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#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
Errors, exceptions, warnings, etc.
"""
import sys
import re
import warnings
import inspect
import subprocess
class ImmutableTaxonNamespaceError(TypeError):
def __init__(self, message):
TypeError.__init__(self, message)
class DataParseError(Exception):
def __init__(self,
message=None,
line_num=None,
col_num=None,
filename=None,
stream=None):
Exception.__init__(self)
self.line_num = line_num
self.col_num = col_num
self.message = message
self.stream = stream
self.filename = None
self.decorate_with_name(filename=filename, stream=stream)
def decorate_with_name(self,
filename=None,
stream=None):
if filename is not None:
self.filename = filename
if stream is not None:
try:
self.filename = stream.name
except AttributeError:
pass
def __str__(self):
f, l, c = "", "", ""
if self.filename:
f = " '{}'".format(self.filename)
if self.line_num is not None:
l = " on line {}".format(self.line_num)
if self.col_num is not None:
c = " at column {}".format(self.col_num)
return "Error parsing data source{}{}{}: {}".format(f, l, c, self.message)
class UnsupportedSchemaError(NotImplementedError):
def __init__(self, *args, **kwargs):
NotImplementedError.__init__(self, *args, **kwargs)
class UnspecifiedSchemaError(Exception):
def __init__(self, *args, **kwargs):
Exception.__init__(self, *args, **kwargs)
class UnspecifiedSourceError(Exception):
def __init__(self, *args, **kwargs):
Exception.__init__(self, *args, **kwargs)
class TooManyArgumentsError(TypeError):
def __init__(self,
message=None,
func_name=None,
max_args=None,
args=None):
if message is None and (func_name is not None and max_args):
message = "{}() takes a maximum of {} arguments ({} given)".format(func_name, max_args, len(args))
TypeError.__init__(self, message)
class InvalidArgumentValueError(ValueError):
def __init__(self, message=None, func_name=None, arg=None):
if message is None and (func_name is not None and arg is not None):
message = "{}() does not accept objects of type '{}' as an argument".format(func_name, arg.__class__.__name__)
ValueError.__init__(self, message)
class MultipleInitializationSourceError(TypeError):
def __init__(self, message=None, class_name=None, arg=None):
if message is None and (class_name is not None and arg is not None):
message = "{}() does not accept data 'stream' or 'schema' arguments when initializing with another object".format(class_name)
TypeError.__init__(self, message)
class TaxonNamespaceIdentityError(ValueError):
def __init__(self, o1, o2):
message = "Non-identical taxon namespace references: {} is not {}".format(
"<TaxonNamespace object at {}>".format(str(hex(id((o1.taxon_namespace))))),
"<TaxonNamespace object at {}>".format(str(hex(id((o2.taxon_namespace))))),
)
ValueError.__init__(self, message)
class SingleTaxonAssemblageException(ValueError):
def __init__(self, message=None):
ValueError.__init__(self, message)
class NullAssemblageException(ValueError):
def __init__(self, message=None):
ValueError.__init__(self, message)
class MixedRootingError(ValueError):
def __init__(self, message=None):
ValueError.__init__(self, message)
class TaxonNamespaceReconstructionError(ValueError):
def __init__(self, message=None):
ValueError.__init__(self, message)
class UltrametricityError(ValueError):
def __init__(self, message=None):
ValueError.__init__(self, message)
class ProcessFailedException(Exception):
"""Exception to be raised when branching process results in all lineages going extinct."""
def __init__(self, *args, **kwargs):
Exception.__init__(self, *args, **kwargs)
class TreeSimTotalExtinctionException(ProcessFailedException):
"""Exception to be raised when branching process results in all lineages going extinct."""
def __init__(self, *args, **kwargs):
ProcessFailedException.__init__(self, *args, **kwargs)
class NullLeafSetException(Exception):
def __init__(self, *args, **kwargs):
Exception.__init__(self, *args, **kwargs)
class SeedNodeDeletionException(Exception):
def __init__(self, *args, **kwargs):
Exception.__init__(self, *args, **kwargs)
class InvalidMultispeciesCoalescentStructureError(Exception):
def __init__(self, *args, **kwargs):
Exception.__init__(self, *args, **kwargs)
class ExternalServiceError(Exception):
def __init__(self,
service_name,
invocation_command,
service_input,
returncode,
stdout,
stderr):
self.service_name = service_name
self.invocation_command = invocation_command
self.service_input = service_input
self.returncode = returncode
self.stdout = stdout
self.stderr = stderr
self.message = self.compose_message()
def __str__(self):
return self.compose_message()
def compose_message(self):
parts = []
parts.append("- Service process {} exited with return code: {}".format(self.service_name, self.returncode))
parts.append("- Service invoked with command:")
parts.append(" {}".format(self.invocation_command))
parts.append("<<<<<<< (SERVICE STANDARD INPUT)")
parts.append(self.service_input)
parts.append(">>>>>>>")
parts.append("<<<<<<< (SERVICE STANDARD OUTPUT)")
parts.append(self.stdout)
parts.append(">>>>>>>")
parts.append("<<<<<<< (SERVICE STANDARD ERROR)")
parts.append(self.stderr)
parts.append(">>>>>>>")
return "\n".join(parts)
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