class Suite(Profile):
paths = related.SequenceField(str, default=None)
queued = related.MappingField(Case, "file_path", default={})
skipped = related.MappingField(Case, "file_path", default={})
def __attrs_post_init__(self):
from . import collect
collect(self)
get_logger().debug("suite constructed",
host=self.host,
paths=self.paths,
prefixes=self.prefixes,
extensions=self.extensions,
includes=self.includes,
excludes=self.excludes,
concurrency=self.concurrency)
def get_case(self, path, filename=None):
file_path = os.path.join(path, filename) if filename else path
return self.queued.get(file_path) or self.skipped.get(file_path)
def add_case(self, case):
if case.is_active(self.includes, self.excludes):
self.queued.add(case)
get_logger().debug("case queued", case=case.file_path)
else:
class Suite(Profile):
paths = related.SequenceField(str, default=None)
queued = related.MappingField(Case, "file_path", default={})
skipped = related.MappingField(Case, "file_path", default={})
semaphores = related.MappingField(Semaphore, "semaphore", default={})
app = related.ChildField(object, default=None)
def __attrs_post_init__(self):
from . import collect
collect(self)
get_logger().debug(
"suite constructed",
host=self.host,
paths=self.paths,
prefixes=self.prefixes,
extensions=self.extensions,
includes=self.includes,
excludes=self.excludes,
concurrency=self.concurrency,
retry_failed=self.retry_failed,
)
def get_case(self, path, filename=None):
file_path = os.path.join(path, filename) if filename else path
return self.queued.get(file_path) or self.skipped.get(file_path)
def add_case(self, case):
if case.is_active(self.includes, self.excludes):
self.queued.add(case)
if (case.semaphore is not None
and case.semaphore not in self.semaphores.keys()):
self.semaphores[case.semaphore] = Semaphore()
get_logger().debug("case queued", case=case.file_path)
class PathReport(object):
url = related.StringField()
obj = related.ChildField(Path)
methods = related.MappingField(MethodReport, "method", default={})
def get_method_report(self, method):
return self.methods.setdefault(method, MethodReport(self.url, method))
class DataLoaderDescription(RelatedLoadSaveMixin):
"""Class representation of dataloader.yaml
"""
type = related.StringField()
defined_as = related.StringField()
args = related.MappingField(DataLoaderArgument, "name")
info = related.ChildField(Info)
output_schema = related.ChildField(DataLoaderSchema)
dependencies = related.ChildField(Dependencies,
default=Dependencies(),
required=False)
path = related.StringField(required=False)
postprocessing = related.ChildField(dict,
default=OrderedDict(),
required=False)
def get_example_kwargs(self):
return example_kwargs(self.args)
def print_kwargs(self, format_examples_json=False):
from kipoi.external.related.fields import UNSPECIFIED
if hasattr(self, "args"):
logger.warn(
"No keyword arguments defined for the given dataloader.")
return None
for k in self.args:
print("Keyword argument: `{0}`".format(k))
for elm in ["doc", "type", "optional", "example"]:
if hasattr(self.args[k], elm) and \
(not isinstance(getattr(self.args[k], elm), UNSPECIFIED)):
print(" {0}: {1}".format(elm,
getattr(self.args[k], elm)))
example_kwargs = self.example_kwargs
print("-" * 80)
if hasattr(self, "example_kwargs"):
if format_examples_json:
import json
example_kwargs = json.dumps(example_kwargs)
print("Example keyword arguments are: {0}".format(
str(example_kwargs)))
def __attrs_post_init__(self):
# load additional objects
for k in self.postprocessing:
k_observed = k
if k == 'variant_effects':
k = 'kipoi_veff'
if is_installed(k):
# Load the config properly if the plugin is installed
try:
parser = get_dataloader_yaml_parser(k)
self.postprocessing[k_observed] = parser.from_config(
self.postprocessing[k_observed])
object.__setattr__(self, "postprocessing",
self.postprocessing)
except Exception:
logger.warn(
"Unable to parse {} filed in DataLoaderDescription: {}"
.format(k_observed, self))
class TestConfig(RelatedConfigMixin):
"""Models config.yaml in the model root
"""
constraints = related.MappingField(TestModelConfig,
"name",
required=False,
repr=True)
class MyModel(object):
is_for = related.StringField(key="for")
criss = related.StringField(key="cross")
cross = related.StringField(key="criss")
is_not = related.BooleanField(key="not")
is_list = related.SequenceField(str, key="list")
is_type = related.ChildField(DataType, key="type")
is_dict = related.MappingField(MyChild, "int", key="dict", required=False)
class Model(object):
# non-child fields
sequence_field = related.SequenceField(str, default=set())
set_field = related.SetField(str, default=[])
mapping_field = related.MappingField(Child, "name", default={})
# child fields
child_list = related.ChildField(list, default=list)
child_set = related.ChildField(set, default=set)
child_dict = related.ChildField(dict, default=dict)
child_obj = related.ChildField(Child, default=Child)
class MethodReport(object):
url = related.StringField()
method = related.StringField()
counts = related.MappingField(Counts, "key", default={})
def add(self, case_pass, scenario_pass, step_pass, params):
self.case_counts.add(case_pass)
self.scenario_counts.add(scenario_pass)
self.step_counts.add(step_pass)
all_pass = case_pass and scenario_pass and step_pass
for param in params:
self.param_counts(param).add(all_pass)
@property
def case_counts(self):
return self.param_counts(CASE)
@property
def scenario_counts(self):
return self.param_counts(SCENARIO)
@property
def step_counts(self):
return self.param_counts(STEP)
def param_counts(self, param):
return self.counts.setdefault(param, Counts(param))
@property
def cases_passed(self):
return self.case_counts.passed
@property
def cases_failed(self):
return self.case_counts.failed
@property
def scenarios_passed(self):
return self.scenario_counts.passed
@property
def scenarios_failed(self):
return self.scenario_counts.failed
@property
def steps_passed(self):
return self.step_counts.passed
@property
def steps_failed(self):
return self.step_counts.failed
class DataLoaderDescription(RelatedLoadSaveMixin):
"""Class representation of dataloader.yaml
"""
defined_as = related.StringField()
args = related.MappingField(DataLoaderArgument, "name")
output_schema = related.ChildField(DataLoaderSchema)
type = related.StringField(required=False)
info = related.ChildField(Info, default=Info(), required=False)
dependencies = related.ChildField(Dependencies,
default=Dependencies(),
required=False)
path = related.StringField(required=False)
writers = related.ChildField(dict, default=OrderedDict(), required=False)
def get_example_kwargs(self):
# return self.download_example()
if self.path is None:
path = "."
else:
path = self.path
return example_kwargs(
self.args,
os.path.join(os.path.dirname(path), "downloaded/example_files"))
def download_example(self, output_dir, absolute_path=False, dry_run=False):
return example_kwargs(self.args,
output_dir,
absolute_path=absolute_path,
dry_run=dry_run)
def print_kwargs(self, format_examples_json=False):
from kipoi_utils.external.related.fields import UNSPECIFIED
if not hasattr(self, "args"):
logger.warning(
"No keyword arguments defined for the given dataloader.")
return None
args = self.args
for k in args:
print("{0}:".format(k))
for elm in ["doc", "type", "optional", "example"]:
if hasattr(args[k], elm) and \
(not isinstance(getattr(args[k], elm), UNSPECIFIED)):
print(" {0}: {1}".format(elm, getattr(args[k], elm)))
# example_kwargs = self.get_example_kwargs()
# if format_examples_json:
# import json
# example_kwargs = json.dumps(example_kwargs)
# print("Example keyword arguments are: {0}".format(str(example_kwargs)))
print_args = print_kwargs
class Operation(object):
responses = related.MappingField(Response, "code", required=True)
tags = related.SequenceField(str, required=False)
summary = related.StringField(required=False)
description = related.StringField(required=False)
operationId = related.StringField(required=False)
parameters = related.SequenceField(Parameter, required=False)
consumes = related.SequenceField(MIMEType, required=False)
produces = related.SequenceField(MIMEType, required=False)
externalDocs = related.ChildField(dict, required=False)
schemes = related.SequenceField(Scheme, required=False)
deprecated = related.BooleanField(required=False)
security = related.ChildField(dict, required=False)
class DashboardSpecification:
version = related.StringField()
date_ranges = related.MappingField(
DateRangeSpecification, 'id', {}, key='dateRanges'
)
filters = related.MappingField(FilterDefinition, 'id', {})
items = related.MappingField(LayoutItem, 'id', {})
queries = related.MappingField(QueryDefinition, 'id', {})
settings = related.MappingField(VisualizationSettings, 'id', {})
sizes = related.MappingField(LayoutSize, 'id', {})
options = related.ChildField(DashboardOptions, DashboardOptions())
class DataLoaderDescription(RelatedLoadSaveMixin):
"""Class representation of dataloader.yaml
"""
type = related.StringField()
defined_as = related.StringField()
args = related.MappingField(DataLoaderArgument, "name")
info = related.ChildField(Info)
output_schema = related.ChildField(DataLoaderSchema)
dependencies = related.ChildField(Dependencies,
default=Dependencies(),
required=False)
path = related.StringField(required=False)
postprocessing = related.ChildField(PostProcDataLoaderStruct,
default=PostProcDataLoaderStruct(),
required=False)
def get_example_kwargs(self):
return example_kwargs(self.args)
def print_kwargs(self, format_examples_json=False):
from kipoi.external.related.fields import UNSPECIFIED
if hasattr(self, "args"):
logger.warn(
"No keyword arguments defined for the given dataloader.")
return None
for k in self.args:
print("Keyword argument: `{0}`".format(k))
for elm in ["doc", "type", "optional", "example"]:
if hasattr(self.args[k], elm) and \
(not isinstance(getattr(self.args[k], elm), UNSPECIFIED)):
print(" {0}: {1}".format(elm,
getattr(self.args[k], elm)))
example_kwargs = self.example_kwargs
print("-" * 80)
if hasattr(self, "example_kwargs"):
if format_examples_json:
import json
example_kwargs = json.dumps(example_kwargs)
print("Example keyword arguments are: {0}".format(
str(example_kwargs)))
class DataLoaderDescription(RelatedLoadSaveMixin):
"""Class representation of dataloader.yaml
"""
defined_as = related.StringField()
args = related.MappingField(DataLoaderArgument, "name")
output_schema = related.ChildField(DataLoaderSchema)
type = related.StringField(required=False)
info = related.ChildField(Info, default=Info(), required=False)
dependencies = related.ChildField(Dependencies, default=Dependencies(), required=False)
path = related.StringField(required=False)
postprocessing = related.ChildField(dict, default=OrderedDict(), required=False)
def get_example_kwargs(self):
# return self.download_example()
if self.path is None:
path = "."
else:
path = self.path
return example_kwargs(self.args, os.path.join(os.path.dirname(path), "downloaded/example_files"))
def download_example(self, output_dir, absolute_path=False, dry_run=False):
return example_kwargs(self.args,
output_dir,
absolute_path=absolute_path,
dry_run=dry_run)
def print_kwargs(self, format_examples_json=False):
from kipoi_utils.external.related.fields import UNSPECIFIED
if not hasattr(self, "args"):
logger.warning("No keyword arguments defined for the given dataloader.")
return None
args = self.args
for k in args:
print("{0}:".format(k))
for elm in ["doc", "type", "optional", "example"]:
if hasattr(args[k], elm) and \
(not isinstance(getattr(args[k], elm), UNSPECIFIED)):
print(" {0}: {1}".format(elm, getattr(args[k], elm)))
# example_kwargs = self.get_example_kwargs()
# if format_examples_json:
# import json
# example_kwargs = json.dumps(example_kwargs)
# print("Example keyword arguments are: {0}".format(str(example_kwargs)))
print_args = print_kwargs
def __attrs_post_init__(self):
# load additional objects
for k in self.postprocessing:
k_observed = k
if k == 'variant_effects':
k = 'kipoi_veff'
if is_installed(k):
# Load the config properly if the plugin is installed
try:
parser = get_dataloader_yaml_parser(k)
self.postprocessing[k_observed] = parser.from_config(self.postprocessing[k_observed])
object.__setattr__(self, "postprocessing", self.postprocessing)
except Exception:
logger.warning("Unable to parse {} filed in DataLoaderDescription: {}".format(k_observed, self))
class Node(object):
name = related.StringField()
node_child = related.ChildField(node_cls, required=False)
node_list = related.SequenceField(node_cls, required=False)
node_map = related.MappingField(node_cls, "name", required=False)
class DataSpec(RelatedLoadSaveMixin):
"""Dataset specification
"""
# Dictionary of different bigwig files
task_specs = related.MappingField(TaskSpec,
"task",
required=True,
repr=True)
# Path to the reference genome fasta file
fasta_file = related.StringField(required=True)
# Bias track specification
bias_specs = related.MappingField(BiasSpec,
"task",
required=False,
repr=True)
# # Set of peaks to consider
# peaks = related.StringField(required=True)
# Original path to the file
path = related.StringField(required=False)
def abspath(self):
return DataSpec(
task_specs={k: v.abspath()
for k, v in self.task_specs.items()},
fasta_file=os.path.abspath(self.fasta_file),
# peaks=os.path.abspath(self.peaks),
path=self.path)
def task2idx(self, task, dtype='counts'):
"""Get the index output
Args:
task: task name
dtype: 'counts' or 'profile'
Returns:
index for the list of predicted arrays
"""
# TODO - this is not the right location for the code
# it should be next to the model
n2idx = {k: i for i, k in enumerate(self.task_specs)}
if dtype == "counts":
return len(self.task_specs) + n2idx[task]
elif dtype == "profile":
return n2idx[task]
else:
raise ValueError("type is not from 'counts' or 'profile'")
def get_bws(self):
return OrderedDict([(task, task_spec.get_bw_dict())
for task, task_spec in self.task_specs.items()])
def touch_all_files(self, verbose=True):
from basepair.utils import touch_file
touch_file(self.fasta_file, verbose)
for ts in self.task_specs.values():
ts.touch_all_files(verbose=verbose)
for ts in self.bias_specs.values():
touch_file(ts.pos_counts, verbose)
touch_file(ts.neg_counts, verbose)
# touch_file(ts.peaks)
def load_counts(self, intervals, use_strand=True, progbar=False):
return {
task: ts.load_counts(intervals,
use_strand=use_strand,
progbar=progbar)
for task, ts in self.task_specs.items()
}
def load_bias_counts(self, intervals, use_strand=True, progbar=False):
return {
task: ts.load_counts(intervals,
use_strand=use_strand,
progbar=progbar)
for task, ts in self.bias_specs.items()
}
class GroupBySettings(object):
groupings = related.MappingField(GroupByObject, 'id', {}, key='groupings')
class SeriesSettings(object):
series_objects = related.MappingField(SeriesSettingsObject,
'id', {},
key='seriesObjects')
series_order = related.SequenceField(str, [], key='seriesOrder')
class DataSpec(RelatedLoadSaveMixin):
"""Dataset specification
"""
# Dictionary of different bigwig files
task_specs = related.MappingField(TaskSpec, "task",
required=True,
repr=True)
# Path to the reference genome fasta file
fasta_file = related.StringField(required=True)
# Bias track specification
bias_specs = related.MappingField(BiasSpec, "task",
required=False,
repr=True)
# # Set of peaks to consider
# peaks = related.StringField(required=True)
# Original path to the file
path = related.StringField(required=False)
def abspath(self):
return DataSpec(
task_specs={k: v.abspath() for k, v in self.task_specs.items()},
fasta_file=os.path.abspath(self.fasta_file),
# peaks=os.path.abspath(self.peaks),
path=self.path)
def get_bws(self):
return OrderedDict([(task, task_spec.tracks)
for task, task_spec in self.task_specs.items()])
def list_all_files(self, include_peaks=False):
"""List all file paths specified
"""
files = []
files.append(self.fasta_file)
for ts in self.task_specs.values():
files += ts.list_all_files(include_peaks=include_peaks)
for ts in self.bias_specs.values():
files += ts.list_all_files(include_peaks=include_peaks)
return files
def touch_all_files(self, verbose=True):
from bpnet.utils import touch_file
touch_file(self.fasta_file, verbose)
for ts in self.task_specs.values():
ts.touch_all_files(verbose=verbose)
for ts in self.bias_specs.values():
ts.touch_all_files(verbose=verbose)
def load_counts(self, intervals, use_strand=True, progbar=False):
return {task: ts.load_counts(intervals, use_strand=use_strand, progbar=progbar)
for task, ts in self.task_specs.items()}
def load_bias_counts(self, intervals, use_strand=True, progbar=False):
return {task: ts.load_counts(intervals, use_strand=use_strand, progbar=progbar)
for task, ts in self.bias_specs.items()}
def get_all_regions(self):
"""Get all the regions
"""
from pybedtools import BedTool
regions = []
for task, task_spec in self.task_specs.items():
if task_spec.peaks is not None:
regions += list(BedTool(task_spec.peaks))
return regions
class Services:
services = related.MappingField(Service, "name")
class CoverageReport(object):
suite_result = related.ChildField(SuiteResult)
schemas = related.SequenceField(Swagger)
paths = related.MappingField(PathReport, "url")
def prepare(self):
"""iterate through all scenario-steps and record the counts."""
for scenario_result, scenario_pass, case_pass in self.iterate():
for step_result in scenario_result.step_results:
step_pass = step_result.success
url, method = step_result.fetch.url, step_result.fetch.method
params = step_result.fetch.kwargs.get("params")
method_report = self.get_method_report(url, method)
if method_report:
method_report.add(case_pass, scenario_pass, step_pass,
params)
def get_method_report(self, url, method):
"""return method report for a given url & method combination"""
path_obj = None
# scan schemas
for schema in self.schemas:
path_obj = schema.resolve(url)
if path_obj is not None:
break
# hard fail
# assert path_obj, "No path report for: %s" % url
# resolve path report and then method report
if path_obj:
path_report = self.paths.get(path_obj.path)
return path_report.get_method_report(method)
def iterate(self): # pragma: no mccabe
"""yields scenario_result, scenario_pass, case_pass"""
for case_result in self.suite_result.passed:
for scenario_result in case_result.passed:
yield scenario_result, True, True
for scenario_result in case_result.failed:
yield scenario_result, False, True # pragma: no cover
for case_result in self.suite_result.failed:
for scenario_result in case_result.passed:
yield scenario_result, True, False # pragma: no cover
for scenario_result in case_result.failed:
yield scenario_result, False, False
def generate(self, output_path):
output_path = output_path or tempfile.mkdtemp()
timestamp = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
output_path = os.path.join(output_path, "coverage-%s.xls" % timestamp)
book = xlwt.Workbook()
sheet = book.add_sheet("coverage")
self.write_row(sheet.row(0), HEADERS, True)
index = 1
for url, path_report in self.paths.items():
for method, method_report in path_report.methods.items():
values = [getattr(method_report, column) for column in COLUMNS]
self.write_row(sheet.row(index), values)
index += 1
for index, width in enumerate(WIDTHS):
sheet.col(index).width = width
book.save(output_path)
return output_path
def write_row(self, row, values, bolded=False):
style = xlwt.XFStyle()
if bolded:
style.font = xlwt.Font()
style.font.bold = True
for index, value in enumerate(values):
row.write(index, value, style=style)
@classmethod
def create(cls, suite_result):
schemas = Swagger.gather_schemas(suite=suite_result.suite)
# populate report with 0 counts for all discovered path/methods
paths = {}
for schema in schemas:
for url, obj in schema.paths.items():
report = PathReport(obj=obj, url=url)
paths[url] = report
for method in obj.methods:
report.get_method_report(method)
# create and prepare report
report = CoverageReport(suite_result=suite_result,
schemas=schemas,
paths=paths)
report.prepare()
return report
class Swagger(object):
swagger = related.StringField(required=True)
info = related.ChildField(Info, required=True)
paths = related.MappingField(Path, "path", required=True)
host = related.StringField(required=False)
basePath = related.StringField(required=False)
schemes = related.SequenceField(Scheme, required=False)
consumes = related.SequenceField(MIMEType, required=False)
produces = related.SequenceField(MIMEType, required=False)
definitions = related.MappingField(Definition, "key", required=False)
_lookup = related.ChildField(dict, required=False)
def __attrs_post_init__(self):
""" populate the nested _lookup dictionary."""
self.populate_lookup()
@classmethod
def loads(cls, content):
as_dict = related.from_yaml(content, object_pairs_hook=dict)
return related.to_model(cls, as_dict)
def resolve(self, url):
""" Resolve to Path object based on the URL path provided. """
return self.descend_lookup(url, try_var=True).get(OBJ)
def populate_lookup(self):
""" Populate the lookup nested dictionary with paths. """
# todo: use basePath to ensure mapping is correct?
self._lookup = {}
for path_url, path_obj in self.paths.items():
nested = self.descend_lookup(path_url)
nested[OBJ] = path_obj
def descend_lookup(self, url, try_var=False):
""" Descend lookup nested dictionary, finding bottom dict and tuple."""
as_tuple = self.path_as_tuple(url)
sub_lookup = self._lookup
for item in as_tuple:
# if in resolve mode, and VAR is only option, return var
if try_var and (item not in sub_lookup) and (VAR in sub_lookup):
sub_lookup = sub_lookup.get(VAR)
# if build mode or item exists, return that.
else:
sub_lookup = sub_lookup.setdefault(item, {})
return sub_lookup
@classmethod
def path_as_tuple(cls, url):
""" Convert URL path into a set of tuples replacing variables. """
# remove leading and trailing blanks
items = hyperlink.URL.from_text(url).path
items = items[1:] if items and not items[0] else items
items = items[:-1] if items and not items[-1] else items
# replace variables with VAR indicator for resolve
return tuple([VAR if cls.is_var(item) else item for item in items])
@staticmethod
def is_var(s):
""" Determines if follows path variable format of {pk}. """
return isinstance(s, str) and s.startswith("{") and s.endswith("}")
@classmethod
def gather_schemas(cls, suite):
from . import utils
schemas = []
for name, path in suite.schemas.items():
json = utils.download_json_with_headers(suite, path)
schema = related.to_model(cls, json)
schemas.append(schema)
return schemas
class Compose(object):
version = related.StringField(required=False, default=None)
services = related.MappingField(Service, "name", required=False)
class DescriptorSet:
agents = related.MappingField(AgentDescriptor, "name")
def __iter__(self):
return self.agents.values().__iter__()
class Config(Profile):
profiles = related.MappingField(Profile, "name", default={})
file_path = related.StringField(required=False, default=None)
def get_profile(self, name):
# todo: determine if name is valid, rather than just returning default.
# todo: handle case insensitivity?
return self.profiles.get(name, self) # return default (self) if fail
@classmethod
def load(cls, paths):
"""Find rigor.yml file and load it into a Config object."""
file_path = cls.find_file_path(paths)
if file_path and os.path.exists(file_path):
content = open(file_path).read()
config = cls.loads(content, file_path)
get_logger().info("config file", file_path=file_path)
get_logger().debug("config details", **related.to_dict(config))
else:
config = cls()
get_logger().info("no config file not found", paths=paths)
return config
@classmethod
def find_file_path(cls, paths):
"""Return valid 'rigor.yml' file in the paths or parents of paths."""
for path in paths:
path = os.path.abspath(path)
file_path = os.path.join(path, const.RIGOR_YML)
reached_top = path == "/"
# iterate until finding a pyconduct.yml file or reaching top
while not os.path.exists(file_path) and not reached_top:
file_path = os.path.join(path, const.RIGOR_YML)
path = os.path.dirname(path)
reached_top = path == "/"
if os.path.exists(file_path):
return file_path
@classmethod
def loads(cls, content, file_path=None):
"""Load JSON string into a Config object."""
vals = related.from_yaml(content,
file_path=file_path,
object_pairs_hook=dict)
# environment namespace (RIGOR_)
env_ns = Namespace(env={
k[6:]: v
for k, v in os.environ.items() if k.startswith("RIGOR_")
})
# pop profiles and file_path from root config
profiles = vals.pop("profiles", {})
file_path = vals.pop("file_path")
# iterate and construct profile sub-dictionaries with root info
for name, profile in profiles.items():
from_root_profile = copy.deepcopy(vals)
profile = utils.nested_update(from_root_profile, profile)
eval_update_ns(profile, env_ns)
profiles[name] = profile
# construct root config profile
vals["name"] = "__root__"
vals["file_path"] = file_path
vals["profiles"] = profiles
eval_update_ns(vals, env_ns)
return related.to_model(cls, vals)
class ProblemSet:
"""Stores all question metadata and defaults"""
uuid = related.UUIDField(required=False)
title = related.StringField('')
questions = related.MappingField(ExamQuestionMeta, 'id', required=False)
question_defaults = related.ChildField(ExamQuestionMeta,
ExamQuestionMeta.from_defaults(),
required=False)
def create_question(self, **kwargs) -> ExamQuestionMeta:
"""Creates a new Question from defaults"""
return ExamQuestionMeta.from_defaults(self.question_defaults.__dict__,
kwargs)
def insert_question(self, allow_edit: bool, id: str,
**kwargs) -> ExamQuestionMeta:
found_question = self.find_question(id)
if found_question:
if not allow_edit:
raise KeyError("Question with specified `id` already exists")
sum_dict = combine_dictionaries(found_question.__dict__, kwargs)
new_question = self.create_question(**sum_dict)
else:
new_question = self.create_question(**kwargs)
self.questions[id] = new_question
return new_question
def find_question(self, id: str) -> ExamQuestionMeta:
"""
Returns the question with specified `id` if it exists; otherwise None
"""
return self.questions.get(id, None)
def generate_exam(self,
num_questions: int,
description: str,
title: str = None) -> Exam:
"""
Creates an Exam instance from randomly selected questions and answers
Args:
num_questions: the number of questions to include
description: exam description shown to user
title: short exam title
"""
questions_meta = weighted_random(self.questions.items(),
lambda q: q[1].likelihood,
num_questions)
questions = [
ExamQuestion.from_meta(id, meta) for id, meta in questions_meta
]
now = datetime.now()
return Exam(meta_uuid=self.uuid,
generated_at=now,
title=title or self.title,
questions=questions,
description=description)
def ensure_exam_compatibility(self, exam: Exam) -> None:
"""
Checks whether the `exam` was created from this problem set.
Raises
SchemeError: if the `exam` isn't compatible
"""
def fail(reason):
raise SchemeError(
f"Problem set `{self.title}` does not match the exam `{self.title}` ({reason})"
)
if self.uuid != exam.meta_uuid:
fail('UUID')
# check for missing questions
for question in exam.questions:
if self.find_question(question.id) is None:
fail(f"missing question: {question.id}")
def save(self, path: str) -> None:
"""
Saves this object instance as YAML to the specified path
"""
self.validate()
with open(path, "w") as file:
related.to_yaml(self,
file,
suppress_empty_values=True,
suppress_map_key_values=True)
def validate(self):
"""Validates object state"""
for key, question in self.questions.items():
question.validate()
@staticmethod
def from_file(path: str):
with open(path, "r") as file:
obj = related.from_yaml(file, ProblemSet)
obj.validate()
return obj