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Refactor yaml validation schemas #141

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Merged
dweindl merged 4 commits into from
Apr 29, 2022
Merged

Refactor yaml validation schemas #141

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6d39656
Refactor yaml validation schemas
dweindl Apr 29, 2022
26ab386
fixup manifest
dweindl Apr 29, 2022
02c24be
..
dweindl Apr 29, 2022
b699a2b
Merge branch 'develop' into refactor_schema
dweindl Apr 29, 2022
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4 changes: 2 additions & 2 deletions MANIFEST.in
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Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
include petab/petab_schema.yaml
recursive-include petab/visualize/templates
recursive-include petab/schemas *.yaml
recursive-include petab/visualize/templates *
0 petab/petab_schema.yaml → petab/schemas/petab_schema.v1.0.0.yaml
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20 changes: 15 additions & 5 deletions petab/yaml.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,14 @@

from .C import * # noqa: F403

SCHEMA = os.path.join(os.path.abspath(os.path.dirname(__file__)),
"petab_schema.yaml")
# directory with PEtab yaml schema files
SCHEMA_DIR = Path(__file__).parent / "schemas"
# map of version number to validation schema
SCHEMAS = {
'1': SCHEMA_DIR / "petab_schema.v1.0.0.yaml",
'1.0.0': SCHEMA_DIR / "petab_schema.v1.0.0.yaml",
}

__all__ = ['validate', 'validate_yaml_syntax', 'validate_yaml_semantics',
'load_yaml', 'is_composite_problem',
'assert_single_condition_and_sbml_file', 'write_yaml',
Expand Down Expand Up @@ -52,13 +58,17 @@ def validate_yaml_syntax(
Raises:
see jsonschema.validate
"""
yaml_config = load_yaml(yaml_config)

if schema is None:
schema = SCHEMA
# try get PEtab version from yaml file
# if this is not the available, the file is not valid anyways,
# but let's still use the latest PEtab schema for full validation
version = yaml_config.get(FORMAT_VERSION, None) \
or list(SCHEMAS.values())[-1]
schema = SCHEMAS[str(version)]

schema = load_yaml(schema)
yaml_config = load_yaml(yaml_config)

jsonschema.validate(instance=yaml_config, schema=schema)


Expand Down