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Schema lint - warn about invalid title + description #701

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Merged
ewels merged 2 commits into from
Jul 29, 2020
Merged

Schema lint - warn about invalid title + description #701

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2bdb026
Schema lint - warn about invalid title + description
ewels Jul 29, 2020
878f841
Update tests
ewels Jul 29, 2020
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5 changes: 5 additions & 0 deletions nf_core/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -482,6 +482,11 @@ def lint(schema_path):
try:
schema_obj.get_schema_path(schema_path)
schema_obj.load_lint_schema()
# Validate title and description - just warnings as schema should still work fine
try:
schema_obj.validate_schema_title_description()
except AssertionError as e:
log.warn(e)
except AssertionError as e:
sys.exit(1)

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8 changes: 8 additions & 0 deletions nf_core/lint.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1237,6 +1237,14 @@ def check_schema_lint(self):
except AssertionError as e:
self.failed.append((14, "Schema lint failed: {}".format(e)))

# Check the title and description - gives warnings instead of fail
if self.schema_obj.schema is not None:
try:
self.schema_obj.validate_schema_title_description()
self.passed.append((14, "Schema title + description lint passed"))
except AssertionError as e:
self.warned.append((14, e))

def check_schema_params(self):
""" Check that the schema describes all flat params in the pipeline """

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23 changes: 10 additions & 13 deletions nf_core/schema.py
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Original file line number Diff line number Diff line change
Expand Up @@ -190,11 +190,11 @@ def validate_schema(self, schema=None):
for allOf in schema["allOf"]:
if allOf["$ref"] == "#/definitions/{}".format(d_key):
in_allOf = True
assert in_allOf, "Definition subschema '{}' not included in schema 'allOf'".format(d_key)
assert in_allOf, "Definition subschema `{}` not included in schema `allOf`".format(d_key)

for d_param_id in d_schema.get("properties", {}):
# Check that we don't have any duplicate parameter IDs in different definitions
assert d_param_id not in param_keys, "Duplicate parameter found in schema 'definitions': '{}'".format(
assert d_param_id not in param_keys, "Duplicate parameter found in schema `definitions`: `{}`".format(
d_param_id
)
param_keys.append(d_param_id)
Expand All @@ -204,16 +204,13 @@ def validate_schema(self, schema=None):
for allOf in schema.get("allOf", []):
assert "definitions" in schema, "Schema has allOf, but no definitions"
def_key = allOf["$ref"][14:]
assert def_key in schema["definitions"], "Subschema '{}' found in 'allOf' but not 'definitions'".format(
assert def_key in schema["definitions"], "Subschema `{}` found in `allOf` but not `definitions`".format(
def_key
)

# Check that the schema describes at least one parameter
assert num_params > 0, "No parameters found in schema"

# Validate title and description
self.validate_schema_title_description(schema)

return num_params

def validate_schema_title_description(self, schema=None):
Expand All @@ -227,30 +224,30 @@ def validate_schema_title_description(self, schema=None):
log.debug("Pipeline schema not set - skipping validation of top-level attributes")
return None

assert "$schema" in self.schema, "Schema missing top-level '$schema' attribute"
assert "$schema" in self.schema, "Schema missing top-level `$schema` attribute"
schema_attr = "https://json-schema.org/draft-07/schema"
assert self.schema["$schema"] == schema_attr, "Schema '$schema' should be '{}'\n Found '{}'".format(
assert self.schema["$schema"] == schema_attr, "Schema `$schema` should be `{}`\n Found `{}`".format(
schema_attr, self.schema["$schema"]
)

if self.pipeline_manifest == {}:
self.get_wf_params()

if "name" not in self.pipeline_manifest:
log.debug("Pipeline manifest 'name' not known - skipping validation of schema id and title")
log.debug("Pipeline manifest `name` not known - skipping validation of schema id and title")
else:
assert "$id" in self.schema, "Schema missing top-level '$id' attribute"
assert "title" in self.schema, "Schema missing top-level 'title' attribute"
assert "$id" in self.schema, "Schema missing top-level `$id` attribute"
assert "title" in self.schema, "Schema missing top-level `title` attribute"
# Validate that id, title and description match the pipeline manifest
id_attr = "https://raw.githubusercontent.com/{}/master/nextflow_schema.json".format(
self.pipeline_manifest["name"].strip("\"'")
)
assert self.schema["$id"] == id_attr, "Schema '$id' should be '{}'\n Found '{}'".format(
assert self.schema["$id"] == id_attr, "Schema `$id` should be `{}`\n Found `{}`".format(
id_attr, self.schema["$id"]
)

title_attr = "{} pipeline parameters".format(self.pipeline_manifest["name"].strip("\"'"))
assert self.schema["title"] == title_attr, "Schema 'title' should be '{}'\n Found: '{}'".format(
assert self.schema["title"] == title_attr, "Schema `title` should be `{}`\n Found: `{}`".format(
title_attr, self.schema["title"]
)

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2 changes: 1 addition & 1 deletion tests/test_lint.py
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@ def pf(wd, path):
]

# The maximum sum of passed tests currently possible
MAX_PASS_CHECKS = 83
MAX_PASS_CHECKS = 84
# The additional tests passed for releases
ADD_PASS_RELEASE = 1

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6 changes: 3 additions & 3 deletions tests/test_schema.py
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Expand Up @@ -161,7 +161,7 @@ def test_validate_schema_fail_duplicate_ids(self):
self.schema_obj.validate_schema(self.schema_obj.schema)
raise UserWarning("Expected AssertionError")
except AssertionError as e:
assert e.args[0] == "Duplicate parameter found in schema 'definitions': 'foo'"
assert e.args[0] == "Duplicate parameter found in schema `definitions`: `foo`"

def test_validate_schema_fail_missing_def(self):
"""
Expand All @@ -175,7 +175,7 @@ def test_validate_schema_fail_missing_def(self):
self.schema_obj.validate_schema(self.schema_obj.schema)
raise UserWarning("Expected AssertionError")
except AssertionError as e:
assert e.args[0] == "Definition subschema 'groupTwo' not included in schema 'allOf'"
assert e.args[0] == "Definition subschema `groupTwo` not included in schema `allOf`"

def test_validate_schema_fail_unexpected_allof(self):
"""
Expand All @@ -193,7 +193,7 @@ def test_validate_schema_fail_unexpected_allof(self):
self.schema_obj.validate_schema(self.schema_obj.schema)
raise UserWarning("Expected AssertionError")
except AssertionError as e:
assert e.args[0] == "Subschema 'groupThree' found in 'allOf' but not 'definitions'"
assert e.args[0] == "Subschema `groupThree` found in `allOf` but not `definitions`"

def test_make_skeleton_schema(self):
""" Test making a new schema skeleton """
Expand Down