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Parameters schema validation: allow oneOf, anyOf and allOf with required #3386

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merged 6 commits into from
Jan 9, 2025
Merged

Parameters schema validation: allow oneOf, anyOf and allOf with required #3386

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4a74d5b
remove required from oneOf, allOf and anyOf instances in a schema
mirpedrol Jan 8, 2025
5782edf
print complete error message from schema validation on debug
mirpedrol Jan 8, 2025
958f58e
[automated] Update CHANGELOG.md
nf-core-bot Jan 8, 2025
51fba5a
reduce code
mirpedrol Jan 8, 2025
2f2950f
handle anyOf, allOf, oneOf in top level
mirpedrol Jan 8, 2025
b1c7a8c
add tests for validate_default_params function
mirpedrol Jan 8, 2025
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,8 @@

### General

- Parameters schema validation: allow oneOf, anyOf and allOf with `required` ([#3386](https://github.com/nf-core/tools/pull/3386))

### Version updates

## [v3.1.1 - Brass Boxfish Patch](https://github.com/nf-core/tools/releases/tag/3.1.1) - [2024-12-20]
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28 changes: 28 additions & 0 deletions nf_core/pipelines/schema.py
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Expand Up @@ -330,8 +330,36 @@ def validate_default_params(self):
for group_key, group in schema_no_required.get(self.defs_notation, {}).items():
if "required" in group:
schema_no_required[self.defs_notation][group_key].pop("required")
if "allOf" in group:
for all_of in group["allOf"]:
if "required" in all_of:
schema_no_required[self.defs_notation][group_key]["allOf"].pop("required")
schema_no_required[self.defs_notation][group_key]["allOf"] = [
all_of for all_of in group["allOf"] if all_of
]
if not group["allOf"]:
schema_no_required[self.defs_notation][group_key].pop("allOf")
if "anyOf" in group:
for any_of in group["anyOf"]:
if "required" in any_of:
schema_no_required[self.defs_notation][group_key]["anyOf"].pop("required")
schema_no_required[self.defs_notation][group_key]["anyOf"] = [
any_of for any_of in group["anyOf"] if any_of
]
if not group["anyOf"]:
schema_no_required[self.defs_notation][group_key].pop("anyOf")
if "oneOf" in group:
for i, one_of in enumerate(group["oneOf"]):
if "required" in one_of:
schema_no_required[self.defs_notation][group_key]["oneOf"][i].pop("required")
schema_no_required[self.defs_notation][group_key]["oneOf"] = [
one_of for one_of in group["oneOf"] if one_of
]
if not group["oneOf"]:
schema_no_required[self.defs_notation][group_key].pop("oneOf")
jsonschema.validate(self.schema_defaults, schema_no_required)
except jsonschema.exceptions.ValidationError as e:
log.debug(f"Complete error message:\n{e}")
raise AssertionError(f"Default parameters are invalid: {e.message}")
for param, default in self.schema_defaults.items():
if default in ("null", "", None, "None") or default is False:
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