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48,200 | zhanglab/psamm | psamm/datasource/reaction.py | parse_compound | def parse_compound(s, global_compartment=None):
"""Parse a compound specification.
If no compartment is specified in the string, the global compartment
will be used.
"""
m = re.match(r'^\|(.*)\|$', s)
if m:
s = m.group(1)
m = re.match(r'^(.+)\[(\S+)\]$', s)
if m:
compou... | python | def parse_compound(s, global_compartment=None):
"""Parse a compound specification.
If no compartment is specified in the string, the global compartment
will be used.
"""
m = re.match(r'^\|(.*)\|$', s)
if m:
s = m.group(1)
m = re.match(r'^(.+)\[(\S+)\]$', s)
if m:
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48,201 | zhanglab/psamm | psamm/randomsparse.py | random_sparse | def random_sparse(strategy, prob, obj_reaction, flux_threshold):
"""Find a random minimal network of model reactions.
Given a reaction to optimize and a threshold, delete entities randomly
until the flux of the reaction to optimize falls under the threshold.
Keep deleting until no more entities can be ... | python | def random_sparse(strategy, prob, obj_reaction, flux_threshold):
"""Find a random minimal network of model reactions.
Given a reaction to optimize and a threshold, delete entities randomly
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48,202 | zhanglab/psamm | psamm/commands/gapcheck.py | GapCheckCommand.run_sink_check | def run_sink_check(self, model, solver, threshold, implicit_sinks=True):
"""Run sink production check method."""
prob = solver.create_problem()
# Create flux variables
v = prob.namespace()
for reaction_id in model.reactions:
lower, upper = model.limits[reaction_id]
... | python | def run_sink_check(self, model, solver, threshold, implicit_sinks=True):
"""Run sink production check method."""
prob = solver.create_problem()
# Create flux variables
v = prob.namespace()
for reaction_id in model.reactions:
lower, upper = model.limits[reaction_id]
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48,203 | zhanglab/psamm | psamm/commands/gapcheck.py | GapCheckCommand.run_reaction_production_check | def run_reaction_production_check(self, model, solver, threshold,
implicit_sinks=True):
"""Run reaction production check method."""
prob = solver.create_problem()
# Create flux variables
v = prob.namespace()
for reaction_id in model.reaction... | python | def run_reaction_production_check(self, model, solver, threshold,
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"""Run reaction production check method."""
prob = solver.create_problem()
# Create flux variables
v = prob.namespace()
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48,204 | zhanglab/psamm | psamm/lpsolver/cplex.py | Problem.add_linear_constraints | def add_linear_constraints(self, *relations):
"""Add constraints to the problem
Each constraint is represented by a Relation, and the
expression in that relation can be a set expression.
"""
constraints = []
for relation in relations:
if self._check_relation... | python | def add_linear_constraints(self, *relations):
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Each constraint is represented by a Relation, and the
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48,205 | zhanglab/psamm | psamm/lpsolver/cplex.py | Problem.set_objective | def set_objective(self, expression):
"""Set objective expression of the problem."""
if isinstance(expression, numbers.Number):
# Allow expressions with no variables as objective,
# represented as a number
expression = Expression(offset=expression)
linear = [... | python | def set_objective(self, expression):
"""Set objective expression of the problem."""
if isinstance(expression, numbers.Number):
# Allow expressions with no variables as objective,
# represented as a number
expression = Expression(offset=expression)
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48,206 | zhanglab/psamm | psamm/lpsolver/cplex.py | Problem._reset_problem_type | def _reset_problem_type(self):
"""Reset problem type to whatever is appropriate."""
# Only need to reset the type after the first solve. This also works
# around a bug in Cplex where get_num_binary() is some rare cases
# causes a segfault.
if self._solve_count > 0:
i... | python | def _reset_problem_type(self):
"""Reset problem type to whatever is appropriate."""
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48,207 | zhanglab/psamm | psamm/lpsolver/cplex.py | Result.get_value | def get_value(self, expression):
"""Return value of expression."""
self._check_valid()
return super(Result, self).get_value(expression) | python | def get_value(self, expression):
"""Return value of expression."""
self._check_valid()
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48,208 | zhanglab/psamm | psamm/formula.py | _parse_formula | def _parse_formula(s):
"""Parse formula string."""
scanner = re.compile(r'''
(\s+) | # whitespace
(\(|\)) | # group
([A-Z][a-z]*) | # element
(\d+) | # number
([a-z]) | # variable
(\Z) | # end
(.) # error
... | python | def _parse_formula(s):
"""Parse formula string."""
scanner = re.compile(r'''
(\s+) | # whitespace
(\(|\)) | # group
([A-Z][a-z]*) | # element
(\d+) | # number
([a-z]) | # variable
(\Z) | # end
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48,209 | hearsaycorp/normalize | normalize/visitor.py | Visitor.copy | def copy(self):
"""Be sure to implement this method when sub-classing, otherwise you
will lose any specialization context."""
doppel = type(self)(
self.unpack, self.apply, self.collect, self.reduce,
apply_empty_slots=self.apply_empty_slots,
extraneous=self.ext... | python | def copy(self):
"""Be sure to implement this method when sub-classing, otherwise you
will lose any specialization context."""
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48,210 | hearsaycorp/normalize | normalize/visitor.py | VisitorPattern.unpack | def unpack(cls, value, value_type, visitor):
"""Unpack a value during a 'visit'
args:
``value=``\ *object*
The instance being visited
``value_type=``\ *RecordType*
The expected type of the instance
``visitor=``\ *Visitor*
... | python | def unpack(cls, value, value_type, visitor):
"""Unpack a value during a 'visit'
args:
``value=``\ *object*
The instance being visited
``value_type=``\ *RecordType*
The expected type of the instance
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48,211 | hearsaycorp/normalize | normalize/visitor.py | VisitorPattern.apply | def apply(cls, value, prop, visitor):
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48,212 | hearsaycorp/normalize | normalize/visitor.py | VisitorPattern.aggregate | def aggregate(self, mapped_coll_generator, coll_type, visitor):
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48,213 | hearsaycorp/normalize | normalize/visitor.py | VisitorPattern.reduce | def reduce(self, mapped_props, aggregated, value_type, visitor):
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48,214 | hearsaycorp/normalize | normalize/visitor.py | VisitorPattern.reflect | def reflect(cls, X, **kwargs):
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48,215 | hearsaycorp/normalize | normalize/visitor.py | VisitorPattern.map | def map(cls, visitor, value, value_type):
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48,216 | zhanglab/psamm | psamm/fluxanalysis.py | _get_fba_problem | def _get_fba_problem(model, tfba, solver):
"""Convenience function for returning the right FBA problem instance"""
p = FluxBalanceProblem(model, solver)
if tfba:
p.add_thermodynamic()
return p | python | def _get_fba_problem(model, tfba, solver):
"""Convenience function for returning the right FBA problem instance"""
p = FluxBalanceProblem(model, solver)
if tfba:
p.add_thermodynamic()
return p | [
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48,217 | zhanglab/psamm | psamm/fluxanalysis.py | flux_balance | def flux_balance(model, reaction, tfba, solver):
"""Run flux balance analysis on the given model.
Yields the reaction id and flux value for each reaction in the model.
This is a convenience function for sertting up and running the
FluxBalanceProblem. If the FBA is solved for more than one parameter
... | python | def flux_balance(model, reaction, tfba, solver):
"""Run flux balance analysis on the given model.
Yields the reaction id and flux value for each reaction in the model.
This is a convenience function for sertting up and running the
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48,218 | zhanglab/psamm | psamm/fluxanalysis.py | flux_variability | def flux_variability(model, reactions, fixed, tfba, solver):
"""Find the variability of each reaction while fixing certain fluxes.
Yields the reaction id, and a tuple of minimum and maximum value for each
of the given reactions. The fixed reactions are given in a dictionary as
a reaction id to value ma... | python | def flux_variability(model, reactions, fixed, tfba, solver):
"""Find the variability of each reaction while fixing certain fluxes.
Yields the reaction id, and a tuple of minimum and maximum value for each
of the given reactions. The fixed reactions are given in a dictionary as
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48,219 | zhanglab/psamm | psamm/fluxanalysis.py | flux_minimization | def flux_minimization(model, fixed, solver, weights={}):
"""Minimize flux of all reactions while keeping certain fluxes fixed.
The fixed reactions are given in a dictionary as reaction id
to value mapping. The weighted L1-norm of the fluxes is minimized.
Args:
model: MetabolicModel to solve.
... | python | def flux_minimization(model, fixed, solver, weights={}):
"""Minimize flux of all reactions while keeping certain fluxes fixed.
The fixed reactions are given in a dictionary as reaction id
to value mapping. The weighted L1-norm of the fluxes is minimized.
Args:
model: MetabolicModel to solve.
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48,220 | zhanglab/psamm | psamm/fluxanalysis.py | flux_randomization | def flux_randomization(model, threshold, tfba, solver):
"""Find a random flux solution on the boundary of the solution space.
The reactions in the threshold dictionary are constrained with the
associated lower bound.
Args:
model: MetabolicModel to solve.
threshold: dict of additional l... | python | def flux_randomization(model, threshold, tfba, solver):
"""Find a random flux solution on the boundary of the solution space.
The reactions in the threshold dictionary are constrained with the
associated lower bound.
Args:
model: MetabolicModel to solve.
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48,221 | zhanglab/psamm | psamm/fluxanalysis.py | consistency_check | def consistency_check(model, subset, epsilon, tfba, solver):
"""Check that reaction subset of model is consistent using FBA.
Yields all reactions that are *not* flux consistent. A reaction is
consistent if there is at least one flux solution to the model that both
respects the model constraints and als... | python | def consistency_check(model, subset, epsilon, tfba, solver):
"""Check that reaction subset of model is consistent using FBA.
Yields all reactions that are *not* flux consistent. A reaction is
consistent if there is at least one flux solution to the model that both
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48,222 | zhanglab/psamm | psamm/fluxanalysis.py | FluxBalanceProblem.add_thermodynamic | def add_thermodynamic(self, em=1000):
"""Apply thermodynamic constraints to the model.
Adding these constraints restricts the solution space to only
contain solutions that have no internal loops [Schilling00]_. This is
solved as a MILP problem as described in [Muller13]_. The time to so... | python | def add_thermodynamic(self, em=1000):
"""Apply thermodynamic constraints to the model.
Adding these constraints restricts the solution space to only
contain solutions that have no internal loops [Schilling00]_. This is
solved as a MILP problem as described in [Muller13]_. The time to so... | [
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48,223 | zhanglab/psamm | psamm/fluxanalysis.py | FluxBalanceProblem.maximize | def maximize(self, reaction):
"""Solve the model by maximizing the given reaction.
If reaction is a dictionary object, each entry is interpreted as a
weight on the objective for that reaction (non-existent reaction will
have zero weight).
"""
self._prob.set_objective(se... | python | def maximize(self, reaction):
"""Solve the model by maximizing the given reaction.
If reaction is a dictionary object, each entry is interpreted as a
weight on the objective for that reaction (non-existent reaction will
have zero weight).
"""
self._prob.set_objective(se... | [
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48,224 | zhanglab/psamm | psamm/fluxanalysis.py | FluxBalanceProblem.flux_bound | def flux_bound(self, reaction, direction):
"""Return the flux bound of the reaction.
Direction must be a positive number to obtain the upper bound or a
negative number to obtain the lower bound. A value of inf or -inf is
returned if the problem is unbounded.
"""
try:
... | python | def flux_bound(self, reaction, direction):
"""Return the flux bound of the reaction.
Direction must be a positive number to obtain the upper bound or a
negative number to obtain the lower bound. A value of inf or -inf is
returned if the problem is unbounded.
"""
try:
... | [
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48,225 | zhanglab/psamm | psamm/fluxanalysis.py | FluxBalanceProblem._add_minimization_vars | def _add_minimization_vars(self):
"""Add variables and constraints for L1 norm minimization."""
self._z = self._prob.namespace(self._model.reactions, lower=0)
# Define constraints
v = self._v.set(self._model.reactions)
z = self._z.set(self._model.reactions)
self._prob.... | python | def _add_minimization_vars(self):
"""Add variables and constraints for L1 norm minimization."""
self._z = self._prob.namespace(self._model.reactions, lower=0)
# Define constraints
v = self._v.set(self._model.reactions)
z = self._z.set(self._model.reactions)
self._prob.... | [
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48,226 | zhanglab/psamm | psamm/fluxanalysis.py | FluxBalanceProblem.minimize_l1 | def minimize_l1(self, weights={}):
"""Solve the model by minimizing the L1 norm of the fluxes.
If the weights dictionary is given, the weighted L1 norm if minimized
instead. The dictionary contains the weights of each reaction
(default 1).
"""
if self._z is None:
... | python | def minimize_l1(self, weights={}):
"""Solve the model by minimizing the L1 norm of the fluxes.
If the weights dictionary is given, the weighted L1 norm if minimized
instead. The dictionary contains the weights of each reaction
(default 1).
"""
if self._z is None:
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48,227 | zhanglab/psamm | psamm/fluxanalysis.py | FluxBalanceProblem.max_min_l1 | def max_min_l1(self, reaction, weights={}):
"""Maximize flux of reaction then minimize the L1 norm.
During minimization the given reaction will be fixed at the maximum
obtained from the first solution. If reaction is a dictionary object,
each entry is interpreted as a weight on the obje... | python | def max_min_l1(self, reaction, weights={}):
"""Maximize flux of reaction then minimize the L1 norm.
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48,228 | zhanglab/psamm | psamm/fluxanalysis.py | FluxBalanceProblem._solve | def _solve(self):
"""Solve the problem with the current objective."""
# Remove temporary constraints
while len(self._remove_constr) > 0:
self._remove_constr.pop().delete()
try:
self._prob.solve(lp.ObjectiveSense.Maximize)
except lp.SolverError as e:
... | python | def _solve(self):
"""Solve the problem with the current objective."""
# Remove temporary constraints
while len(self._remove_constr) > 0:
self._remove_constr.pop().delete()
try:
self._prob.solve(lp.ObjectiveSense.Maximize)
except lp.SolverError as e:
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48,229 | zhanglab/psamm | psamm/fluxanalysis.py | FluxBalanceProblem.flux_expr | def flux_expr(self, reaction):
"""Get LP expression representing the reaction flux."""
if isinstance(reaction, dict):
return self._v.expr(iteritems(reaction))
return self._v(reaction) | python | def flux_expr(self, reaction):
"""Get LP expression representing the reaction flux."""
if isinstance(reaction, dict):
return self._v.expr(iteritems(reaction))
return self._v(reaction) | [
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48,230 | zhanglab/psamm | psamm/fluxanalysis.py | FluxBalanceProblem.get_flux | def get_flux(self, reaction):
"""Get resulting flux value for reaction."""
return self._prob.result.get_value(self._v(reaction)) | python | def get_flux(self, reaction):
"""Get resulting flux value for reaction."""
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48,231 | zhanglab/psamm | psamm/lpsolver/qsoptex.py | Problem.set_objective | def set_objective(self, expression):
"""Set linear objective of problem"""
if isinstance(expression, numbers.Number):
# Allow expressions with no variables as objective,
# represented as a number
expression = Expression()
self._p.set_linear_objective(
... | python | def set_objective(self, expression):
"""Set linear objective of problem"""
if isinstance(expression, numbers.Number):
# Allow expressions with no variables as objective,
# represented as a number
expression = Expression()
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48,232 | zhanglab/psamm | psamm/lpsolver/qsoptex.py | Result.unbounded | def unbounded(self):
"""Whether the solution is unbounded"""
self._check_valid()
return (self._problem._p.get_status() ==
qsoptex.SolutionStatus.UNBOUNDED) | python | def unbounded(self):
"""Whether the solution is unbounded"""
self._check_valid()
return (self._problem._p.get_status() ==
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48,233 | smartfile/python-librsync | librsync/__init__.py | _execute | def _execute(job, f, o=None):
"""
Executes a librsync "job" by reading bytes from `f` and writing results to
`o` if provided. If `o` is omitted, the output is ignored.
"""
# Re-use the same buffer for output, we will read from it after each
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out = ctypes.create_string_buffer(RS_J... | python | def _execute(job, f, o=None):
"""
Executes a librsync "job" by reading bytes from `f` and writing results to
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"""
# Re-use the same buffer for output, we will read from it after each
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48,234 | smartfile/python-librsync | librsync/__init__.py | signature | def signature(f, s=None, block_size=RS_DEFAULT_BLOCK_LEN):
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Generate a signature for the file `f`. The signature will be written to `s`.
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48,235 | smartfile/python-librsync | librsync/__init__.py | delta | def delta(f, s, d=None):
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d ... | python | def delta(f, s, d=None):
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48,236 | smartfile/python-librsync | librsync/__init__.py | patch | def patch(f, d, o=None):
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48,237 | zhanglab/psamm | psamm/gapfill.py | _find_integer_tolerance | def _find_integer_tolerance(epsilon, v_max, min_tol):
"""Find appropriate integer tolerance for gap-filling problems."""
int_tol = min(epsilon / (10 * v_max), 0.1)
min_tol = max(1e-10, min_tol)
if int_tol < min_tol:
eps_lower = min_tol * 10 * v_max
logger.warning(
'When the m... | python | def _find_integer_tolerance(epsilon, v_max, min_tol):
"""Find appropriate integer tolerance for gap-filling problems."""
int_tol = min(epsilon / (10 * v_max), 0.1)
min_tol = max(1e-10, min_tol)
if int_tol < min_tol:
eps_lower = min_tol * 10 * v_max
logger.warning(
'When the m... | [
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48,238 | zhanglab/psamm | psamm/gapfill.py | gapfind | def gapfind(model, solver, epsilon=0.001, v_max=1000, implicit_sinks=True):
"""Identify compounds in the model that cannot be produced.
Yields all compounds that cannot be produced. This method
assumes implicit sinks for all compounds in the model so
the only factor that influences whether a compound c... | python | def gapfind(model, solver, epsilon=0.001, v_max=1000, implicit_sinks=True):
"""Identify compounds in the model that cannot be produced.
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48,239 | zhanglab/psamm | psamm/datasource/native.py | float_constructor | def float_constructor(loader, node):
"""Construct Decimal from YAML float encoding."""
s = loader.construct_scalar(node)
if s == '.inf':
return Decimal('Infinity')
elif s == '-.inf':
return -Decimal('Infinity')
elif s == '.nan':
return Decimal('NaN')
return Decimal(s) | python | def float_constructor(loader, node):
"""Construct Decimal from YAML float encoding."""
s = loader.construct_scalar(node)
if s == '.inf':
return Decimal('Infinity')
elif s == '-.inf':
return -Decimal('Infinity')
elif s == '.nan':
return Decimal('NaN')
return Decimal(s) | [
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48,240 | zhanglab/psamm | psamm/datasource/native.py | yaml_load | def yaml_load(stream):
"""Load YAML file using safe loader."""
# Surprisingly, the CSafeLoader does not seem to be used by default.
# Check whether the CSafeLoader is available and provide a log message
# if it is not available.
global _HAS_YAML_LIBRARY
if _HAS_YAML_LIBRARY is None:
_HA... | python | def yaml_load(stream):
"""Load YAML file using safe loader."""
# Surprisingly, the CSafeLoader does not seem to be used by default.
# Check whether the CSafeLoader is available and provide a log message
# if it is not available.
global _HAS_YAML_LIBRARY
if _HAS_YAML_LIBRARY is None:
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48,241 | zhanglab/psamm | psamm/datasource/native.py | _check_id | def _check_id(entity, entity_type):
"""Check whether the ID is valid.
First check if the ID is missing, and then check if it is a qualified
string type, finally check if the string is empty. For all checks, it
would raise a ParseError with the corresponding message.
Args:
entity: a string ... | python | def _check_id(entity, entity_type):
"""Check whether the ID is valid.
First check if the ID is missing, and then check if it is a qualified
string type, finally check if the string is empty. For all checks, it
would raise a ParseError with the corresponding message.
Args:
entity: a string ... | [
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48,242 | zhanglab/psamm | psamm/datasource/native.py | parse_compound | def parse_compound(compound_def, context=None):
"""Parse a structured compound definition as obtained from a YAML file
Returns a CompoundEntry."""
compound_id = compound_def.get('id')
_check_id(compound_id, 'Compound')
mark = FileMark(context, None, None)
return CompoundEntry(compound_def, ma... | python | def parse_compound(compound_def, context=None):
"""Parse a structured compound definition as obtained from a YAML file
Returns a CompoundEntry."""
compound_id = compound_def.get('id')
_check_id(compound_id, 'Compound')
mark = FileMark(context, None, None)
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48,243 | zhanglab/psamm | psamm/datasource/native.py | parse_compound_list | def parse_compound_list(path, compounds):
"""Parse a structured list of compounds as obtained from a YAML file
Yields CompoundEntries. Path can be given as a string or a context.
"""
context = FilePathContext(path)
for compound_def in compounds:
if 'include' in compound_def:
f... | python | def parse_compound_list(path, compounds):
"""Parse a structured list of compounds as obtained from a YAML file
Yields CompoundEntries. Path can be given as a string or a context.
"""
context = FilePathContext(path)
for compound_def in compounds:
if 'include' in compound_def:
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48,244 | zhanglab/psamm | psamm/datasource/native.py | parse_compound_table_file | def parse_compound_table_file(path, f):
"""Parse a tab-separated file containing compound IDs and properties
The compound properties are parsed according to the header which specifies
which property is contained in each column.
"""
context = FilePathContext(path)
for i, row in enumerate(csv.D... | python | def parse_compound_table_file(path, f):
"""Parse a tab-separated file containing compound IDs and properties
The compound properties are parsed according to the header which specifies
which property is contained in each column.
"""
context = FilePathContext(path)
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48,245 | zhanglab/psamm | psamm/datasource/native.py | parse_compound_file | def parse_compound_file(path, format):
"""Open and parse reaction file based on file extension or given format
Path can be given as a string or a context.
"""
context = FilePathContext(path)
# YAML files do not need to explicitly specify format
format = resolve_format(format, context.filepath... | python | def parse_compound_file(path, format):
"""Open and parse reaction file based on file extension or given format
Path can be given as a string or a context.
"""
context = FilePathContext(path)
# YAML files do not need to explicitly specify format
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48,246 | zhanglab/psamm | psamm/datasource/native.py | parse_reaction_equation_string | def parse_reaction_equation_string(equation, default_compartment):
"""Parse a string representation of a reaction equation.
Converts undefined compartments to the default compartment.
"""
def _translate_compartments(reaction, compartment):
"""Translate compound with missing compartments.
... | python | def parse_reaction_equation_string(equation, default_compartment):
"""Parse a string representation of a reaction equation.
Converts undefined compartments to the default compartment.
"""
def _translate_compartments(reaction, compartment):
"""Translate compound with missing compartments.
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48,247 | zhanglab/psamm | psamm/datasource/native.py | parse_reaction_equation | def parse_reaction_equation(equation_def, default_compartment):
"""Parse a structured reaction equation as obtained from a YAML file
Returns a Reaction.
"""
def parse_compound_list(l, compartment):
"""Parse a list of reactants or metabolites"""
for compound_def in l:
compou... | python | def parse_reaction_equation(equation_def, default_compartment):
"""Parse a structured reaction equation as obtained from a YAML file
Returns a Reaction.
"""
def parse_compound_list(l, compartment):
"""Parse a list of reactants or metabolites"""
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48,248 | zhanglab/psamm | psamm/datasource/native.py | parse_reaction | def parse_reaction(reaction_def, default_compartment, context=None):
"""Parse a structured reaction definition as obtained from a YAML file
Returns a ReactionEntry.
"""
reaction_id = reaction_def.get('id')
_check_id(reaction_id, 'Reaction')
reaction_props = dict(reaction_def)
# Parse rea... | python | def parse_reaction(reaction_def, default_compartment, context=None):
"""Parse a structured reaction definition as obtained from a YAML file
Returns a ReactionEntry.
"""
reaction_id = reaction_def.get('id')
_check_id(reaction_id, 'Reaction')
reaction_props = dict(reaction_def)
# Parse rea... | [
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48,249 | zhanglab/psamm | psamm/datasource/native.py | parse_reaction_list | def parse_reaction_list(path, reactions, default_compartment=None):
"""Parse a structured list of reactions as obtained from a YAML file
Yields tuples of reaction ID and reaction object. Path can be given as a
string or a context.
"""
context = FilePathContext(path)
for reaction_def in reacti... | python | def parse_reaction_list(path, reactions, default_compartment=None):
"""Parse a structured list of reactions as obtained from a YAML file
Yields tuples of reaction ID and reaction object. Path can be given as a
string or a context.
"""
context = FilePathContext(path)
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48,250 | zhanglab/psamm | psamm/datasource/native.py | parse_reaction_table_file | def parse_reaction_table_file(path, f, default_compartment):
"""Parse a tab-separated file containing reaction IDs and properties
The reaction properties are parsed according to the header which specifies
which property is contained in each column.
"""
context = FilePathContext(path)
for line... | python | def parse_reaction_table_file(path, f, default_compartment):
"""Parse a tab-separated file containing reaction IDs and properties
The reaction properties are parsed according to the header which specifies
which property is contained in each column.
"""
context = FilePathContext(path)
for line... | [
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48,251 | zhanglab/psamm | psamm/datasource/native.py | parse_reaction_file | def parse_reaction_file(path, default_compartment=None):
"""Open and parse reaction file based on file extension
Path can be given as a string or a context.
"""
context = FilePathContext(path)
format = resolve_format(None, context.filepath)
if format == 'tsv':
logger.debug('Parsing re... | python | def parse_reaction_file(path, default_compartment=None):
"""Open and parse reaction file based on file extension
Path can be given as a string or a context.
"""
context = FilePathContext(path)
format = resolve_format(None, context.filepath)
if format == 'tsv':
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48,252 | zhanglab/psamm | psamm/datasource/native.py | parse_exchange | def parse_exchange(exchange_def, default_compartment):
"""Parse a structured exchange definition as obtained from a YAML file.
Returns in iterator of compound, reaction, lower and upper bounds.
"""
default_compartment = exchange_def.get('compartment', default_compartment)
for compound_def in exch... | python | def parse_exchange(exchange_def, default_compartment):
"""Parse a structured exchange definition as obtained from a YAML file.
Returns in iterator of compound, reaction, lower and upper bounds.
"""
default_compartment = exchange_def.get('compartment', default_compartment)
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48,253 | zhanglab/psamm | psamm/datasource/native.py | parse_exchange_list | def parse_exchange_list(path, exchange, default_compartment):
"""Parse a structured exchange list as obtained from a YAML file.
Yields tuples of compound, reaction ID, lower and upper flux bounds. Path
can be given as a string or a context.
"""
context = FilePathContext(path)
for exchange_def... | python | def parse_exchange_list(path, exchange, default_compartment):
"""Parse a structured exchange list as obtained from a YAML file.
Yields tuples of compound, reaction ID, lower and upper flux bounds. Path
can be given as a string or a context.
"""
context = FilePathContext(path)
for exchange_def... | [
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48,254 | zhanglab/psamm | psamm/datasource/native.py | parse_exchange_table_file | def parse_exchange_table_file(f):
"""Parse a space-separated file containing exchange compound flux limits.
The first two columns contain compound IDs and compartment while the
third column contains the lower flux limits. The fourth column is
optional and contains the upper flux limit.
"""
for... | python | def parse_exchange_table_file(f):
"""Parse a space-separated file containing exchange compound flux limits.
The first two columns contain compound IDs and compartment while the
third column contains the lower flux limits. The fourth column is
optional and contains the upper flux limit.
"""
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48,255 | zhanglab/psamm | psamm/datasource/native.py | parse_exchange_file | def parse_exchange_file(path, default_compartment):
"""Parse a file as a list of exchange compounds with flux limits.
The file format is detected and the file is parsed accordingly. Path can
be given as a string or a context.
"""
context = FilePathContext(path)
format = resolve_format(None, c... | python | def parse_exchange_file(path, default_compartment):
"""Parse a file as a list of exchange compounds with flux limits.
The file format is detected and the file is parsed accordingly. Path can
be given as a string or a context.
"""
context = FilePathContext(path)
format = resolve_format(None, c... | [
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48,256 | zhanglab/psamm | psamm/datasource/native.py | parse_limit | def parse_limit(limit_def):
"""Parse a structured flux limit definition as obtained from a YAML file
Returns a tuple of reaction, lower and upper bound.
"""
lower, upper = get_limits(limit_def)
reaction = limit_def.get('reaction')
return reaction, lower, upper | python | def parse_limit(limit_def):
"""Parse a structured flux limit definition as obtained from a YAML file
Returns a tuple of reaction, lower and upper bound.
"""
lower, upper = get_limits(limit_def)
reaction = limit_def.get('reaction')
return reaction, lower, upper | [
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48,257 | zhanglab/psamm | psamm/datasource/native.py | parse_limits_list | def parse_limits_list(path, limits):
"""Parse a structured list of flux limits as obtained from a YAML file
Yields tuples of reaction ID, lower and upper flux bounds. Path can be
given as a string or a context.
"""
context = FilePathContext(path)
for limit_def in limits:
if 'include' ... | python | def parse_limits_list(path, limits):
"""Parse a structured list of flux limits as obtained from a YAML file
Yields tuples of reaction ID, lower and upper flux bounds. Path can be
given as a string or a context.
"""
context = FilePathContext(path)
for limit_def in limits:
if 'include' ... | [
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48,258 | zhanglab/psamm | psamm/datasource/native.py | parse_limits_table_file | def parse_limits_table_file(f):
"""Parse a space-separated file containing reaction flux limits
The first column contains reaction IDs while the second column contains
the lower flux limits. The third column is optional and contains the
upper flux limit.
"""
for line in f:
line, _, com... | python | def parse_limits_table_file(f):
"""Parse a space-separated file containing reaction flux limits
The first column contains reaction IDs while the second column contains
the lower flux limits. The third column is optional and contains the
upper flux limit.
"""
for line in f:
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48,259 | zhanglab/psamm | psamm/datasource/native.py | parse_limits_file | def parse_limits_file(path):
"""Parse a file as a list of reaction flux limits
The file format is detected and the file is parsed accordingly. Path can
be given as a string or a context.
"""
context = FilePathContext(path)
format = resolve_format(None, context.filepath)
if format == 'tsv'... | python | def parse_limits_file(path):
"""Parse a file as a list of reaction flux limits
The file format is detected and the file is parsed accordingly. Path can
be given as a string or a context.
"""
context = FilePathContext(path)
format = resolve_format(None, context.filepath)
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48,260 | zhanglab/psamm | psamm/datasource/native.py | parse_model_group | def parse_model_group(path, group):
"""Parse a structured model group as obtained from a YAML file
Path can be given as a string or a context.
"""
context = FilePathContext(path)
for reaction_id in group.get('reactions', []):
yield reaction_id
# Parse subgroups
for reaction_id in... | python | def parse_model_group(path, group):
"""Parse a structured model group as obtained from a YAML file
Path can be given as a string or a context.
"""
context = FilePathContext(path)
for reaction_id in group.get('reactions', []):
yield reaction_id
# Parse subgroups
for reaction_id in... | [
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48,261 | zhanglab/psamm | psamm/datasource/native.py | parse_model_group_list | def parse_model_group_list(path, groups):
"""Parse a structured list of model groups as obtained from a YAML file
Yields reaction IDs. Path can be given as a string or a context.
"""
context = FilePathContext(path)
for model_group in groups:
if 'include' in model_group:
include... | python | def parse_model_group_list(path, groups):
"""Parse a structured list of model groups as obtained from a YAML file
Yields reaction IDs. Path can be given as a string or a context.
"""
context = FilePathContext(path)
for model_group in groups:
if 'include' in model_group:
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48,262 | zhanglab/psamm | psamm/datasource/native.py | _reaction_representer | def _reaction_representer(dumper, data):
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then transform the reaction data into a list of directories with all
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48,263 | zhanglab/psamm | psamm/datasource/native.py | ModelReader.reader_from_path | def reader_from_path(cls, path):
"""Create a model from specified path.
Path can be a directory containing a ``model.yaml`` or ``model.yml``
file or it can be a path naming the central model file directly.
"""
context = FilePathContext(path)
try:
with open(co... | python | def reader_from_path(cls, path):
"""Create a model from specified path.
Path can be a directory containing a ``model.yaml`` or ``model.yml``
file or it can be a path naming the central model file directly.
"""
context = FilePathContext(path)
try:
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48,264 | zhanglab/psamm | psamm/datasource/native.py | ModelReader.parse_compartments | def parse_compartments(self):
"""Parse compartment information from model.
Return tuple of: 1) iterator of
:class:`psamm.datasource.entry.CompartmentEntry`; 2) Set of pairs
defining the compartment boundaries of the model.
"""
compartments = OrderedDict()
bounda... | python | def parse_compartments(self):
"""Parse compartment information from model.
Return tuple of: 1) iterator of
:class:`psamm.datasource.entry.CompartmentEntry`; 2) Set of pairs
defining the compartment boundaries of the model.
"""
compartments = OrderedDict()
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48,265 | zhanglab/psamm | psamm/datasource/native.py | ModelReader.parse_reactions | def parse_reactions(self):
"""Yield tuples of reaction ID and reactions defined in the model"""
# Parse reactions defined in the main model file
if 'reactions' in self._model:
for reaction in parse_reaction_list(
self._context, self._model['reactions'],
... | python | def parse_reactions(self):
"""Yield tuples of reaction ID and reactions defined in the model"""
# Parse reactions defined in the main model file
if 'reactions' in self._model:
for reaction in parse_reaction_list(
self._context, self._model['reactions'],
... | [
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48,266 | zhanglab/psamm | psamm/datasource/native.py | ModelReader.parse_model | def parse_model(self):
"""Yield reaction IDs of model reactions"""
if self.has_model_definition():
for reaction_id in parse_model_group_list(
self._context, self._model['model']):
yield reaction_id | python | def parse_model(self):
"""Yield reaction IDs of model reactions"""
if self.has_model_definition():
for reaction_id in parse_model_group_list(
self._context, self._model['model']):
yield reaction_id | [
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48,267 | zhanglab/psamm | psamm/datasource/native.py | ModelReader.parse_limits | def parse_limits(self):
"""Yield tuples of reaction ID, lower, and upper bound flux limits"""
if 'limits' in self._model:
if not isinstance(self._model['limits'], list):
raise ParseError('Expected limits to be a list')
for limit in parse_limits_list(
... | python | def parse_limits(self):
"""Yield tuples of reaction ID, lower, and upper bound flux limits"""
if 'limits' in self._model:
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raise ParseError('Expected limits to be a list')
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48,268 | zhanglab/psamm | psamm/datasource/native.py | ModelReader.parse_exchange | def parse_exchange(self):
"""Yield tuples of exchange compounds.
Each exchange compound is a tuple of compound, reaction ID, lower and
upper flux limits.
"""
if 'media' in self._model:
if 'exchange' in self._model:
raise ParseError('Both "media" and ... | python | def parse_exchange(self):
"""Yield tuples of exchange compounds.
Each exchange compound is a tuple of compound, reaction ID, lower and
upper flux limits.
"""
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48,269 | zhanglab/psamm | psamm/datasource/native.py | ModelReader.parse_compounds | def parse_compounds(self):
"""Yield CompoundEntries for defined compounds"""
if 'compounds' in self._model:
for compound in parse_compound_list(
self._context, self._model['compounds']):
yield compound | python | def parse_compounds(self):
"""Yield CompoundEntries for defined compounds"""
if 'compounds' in self._model:
for compound in parse_compound_list(
self._context, self._model['compounds']):
yield compound | [
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48,270 | zhanglab/psamm | psamm/datasource/native.py | ModelWriter.convert_compartment_entry | def convert_compartment_entry(self, compartment, adjacencies):
"""Convert compartment entry to YAML dict.
Args:
compartment: :class:`psamm.datasource.entry.CompartmentEntry`.
adjacencies: Sequence of IDs or a single ID of adjacent
compartments (or None).
... | python | def convert_compartment_entry(self, compartment, adjacencies):
"""Convert compartment entry to YAML dict.
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compartment: :class:`psamm.datasource.entry.CompartmentEntry`.
adjacencies: Sequence of IDs or a single ID of adjacent
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48,271 | zhanglab/psamm | psamm/datasource/native.py | ModelWriter.convert_compound_entry | def convert_compound_entry(self, compound):
"""Convert compound entry to YAML dict."""
d = OrderedDict()
d['id'] = compound.id
order = {
key: i for i, key in enumerate(
['name', 'formula', 'formula_neutral', 'charge', 'kegg',
'cas'])}
... | python | def convert_compound_entry(self, compound):
"""Convert compound entry to YAML dict."""
d = OrderedDict()
d['id'] = compound.id
order = {
key: i for i, key in enumerate(
['name', 'formula', 'formula_neutral', 'charge', 'kegg',
'cas'])}
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48,272 | zhanglab/psamm | psamm/datasource/native.py | ModelWriter.convert_reaction_entry | def convert_reaction_entry(self, reaction):
"""Convert reaction entry to YAML dict."""
d = OrderedDict()
d['id'] = reaction.id
def is_equation_valid(equation):
# If the equation is a Reaction object, it must have non-zero
# number of compounds.
return... | python | def convert_reaction_entry(self, reaction):
"""Convert reaction entry to YAML dict."""
d = OrderedDict()
d['id'] = reaction.id
def is_equation_valid(equation):
# If the equation is a Reaction object, it must have non-zero
# number of compounds.
return... | [
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48,273 | zhanglab/psamm | psamm/datasource/native.py | ModelWriter._write_entries | def _write_entries(self, stream, entries, converter, properties=None):
"""Write iterable of entries as YAML object to stream.
Args:
stream: File-like object.
entries: Iterable of entries.
converter: Conversion function from entry to YAML object.
propertie... | python | def _write_entries(self, stream, entries, converter, properties=None):
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Args:
stream: File-like object.
entries: Iterable of entries.
converter: Conversion function from entry to YAML object.
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48,274 | zhanglab/psamm | psamm/datasource/native.py | ModelWriter.write_compartments | def write_compartments(self, stream, compartments, adjacencies,
properties=None):
"""Write iterable of compartments as YAML object to stream.
Args:
stream: File-like object.
compartments: Iterable of compartment entries.
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"""Write iterable of compartments as YAML object to stream.
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stream: File-like object.
compartments: Iterable of compartment entries.
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48,275 | zhanglab/psamm | psamm/datasource/native.py | ModelWriter.write_compounds | def write_compounds(self, stream, compounds, properties=None):
"""Write iterable of compounds as YAML object to stream.
Args:
stream: File-like object.
compounds: Iterable of compound entries.
properties: Set of compound properties to output (or None to output
... | python | def write_compounds(self, stream, compounds, properties=None):
"""Write iterable of compounds as YAML object to stream.
Args:
stream: File-like object.
compounds: Iterable of compound entries.
properties: Set of compound properties to output (or None to output
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48,276 | zhanglab/psamm | psamm/datasource/native.py | ModelWriter.write_reactions | def write_reactions(self, stream, reactions, properties=None):
"""Write iterable of reactions as YAML object to stream.
Args:
stream: File-like object.
compounds: Iterable of reaction entries.
properties: Set of reaction properties to output (or None to output
... | python | def write_reactions(self, stream, reactions, properties=None):
"""Write iterable of reactions as YAML object to stream.
Args:
stream: File-like object.
compounds: Iterable of reaction entries.
properties: Set of reaction properties to output (or None to output
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48,277 | inveniosoftware/invenio-rest | invenio_rest/views.py | create_api_errorhandler | def create_api_errorhandler(**kwargs):
r"""Create an API error handler.
E.g. register a 404 error:
.. code-block:: python
app.errorhandler(404)(create_api_errorhandler(
status=404, message='Not Found'))
:param \*\*kwargs: It contains the ``'status'`` and the ``'message'``
... | python | def create_api_errorhandler(**kwargs):
r"""Create an API error handler.
E.g. register a 404 error:
.. code-block:: python
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48,279 | inveniosoftware/invenio-rest | invenio_rest/views.py | ContentNegotiatedMethodView._match_serializers_by_query_arg | def _match_serializers_by_query_arg(self, serializers):
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"""Match serializer by query arg."""
# if the format query argument is present, match the serializer
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48,280 | inveniosoftware/invenio-rest | invenio_rest/views.py | ContentNegotiatedMethodView._match_serializers_by_accept_headers | def _match_serializers_by_accept_headers(self, serializers,
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"""Match serializer by `Accept` headers."""
# Bail out fast if no accept headers were given.
if len(request.accept_mimetypes) == 0:
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48,281 | inveniosoftware/invenio-rest | invenio_rest/views.py | ContentNegotiatedMethodView.match_serializers | def match_serializers(self, serializers, default_media_type):
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48,282 | inveniosoftware/invenio-rest | invenio_rest/views.py | ContentNegotiatedMethodView.make_response | def make_response(self, *args, **kwargs):
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"""Create a Flask Response.
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48,283 | inveniosoftware/invenio-rest | invenio_rest/views.py | ContentNegotiatedMethodView.dispatch_request | def dispatch_request(self, *args, **kwargs):
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48,284 | inveniosoftware/invenio-rest | invenio_rest/views.py | ContentNegotiatedMethodView.check_etag | def check_etag(self, etag, weak=False):
"""Validate the given ETag with current request conditions.
Compare the given ETag to the ones in the request header If-Match
and If-None-Match conditions.
The result is unspecified for requests having If-Match and
If-None-Match being bot... | python | def check_etag(self, etag, weak=False):
"""Validate the given ETag with current request conditions.
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48,285 | inveniosoftware/invenio-rest | invenio_rest/views.py | ContentNegotiatedMethodView.check_if_modified_since | def check_if_modified_since(self, dt, etag=None):
"""Validate If-Modified-Since with current request conditions."""
dt = dt.replace(microsecond=0)
if request.if_modified_since and dt <= request.if_modified_since:
raise SameContentException(etag, last_modified=dt) | python | def check_if_modified_since(self, dt, etag=None):
"""Validate If-Modified-Since with current request conditions."""
dt = dt.replace(microsecond=0)
if request.if_modified_since and dt <= request.if_modified_since:
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48,286 | zhanglab/psamm | psamm/importer.py | get_default_compartment | def get_default_compartment(model):
"""Return what the default compartment should be set to.
If some compounds have no compartment, unique compartment
name is returned to avoid collisions.
"""
default_compartment = 'c'
default_key = set()
for reaction in model.reactions:
equation = ... | python | def get_default_compartment(model):
"""Return what the default compartment should be set to.
If some compounds have no compartment, unique compartment
name is returned to avoid collisions.
"""
default_compartment = 'c'
default_key = set()
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48,287 | zhanglab/psamm | psamm/importer.py | detect_best_flux_limit | def detect_best_flux_limit(model):
"""Detect the best default flux limit to use for model output.
The default flux limit does not change the model but selecting a good
value reduced the amount of output produced and reduces clutter in the
output files.
"""
flux_limit_count = Counter()
for ... | python | def detect_best_flux_limit(model):
"""Detect the best default flux limit to use for model output.
The default flux limit does not change the model but selecting a good
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"""
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48,288 | zhanglab/psamm | psamm/importer.py | reactions_to_files | def reactions_to_files(model, dest, writer, split_subsystem):
"""Turn the reaction subsystems into their own files.
If a subsystem has a number of reactions over the threshold, it gets its
own YAML file. All other reactions, those that don't have a subsystem or
are in a subsystem that falls below the t... | python | def reactions_to_files(model, dest, writer, split_subsystem):
"""Turn the reaction subsystems into their own files.
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48,289 | zhanglab/psamm | psamm/importer.py | _generate_limit_items | def _generate_limit_items(lower, upper):
"""Yield key, value pairs for limits dictionary.
Yield pairs of key, value where key is ``lower``, ``upper`` or ``fixed``.
A key, value pair is emitted if the bounds are not None.
"""
# Use value + 0 to convert any -0.0 to 0.0 which looks better.
if lowe... | python | def _generate_limit_items(lower, upper):
"""Yield key, value pairs for limits dictionary.
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48,290 | zhanglab/psamm | psamm/importer.py | model_exchange | def model_exchange(model):
"""Return exchange definition as YAML dict."""
# Determine the default flux limits. If the value is already at the
# default it does not need to be included in the output.
lower_default, upper_default = None, None
if model.default_flux_limit is not None:
lower_defa... | python | def model_exchange(model):
"""Return exchange definition as YAML dict."""
# Determine the default flux limits. If the value is already at the
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lower_default, upper_default = None, None
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48,291 | zhanglab/psamm | psamm/importer.py | model_reaction_limits | def model_reaction_limits(model):
"""Yield model reaction limits as YAML dicts."""
for reaction in sorted(model.reactions, key=lambda r: r.id):
equation = reaction.properties.get('equation')
if equation is None:
continue
# Determine the default flux limits. If the value is a... | python | def model_reaction_limits(model):
"""Yield model reaction limits as YAML dicts."""
for reaction in sorted(model.reactions, key=lambda r: r.id):
equation = reaction.properties.get('equation')
if equation is None:
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48,292 | zhanglab/psamm | psamm/importer.py | infer_compartment_entries | def infer_compartment_entries(model):
"""Infer compartment entries for model based on reaction compounds."""
compartment_ids = set()
for reaction in model.reactions:
equation = reaction.equation
if equation is None:
continue
for compound, _ in equation.compounds:
... | python | def infer_compartment_entries(model):
"""Infer compartment entries for model based on reaction compounds."""
compartment_ids = set()
for reaction in model.reactions:
equation = reaction.equation
if equation is None:
continue
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] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/importer.py#L386-L407 |
48,293 | zhanglab/psamm | psamm/importer.py | infer_compartment_adjacency | def infer_compartment_adjacency(model):
"""Infer compartment adjacency for model based on reactions."""
def reaction_compartments(seq):
for compound, _ in seq:
compartment = compound.compartment
if compartment is None:
compartment = model.default_compartment
... | python | def infer_compartment_adjacency(model):
"""Infer compartment adjacency for model based on reactions."""
def reaction_compartments(seq):
for compound, _ in seq:
compartment = compound.compartment
if compartment is None:
compartment = model.default_compartment
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48,294 | zhanglab/psamm | psamm/importer.py | count_genes | def count_genes(model):
"""Count the number of distinct genes in model reactions."""
genes = set()
for reaction in model.reactions:
if reaction.genes is None:
continue
if isinstance(reaction.genes, boolean.Expression):
genes.update(v.symbol for v in reaction.genes.va... | python | def count_genes(model):
"""Count the number of distinct genes in model reactions."""
genes = set()
for reaction in model.reactions:
if reaction.genes is None:
continue
if isinstance(reaction.genes, boolean.Expression):
genes.update(v.symbol for v in reaction.genes.va... | [
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] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/importer.py#L435-L447 |
48,295 | zhanglab/psamm | psamm/importer.py | Importer._try_parse_formula | def _try_parse_formula(self, compound_id, s):
"""Try to parse the given compound formula string.
Logs a warning if the formula could not be parsed.
"""
s = s.strip()
if s == '':
return None
try:
# Do not return the parsed formula. For now it is b... | python | def _try_parse_formula(self, compound_id, s):
"""Try to parse the given compound formula string.
Logs a warning if the formula could not be parsed.
"""
s = s.strip()
if s == '':
return None
try:
# Do not return the parsed formula. For now it is b... | [
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] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/importer.py#L79-L96 |
48,296 | zhanglab/psamm | psamm/importer.py | Importer._try_parse_reaction | def _try_parse_reaction(self, reaction_id, s,
parser=parse_reaction, **kwargs):
"""Try to parse the given reaction equation string.
Returns the parsed Reaction object, or raises an error if the reaction
could not be parsed.
"""
try:
return... | python | def _try_parse_reaction(self, reaction_id, s,
parser=parse_reaction, **kwargs):
"""Try to parse the given reaction equation string.
Returns the parsed Reaction object, or raises an error if the reaction
could not be parsed.
"""
try:
return... | [
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48,297 | zhanglab/psamm | psamm/importer.py | Importer._try_parse_gene_association | def _try_parse_gene_association(self, reaction_id, s):
"""Try to parse the given gene association rule.
Logs a warning if the association rule could not be parsed and returns
the original string. Otherwise, returns the boolean.Expression object.
"""
s = s.strip()
if s ==... | python | def _try_parse_gene_association(self, reaction_id, s):
"""Try to parse the given gene association rule.
Logs a warning if the association rule could not be parsed and returns
the original string. Otherwise, returns the boolean.Expression object.
"""
s = s.strip()
if s ==... | [
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48,298 | inveniosoftware/invenio-rest | invenio_rest/decorators.py | require_content_types | def require_content_types(*allowed_content_types):
r"""Decorator to test if proper Content-Type is provided.
:param \*allowed_content_types: List of allowed content types.
:raises invenio_rest.errors.InvalidContentType: It's rised if a content
type not allowed is required.
"""
def decorator... | python | def require_content_types(*allowed_content_types):
r"""Decorator to test if proper Content-Type is provided.
:param \*allowed_content_types: List of allowed content types.
:raises invenio_rest.errors.InvalidContentType: It's rised if a content
type not allowed is required.
"""
def decorator... | [
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48,299 | merll/docker-fabric | dockerfabric/base.py | DockerConnectionDict.get_connection | def get_connection(self, *args, **kwargs):
"""
Create a new connection, or return an existing one from the cache. Uses Fabric's current ``env.host_string``
and the URL to the Docker service.
:param args: Additional arguments for the client constructor, if a new client has to be instanti... | python | def get_connection(self, *args, **kwargs):
"""
Create a new connection, or return an existing one from the cache. Uses Fabric's current ``env.host_string``
and the URL to the Docker service.
:param args: Additional arguments for the client constructor, if a new client has to be instanti... | [
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