def _convert_to_j(self, annotation):
if annotation is not None:
return Env.jutils().arrayListToISeq(
[self.element_type._convert_to_j(elt) for elt in annotation]
)
else:
return annotation
def _convert_to_j(self, annotation):
if annotation is not None:
return Env.jutils().javaMapToMap(
{self.key_type._convert_to_j(k): self.value_type._convert_to_j(v) for k, v in annotation.iteritems()}
)
else:
return annotation
def _convert_to_j(self, annotation):
if annotation is not None:
return Env.jutils().javaMapToMap(
{self.key_type._convert_to_j(k): self.value_type._convert_to_j(v) for k, v in annotation.iteritems()}
)
else:
return annotation
def _convert_to_j(self, annotation):
if annotation is not None:
return Env.jutils().arrayListToSet(
[self.element_type._convert_to_j(elt) for elt in annotation]
)
else:
return annotation
def _init_from_java(self, jtype):
jfields = Env.jutils().iterableToArrayList(jtype.fields())
self.fields = [
Field(f.name(), Type._from_java(f.typ()), dict(f.attrsJava()))
for f in jfields
]
def hadoop_copy(src, dest):
"""Copy a file through the Hadoop filesystem API.
Supports distributed file systems like hdfs, gs, and s3.
**Examples**
>>> hadoop_copy('gs://hail-common/LCR.interval_list', 'file:///mnt/data/LCR.interval_list') # doctest: +SKIP
**Notes**
The provided source and destination file paths must be URIs
(uniform resource identifiers).
:param str src: Source file URI.
:param str dest: Destination file URI.
"""
Env.jutils().copyFile(src, dest, Env.hc()._jhc)
def hadoop_copy(src, dest):
"""Copy a file through the Hadoop filesystem API.
Supports distributed file systems like hdfs, gs, and s3.
**Examples**
>>> hadoop_copy('gs://hail-common/LCR.interval_list', 'file:///mnt/data/LCR.interval_list') # doctest: +SKIP
**Notes**
The provided source and destination file paths must be URIs
(uniform resource identifiers).
:param str src: Source file URI.
:param str dest: Destination file URI.
"""
Env.jutils().copyFile(src, dest, Env.hc()._jhc)
def _convert_to_j(self, annotation):
if annotation is not None:
return scala_object(Env.hail().annotations, 'Annotation').fromSeq(
Env.jutils().arrayListToISeq([
f.typ._convert_to_j(annotation[f.name])
for f in self.fields
]))
else:
return annotation
def _convert_to_py(self, annotation):
if annotation:
lst = Env.jutils().iterableToArrayList(annotation)
d = dict()
for x in lst:
d[self.key_type._convert_to_py(x._1())] = self.value_type._convert_to_py(x._2())
return d
else:
return annotation
def _convert_to_py(self, annotation):
if annotation:
lst = Env.jutils().iterableToArrayList(annotation)
d = dict()
for x in lst:
d[self.key_type._convert_to_py(x._1())] = self.value_type._convert_to_py(x._2())
return d
else:
return annotation
def _convert_to_j(self, annotation):
if annotation is not None:
return scala_object(Env.hail().annotations, 'Annotation').fromSeq(
Env.jutils().arrayListToISeq(
[f.typ._convert_to_j(annotation.get(f.name)) for f in self.fields]
)
)
else:
return annotation
def from_fields(cls, fields, required=False):
"""Creates a new TStruct from field objects.
:param fields: The TStruct fields.
:type fields: list of :class:`.Field`
:param bool required: Flag for whether the struct can be missing.
:return: TStruct from input fields
:rtype: :class:`.TStruct`
"""
struct = TStruct.__new__(cls)
struct.fields = fields
jfields = [scala_object(Env.hail().expr, 'Field').apply(
f.name, f.typ._jtype, i, Env.jutils().javaMapToMap(f.attributes)) for i,f in enumerate(fields)]
jtype = scala_object(Env.hail().expr, 'TStruct').apply(jindexed_seq(jfields), required)
return TStruct._from_java(jtype)
def _convert_to_py(self, annotation):
if annotation:
lst = Env.jutils().iterableToArrayList(annotation)
return set([self.element_type._convert_to_py(x) for x in lst])
else:
return annotation
def __init__(self, path):
self._jfile = Env.jutils().writeFile(path, Env.hc()._jhc)
super(HadoopWriter, self).__init__()
def _convert_to_j(self, annotation):
if annotation:
return Env.jutils().makeInt(annotation)
else:
return annotation
def __init__(self, path):
self._jfile = Env.jutils().readFile(path, Env.hc()._jhc)
super(HadoopReader, self).__init__()
def _init_from_java(self, jtype):
jfields = Env.jutils().iterableToArrayList(jtype.fields())
self.fields = [Field(f.name(), Type._from_java(f.typ()), dict(f.attrsJava())) for f in jfields]
def __init__(self, path):
self._jfile = Env.jutils().writeFile(path, Env.hc()._jhc)
super(HadoopWriter, self).__init__()
def __init__(self, path):
self._jfile = Env.jutils().readFile(path, Env.hc()._jhc)
super(HadoopReader, self).__init__()
def _convert_to_j(self, annotation):
if annotation:
return Env.jutils().makeInt(annotation)
else:
return annotation
def _convert_to_py(self, annotation):
if annotation:
lst = Env.jutils().iterableToArrayList(annotation)
return set([self.element_type._convert_to_py(x) for x in lst])
else:
return annotation
