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Extend the Specification interface to break out loading from streams. #198

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merged 6 commits into from
Sep 26, 2019
Merged

Extend the Specification interface to break out loading from streams. #198

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9f77450
Addition of loading specification "from_str".
Sep 25, 2019
981027d
Updates to Specification docstrings.
Sep 25, 2019
ad133bb
Updates to abstract Specification to change from str to stream.
Sep 25, 2019
b949c61
Updates to YAMLSpecification to use the new stream API.
Sep 25, 2019
2b68968
Removal of IOString
Sep 25, 2019
b0e39ca
Update to the YAMLSpecification load stream method.
Sep 25, 2019
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15 changes: 13 additions & 2 deletions maestrowf/abstracts/specification.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,10 +42,21 @@ class Specification(object):
@abstractclassmethod
def load_specification(cls, path):
"""
Method for loading a study specification.
Method for loading a study specification from a file.

:param path: Path to a study specification.
:returns: A specification object containing the information from path.
:returns: A specification object containing the information loaded
from path.
"""
pass

@abstractclassmethod
def load_specification_from_stream(cls, stream):
"""
Method for loading a study specification from a stream.

:param stream: Raw text stream containing specification data.
:returns: A specification object containing the information in string.
"""
pass

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32 changes: 22 additions & 10 deletions maestrowf/datastructures/yamlspecification.py
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Expand Up @@ -95,22 +95,34 @@ def load_specification(cls, path):
try:
# Load the YAML spec from the file.
with open(path, 'r') as data:
try:
spec = yaml.load(data, yaml.FullLoader)
except AttributeError:
logger.warning(
"*** PyYAML is using an unsafe version with a known "
"load vulnerability. Please upgrade your installation "
"to a more recent version! ***")
spec = yaml.load(data)

specification = cls.load_specification_from_stream(data)
except Exception as e:
logger.exception(e.args)
raise

return specification

@classmethod
def load_specification_from_stream(cls, stream):
"""
Load a study specification.

:param stream: Raw text stream to study YAML specification data.
:returns: A specification object containing the information from the
passed stream.
"""

try:
spec = yaml.load(stream, yaml.FullLoader)
except AttributeError:
logger.warning(
"*** PyYAML is using an unsafe version with a known "
"load vulnerability. Please upgrade your installation "
"to a more recent version! ***")
spec = yaml.load(stream)

logger.debug("Loaded specification -- \n%s", spec["description"])
specification = cls()
specification.path = path
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specification.description = spec.pop("description", {})
specification.environment = spec.pop("env",
{'variables': {},
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