __init__(self):
self.name = None
self.constituents = None
self.sublattices = []
self.model_hints = {}
def __eq__(self, other):
if type(self) == type(other):
return self.__dict__ == other.__dict__
else:
return False
def __ne__(self, other):
return not self.__eq__(other)
def __repr__(self):
return 'Phase({0!r})'.format(self.__dict__)
def __hash__(self):
return hash((self.name, self.constituents, tuple(self.sublattices),
tuple(sorted(recursive_tuplify(self.model_hints.items())))))
DatabaseFormat = namedtuple('DatabaseFormat', ['read', 'write'])
format_registry = {}
[docs]
class Database(object): #pylint: disable=R0902
"""
Structured thermodynamic and/or kinetic data.
Attributes
----------
elements : set
Set of elements in database.
species : set
Set of species in database.
phases : dict
Phase objects indexed by their system-local name.
symbols : dict
SymEngine objects indexed by their name (FUNCTIONs in Thermo-Calc).
references : dict
Reference objects indexed by their system-local identifier.
Examples
--------
>>> mydb = Database(open('crfeni_mie.tdb'))
>>> mydb = Database('crfeni_mie.tdb')
>>> f = StringIO(u'$a complete TDB file as a string\\n')
>>> mydb = Database(f)
"""
def __new__(cls, *args):
if len(args) == 0:
obj = super(Database, cls).__new__(cls, *args)
# Should elements be rolled into a special case of species?
obj.elements = set()
obj.species = set()
obj.phases = {}
obj.refstates = {}
obj._structure_dict = {} # System-local phase names to global IDs
obj._parameters = TinyDB(storage=MemoryStorage)
obj._parameter_queue = []
obj.symbols = {}
obj.references = {}
# Note: No public typedefs here (from TDB files)
# Instead we put that information in the model_hint for phases
return obj
elif len(args) == 1:
fname = args[0]
# Backwards compatibility: assume TDB by default
fmt = 'tdb'
# Attempt to auto-detect the correct format based on the file extension
try:
path, ext = os.path.splitext(fname)
if '.' in ext and ext[1:].lower() in format_registry:
fmt = ext[1:].lower()
except (AttributeError, TypeError):
pass
if hasattr(fname, 'read'):
# File descriptor
return cls.from_file(fname, fmt=fmt)
elif fname.find('\n') == -1:
# Single-line string; it's probably a filename
return cls.from_file(fname, fmt=fmt)
else:
# Newlines found: probably a full database string
return cls.from_string(fname, fmt=fmt)
else:
raise ValueError('Invalid number of parameters: '+len(args))
def __hash__(self):
return fhash(self.__dict__)
def __getstate__(self):
pickle_dict = {}
for key, value in self.__dict__.items():
if key == '_parameters':
pickle_dict[key] = value.all()
else:
pickle_dict[key] = value
return pickle_dict
def __setstate__(self, state):
for key, value in state.items():
if key == '_parameters':
self._parameters = TinyDB(storage=MemoryStorage)
self._parameters.insert_multiple(value)
else:
setattr(self, key, value)
def __deepcopy__(self, memo):
copy = type(self)()
memo[id(self)] = copy
for key, value in self.__dict__.items():
if key == '_parameters':
copy._parameters = TinyDB(storage=MemoryStorage)
copy._parameters.insert_multiple(value.all())
else:
setattr(copy, key, value)
return copy
[docs]
@staticmethod
def from_file(fname, fmt=None):
"""
Create a Database from a file.
Parameters
----------
fname: str or file-like
File name/descriptor to read.
fmt : str, optional
File format. If not specified, an attempt at auto-detection is made.
Returns
-------
dbf : Database
Database from file.
Examples
--------
None yet.
"""
if fmt is None:
# Attempt to auto-detect the correct format based on the file extension
try:
path, ext = os.path.splitext(fname)
except (AttributeError, TypeError):
# fname isn't actually a path, so we don't know the correct format
raise ValueError('\'fmt\' keyword argument must be specified when passing a file descriptor.')
if '.' in ext and ext[1:].lower() in format_registry:
fmt = ext[1:].lower()
else:
fmt = fmt.lower()
if fmt not in format_registry or format_registry[fmt].read is None:
supported_reads = [key for key, value in format_registry.items() if value.read is not None]
raise NotImplementedError('Unsupported read format \'{0}\'. Supported formats: {1}'.format(fmt,
supported_reads))
# Is it a file descriptor?
if hasattr(fname, 'read'):
fd = fname
need_to_close = False
else:
# It's not file-like, so it's probably a filename
need_to_close = True
fd = open(fname, mode='r')
try:
dbf = Database()
format_registry[fmt.lower()].read(dbf, fd)
finally:
# Close file descriptors created in this routine
# Otherwise that's left up to the calling function
if need_to_close:
fd.close()
return dbf
[docs]
@classmethod
def from_string(cls, data, **kwargs):
"""
Returns Database from a string in the specified format.
This function is a wrapper for calling `from_file` with StringIO.
Parameters
----------
data : str
Raw database string in the specified format.
kwargs : optional
See keyword arguments for `from_file`.
Returns
-------
dbf : Database
"""
return cls.from_file(StringIO(data), **kwargs)
[docs]
def to_file(self, fname, fmt=None, if_exists='raise', **write_kwargs):
"""
Write the Database to a file.
Parameters
----------
fname: str or file-like
File name/descriptor to write.
fmt : str, optional
File format. If not specified, an attempt at auto-detection is made.
if_exists : string, optional ['raise', 'rename', 'overwrite']
Strategy if 'fname' already exists.
The 'raise' option (default) will raise a FileExistsError.
The 'rename' option will append the date/time to the filename.
The 'overwrite' option will overwrite the file.
This argument is ignored if 'fname' is file-like.
write_kwargs : optional
Keyword arguments to pass to write function.
Examples
--------
None yet.
"""
if fmt is None:
# Attempt to auto-detect the correct format based on the file extension
try:
path, ext = os.path.splitext(fname)
except (AttributeError, TypeError):
# fname isn't actually a path, so we don't know the correct format
raise ValueError('\'fmt\' keyword argument must be specified when passing a file descriptor.')
if '.' in ext and ext[1:].lower() in format_registry:
fmt = ext[1:].lower()
else:
fmt = fmt.lower()
if fmt not in format_registry or format_registry[fmt].write is None:
supported_writes = [key for key, value in format_registry.items() if value.write is not None]
raise NotImplementedError('Unsupported write format \'{0}\'. Supported formats: {1}'.format(fmt,
supported_writes))
# Is this a file descriptor?
if hasattr(fname, 'write'):
format_registry[fmt].write(self, fname, **write_kwargs)
else:
if os.path.exists(fname) and if_exists != 'overwrite':
if if_exists == 'rename':
writetime = datetime.now()
fname = os.path.splitext(fname)
fname = fname[0] + "." + writetime.strftime("%Y-%m-%d-%H-%M") + fname[1]
else:
# equivalent to 'raise'
raise FileExistsError('File {} already exists'.format(fname))
with open(fname, mode='w') as fd:
format_registry[fmt].write(self, fd, **write_kwargs)
[docs]
def to_string(self, **kwargs):
"""
Returns Database as a string.
This function is a wrapper for calling `to_file` with StringIO.
Parameters
----------
kwargs : optional
See keyword arguments for `to_file`.
Returns
-------
result : str
"""
result = StringIO()
self.to_file(result, **kwargs)
return result.getvalue()
def __str__(self):
result = 'Elements: {0}\n'.format(sorted(self.elements))
result += 'Species: {0}\n'.format(sorted(self.species, key=lambda s: s.name))
for name, phase in sorted(self.phases.items()):
result += str(phase)+'\n'
result += '{0} symbols in database\n'.format(len(self.symbols))
result += '{0} parameters in database\n'.format(len(self._parameters))
return result
def __eq__(self, other):
if self is other:
return True
elif type(self) != type(other):
return False
elif sorted(self.__dict__.keys()) != sorted(other.__dict__.keys()):
return False
else:
def param_sort_key(x):
return x['phase_name'], x['parameter_type'], x['constituent_array'], \
x['parameter_order'], x['diffusing_species']
for key in self.__dict__.keys():
if key == '_parameters':
# Special handling for TinyDB objects
if len(self._parameters.all()) != len(other._parameters.all()):
return False
self_params = sorted(self._parameters.all(), key=param_sort_key)
other_params = sorted(other._parameters.all(), key=param_sort_key)
if self_params != other_params:
return False
elif self.__dict__[key] != other.__dict__[key]:
return False
return True
def __ne__(self, other):
return not self.__eq__(other)
[docs]
def add_structure_entry(self, local_name, global_name):
"""
Define a relation between the system-local name of a phase and a
"global" identifier. This is used to link crystallographically
similar phases known by different colloquial names.
Parameters
----------
local_name : string
System-local name of the phase.
global_name : object
Abstract representation of symbol, e.g., in SymEngine format.
Examples
--------
None yet.
"""
self._structure_dict[local_name] = global_name
[docs]
def add_parameter(
self, param_type, phase_name, constituent_array, param_order, param, ref=None,
diffusing_species=None, force_insert=True, **kwargs,
):
"""
Add a parameter.
Parameters
----------
param_type : str
Type name of the parameter, e.g., G, L, BMAGN.
phase_name : str
Name of the phase.
constituent_array : list
Configuration of the sublattices (elements and/or species).
param_order : int
Polynomial order of the parameter.
param : object
Abstract representation of the parameter, e.g., in SymEngine format.
ref : str, optional
Reference for the parameter.
diffusing_species : str, optional
(If kinetic parameter) Diffusing species for this parameter.
force_insert : bool, optional
If True, inserts into the database immediately. False is a delayed insert (for performance).
kwargs : Any
Additional metadata to insert into the parameter dictionary
Examples
--------
None yet.
"""
species_dict = {s.name: s for s in self.species}
new_parameter = {
'phase_name': phase_name,
'constituent_array': tuple(tuple(species_dict.get(s.upper(), Species(s)) for s in xs) for xs in constituent_array), # must be hashable type
'parameter_type': param_type,
'parameter_order': param_order,
'parameter': param,
'diffusing_species': Species(diffusing_species),
'reference': ref
}
new_parameter.update(kwargs)
if force_insert:
self._parameters.insert(new_parameter)
else:
self._parameter_queue.append(new_parameter)
[docs]
def add_phase(self, phase_name, model_hints, sublattices):
"""
Add a phase.
Parameters
----------
phase_name : string
System-local name of the phase.
model_hints : dict
Structured "hints" for a Model trying to read this phase.
Hints for major constituents and typedefs (Thermo-Calc) go here.
sublattices : list
Site ratios of sublattices.
Examples
--------
None yet.
"""
new_phase = Phase()
new_phase.name = phase_name
# Need to convert from ParseResults or else equality testing will break
new_phase.sublattices = tuple(sublattices)
new_phase.model_hints = model_hints
self.phases[phase_name] = new_phase
[docs]
def add_phase_constituents(self, phase_name, constituents):
"""
Add a phase.
Parameters
----------
phase_name : string
System-local name of the phase.
constituents : list
Possible phase constituents (elements and/or species).
Examples
--------
None yet.
"""
species_dict = {s.name: s for s in self.species}
try:
# Need to convert constituents from ParseResults
# Otherwise equality testing will be broken
self.phases[phase_name].constituents = tuple([frozenset([species_dict[s.upper()] for s in xs]) for xs in constituents])
except KeyError:
print("Undefined phase "+phase_name)
raise
[docs]
def search(self, query):
"""
Search for parameters matching the specified query.
Parameters
----------
query : object
Structured database query in TinyDB format.
Examples
--------
>>>> from tinydb import where
>>>> db = Database()
>>>> eid = db.add_parameter(...) #TODO
>>>> db.search(where('eid') == eid)
"""
return self._parameters.search(query)
[docs]
def process_parameter_queue(self):
"""
Process the queue of parameters so they are added to the TinyDB in one transaction.
This avoids repeated (expensive) calls to insert().
"""
result = self._parameters.insert_multiple(self._parameter_queue)
self._parameter_queue = []
return result