def write_biom_table(result_key, data, option_value=None):
"""Write a string to a file"""
if option_value is None:
raise IncompetentDeveloperError("Cannot write output without a "
"filepath.")
if exists(option_value):
raise IOError("Output path '%s' already exists." % option_value)
table, fmt = data
if fmt not in ['hdf5', 'json', 'tsv']:
raise IncompetentDeveloperError("Unknown file format")
if fmt == 'json':
with open(option_value, 'w') as f:
f.write(table.to_json(generatedby()))
elif fmt == 'tsv':
with open(option_value, 'w') as f:
f.write(table)
f.write('\n')
else:
if HAVE_H5PY:
import h5py
else:
raise ImportError("h5py is not available, cannot write HDF5!")
with h5py.File(option_value, 'w') as f:
table.to_hdf5(f, generatedby())
def __init__(self,
Parameter=None,
Type=None,
Handler=None,
Name=None,
Help=None):
self.Parameter = Parameter
if self.Parameter is None:
if Name is None:
raise IncompetentDeveloperError("Must specify a Name for the "
"InterfaceOption since it "
"doesn't have a Parameter.")
if Help is None:
raise IncompetentDeveloperError("Must specify Help for the "
"InterfaceOption since it "
"doesn't have a Parameter.")
self.Name = Name
self.Help = Help
else:
# Transfer information from Parameter unless overridden here.
self.Name = Parameter.Name if Name is None else Name
self.Help = Parameter.Description if Help is None else Help
# This information is never contained in a Parameter.
self.Type = Type
self.Handler = Handler
def _validate_inputs_outputs(self, inputs, outputs):
"""Perform validation on interface IO objects.
``inputs`` will be the output of ``self._get_inputs()``. Subclasses can
override to perform validation that requires a list of all input
options. Validation that should be performed on a per-option basis
should instead go into ``InterfaceOption._validate_option``.
``outputs`` will be the output of ``self._get_outputs()``. Subclasses
can override to perform validation that requires a list of all
interface results. Validation that should be performed on a
per-interface result basis should instead go into
``InterfaceOutputOption._validate_result``.
"""
param_names = [
input_.getParameterName() for input_ in inputs
if input_.getParameterName() is not None
]
if len(param_names) != len(set(param_names)):
raise IncompetentDeveloperError("Found more than one "
"InterfaceOption mapping to the "
"same Parameter.")
input_names = set([i.Name for i in inputs])
for ifout in outputs:
if ifout.InputName is None:
continue
if ifout.InputName not in input_names:
raise IncompetentDeveloperError(\
"Could not link %s to an input!" % ifout.InputName)
def _validate_usage_example(self):
if self.ShortDesc is None:
raise IncompetentDeveloperError("Must define ShortDesc")
if self.LongDesc is None:
raise IncompetentDeveloperError("Must define LongDesc")
if self.Ex is None:
raise IncompetentDeveloperError("Must define Ex")
def write_subsetted_biom_table(result_key, data, option_value=None):
"""Write a string to a file"""
if option_value is None:
raise IncompetentDeveloperError("Cannot write output without a "
"filepath.")
if exists(option_value):
raise IOError("Output path '%s' already exists." % option_value)
table, fmt = data
if fmt not in ['hdf5', 'json']:
raise IncompetentDeveloperError("Unknown file format")
if fmt == 'json':
write_list_of_strings(result_key, table, option_value)
else:
if HAVE_H5PY:
import h5py
else:
# This should never be raised here
raise ImportError("h5py is not available, cannot write HDF5!")
with h5py.File(option_value, 'w') as f:
table.to_hdf5(f, generatedby())
def _validate_inputs_outputs(self, inputs, outputs):
super(HTMLInterface, self)._validate_inputs_outputs(inputs, outputs)
if len(outputs) > 1:
raise IncompetentDeveloperError("There can be only one... output")
if not (isinstance(outputs[0], HTMLPage)
or isinstance(outputs[0], HTMLDownload)):
raise IncompetentDeveloperError(
"Output must subclass HTMLPage or HTMLDownload")
def _validate_usage_examples(self, usage_examples):
super(HTMLInterface, self)._validate_usage_examples(usage_examples)
if usage_examples:
raise IncompetentDeveloperError(
"There shouldn't be usage examples "
"associated with this command.")
def _validate_option(self):
if self.Type not in self._type_handlers:
raise IncompetentDeveloperError(
"Unsupported Type in HTMLInputOption: %s" % self.Type)
#From optparse's __init__.py, inside class PyqiOption
if self.Type == "multiple_choice":
if self.Choices is None:
raise IncompetentDeveloperError(
"must supply a list of Choices for type '%s'" % self.type,
self)
elif type(self.Choices) not in (types.TupleType, types.ListType):
raise IncompetentDeveloperError(
"choices must be a list of strings ('%s' supplied)" %
str(type(self.Choices)).split("'")[1], self)
elif self.Choices is not None:
raise IncompetentDeveloperError(
"must not supply Choices for type %r" % self.type, self)
def load_file_lines(option_value):
"""Return a list of strings, one per line in the file.
Each line will have leading and trailing whitespace stripped from it.
"""
if not hasattr(option_value, 'read'):
raise IncompetentDeveloperError("Input type must be a file object.")
return [line.strip() for line in option_value]
def __init__(self, Parameters):
self.Parameters = Parameters
for p in self.Parameters:
if p.Name in self:
raise IncompetentDeveloperError("Found duplicate Parameter "
"name '%s'. Parameter names "
"must be unique." % p.Name)
else:
super(ParameterCollection, self).__setitem__(p.Name, p)
def __init__(self, **kwargs):
""" """
self.CmdInstance = None
if self.CommandConstructor is None:
raise IncompetentDeveloperError("Cannot construct an Interface "
"without a CommandConstructor.")
self.CmdInstance = self.CommandConstructor(**kwargs)
self._validate_usage_examples(self._get_usage_examples())
self._validate_inputs_outputs(self._get_inputs(), self._get_outputs())
def write_string(result_key, data, option_value=None):
"""Write a string to a file.
A newline will be added to the end of the file.
"""
if option_value is None:
raise IncompetentDeveloperError("Cannot write output without a "
"filepath.")
if os.path.exists(option_value):
raise IOError("Output path '%s' already exists." % option_value)
with open(option_value, 'w') as f:
f.write(data)
f.write('\n')
def write_summarized_results(result_key, data, option_value=None):
"""Write the benchmark results in a tab-delimited format
option_value is the base output directory
Writes a file with the benchmark results in a tab-delimited form,
with the following headers: label, wall_mean, wall_std, user_mean, user_std,
kernel_mean, kernel_std, mem_mean, mem_std
Each row contains the results for a single experiment
"""
if option_value is None:
raise IncompetentDeveloperError("Cannot write output without an "
"output directory.")
if os.path.exists(option_value):
if os.path.isfile(option_value):
raise IOError(
"Output directory '%s' already exists and it is a file." %
option_value)
else:
os.mkdir(option_value)
output_fp = os.path.join(option_value, "%s.txt" % result_key)
lines = []
headers = [
"#label", "wall_mean", "wall_std", "user_mean", "user_std",
"kernel_mean", "kernel_std", "mem_mean", "mem_std"
]
lines.append("\t".join(headers))
# Loop over all the experiments
for i, label in enumerate(data['label']):
values = [str(label)]
values.append(str(data['wall_time'][0][i]))
values.append(str(data['wall_time'][1][i]))
values.append(str(data['cpu_user'][0][i]))
values.append(str(data['cpu_user'][1][i]))
values.append(str(data['cpu_kernel'][0][i]))
values.append(str(data['cpu_kernel'][1][i]))
values.append(str(data['memory'][0][i]))
values.append(str(data['memory'][1][i]))
lines.append("\t".join(values))
write_list_of_strings(result_key, lines, option_value=output_fp)
def write_string_to_dir(result_key, data, option_value=None):
"""Write a string to a file
option_value is the base output directory
"""
if option_value is None:
raise IncompetentDeveloperError("Cannot write output without an "
"output directory.")
if os.path.exists(option_value):
if os.path.isfile(option_value):
raise IOError(
"Output directory '%s' already exists and it is a file." %
option_value)
else:
os.mkdir(option_value)
output_fp = os.path.join(option_value, "%s.txt" % result_key)
write_string(result_key, data, option_value=output_fp)
def __init__(self,
Name,
DataType,
Description,
Required=False,
Default=None,
DefaultDescription=None,
**kwargs):
self.Required = Required
self.Default = Default
self.DefaultDescription = DefaultDescription
if Required and Default is not None:
raise IncompetentDeveloperError(
"Found required CommandIn '%s' "
"with default value '%r'. Required CommandIns cannot have "
"default values." % (Name, Default))
super(CommandIn, self).__init__(Name, DataType, Description, **kwargs)
def write_comp_results(result_key, data, option_value=None):
"""Output handler for the bench_results_processer command
Parameters
----------
result_key : string
The key used in the results dictionary
data : CompData namedtuple
The results of the command
option_value : string
Path to the output directory
Raises
------
IOError
If the output directory exists and it's a file
"""
# Check that we are not dealing with incompetent developers
if option_value is None:
raise IncompetentDeveloperError("Cannot write output without an "
"output directory.")
# Check that the output directory exists
if exists(option_value):
# Check that it is not a file, so we can use it
if isfile(option_value):
raise IOError("Output directory '%s' already exists and it is a "
"file." % option_value)
else:
# The output directory does not exists, create it
mkdir(option_value)
# Create the plots with the benchmark comparison
time_plot_fp = join(option_value, "time_fig.png")
make_comparison_plot(data.x, data.time, "Running time", "Time (seconds)",
time_plot_fp)
mem_plot_fp = join(option_value, "mem_fig.png")
make_comparison_plot(data.x,
data.mem,
"Memory usage",
"Memory (GB)",
mem_plot_fp,
scale=1024 * 1024)
def __init__(self,
Action=None,
Required=False,
Default=None,
ShortName=None,
DefaultDescription=None,
convert_to_dashed_name=True,
**kwargs):
super(InterfaceInputOption, self).__init__(**kwargs)
self.Required = Required
self.Default = Default
self.DefaultDescription = DefaultDescription
self.ShortName = ShortName
self.Action = Action
if convert_to_dashed_name:
self.Name = self.Name.replace('_', '-')
if self.Required and self.Default is not None:
raise IncompetentDeveloperError(
"Found required option '%s' "
"with default value '%s'. Required options cannot have "
"default values." % (self.Name, self.Default))
if self.Default is None and self.Parameter is not None:
self.Default = self.Parameter.Default
self.DefaultDescription = self.Parameter.DefaultDescription
# If a parameter is required, the option is always required, but
# if a parameter is not required, but the option does require it,
# then we make the option required.
if self.Parameter is not None:
self.Required = self.Parameter.Required
if not self.Parameter.Required and Required:
self.Required = True
self._convert_primitive_strings()
self._validate_option()
def write_matplotlib_figure(result_key, data, option_value=None):
"""Write a matplotlib figure to disk
option_value is the base output directory
"""
if option_value is None:
raise IncompetentDeveloperError("Cannot write output without an "
"output directory.")
if os.path.exists(option_value):
if os.path.isfile(option_value):
raise IOError(
"Output directory '%s' already exists and it is a file." %
option_value)
else:
os.mkdir(option_value)
output_fp = os.path.join(option_value, "%s.png" % result_key)
if os.path.exists(output_fp):
raise IOError("Output path %s already exists." % output_fp)
data.savefig(output_fp)
def __init__(self, Name, DataType, Description, ValidateValue=None):
"""
``Name`` should be a valid Python name so that users can supply either
a dictionary as input or named arguments.
``DataType`` specifies the type that the input must be. The input
should be an instance of type ``DataType``.
``ValidateValue`` can be set as a function that will validate the
value associated with a ``Parameter``.
"""
if not self._is_valid_name(Name):
raise IncompetentDeveloperError("Parameter '%s' is not a valid "
"Python variable name. Parameter "
"names must be alphanumeric and "
"start with a letter or "
"underscore." % Name)
self.Name = Name
self.DataType = DataType
self.Description = Description
self.ValidateValue = ValidateValue
def __init__(self, MIMEType=None, **kwargs):
super(HTMLResult, self).__init__(**kwargs)
if MIMEType is None:
raise IncompetentDeveloperError(
"A valid MIMEType must be provided")
self.MIMEType = MIMEType
def _the_out_validator(self, out_):
"""Validate output coming from the command call"""
if not isinstance(out_, dict):
raise IncompetentDeveloperError("Unsupported result '%r'. Result "
"must be a dict." % out_)
def _the_in_validator(self, in_):
"""Validate input coming from the command line"""
if not isinstance(in_, list):
raise IncompetentDeveloperError("Unsupported input '%r'. Input "
"must be a list." % in_)
def _validate_usage_examples(self, usage_examples):
super(OptparseInterface, self)._validate_usage_examples(usage_examples)
if len(usage_examples) < 1:
raise IncompetentDeveloperError("There are no usage examples "
"associated with this command.")
def load_file_contents(option_value):
"""Return the contents of a file as a single string."""
if not hasattr(option_value, 'read'):
raise IncompetentDeveloperError("Input type must be a file object.")
return option_value.read()
def _the_in_validator(self, in_):
"""Validate input coming from the postvars"""
if not isinstance(in_, FieldStorage):
raise IncompetentDeveloperError("Unsupported input '%r'. Input "
"must be FieldStorage." % in_)
def write_bench_results(result_key, data, option_value=None):
"""Output handler for the bench_results_processer command
Parameters
----------
result_key : string
The key used in the results dictionary
data : BenchData namedtuple
The results of the command
option_value : string
Path to the output directory
Raises
------
IOError
If the output directory exists and it's a file
"""
# Check that we are not dealing with incompetent developers
if option_value is None:
raise IncompetentDeveloperError("Cannot write output without an "
"output directory.")
# Check that the output directory exists
if exists(option_value):
# Check that it is not a file, so we can use it
if isfile(option_value):
raise IOError("Output directory '%s' already exists and it is a "
"file." % option_value)
else:
# The output directory does not exists, create it
mkdir(option_value)
# Write a tab delimited file with a summary of the benchmark results
summary_fp = join(option_value, "summarized_results.txt")
lines = [
"\t".join([
"#label", "wall_mean", "wall_std", "user_mean", "user_std",
"kernel_mean", "kernel_std", "mem_mean", "mem_std"
])
]
# Loop over all the tests cases
for i, label in enumerate(data.labels):
lines.append("\t".join([
label,
str(data.means.wall[i]),
str(data.stdevs.wall[i]),
str(data.means.user[i]),
str(data.stdevs.user[i]),
str(data.means.kernel[i]),
str(data.stdevs.kernel[i]),
str(data.means.mem[i]),
str(data.stdevs.mem[i])
]))
write_list_of_strings(result_key, lines, option_value=summary_fp)
# Write the polynomials that fit the wall time and memory usage in
# human-readable form
poly_fp = join(option_value, "curves.txt")
lines = [
"Wall time fitted curve",
generate_poly_label(data.wall_curve.poly, data.wall_curve.deg),
"Memory usage fitted curve",
generate_poly_label(data.mem_curve.poly, data.mem_curve.deg)
]
write_list_of_strings(result_key, lines, option_value=poly_fp)
# Create plots with benchmark results
# Create a plot with the time results
time_plot_fp = join(option_value, "time_fig.png")
ys = [data.means.wall, data.means.user, data.means.kernel]
y_errors = [data.stdevs.wall, data.stdevs.user, data.stdevs.kernel]
labels = ['wall', 'user', 'kernel']
make_bench_plot(data.labels, ys, y_errors, labels, "Running time",
"Time (seconds)", data.wall_curve.poly,
data.wall_curve.deg, time_plot_fp)
# Create a plot with the memory results
mem_plot_fp = join(option_value, "mem_fig.png")
y_errors = [data.stdevs.mem]
labels = ['memory']
make_bench_plot(data.labels,
ys,
y_errors,
labels,
"Memory usage",
"Memory (GB)",
data.mem_curve.poly,
data.mem_curve.deg,
mem_plot_fp,
scale=1024 * 1024)