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"""Functions to process Schema Salad schemas."""
import copy
import hashlib
from typing import (
IO,
Any,
Dict,
List,
Mapping,
MutableMapping,
MutableSequence,
Optional,
Set,
Tuple,
TypeVar,
Union,
cast,
)
from urllib.parse import urldefrag, urlparse
from pkg_resources import resource_stream
from ruamel import yaml
from ruamel.yaml.comments import CommentedMap, CommentedSeq
from schema_salad.utils import (
CacheType,
ResolveType,
add_dictlist,
aslist,
convert_to_dict,
flatten,
json_dumps,
)
from . import _logger, jsonld_context, ref_resolver, validate
from .avro.schema import Names, SchemaParseException, make_avsc_object
from .exceptions import (
ClassValidationException,
SchemaSaladException,
ValidationException,
)
from .ref_resolver import Loader
from .sourceline import SourceLine, add_lc_filename, relname
SALAD_FILES = (
"metaschema.yml",
"metaschema_base.yml",
"salad.md",
"field_name.yml",
"import_include.md",
"link_res.yml",
"ident_res.yml",
"vocab_res.yml",
"vocab_res.yml",
"field_name_schema.yml",
"field_name_src.yml",
"field_name_proc.yml",
"ident_res_schema.yml",
"ident_res_src.yml",
"ident_res_proc.yml",
"link_res_schema.yml",
"link_res_src.yml",
"link_res_proc.yml",
"vocab_res_schema.yml",
"vocab_res_src.yml",
"vocab_res_proc.yml",
"map_res.yml",
"map_res_schema.yml",
"map_res_src.yml",
"map_res_proc.yml",
"typedsl_res.yml",
"typedsl_res_schema.yml",
"typedsl_res_src.yml",
"typedsl_res_proc.yml",
"sfdsl_res.yml",
"sfdsl_res_schema.yml",
"sfdsl_res_src.yml",
"sfdsl_res_proc.yml",
)
saladp = "https://w3id.org/cwl/salad#"
def get_metaschema() -> Tuple[Names, List[Dict[str, str]], Loader]:
"""Instantiate the metaschema."""
loader = ref_resolver.Loader(
{
"Any": saladp + "Any",
"ArraySchema": saladp + "ArraySchema",
"Array_symbol": saladp + "ArraySchema/type/Array_symbol",
"DocType": saladp + "DocType",
"Documentation": saladp + "Documentation",
"Documentation_symbol": saladp + "Documentation/type/Documentation_symbol",
"Documented": saladp + "Documented",
"EnumSchema": saladp + "EnumSchema",
"Enum_symbol": saladp + "EnumSchema/type/Enum_symbol",
"JsonldPredicate": saladp + "JsonldPredicate",
"NamedType": saladp + "NamedType",
"PrimitiveType": saladp + "PrimitiveType",
"RecordField": saladp + "RecordField",
"RecordSchema": saladp + "RecordSchema",
"Record_symbol": saladp + "RecordSchema/type/Record_symbol",
"SaladEnumSchema": saladp + "SaladEnumSchema",
"SaladRecordField": saladp + "SaladRecordField",
"SaladRecordSchema": saladp + "SaladRecordSchema",
"SchemaDefinedType": saladp + "SchemaDefinedType",
"SpecializeDef": saladp + "SpecializeDef",
"_container": saladp + "JsonldPredicate/_container",
"_id": {"@id": saladp + "_id", "@type": "@id", "identity": True},
"_type": saladp + "JsonldPredicate/_type",
"abstract": saladp + "SaladRecordSchema/abstract",
"array": saladp + "array",
"boolean": "http://www.w3.org/2001/XMLSchema#boolean",
"dct": "http://purl.org/dc/terms/",
"default": {"@id": saladp + "default", "noLinkCheck": True},
"doc": "rdfs:comment",
"docAfter": {"@id": saladp + "docAfter", "@type": "@id"},
"docChild": {"@id": saladp + "docChild", "@type": "@id"},
"docParent": {"@id": saladp + "docParent", "@type": "@id"},
"documentRoot": saladp + "SchemaDefinedType/documentRoot",
"documentation": saladp + "documentation",
"double": "http://www.w3.org/2001/XMLSchema#double",
"enum": saladp + "enum",
"extends": {"@id": saladp + "extends", "@type": "@id", "refScope": 1},
"fields": {
"@id": saladp + "fields",
"mapPredicate": "type",
"mapSubject": "name",
},
"float": "http://www.w3.org/2001/XMLSchema#float",
"identity": saladp + "JsonldPredicate/identity",
"inVocab": saladp + "NamedType/inVocab",
"int": "http://www.w3.org/2001/XMLSchema#int",
"items": {"@id": saladp + "items", "@type": "@vocab", "refScope": 2},
"jsonldPredicate": "sld:jsonldPredicate",
"long": "http://www.w3.org/2001/XMLSchema#long",
"mapPredicate": saladp + "JsonldPredicate/mapPredicate",
"mapSubject": saladp + "JsonldPredicate/mapSubject",
"name": "@id",
"noLinkCheck": saladp + "JsonldPredicate/noLinkCheck",
"null": saladp + "null",
"rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdfs": "http://www.w3.org/2000/01/rdf-schema#",
"record": saladp + "record",
"refScope": saladp + "JsonldPredicate/refScope",
"sld": saladp,
"specialize": {
"@id": saladp + "specialize",
"mapPredicate": "specializeTo",
"mapSubject": "specializeFrom",
},
"specializeFrom": {
"@id": saladp + "specializeFrom",
"@type": "@id",
"refScope": 1,
},
"specializeTo": {
"@id": saladp + "specializeTo",
"@type": "@id",
"refScope": 1,
},
"string": "http://www.w3.org/2001/XMLSchema#string",
"subscope": saladp + "JsonldPredicate/subscope",
"symbols": {"@id": saladp + "symbols", "@type": "@id", "identity": True},
"type": {
"@id": saladp + "type",
"@type": "@vocab",
"refScope": 2,
"typeDSL": True,
},
"typeDSL": saladp + "JsonldPredicate/typeDSL",
"xsd": "http://www.w3.org/2001/XMLSchema#",
}
)
for salad in SALAD_FILES:
with resource_stream("schema_salad", "metaschema/" + salad) as stream:
loader.cache["https://w3id.org/cwl/" + salad] = stream.read().decode(
"UTF-8"
)
with resource_stream("schema_salad", "metaschema/metaschema.yml") as stream:
loader.cache["https://w3id.org/cwl/salad"] = stream.read().decode("UTF-8")
j = yaml.main.round_trip_load(loader.cache["https://w3id.org/cwl/salad"])
add_lc_filename(j, "metaschema.yml")
j2 = loader.resolve_all(j, saladp)[0]
if not isinstance(j2, list):
_logger.error("%s", j2)
raise SchemaParseException(f"Not a list: {j2}")
else:
sch_obj = make_avro(j2, loader)
try:
sch_names = make_avro_schema_from_avro(sch_obj)
except SchemaParseException:
_logger.error("Metaschema error, avro was:\n%s", json_dumps(sch_obj, indent=4))
raise
validate_doc(sch_names, j2, loader, strict=True)
return (sch_names, j2, loader)
def add_namespaces(
metadata: Mapping[str, Any], namespaces: MutableMapping[str, str]
) -> None:
"""Collect the provided namespaces, checking for conflicts."""
for key, value in metadata.items():
if key not in namespaces:
namespaces[key] = value
elif namespaces[key] != value:
raise ValidationException(
"Namespace prefix '{}' has conflicting definitions '{}'"
" and '{}'.".format(key, namespaces[key], value)
)
def collect_namespaces(metadata: Mapping[str, Any]) -> Dict[str, str]:
"""Walk through the metadata object, collecting namespace declarations."""
namespaces = {} # type: Dict[str, str]
if "$import_metadata" in metadata:
for value in metadata["$import_metadata"].values():
add_namespaces(collect_namespaces(value), namespaces)
if "$namespaces" in metadata:
add_namespaces(metadata["$namespaces"], namespaces)
return namespaces
schema_type = Tuple[Loader, Union[Names, SchemaParseException], Dict[str, Any], Loader]
def load_schema(
schema_ref: ResolveType,
cache: Optional[CacheType] = None,
) -> schema_type:
"""
Load a schema that can be used to validate documents using load_and_validate.
return: document_loader, avsc_names, schema_metadata, metaschema_loader
"""
metaschema_names, _metaschema_doc, metaschema_loader = get_metaschema()
if cache is not None:
metaschema_loader.cache.update(cache)
schema_doc, schema_metadata = metaschema_loader.resolve_ref(schema_ref, "")
if not isinstance(schema_doc, MutableSequence):
raise ValidationException("Schema reference must resolve to a list.")
validate_doc(metaschema_names, schema_doc, metaschema_loader, True)
metactx = schema_metadata.get("@context", {})
metactx.update(collect_namespaces(schema_metadata))
schema_ctx = jsonld_context.salad_to_jsonld_context(schema_doc, metactx)[0]
# Create the loader that will be used to load the target document.
document_loader = Loader(schema_ctx, cache=cache)
# Make the Avro validation that will be used to validate the target
# document
avsc_names = make_avro_schema(schema_doc, document_loader)
return document_loader, avsc_names, schema_metadata, metaschema_loader
def load_and_validate(
document_loader: Loader,
avsc_names: Names,
document: Union[CommentedMap, str],
strict: bool,
strict_foreign_properties: bool = False,
) -> Tuple[Any, Dict[str, Any]]:
"""Load a document and validate it with the provided schema.
return data, metadata
"""
try:
if isinstance(document, CommentedMap):
data, metadata = document_loader.resolve_all(
document,
document["id"],
checklinks=True,
strict_foreign_properties=strict_foreign_properties,
)
else:
data, metadata = document_loader.resolve_ref(
document,
checklinks=True,
strict_foreign_properties=strict_foreign_properties,
)
validate_doc(
avsc_names,
data,
document_loader,
strict,
strict_foreign_properties=strict_foreign_properties,
)
except ValidationException as exc:
raise ValidationException("", None, [exc]) from exc
return data, metadata
def validate_doc(
schema_names: Names,
doc: ResolveType,
loader: Loader,
strict: bool,
strict_foreign_properties: bool = False,
) -> None:
"""Validate a document using the provided schema."""
has_root = False
for root in schema_names.names.values():
if (hasattr(root, "get_prop") and root.get_prop("documentRoot")) or (
"documentRoot" in root.props
):
has_root = True
break
if not has_root:
raise ValidationException("No document roots defined in the schema")
if isinstance(doc, MutableSequence):
vdoc = doc
elif isinstance(doc, CommentedMap):
vdoc = CommentedSeq([doc])
vdoc.lc.add_kv_line_col(0, [doc.lc.line, doc.lc.col])
vdoc.lc.filename = doc.lc.filename
else:
raise ValidationException("Document must be dict or list")
roots = []
for root in schema_names.names.values():
if (hasattr(root, "get_prop") and root.get_prop("documentRoot")) or (
root.props.get("documentRoot")
):
roots.append(root)
anyerrors = []
for pos, item in enumerate(vdoc):
sourceline = SourceLine(vdoc, pos, str)
success = False
for root in roots:
success = validate.validate_ex(
root,
item,
loader.identifiers,
strict,
foreign_properties=loader.foreign_properties,
raise_ex=False,
skip_foreign_properties=loader.skip_schemas,
strict_foreign_properties=strict_foreign_properties,
)
if success:
break
if not success:
errors = [] # type: List[SchemaSaladException]
for root in roots:
if hasattr(root, "get_prop"):
name = root.get_prop("name")
elif hasattr(root, "name"):
name = root.name
try:
validate.validate_ex(
root,
item,
loader.identifiers,
strict,
foreign_properties=loader.foreign_properties,
raise_ex=True,
skip_foreign_properties=loader.skip_schemas,
strict_foreign_properties=strict_foreign_properties,
)
except ClassValidationException as exc1:
errors = [
ClassValidationException(
f"tried `{name}` but", sourceline, [exc1]
)
]
break
except ValidationException as exc2:
errors.append(
ValidationException(f"tried `{name}` but", sourceline, [exc2])
)
objerr = "Invalid"
for ident in loader.identifiers:
if ident in item:
objerr = "Object `{}` is not valid because".format(
relname(item[ident])
)
break
anyerrors.append(ValidationException(objerr, sourceline, errors, "-"))
if anyerrors:
raise ValidationException("", None, anyerrors, "*")
def get_anon_name(
rec: MutableMapping[str, Union[str, Dict[str, str], List[str]]]
) -> str:
"""Calculate a reproducible name for anonymous types."""
if "name" in rec:
name = rec["name"]
if isinstance(name, str):
return name
raise ValidationException(f"Expected name field to be a string, was {name}")
anon_name = ""
if rec["type"] in ("enum", saladp + "enum"):
for sym in rec["symbols"]:
anon_name += sym
return "enum_" + hashlib.sha1(anon_name.encode("UTF-8")).hexdigest()
if rec["type"] in ("record", saladp + "record"):
for field in rec["fields"]:
if isinstance(field, Mapping):
anon_name += field["name"]
else:
raise ValidationException(
"Expected entries in 'fields' to also be maps, was {}.".format(
field
)
)
return "record_" + hashlib.sha1(anon_name.encode("UTF-8")).hexdigest()
if rec["type"] in ("array", saladp + "array"):
return ""
raise ValidationException("Expected enum or record, was {}".format(rec["type"]))
def replace_type(
items: Any,
spec: Dict[str, Any],
loader: Loader,
found: Set[str],
find_embeds: bool = True,
deepen: bool = True,
) -> Any:
""" Go through and replace types in the 'spec' mapping"""
if isinstance(items, MutableMapping):
# recursively check these fields for types to replace
if items.get("type") in ("record", "enum") and items.get("name"):
if items["name"] in found:
return items["name"]
found.add(items["name"])
if not deepen:
return items
items = copy.copy(items)
if not items.get("name"):
items["name"] = get_anon_name(items)
for name in ("type", "items", "fields"):
if name in items:
items[name] = replace_type(
items[name],
spec,
loader,
found,
find_embeds=find_embeds,
deepen=find_embeds,
)
if isinstance(items[name], MutableSequence):
items[name] = flatten(items[name])
return items
if isinstance(items, MutableSequence):
# recursively transform list
return [
replace_type(i, spec, loader, found, find_embeds=find_embeds, deepen=deepen)
for i in items
]
if isinstance(items, str):
# found a string which is a symbol corresponding to a type.
replace_with = None
if items in loader.vocab:
# If it's a vocabulary term, first expand it to its fully qualified
# URI
items = loader.vocab[items]
if items in spec:
# Look up in specialization map
replace_with = spec[items]
if replace_with:
return replace_type(
replace_with, spec, loader, found, find_embeds=find_embeds
)
found.add(items)
return items
def avro_name(url: str) -> str:
"""
Turn a URL into an Avro-safe name.
If the URL has no fragment, return this plain URL.
Extract either the last part of the URL fragment past the slash, otherwise
the whole fragment.
"""
frg = urldefrag(url)[1]
if frg != "":
if "/" in frg:
return frg[frg.rindex("/") + 1 :]
return frg
return url
Avro = TypeVar("Avro", MutableMapping[str, Any], MutableSequence[Any], str)
def make_valid_avro(
items: Avro,
alltypes: Dict[str, Dict[str, Any]],
found: Set[str],
union: bool = False,
) -> Union[
Avro, MutableMapping[str, str], str, List[Union[Any, MutableMapping[str, str], str]]
]:
"""Convert our schema to be more avro like."""
# Possibly could be integrated into our fork of avro/schema.py?
if isinstance(items, MutableMapping):
avro = copy.copy(items)
if avro.get("name") and avro.get("inVocab", True):
avro["name"] = avro_name(avro["name"])
if "type" in avro and avro["type"] in (
saladp + "record",
saladp + "enum",
"record",
"enum",
):
if (hasattr(avro, "get") and avro.get("abstract")) or ("abstract" in avro):
return avro
if avro["name"] in found:
return cast(str, avro["name"])
found.add(avro["name"])
for field in ("type", "items", "values", "fields"):
if field in avro:
avro[field] = make_valid_avro(avro[field], alltypes, found, union=True)
if "symbols" in avro:
avro["symbols"] = [avro_name(sym) for sym in avro["symbols"]]
return avro
if isinstance(items, MutableSequence):
ret = []
for i in items:
ret.append(make_valid_avro(i, alltypes, found, union=union))
return ret
if union and isinstance(items, str):
if items in alltypes and avro_name(items) not in found:
return make_valid_avro(alltypes[items], alltypes, found, union=union)
return avro_name(items)
else:
return items
def deepcopy_strip(item: Any) -> Any:
"""
Make a deep copy of list and dict objects.
Intentionally do not copy attributes. This is to discard CommentedMap and
CommentedSeq metadata which is very expensive with regular copy.deepcopy.
"""
if isinstance(item, MutableMapping):
return {k: deepcopy_strip(v) for k, v in item.items()}
if isinstance(item, MutableSequence):
return [deepcopy_strip(k) for k in item]
return item
def extend_and_specialize(
items: List[Dict[str, Any]], loader: Loader
) -> List[Dict[str, Any]]:
"""
Apply 'extend' and 'specialize' to fully materialize derived record types.
"""
items2 = deepcopy_strip(items)
types = {i["name"]: i for i in items2} # type: Dict[str, Any]
results = []
for stype in items2:
if "extends" in stype:
specs = {} # type: Dict[str, str]
if "specialize" in stype:
for spec in aslist(stype["specialize"]):
specs[spec["specializeFrom"]] = spec["specializeTo"]
exfields = [] # type: List[str]
exsym = [] # type: List[str]
for ex in aslist(stype["extends"]):
if ex not in types:
raise ValidationException(
"Extends {} in {} refers to invalid base type.".format(
stype["extends"], stype["name"]
)
)
basetype = copy.copy(types[ex])
if stype["type"] == "record":
if specs:
basetype["fields"] = replace_type(
basetype.get("fields", []), specs, loader, set()
)
for field in basetype.get("fields", []):
if "inherited_from" not in field:
field["inherited_from"] = ex
exfields.extend(basetype.get("fields", []))
elif stype["type"] == "enum":
exsym.extend(basetype.get("symbols", []))
if stype["type"] == "record":
stype = copy.copy(stype)
exfields.extend(stype.get("fields", []))
stype["fields"] = exfields
fieldnames = set() # type: Set[str]
for field in stype["fields"]:
if field["name"] in fieldnames:
raise ValidationException(
"Field name {} appears twice in {}".format(
field["name"], stype["name"]
)
)
else:
fieldnames.add(field["name"])
elif stype["type"] == "enum":
stype = copy.copy(stype)
exsym.extend(stype.get("symbols", []))
stype["symbol"] = exsym
types[stype["name"]] = stype
results.append(stype)
ex_types = {}
for result in results:
ex_types[result["name"]] = result
extended_by = {} # type: Dict[str, str]
for result in results:
if "extends" in result:
for ex in aslist(result["extends"]):
if ex_types[ex].get("abstract"):
add_dictlist(extended_by, ex, ex_types[result["name"]])
add_dictlist(extended_by, avro_name(ex), ex_types[ex])
for result in results:
if result.get("abstract") and result["name"] not in extended_by:
raise ValidationException(
"{} is abstract but missing a concrete subtype".format(result["name"])
)
for result in results:
if "fields" in result:
result["fields"] = replace_type(
result["fields"], extended_by, loader, set()
)
return results
def make_avro(
i: List[Dict[str, Any]],
loader: Loader,
) -> List[Any]:
j = extend_and_specialize(i, loader)
name_dict = {} # type: Dict[str, Dict[str, Any]]
for entry in j:
name_dict[entry["name"]] = entry
avro = make_valid_avro(j, name_dict, set())
return [
t
for t in avro
if isinstance(t, MutableMapping)
and not t.get("abstract")
and t.get("type") != "documentation"
]
def make_avro_schema(
i: List[Any],
loader: Loader,
) -> Names:
"""
All in one convenience function.
Call make_avro() and make_avro_schema_from_avro() separately if you need
the intermediate result for diagnostic output.
"""
names = Names()
avro = make_avro(i, loader)
make_avsc_object(convert_to_dict(avro), names)
return names
def make_avro_schema_from_avro(avro: List[Union[Avro, Dict[str, str], str]]) -> Names:
names = Names()
make_avsc_object(convert_to_dict(avro), names)
return names
def shortname(inputid: str) -> str:
"""Returns the last segment of the provided fragment or path."""
parsed_id = urlparse(inputid)
if parsed_id.fragment:
return parsed_id.fragment.split("/")[-1]
return parsed_id.path.split("/")[-1]
def print_inheritance(doc: List[Dict[str, Any]], stream: IO[Any]) -> None:
"""Write a Grapviz inheritance graph for the supplied document."""
stream.write("digraph {\n")
for entry in doc:
if entry["type"] == "record":
label = name = shortname(entry["name"])
fields = entry.get("fields", [])
if fields:
label += "\\n* {}\\l".format(
"\\l* ".join(shortname(field["name"]) for field in fields)
)
shape = "ellipse" if entry.get("abstract") else "box"
stream.write(f'"{name}" [shape={shape} label="{label}"];\n')
if "extends" in entry:
for target in aslist(entry["extends"]):
stream.write('"{}" -> "{}";\n'.format(shortname(target), name))
stream.write("}\n")
def print_fieldrefs(doc: List[Dict[str, Any]], loader: Loader, stream: IO[Any]) -> None:
"""Write a GraphViz graph of the relationships between the fields."""
obj = extend_and_specialize(doc, loader)
primitives = {
"http://www.w3.org/2001/XMLSchema#string",
"http://www.w3.org/2001/XMLSchema#boolean",
"http://www.w3.org/2001/XMLSchema#int",
"http://www.w3.org/2001/XMLSchema#long",
saladp + "null",
saladp + "enum",
saladp + "array",
saladp + "record",
saladp + "Any",
}
stream.write("digraph {\n")
for entry in obj:
if entry.get("abstract"):
continue
if entry["type"] == "record":
label = shortname(entry["name"])
for field in entry.get("fields", []):
found = set() # type: Set[str]
field_name = shortname(field["name"])
replace_type(field["type"], {}, loader, found, find_embeds=False)
for each_type in found:
if each_type not in primitives:
stream.write(
'"{}" -> "{}" [label="{}"];\n'.format(
label, shortname(each_type), field_name
)
)
stream.write("}\n")
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