def test_rdf_datetime() -> None:
"""Affirm that datetime objects can be serialized in makerdf()."""
ldr = Loader({})
ctx: ContextType = {
"id": "@id",
"location": {"@id": "@id", "@type": "@id"},
"bar": "http://example.com/bar",
"ex": "http://example.com/",
}
ldr.add_context(ctx)
ra: CommentedMap = cast(
CommentedMap,
ldr.resolve_all(
cmap(
{
"id": "foo",
"bar": {"id": "baz"},
}
),
"http://example.com",
)[0],
)
ra["s:dateCreated"] = datetime.datetime(2020, 10, 8)
g = makerdf(None, ra, ctx)
g.serialize(destination=stdout(), format="n3")
g2 = makerdf(None, CommentedSeq([ra]), ctx)
g2.serialize(destination=stdout(), format="n3")
def test_scoped_id() -> None:
ldr = Loader({})
ctx = {
"id": "@id",
"location": {"@id": "@id", "@type": "@id"},
"bar": "http://example.com/bar",
"ex": "http://example.com/",
} # type: ContextType
ldr.add_context(ctx)
ra, _ = ldr.resolve_all(
cmap({"id": "foo", "bar": {"id": "baz"}}), "http://example.com"
)
assert {
"id": "http://example.com/#foo",
"bar": {"id": "http://example.com/#foo/baz"},
} == ra
g = makerdf(None, ra, ctx)
print(g.serialize(format="n3"))
ra, _ = ldr.resolve_all(
cmap({"location": "foo", "bar": {"location": "baz"}}),
"http://example.com",
checklinks=False,
)
assert {
"location": "http://example.com/foo",
"bar": {"location": "http://example.com/baz"},
} == ra
g = makerdf(None, ra, ctx)
print(g.serialize(format="n3"))
ra, _ = ldr.resolve_all(
cmap({"id": "foo", "bar": {"location": "baz"}}),
"http://example.com",
checklinks=False,
)
assert {
"id": "http://example.com/#foo",
"bar": {"location": "http://example.com/baz"},
} == ra
g = makerdf(None, ra, ctx)
print(g.serialize(format="n3"))
ra, _ = ldr.resolve_all(
cmap({"location": "foo", "bar": {"id": "baz"}}),
"http://example.com",
checklinks=False,
)
assert {
"location": "http://example.com/foo",
"bar": {"id": "http://example.com/#baz"},
} == ra
g = makerdf(None, ra, ctx)
print(g.serialize(format="n3"))
def expand_cwl(cwl, uri, g):
try:
document_loader = Loader(
{"cwl": "https://w3id.org/cwl/cwl#", "id": "@id"})
cwl = yaml.load(cwl)
document_loader, avsc_names, processobj, metadata, uri = validate_document(
document_loader, cwl, uri, strict=False)
jsonld_context.makerdf(uri, processobj, document_loader.ctx, graph=g)
sys.stderr.write("\n%s: imported ok\n" % (uri))
except Exception as e:
sys.stderr.write("\n%s: %s\n" % (uri, e))
def expand_cwl(cwl, uri, g):
try:
document_loader = Loader({
"cwl": "https://w3id.org/cwl/cwl#",
"id": "@id"
})
cwl = yaml.load(cwl)
document_loader, avsc_names, processobj, metadata, uri = validate_document(
document_loader, cwl, uri, strict=False)
jsonld_context.makerdf(uri, processobj, document_loader.ctx, graph=g)
sys.stderr.write("\n%s: imported ok\n" % (uri))
except Exception as e:
sys.stderr.write("\n%s: %s\n" % (uri, e))
def main():
parser = argparse.ArgumentParser()
parser.add_argument("swagger")
parser.add_argument("annotations")
parser.add_argument("url")
parser.add_argument("--dockstore-fixup",
action="store_true",
default=False)
parser.add_argument("--print-rdf", action="store_true", default=False)
parser.add_argument("--serve", action="store_true", default=False)
parser.add_argument("--fuseki-path", type=str, default=".")
args = parser.parse_args()
with open(args.annotations) as f2:
annotations = yaml.load(f2)
with open(args.swagger) as f:
sld = swg2salad.swg2salad(yaml.load(f), annotations)
sld["$base"] = "http://ga4gh.org/schemas/tool-registry-schemas"
sld["name"] = "file://" + os.path.realpath(args.swagger)
document_loader, avsc_names, schema_metadata, metaschema_loader = load_schema(
sld)
txt = document_loader.fetch_text(
urlparse.urljoin("file://" + os.getcwd() + "/", args.url))
r = yaml.load(txt)
if args.dockstore_fixup:
dockstore_fixup(r)
validate_doc(avsc_names, r, document_loader, True)
sys.stderr.write("API returned valid response\n")
toolreg = Namespace("http://ga4gh.org/schemas/tool-registry-schemas#")
td = Namespace(
"http://ga4gh.org/schemas/tool-registry-schemas#ToolDescriptor/")
if args.print_rdf or args.serve:
g = jsonld_context.makerdf(args.url, r, document_loader.ctx)
for s, _, o in g.triples((None, td["type"], Literal("CWL"))):
for _, _, d in g.triples((s, toolreg["descriptor"], None)):
expand_cwl(d, unicode(s), g)
if args.print_rdf:
print(g.serialize(format="turtle"))
if args.serve:
t = tempfile.NamedTemporaryFile(suffix=".ttl")
g.serialize(t, format="turtle")
t.flush()
subprocess.check_call(
["./fuseki-server", "--file=" + t.name, "/tools"],
cwd=args.fuseki_path)
def main():
parser = argparse.ArgumentParser()
parser.add_argument("swagger")
parser.add_argument("annotations")
parser.add_argument("url")
parser.add_argument("--print-rdf", action="store_true", default=False)
parser.add_argument("--serve", action="store_true", default=False)
parser.add_argument("--fuseki-path", type=str, default=".")
args = parser.parse_args()
warnings.simplefilter('ignore', yaml.error.UnsafeLoaderWarning)
with open(args.annotations) as f2:
annotations = yaml.load(f2)
with open(args.swagger) as f:
sld = swg2salad.swg2salad(yaml.load(f), annotations)
sld["$base"] = "http://ga4gh.org/schemas/tool-registry-schemas"
sld["name"] = "file://" + os.path.realpath(args.swagger)
document_loader, avsc_names, schema_metadata, metaschema_loader = load_schema(
cmap(sld))
txt = document_loader.fetch_text(
urlparse.urljoin(
"file://" +
os.getcwd() +
"/",
args.url))
r = yaml.load(txt)
validate_doc(avsc_names, r, document_loader, True)
sys.stderr.write("API returned valid response\n")
toolreg = Namespace("http://ga4gh.org/schemas/tool-registry-schemas#")
td = Namespace(
"http://ga4gh.org/schemas/tool-registry-schemas#ToolDescriptor/")
if args.print_rdf or args.serve:
g = jsonld_context.makerdf(args.url, r, document_loader.ctx)
for s, _, o in g.triples((None, td["type"], Literal("CWL"))):
for _, _, d in g.triples((s, toolreg["descriptor"], None)):
expand_cwl(d, unicode(s), g)
if args.print_rdf:
print(g.serialize(format="turtle"))
if args.serve:
t = tempfile.NamedTemporaryFile(suffix=".ttl")
g.serialize(t, format="turtle")
t.flush()
subprocess.check_call(
["./fuseki-server", "--file=" + t.name, "/tools"], cwd=args.fuseki_path)
def visitor(t):
makerdf(t["id"], t, ctx, graph=g)
def visitor(t):
makerdf(t["id"], t, ctx, graph=g)
def visitor(t: CommentedMap) -> None:
makerdf(t["id"], t, ctx, graph=g)
def test_scoped_id(self):
ldr = schema_salad.ref_resolver.Loader({})
ctx = {
"id": "@id",
"location": {
"@id": "@id",
"@type": "@id"
},
"bar": "http://example.com/bar",
"ex": "http://example.com/"
}
ldr.add_context(ctx)
ra, _ = ldr.resolve_all(cmap({
"id": "foo",
"bar": {
"id": "baz"
}
}), "http://example.com")
self.assertEqual(
{
'id': 'http://example.com/#foo',
'bar': {
'id': 'http://example.com/#foo/baz'
},
}, ra)
g = makerdf(None, ra, ctx)
print(g.serialize(format="n3"))
ra, _ = ldr.resolve_all(cmap({
"location": "foo",
"bar": {
"location": "baz"
}
}),
"http://example.com",
checklinks=False)
self.assertEqual(
{
'location': 'http://example.com/foo',
'bar': {
'location': 'http://example.com/baz'
},
}, ra)
g = makerdf(None, ra, ctx)
print(g.serialize(format="n3"))
ra, _ = ldr.resolve_all(cmap({
"id": "foo",
"bar": {
"location": "baz"
}
}),
"http://example.com",
checklinks=False)
self.assertEqual(
{
'id': 'http://example.com/#foo',
'bar': {
'location': 'http://example.com/baz'
},
}, ra)
g = makerdf(None, ra, ctx)
print(g.serialize(format="n3"))
ra, _ = ldr.resolve_all(cmap({
"location": "foo",
"bar": {
"id": "baz"
}
}),
"http://example.com",
checklinks=False)
self.assertEqual(
{
'location': 'http://example.com/foo',
'bar': {
'id': 'http://example.com/#baz'
},
}, ra)
g = makerdf(None, ra, ctx)
print(g.serialize(format="n3"))
def test_scoped_id(self):
ldr = schema_salad.ref_resolver.Loader({})
ctx = {
"id": "@id",
"location": {
"@id": "@id",
"@type": "@id"
},
"bar": "http://example.com/bar",
"ex": "http://example.com/"
}
ldr.add_context(ctx)
ra, _ = ldr.resolve_all({
"id": "foo",
"bar": {
"id": "baz"
}
}, "http://example.com")
self.assertEqual({'id': 'http://example.com/#foo',
'bar': {
'id': 'http://example.com/#foo/baz'},
}, ra)
g = makerdf(None, ra, ctx)
print(g.serialize(format="n3"))
ra, _ = ldr.resolve_all({
"location": "foo",
"bar": {
"location": "baz"
}
}, "http://example.com", checklinks=False)
self.assertEqual({'location': 'http://example.com/foo',
'bar': {
'location': 'http://example.com/baz'},
}, ra)
g = makerdf(None, ra, ctx)
print(g.serialize(format="n3"))
ra, _ = ldr.resolve_all({
"id": "foo",
"bar": {
"location": "baz"
}
}, "http://example.com", checklinks=False)
self.assertEqual({'id': 'http://example.com/#foo',
'bar': {
'location': 'http://example.com/baz'},
}, ra)
g = makerdf(None, ra, ctx)
print(g.serialize(format="n3"))
ra, _ = ldr.resolve_all({
"location": "foo",
"bar": {
"id": "baz"
}
}, "http://example.com", checklinks=False)
self.assertEqual({'location': 'http://example.com/foo',
'bar': {
'id': 'http://example.com/#baz'},
}, ra)
g = makerdf(None, ra, ctx)
print(g.serialize(format="n3"))
def visitor(t): # type: (CommentedMap) -> None
makerdf(t["id"], t, ctx, graph=g)
def visitor(t): # type: (MutableMapping[str, Any]) -> None
makerdf(t["id"], t, ctx, graph=g)
