Improve validation of modules.yaml (#9878)

This PR improves the validation of `modules.yaml` by introducing a custom validator that checks if an attribute listed in `properties` or `patternProperties` is a valid spec. This new check applied to the test case in #9857 gives:

```console
$ spack install szip
==> Error: /home/mculpo/.spack/linux/modules.yaml:5: "^python@2.7@" is an invalid spec [Invalid version specifier]
```

Details: 
* Moved the set-up of a custom validator class to spack.schema
  * In Spack we use `jsonschema` to validate configuration files 
    against a schema. We also need custom validators to enforce
    writing default values within "properties" or "patternProperties"
    attributes.

  * Currently, validators were customized at the place of use and with the
    recent introduction of environments that meant we were setting-up and
    using 2 different validator classes in two different modules.

  * This commit moves the set-up of a custom validator class in the
    `spack.schema` module and refactors the code in `spack.config` and
    `spack.environments` to use it.

* Added a custom validator to check if an attribute is a valid spec
  * Added a custom validator that can be used on objects, which yields an
    error if the attribute is not a valid spec.

* Updated the schema for modules.yaml

* Updated modules.yaml to fix a few inconsistencies:
  - a few attributes were not tested properly using 'anyOf'
  - suffixes has been updated to also check that the attribute is a spec
  - hierarchical_scheme has been updated to hierarchy

* Removed $ref from every schema
  * $ref is not composable or particularly legible
  * Use python dicts and regular old variables instead.

lib/spack/llnl/util/lang.py

@@ -562,6 +562,9 @@ def __getitem__(self, name):
     def __contains__(self, element):
         return element in self.instance
 
+    def __call__(self, *args, **kwargs):
+        return self.instance(*args, **kwargs)
+
     def __iter__(self):
         return iter(self.instance)
 

lib/spack/spack/config.py

@@ -32,7 +32,6 @@
 
 import copy
 import os
-import re
 import sys
 import multiprocessing
 from contextlib import contextmanager
@@ -49,6 +48,7 @@
 
 import spack.paths
 import spack.architecture
+import spack.schema
 import spack.schema.compilers
 import spack.schema.mirrors
 import spack.schema.repos
@@ -115,47 +115,6 @@ def first_existing(dictionary, keys):
         raise KeyError("None of %s is in dict!" % keys)
 
 
-def _extend_with_default(validator_class):
-    """Add support for the 'default' attr for properties and patternProperties.
-
-       jsonschema does not handle this out of the box -- it only
-       validates.  This allows us to set default values for configs
-       where certain fields are `None` b/c they're deleted or
-       commented out.
-
-    """
-    import jsonschema
-    validate_properties = validator_class.VALIDATORS["properties"]
-    validate_pattern_properties = validator_class.VALIDATORS[
-        "patternProperties"]
-
-    def set_defaults(validator, properties, instance, schema):
-        for property, subschema in iteritems(properties):
-            if "default" in subschema:
-                instance.setdefault(
-                    property, copy.deepcopy(subschema["default"]))
-        for err in validate_properties(
-                validator, properties, instance, schema):
-            yield err
-
-    def set_pp_defaults(validator, properties, instance, schema):
-        for property, subschema in iteritems(properties):
-            if "default" in subschema:
-                if isinstance(instance, dict):
-                    for key, val in iteritems(instance):
-                        if re.match(property, key) and val is None:
-                            instance[key] = copy.deepcopy(subschema["default"])
-
-        for err in validate_pattern_properties(
-                validator, properties, instance, schema):
-            yield err
-
-    return jsonschema.validators.extend(validator_class, {
-        "properties": set_defaults,
-        "patternProperties": set_pp_defaults
-    })
-
-
 class ConfigScope(object):
     """This class represents a configuration scope.
 
@@ -697,17 +656,10 @@ def _validate(data, schema, set_defaults=True):
 
     This leverages the line information (start_mark, end_mark) stored
     on Spack YAML structures.
-
     """
     import jsonschema
-
-    if not hasattr(_validate, 'validator'):
-        default_setting_validator = _extend_with_default(
-            jsonschema.Draft4Validator)
-        _validate.validator = default_setting_validator
-
     try:
-        _validate.validator(schema).validate(data)
+        spack.schema.Validator(schema).validate(data)
     except jsonschema.ValidationError as e:
         raise ConfigFormatError(e, data)
 

lib/spack/spack/environment.py

@@ -8,7 +8,6 @@
 import sys
 import shutil
 
-import jsonschema
 import ruamel.yaml
 
 import llnl.util.filesystem as fs
@@ -67,9 +66,6 @@
 #: legal first keys in the spack.yaml manifest file
 env_schema_keys = ('spack', 'env')
 
-#: jsonschema validator for environments
-_validator = None
-
 
 def valid_env_name(name):
     return re.match(valid_environment_name_re, name)
@@ -306,11 +302,9 @@ def all_environments():
 
 
 def validate(data, filename=None):
-    global _validator
+    import jsonschema
-    if _validator is None:
-        _validator = jsonschema.Draft4Validator(spack.schema.env.schema)
     try:
-        _validator.validate(data)
+        spack.schema.Validator(spack.schema.env.schema).validate(data)
     except jsonschema.ValidationError as e:
         raise spack.config.ConfigFormatError(
             e, data, filename, e.instance.lc.line + 1)

lib/spack/spack/schema/__init__.py

@@ -4,3 +4,81 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 """This module contains jsonschema files for all of Spack's YAML formats."""
+
+import copy
+import re
+
+import six
+
+import llnl.util.lang
+import spack.spec
+
+
+# jsonschema is imported lazily as it is heavy to import
+# and increases the start-up time
+def _make_validator():
+    import jsonschema
+    _validate_properties = jsonschema.Draft4Validator.VALIDATORS["properties"]
+    _validate_pattern_properties = jsonschema.Draft4Validator.VALIDATORS[
+        "patternProperties"
+    ]
+
+    def _set_defaults(validator, properties, instance, schema):
+        """Adds support for the 'default' attribute in 'properties'.
+
+        ``jsonschema`` does not handle this out of the box -- it only
+        validates. This allows us to set default values for configs
+        where certain fields are `None` b/c they're deleted or
+        commented out.
+        """
+        for property, subschema in six.iteritems(properties):
+            if "default" in subschema:
+                instance.setdefault(
+                    property, copy.deepcopy(subschema["default"]))
+        for err in _validate_properties(
+                validator, properties, instance, schema):
+            yield err
+
+    def _set_pp_defaults(validator, properties, instance, schema):
+        """Adds support for the 'default' attribute in 'patternProperties'.
+
+        ``jsonschema`` does not handle this out of the box -- it only
+        validates. This allows us to set default values for configs
+        where certain fields are `None` b/c they're deleted or
+        commented out.
+        """
+        for property, subschema in six.iteritems(properties):
+            if "default" in subschema:
+                if isinstance(instance, dict):
+                    for key, val in six.iteritems(instance):
+                        if re.match(property, key) and val is None:
+                            instance[key] = copy.deepcopy(subschema["default"])
+
+        for err in _validate_pattern_properties(
+                validator, properties, instance, schema):
+            yield err
+
+    def _validate_spec(validator, is_spec, instance, schema):
+        """Check if the attributes on instance are valid specs."""
+        import jsonschema
+        if not validator.is_type(instance, "object"):
+            return
+
+        for spec_str in instance:
+            try:
+                spack.spec.parse(spec_str)
+            except spack.spec.SpecParseError as e:
+                yield jsonschema.ValidationError(
+                    '"{0}" is an invalid spec [{1}]'.format(spec_str, str(e))
+                )
+
+    return jsonschema.validators.extend(
+        jsonschema.Draft4Validator, {
+            "validate_spec": _validate_spec,
+            "properties": _set_defaults,
+            "patternProperties": _set_pp_defaults
+        }
+    )
+
+
+Validator = llnl.util.lang.Singleton(_make_validator)

lib/spack/spack/schema/env.py

@@ -11,13 +11,11 @@
 from llnl.util.lang import union_dicts
 
 import spack.schema.merged
-import spack.schema.modules
 
 
 schema = {
     '$schema': 'http://json-schema.org/schema#',
     'title': 'Spack environment file schema',
-    'definitions': spack.schema.modules.definitions,
     'type': 'object',
     'additionalProperties': False,
     'patternProperties': {

lib/spack/spack/schema/merged.py

@@ -6,7 +6,7 @@
 """Schema for configuration merged into one file.
 
 .. literalinclude:: ../spack/schema/merged.py
-   :lines: 40-
+   :lines: 39-
 """
 from llnl.util.lang import union_dicts
 
@@ -33,7 +33,6 @@
 schema = {
     '$schema': 'http://json-schema.org/schema#',
     'title': 'Spack merged configuration file schema',
-    'definitions': spack.schema.modules.definitions,
     'type': 'object',
     'additionalProperties': False,
     'properties': properties,

lib/spack/spack/schema/modules.py

@@ -9,110 +9,110 @@
    :lines: 13-
 """
 
+#: Matches a spec or a multi-valued variant but not another
+#: valid keyword.
+#:
+#: THIS NEEDS TO BE UPDATED FOR EVERY NEW KEYWORD THAT
+#: IS ADDED IMMEDIATELY BELOW THE MODULE TYPE ATTRIBUTE
+spec_regex = r'(?!hierarchy|verbose|hash_length|whitelist|' \
+             r'blacklist|naming_scheme|core_compilers|all)(^\w[\w-]*)'
+
+#: Matches an anonymous spec, i.e. a spec without a root name
+anonymous_spec_regex = r'^[\^@%+~]'
 
 #: Definitions for parts of module schema
-definitions = {
+array_of_strings = {
-    'array_of_strings': {
+    'type': 'array', 'default': [], 'items': {'type': 'string'}
-        'type': 'array',
+}
-        'default': [],
+
-        'items': {
+dictionary_of_strings = {
-            'type': 'string'
+    'type': 'object', 'patternProperties': {r'\w[\w-]*': {'type': 'string'}}
-        }
+}
-    },
+
-    'dictionary_of_strings': {
+dependency_selection = {'type': 'string', 'enum': ['none', 'direct', 'all']}
-        'type': 'object',
+
-        'patternProperties': {
+module_file_configuration = {
-            r'\w[\w-]*': {  # key
+    'type': 'object',
-                'type': 'string'
+    'default': {},
-            }
+    'additionalProperties': False,
-        }
+    'properties': {
-    },
+        'filter': {
-    'dependency_selection': {
+            'type': 'object',
-        'type': 'string',
+            'default': {},
-        'enum': ['none', 'direct', 'all']
+            'additionalProperties': False,
-    },
+            'properties': {
-    'module_file_configuration': {
+                'environment_blacklist': {
-        'type': 'object',
+                    'type': 'array',
-        'default': {},
+                    'default': [],
-        'additionalProperties': False,
+                    'items': {
-        'properties': {
+                        'type': 'string'
-            'filter': {
-                'type': 'object',
-                'default': {},
-                'additionalProperties': False,
-                'properties': {
-                    'environment_blacklist': {
-                        'type': 'array',
-                        'default': [],
-                        'items': {
-                            'type': 'string'
-                        }
                     }
                 }
-            },
+            }
-            'template': {
+        },
-                'type': 'string'
+        'template': {
-            },
+            'type': 'string'
-            'autoload': {
+        },
-                '$ref': '#/definitions/dependency_selection'},
+        'autoload': dependency_selection,
-            'prerequisites': {
+        'prerequisites': dependency_selection,
-                '$ref': '#/definitions/dependency_selection'},
+        'conflict': array_of_strings,
-            'conflict': {
+        'load': array_of_strings,
-                '$ref': '#/definitions/array_of_strings'},
+        'suffixes': {
-            'load': {
+            'type': 'object',
-                '$ref': '#/definitions/array_of_strings'},
+            'validate_spec': True,
-            'suffixes': {
+            'patternProperties': {
-                '$ref': '#/definitions/dictionary_of_strings'},
+                r'\w[\w-]*': {  # key
-            'environment': {
+                    'type': 'string'
-                'type': 'object',
-                'default': {},
-                'additionalProperties': False,
-                'properties': {
-                    'set': {
-                        '$ref': '#/definitions/dictionary_of_strings'},
-                    'unset': {
-                        '$ref': '#/definitions/array_of_strings'},
-                    'prepend_path': {
-                        '$ref': '#/definitions/dictionary_of_strings'},
-                    'append_path': {
-                        '$ref': '#/definitions/dictionary_of_strings'}
                 }
             }
+        },
+        'environment': {
+            'type': 'object',
+            'default': {},
+            'additionalProperties': False,
+            'properties': {
+                'set': dictionary_of_strings,
+                'unset': array_of_strings,
+                'prepend_path': dictionary_of_strings,
+                'append_path': dictionary_of_strings
+            }
         }
-    },
-    'module_type_configuration': {
-        'type': 'object',
-        'default': {},
-        'anyOf': [
-            {'properties': {
-                'verbose': {
-                    'type': 'boolean',
-                    'default': False
-                },
-                'hash_length': {
-                    'type': 'integer',
-                    'minimum': 0,
-                    'default': 7
-                },
-                'whitelist': {
-                    '$ref': '#/definitions/array_of_strings'},
-                'blacklist': {
-                    '$ref': '#/definitions/array_of_strings'},
-                'blacklist_implicits': {
-                    'type': 'boolean',
-                    'default': False
-                },
-                'naming_scheme': {
-                    'type': 'string'  # Can we be more specific here?
-                }
-            }},
-            {'patternProperties': {
-                r'\w[\w-]*': {
-                    '$ref': '#/definitions/module_file_configuration'
-                }
-            }}
-        ]
     }
+},
+
+module_type_configuration = {
+    'type': 'object',
+    'default': {},
+    'allOf': [
+        {'properties': {
+            'verbose': {
+                'type': 'boolean',
+                'default': False
+            },
+            'hash_length': {
+                'type': 'integer',
+                'minimum': 0,
+                'default': 7
+            },
+            'whitelist': array_of_strings,
+            'blacklist': array_of_strings,
+            'blacklist_implicits': {
+                'type': 'boolean',
+                'default': False
+            },
+            'naming_scheme': {
+                'type': 'string'  # Can we be more specific here?
+            },
+            'all': module_file_configuration,
+        }
+        },
+        {'validate_spec': True,
+         'patternProperties': {
+             spec_regex: module_file_configuration,
+             anonymous_spec_regex: module_file_configuration,
+         }
+         }
+    ]
 }
 
 
@@ -127,8 +127,9 @@
                 'type': 'object',
                 'patternProperties': {
                     # prefix-relative path to be inspected for existence
-                    r'\w[\w-]*': {
+                    r'\w[\w-]*': array_of_strings
-                        '$ref': '#/definitions/array_of_strings'}}},
+                }
+            },
             'enable': {
                 'type': 'array',
                 'default': [],
@@ -138,28 +139,27 @@
             'lmod': {
                 'allOf': [
                     # Base configuration
-                    {'$ref': '#/definitions/module_type_configuration'},
+                    module_type_configuration,
                     {
-                        'core_compilers': {
+                        'type': 'object',
-                            '$ref': '#/definitions/array_of_strings'
+                        'properties': {
+                            'core_compilers': array_of_strings,
+                            'hierarchy': array_of_strings
                         },
-                        'hierarchical_scheme': {
-                            '$ref': '#/definitions/array_of_strings'
-                        }
                     }  # Specific lmod extensions
                 ]
             },
             'tcl': {
                 'allOf': [
                     # Base configuration
-                    {'$ref': '#/definitions/module_type_configuration'},
+                    module_type_configuration,
                     {}  # Specific tcl extensions
                 ]
             },
             'dotkit': {
                 'allOf': [
                     # Base configuration
-                    {'$ref': '#/definitions/module_type_configuration'},
+                    module_type_configuration,
                     {}  # Specific dotkit extensions
                 ]
             },
@@ -172,7 +172,6 @@
 schema = {
     '$schema': 'http://json-schema.org/schema#',
     'title': 'Spack module file configuration file schema',
-    'definitions': definitions,
     'type': 'object',
     'additionalProperties': False,
     'properties': properties,

lib/spack/spack/test/schema.py

@@ -0,0 +1,77 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import jsonschema
+import pytest
+
+
+import spack.schema
+
+
+@pytest.fixture()
+def validate_spec_schema():
+    return {
+        'type': 'object',
+        'validate_spec': True,
+        'patternProperties': {
+            r'\w[\w-]*': {
+                'type': 'string'
+            }
+        }
+    }
+
+
+@pytest.fixture()
+def module_suffixes_schema():
+    return {
+        'type': 'object',
+        'properties': {
+            'tcl': {
+                'type': 'object',
+                'patternProperties': {
+                    r'\w[\w-]*': {
+                        'type': 'object',
+                        'properties': {
+                            'suffixes': {
+                                'validate_spec': True,
+                                'patternProperties': {
+                                    r'\w[\w-]*': {
+                                        'type': 'string',
+                                    }
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+        }
+    }
+
+
+@pytest.mark.regression('9857')
+def test_validate_spec(validate_spec_schema):
+    v = spack.schema.Validator(validate_spec_schema)
+    data = {'foo@3.7': 'bar'}
+
+    # Validate good data (the key is a spec)
+    v.validate(data)
+
+    # Check that invalid data throws
+    data['^python@3.7@'] = 'baz'
+    with pytest.raises(jsonschema.ValidationError) as exc_err:
+        v.validate(data)
+
+    assert 'is an invalid spec' in str(exc_err.value)
+
+
+@pytest.mark.regression('9857')
+def test_module_suffixes(module_suffixes_schema):
+    v = spack.schema.Validator(module_suffixes_schema)
+    data = {'tcl': {'all': {'suffixes': {'^python@2.7@': 'py2.7'}}}}
+
+    with pytest.raises(jsonschema.ValidationError) as exc_err:
+        v.validate(data)
+
+    assert 'is an invalid spec' in str(exc_err.value)