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import avro
import copy
from .add_dictlist import add_dictlist
import sys
import pprint
from pkg_resources import resource_stream
import ruamel.yaml as yaml
import avro.schema
from . import validate
import json
import urlparse
import os
AvroSchemaFromJSONData = avro.schema.make_avsc_object
# AvroSchemaFromJSONData=avro.schema.SchemaFromJSONData
from avro.schema import Names, SchemaParseException
from . import ref_resolver
from .ref_resolver import Loader, DocumentType
from .flatten import flatten
import logging
from .aslist import aslist
from . import jsonld_context
from .sourceline import SourceLine, strip_dup_lineno, add_lc_filename, bullets, relname
from typing import Any, AnyStr, cast, Dict, List, Tuple, TypeVar, Union
from ruamel.yaml.comments import CommentedSeq, CommentedMap
_logger = logging.getLogger("salad")
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')
def get_metaschema():
# type: () -> Tuple[Names, List[Dict[unicode, Any]], Loader]
loader = ref_resolver.Loader({
"Any": "https://w3id.org/cwl/salad#Any",
"ArraySchema": "https://w3id.org/cwl/salad#ArraySchema",
"DocType": "https://w3id.org/cwl/salad#DocType",
"Documentation": "https://w3id.org/cwl/salad#Documentation",
"EnumSchema": "https://w3id.org/cwl/salad#EnumSchema",
"JsonldPredicate": "https://w3id.org/cwl/salad#JsonldPredicate",
"NamedType": "https://w3id.org/cwl/salad#NamedType",
"RecordField": "https://w3id.org/cwl/salad#RecordField",
"RecordSchema": "https://w3id.org/cwl/salad#RecordSchema",
"SaladEnumSchema": "https://w3id.org/cwl/salad#SaladEnumSchema",
"SaladRecordField": "https://w3id.org/cwl/salad#SaladRecordField",
"SaladRecordSchema": "https://w3id.org/cwl/salad#SaladRecordSchema",
"SchemaDefinedType": "https://w3id.org/cwl/salad#SchemaDefinedType",
"SpecializeDef": "https://w3id.org/cwl/salad#SpecializeDef",
"_container": "https://w3id.org/cwl/salad#JsonldPredicate/_container",
"_id": {
"@id": "https://w3id.org/cwl/salad#_id",
"@type": "@id",
"identity": True
},
"_type": "https://w3id.org/cwl/salad#JsonldPredicate/_type",
"abstract": "https://w3id.org/cwl/salad#SaladRecordSchema/abstract",
"array": "https://w3id.org/cwl/salad#array",
"boolean": "http://www.w3.org/2001/XMLSchema#boolean",
"dct": "http://purl.org/dc/terms/",
"doc": "sld:doc",
"docAfter": {
"@id": "https://w3id.org/cwl/salad#docAfter",
"@type": "@id"
},
"docChild": {
"@id": "https://w3id.org/cwl/salad#docChild",
"@type": "@id"
},
"docParent": {
"@id": "https://w3id.org/cwl/salad#docParent",
"@type": "@id"
},
"documentRoot": "https://w3id.org/cwl/salad#SchemaDefinedType/documentRoot",
"documentation": "https://w3id.org/cwl/salad#documentation",
"double": "http://www.w3.org/2001/XMLSchema#double",
"enum": "https://w3id.org/cwl/salad#enum",
"extends": {
"@id": "https://w3id.org/cwl/salad#extends",
"@type": "@id",
"refScope": 1
},
"fields": {
"@id": "https://w3id.org/cwl/salad#fields",
"mapPredicate": "type",
"mapSubject": "name"
},
"float": "http://www.w3.org/2001/XMLSchema#float",
"identity": "https://w3id.org/cwl/salad#JsonldPredicate/identity",
"int": "http://www.w3.org/2001/XMLSchema#int",
"items": {
"@id": "https://w3id.org/cwl/salad#items",
"@type": "@vocab",
"refScope": 2
},
"jsonldPredicate": "sld:jsonldPredicate",
"long": "http://www.w3.org/2001/XMLSchema#long",
"mapPredicate": "https://w3id.org/cwl/salad#JsonldPredicate/mapPredicate",
"mapSubject": "https://w3id.org/cwl/salad#JsonldPredicate/mapSubject",
"name": "@id",
"noLinkCheck": "https://w3id.org/cwl/salad#JsonldPredicate/noLinkCheck",
"null": "https://w3id.org/cwl/salad#null",
"rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdfs": "http://www.w3.org/2000/01/rdf-schema#",
"record": "https://w3id.org/cwl/salad#record",
"refScope": "https://w3id.org/cwl/salad#JsonldPredicate/refScope",
"sld": "https://w3id.org/cwl/salad#",
"specialize": {
"@id": "https://w3id.org/cwl/salad#specialize",
"mapPredicate": "specializeTo",
"mapSubject": "specializeFrom"
},
"specializeFrom": {
"@id": "https://w3id.org/cwl/salad#specializeFrom",
"@type": "@id",
"refScope": 1
},
"specializeTo": {
"@id": "https://w3id.org/cwl/salad#specializeTo",
"@type": "@id",
"refScope": 1
},
"string": "http://www.w3.org/2001/XMLSchema#string",
"symbols": {
"@id": "https://w3id.org/cwl/salad#symbols",
"@type": "@id",
"identity": True
},
"type": {
"@id": "https://w3id.org/cwl/salad#type",
"@type": "@vocab",
"refScope": 2,
"typeDSL": True
},
"typeDSL": "https://w3id.org/cwl/salad#JsonldPredicate/typeDSL",
"xsd": "http://www.w3.org/2001/XMLSchema#"
})
for f in salad_files:
rs = resource_stream(__name__, 'metaschema/' + f)
loader.cache["https://w3id.org/cwl/" + f] = rs.read()
rs.close()
rs = resource_stream(__name__, 'metaschema/metaschema.yml')
loader.cache["https://w3id.org/cwl/salad"] = rs.read()
rs.close()
j = yaml.round_trip_load(loader.cache["https://w3id.org/cwl/salad"]) # type: ignore
add_lc_filename(j, "metaschema.yml")
j, _ = loader.resolve_all(j, "https://w3id.org/cwl/salad#")
# pprint.pprint(j)
(sch_names, sch_obj) = make_avro_schema(j, loader)
if isinstance(sch_names, Exception):
_logger.error("Metaschema error, avro was:\n%s",
json.dumps(sch_obj, indent=4))
raise sch_names
validate_doc(sch_names, j, loader, strict=True)
return (sch_names, j, loader)
def load_schema(schema_ref, # type: Union[CommentedMap, CommentedSeq, unicode]
cache=None # type: Dict
):
# type: (...) -> Tuple[Loader, Union[Names, SchemaParseException], Dict[unicode, Any], Loader]
"""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, list):
raise ValueError("Schema reference must resolve to a list.")
validate_doc(metaschema_names, schema_doc, metaschema_loader, True)
metactx = schema_metadata.get("@context", {})
metactx.update(schema_metadata.get("$namespaces", {}))
(schema_ctx, rdfs) = jsonld_context.salad_to_jsonld_context(
schema_doc, metactx)
# 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, avsc_obj) = make_avro_schema(schema_doc, document_loader)
return document_loader, avsc_names, schema_metadata, metaschema_loader
def load_and_validate(document_loader, # type: Loader
avsc_names, # type: Names
document, # type: Union[CommentedMap, unicode]
strict # type: bool
):
# type: (...) -> Tuple[Any, Dict[unicode, Any]]
"""Load a document and validate it with the provided schema.
return data, metadata
"""
try:
if isinstance(document, CommentedMap):
source = document["id"]
data, metadata = document_loader.resolve_all(
document, document["id"], checklinks=False)
else:
source = document
data, metadata = document_loader.resolve_ref(
document, checklinks=False)
except validate.ValidationException as v:
raise validate.ValidationException(strip_dup_lineno(str(v)))
validationErrors = u""
try:
document_loader.validate_links(data, u"")
except validate.ValidationException as v:
validationErrors = unicode(v) + "\n"
try:
validate_doc(avsc_names, data, document_loader, strict, source=source)
except validate.ValidationException as v:
validationErrors += unicode(v)
if validationErrors:
raise validate.ValidationException(validationErrors)
return data, metadata
def validate_doc(schema_names, # type: Names
doc, # type: Union[Dict[unicode, Any], List[Dict[unicode, Any]], unicode]
loader, # type: Loader
strict, # type: bool
source=None
):
# type: (...) -> None
has_root = False
for r in schema_names.names.values():
if ((hasattr(r, 'get_prop') and r.get_prop(u"documentRoot")) or (
u"documentRoot" in r.props)):
has_root = True
break
if not has_root:
raise validate.ValidationException(
"No document roots defined in the schema")
if isinstance(doc, list):
validate_doc = doc
elif isinstance(doc, CommentedMap):
validate_doc = CommentedSeq([doc])
validate_doc.lc.add_kv_line_col(0, [doc.lc.line, doc.lc.col])
validate_doc.lc.filename = doc.lc.filename
else:
raise validate.ValidationException("Document must be dict or list")
roots = []
for r in schema_names.names.values():
if ((hasattr(r, "get_prop") and r.get_prop(u"documentRoot")) or (
r.props.get(u"documentRoot"))):
roots.append(r)
anyerrors = []
for pos, item in enumerate(validate_doc):
sl = SourceLine(validate_doc, pos, unicode)
success = False
for r in roots:
success = validate.validate_ex(
r, item, loader.identifiers, strict,
foreign_properties=loader.foreign_properties, raise_ex=False)
if success:
break
if not success:
errors = [] # type: List[unicode]
for r in roots:
if hasattr(r, "get_prop"):
name = r.get_prop(u"name")
elif hasattr(r, "name"):
name = r.name
try:
validate.validate_ex(
r, item, loader.identifiers, strict,
foreign_properties=loader.foreign_properties,
raise_ex=True)
except validate.ClassValidationException as e:
errors = [sl.makeError(u"tried `%s` but\n%s" % (
name, validate.indent(str(e), nolead=False)))]
break
except validate.ValidationException as e:
errors.append(sl.makeError(u"tried `%s` but\n%s" % (
name, validate.indent(str(e), nolead=False))))
objerr = sl.makeError(u"Invalid")
for ident in loader.identifiers:
if ident in item:
objerr = sl.makeError(
u"Object `%s` is not valid because"
% (relname(item[ident])))
break
anyerrors.append(u"%s\n%s" %
(objerr, validate.indent(bullets(errors, "- "))))
if anyerrors:
raise validate.ValidationException(
strip_dup_lineno(bullets(anyerrors, "* ")))
def replace_type(items, spec, loader, found):
# type: (Any, Dict[unicode, Any], Loader, Set[unicode]) -> Any
""" Go through and replace types in the 'spec' mapping"""
items = copy.deepcopy(items)
if isinstance(items, dict):
# recursively check these fields for types to replace
if "type" in items and items["type"] in ("record", "enum"):
if items.get("name"):
if items["name"] in found:
return items["name"]
else:
found.add(items["name"])
for n in ("type", "items", "fields"):
if n in items:
items[n] = replace_type(items[n], spec, loader, found)
if isinstance(items[n], list):
items[n] = flatten(items[n])
return items
elif isinstance(items, list):
# recursively transform list
return [replace_type(i, spec, loader, found) for i in items]
elif isinstance(items, (str, unicode)):
# 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)
return items
def avro_name(url): # type: (AnyStr) -> AnyStr
doc_url, frg = urlparse.urldefrag(url)
if frg:
if '/' in frg:
return frg[frg.rindex('/') + 1:]
else:
return frg
return url
Avro = TypeVar('Avro', Dict[unicode, Any], List[Any], unicode)
def make_valid_avro(items, # type: Avro
alltypes, # type: Dict[unicode, Dict[unicode, Any]]
found, # type: Set[unicode]
union=False # type: bool
):
# type: (...) -> Union[Avro, Dict]
items = copy.deepcopy(items)
if isinstance(items, dict):
if items.get("name"):
items["name"] = avro_name(items["name"])
if "type" in items and items["type"] in ("https://w3id.org/cwl/salad#record", "https://w3id.org/cwl/salad#enum", "record", "enum"):
if (hasattr(items, "get") and items.get("abstract")) or ("abstract"
in items):
return items
if not items.get("name"):
raise Exception(
"Named schemas must have a non-empty name: %s" % items)
if items["name"] in found:
return items["name"]
else:
found.add(items["name"])
for n in ("type", "items", "values", "fields"):
if n in items:
items[n] = make_valid_avro(
items[n], alltypes, found, union=True)
if "symbols" in items:
items["symbols"] = [avro_name(sym) for sym in items["symbols"]]
return items
if isinstance(items, list):
ret = []
for i in items:
ret.append(make_valid_avro(i, alltypes, found, union=union))
return ret
if union and isinstance(items, (str, unicode)):
if items in alltypes and avro_name(items) not in found:
return cast(Dict, make_valid_avro(alltypes[items], alltypes, found,
union=union))
items = avro_name(items)
return items
def extend_and_specialize(items, loader):
# type: (List[Dict[unicode, Any]], Loader) -> List[Dict[unicode, Any]]
"""Apply 'extend' and 'specialize' to fully materialize derived record
types."""
types = {} # type: Dict[unicode, Any]
for t in items:
types[t["name"]] = t
n = []
for t in items:
t = copy.deepcopy(t)
if "extends" in t:
spec = {} # type: Dict[unicode, unicode]
if "specialize" in t:
for sp in aslist(t["specialize"]):
spec[sp["specializeFrom"]] = sp["specializeTo"]
exfields = [] # type: List[unicode]
exsym = [] # type: List[unicode]
for ex in aslist(t["extends"]):
if ex not in types:
raise Exception("Extends %s in %s refers to invalid base type" % (
t["extends"], t["name"]))
basetype = copy.deepcopy(types[ex])
if t["type"] == "record":
if spec:
basetype["fields"] = replace_type(
basetype.get("fields", []), spec, loader, set())
for f in basetype.get("fields", []):
if "inherited_from" not in f:
f["inherited_from"] = ex
exfields.extend(basetype.get("fields", []))
elif t["type"] == "enum":
exsym.extend(basetype.get("symbols", []))
if t["type"] == "record":
exfields.extend(t.get("fields", []))
t["fields"] = exfields
fieldnames = set() # type: Set[unicode]
for field in t["fields"]:
if field["name"] in fieldnames:
raise validate.ValidationException(
"Field name %s appears twice in %s" % (field["name"], t["name"]))
else:
fieldnames.add(field["name"])
elif t["type"] == "enum":
exsym.extend(t.get("symbols", []))
t["symbol"] = exsym
types[t["name"]] = t
n.append(t)
ex_types = {}
for t in n:
ex_types[t["name"]] = t
extended_by = {} # type: Dict[unicode, unicode]
for t in n:
if "extends" in t:
for ex in aslist(t["extends"]):
if ex_types[ex].get("abstract"):
add_dictlist(extended_by, ex, ex_types[t["name"]])
add_dictlist(extended_by, avro_name(ex), ex_types[ex])
for t in n:
if t.get("abstract") and t["name"] not in extended_by:
raise validate.ValidationException(
"%s is abstract but missing a concrete subtype" % t["name"])
for t in n:
if "fields" in t:
t["fields"] = replace_type(t["fields"], extended_by, loader, set())
return n
def make_avro_schema(i, # type: List[Dict[unicode, Any]]
loader # type: Loader
):
# type: (...) -> Tuple[Union[Names, SchemaParseException], List[Dict[unicode, Any]]]
names = avro.schema.Names()
j = extend_and_specialize(i, loader)
name_dict = {} # type: Dict[unicode, Dict[unicode, Any]]
for t in j:
name_dict[t["name"]] = t
j2 = make_valid_avro(j, name_dict, set())
j3 = [t for t in j2 if isinstance(t, dict) and not t.get(
"abstract") and t.get("type") != "documentation"]
try:
AvroSchemaFromJSONData(j3, names)
except avro.schema.SchemaParseException as e:
return (e, j3)
return (names, j3)
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