def document1_loader():
class Document1Loader(yatiml.Loader):
pass
yatiml.add_to_loader(Document1Loader, Document1)
yatiml.set_document_type(Document1Loader, Document1)
return Document1Loader
def vector_loader():
class VectorLoader(yatiml.Loader):
pass
yatiml.add_to_loader(VectorLoader, Vector2D)
yatiml.set_document_type(VectorLoader, Vector2D)
return VectorLoader
def dict_attribute_loader():
class DictAttributeLoader(yatiml.Loader):
pass
yatiml.add_to_loader(DictAttributeLoader, DictAttribute)
yatiml.set_document_type(DictAttributeLoader, DictAttribute)
return DictAttributeLoader
def parsed_class_loader():
class ParsedClassLoader(yatiml.Loader):
pass
yatiml.add_to_loader(ParsedClassLoader, Postcode)
yatiml.set_document_type(ParsedClassLoader, Postcode)
return ParsedClassLoader
def enum_list_loader():
class EnumListLoader(yatiml.Loader):
pass
yatiml.add_to_loader(EnumListLoader, Color2)
yatiml.set_document_type(EnumListLoader, List[Color2])
return EnumListLoader
def bool_fix_union_loader():
class BoolUnionFixLoader(yatiml.Loader):
pass
yatiml.set_document_type(BoolUnionFixLoader, Union[int, bool,
yatiml.bool_union_fix])
return BoolUnionFixLoader
def union_attribute_loader():
class UnionAttributeLoader(yatiml.Loader):
pass
yatiml.add_to_loader(UnionAttributeLoader, UnionAttribute)
yatiml.set_document_type(UnionAttributeLoader, UnionAttribute)
return UnionAttributeLoader
def enum_dict_loader():
class EnumDictLoader(yatiml.Loader):
pass
yatiml.add_to_loader(EnumDictLoader, Color2)
yatiml.set_document_type(EnumDictLoader, Dict[str, Color2])
return EnumDictLoader
def universal_loader():
class UniversalLoader(yatiml.Loader):
pass
yatiml.add_to_loader(UniversalLoader, Universal)
yatiml.set_document_type(UniversalLoader, Universal)
return UniversalLoader
def extensible_loader():
class ExtensibleLoader(yatiml.Loader):
pass
yatiml.add_to_loader(ExtensibleLoader, Extensible)
yatiml.set_document_type(ExtensibleLoader, Extensible)
return ExtensibleLoader
def super_loader():
class SuperLoader(yatiml.Loader):
pass
yatiml.add_to_loader(SuperLoader, [Super, SubA, SubB])
yatiml.set_document_type(SuperLoader, Super)
return SuperLoader
def super2_loader():
class Super2Loader(yatiml.Loader):
pass
yatiml.add_to_loader(Super2Loader, [Super2, SubA2, SubB2])
yatiml.set_document_type(Super2Loader, Super2)
return Super2Loader
def user_string_loader():
class UserStringLoader(yatiml.Loader):
pass
yatiml.add_to_loader(UserStringLoader, ConstrainedString)
yatiml.set_document_type(UserStringLoader, ConstrainedString)
return UserStringLoader
def enum_loader2():
class EnumLoader2(yatiml.Loader):
pass
yatiml.add_to_loader(EnumLoader2, Color2)
yatiml.set_document_type(EnumLoader2, Color2)
return EnumLoader2
def bool_fix_tester_loader():
class BoolFixTesterLoader(yatiml.Loader):
pass
yatiml.set_document_type(BoolFixTesterLoader, BoolFixTester)
yatiml.add_to_loader(BoolFixTesterLoader, BoolFixTester)
return BoolFixTesterLoader
def dashed_attribute_loader():
class DashedAttributeLoader(yatiml.Loader):
pass
yatiml.add_to_loader(DashedAttributeLoader, DashedAttribute)
yatiml.set_document_type(DashedAttributeLoader, DashedAttribute)
return DashedAttributeLoader
def missing_circle_loader():
class MissingCircleLoader(yatiml.Loader):
pass
yatiml.add_to_loader(MissingCircleLoader,
[Shape, Rectangle, Ellipse, Vector2D])
yatiml.set_document_type(MissingCircleLoader, Shape)
return MissingCircleLoader
def shape_loader():
class ShapeLoader(yatiml.Loader):
pass
yatiml.add_to_loader(ShapeLoader,
[Shape, Rectangle, Circle, Ellipse, Vector2D])
yatiml.set_document_type(ShapeLoader, Shape)
return ShapeLoader
def test_load_dict_invalid_key():
class IntKeyDictLoader(yatiml.Loader):
pass
yatiml.set_document_type(IntKeyDictLoader, Dict[int, str])
text = ('1: one\n' '2: two\n' '3: three\n')
with pytest.raises(RuntimeError):
yaml.load(text, Loader=IntKeyDictLoader)
def document2_loader():
class Document2Loader(yatiml.Loader):
pass
yatiml.add_to_loader(
Document2Loader,
[Color2, Document2, Shape, Rectangle, Circle, Vector2D])
yatiml.set_document_type(Document2Loader, Document2)
return Document2Loader
def test_load_bool():
class BoolLoader(yatiml.Loader):
pass
yatiml.set_document_type(BoolLoader, bool)
text = 'True'
data = yaml.load(text, Loader=BoolLoader)
assert isinstance(data, bool)
assert data is True
def test_load_float():
class FloatLoader(yatiml.Loader):
pass
yatiml.set_document_type(FloatLoader, float)
text = '3.1415'
data = yaml.load(text, Loader=FloatLoader)
assert isinstance(data, float)
assert data == 3.1415
def test_load_int():
class IntLoader(yatiml.Loader):
pass
yatiml.set_document_type(IntLoader, int)
text = '42'
data = yaml.load(text, Loader=IntLoader)
assert isinstance(data, int)
assert data == 42
self.echo_run = echo_run
self.enable_callers = enable_callers
self.mode = mode
self.genome = genome
self.exclusion_list = exclusion_list
self.exclude_regions = exclude_regions
self.file_exts = file_exts
self.samples = samples
self.callers = callers
self.postproc = postproc
# Create loader
class MyLoader(yatiml.Loader):
"""
MyLoader class.
"""
pass
def load_configfile(yaml_file: str) -> Dict:
with open(yaml_file, 'r') as conf:
return yaml.load(conf, MyLoader)
yatiml.logger.setLevel(logging.DEBUG)
yatiml.add_to_loader(MyLoader, [Mode, FileExtension, Resource, Manta, Delly,
Lumpy, Gridss, Caller, SurvivorFilter, SurvivorMerge,
Survivor, PostProcess, Analysis])
yatiml.set_document_type(MyLoader, Analysis)
from ruamel import yaml
from typing import Dict
import yatiml
# Create loader
class MyLoader(yatiml.Loader):
pass
yatiml.set_document_type(MyLoader, Dict[str, str])
# Load YAML
yaml_text = ('name: Janice\n'
'age: Six\n')
doc = yaml.load(yaml_text, Loader=MyLoader)
print(doc)
def bool_union_loader():
class BoolUnionLoader(yatiml.Loader):
pass
yatiml.set_document_type(BoolUnionLoader, Union[int, bool])
return BoolUnionLoader
def bool_fix_loader():
class BoolFixLoader(yatiml.Loader):
pass
yatiml.set_document_type(BoolFixLoader, yatiml.bool_union_fix)
return BoolFixLoader
def bool_loader():
class BoolLoader(yatiml.Loader):
pass
yatiml.set_document_type(BoolLoader, bool)
return BoolLoader
@classmethod
def _yatiml_savorize(cls, node: yatiml.Node) -> None:
str_to_int = {
'five': 5,
'six': 6,
'seven': 7,
}
if node.has_attribute_type('age', str):
str_val = node.get_attribute('age').get_value()
if str_val in str_to_int:
node.set_attribute('age', str_to_int[str_val])
else:
raise yatiml.SeasoningError('Invalid age string')
# Create loader
class MyLoader(yatiml.Loader):
pass
yatiml.add_to_loader(MyLoader, Submission)
yatiml.set_document_type(MyLoader, Submission)
# Load YAML
yaml_text = ('name: Janice\n' 'age: six\n')
doc = yaml.load(yaml_text, Loader=MyLoader)
print(doc.name)
print(doc.age)
print(doc.tool)
def union_loader():
class UnionLoader(yatiml.Loader):
pass
yatiml.set_document_type(UnionLoader, Union[str, int])
return UnionLoader
