def test_idmap() -> None:
doc = {
"type": "record",
"fields": {
"hello": {
"doc": "Hello test case",
"type": "string"
}
},
}
rs = cg_metaschema.RecordSchema.fromDoc(doc, "http://example.com/",
cg_metaschema.LoadingOptions())
assert "record" == rs.type
assert "http://example.com/#hello" == rs.fields[0].name
assert "Hello test case" == rs.fields[0].doc
assert "string" == rs.fields[0].type
assert {
"type":
"record",
"fields": [{
"name": "http://example.com/#hello",
"doc": "Hello test case",
"type": "string",
}],
} == rs.save()
def test_err2() -> None:
doc = {
"type": "rucord",
"fields": [{"name": "hello", "doc": "Hello test case", "type": "string"}],
}
with pytest.raises(ValidationException):
cg_metaschema.RecordSchema.fromDoc(doc, "", cg_metaschema.LoadingOptions())
def test_idmap(self):
doc = {
"type": "record",
"fields": {
"hello": {
"doc": "Hello test case",
"type": "string"
}
}
}
rs = cg_metaschema.RecordSchema(doc, "http://example.com/",
cg_metaschema.LoadingOptions())
self.assertEqual("record", rs.type)
self.assertEqual("http://example.com/#hello", rs.fields[0].name)
self.assertEqual("Hello test case", rs.fields[0].doc)
self.assertEqual("string", rs.fields[0].type)
self.assertEqual(
{
"type":
"record",
"fields": [{
"name": "http://example.com/#hello",
"doc": "Hello test case",
"type": "string"
}]
}, rs.save())
def test_load_cwlschema(self):
doc = cg_metaschema.load_document(
file_uri(get_data("tests/test_schema/CommonWorkflowLanguage.yml")),
"", cg_metaschema.LoadingOptions())
with open(get_data("tests/cwl-pre.yml")) as f:
pre = json.load(f)
saved = [d.save() for d in doc]
self.assertEqual(saved, JsonDiffMatcher(pre))
def test_load_metaschema(self):
doc = cg_metaschema.load_document(
file_uri(get_data("metaschema/metaschema.yml")), "",
cg_metaschema.LoadingOptions())
with open(get_data("tests/metaschema-pre.yml")) as f:
pre = json.load(f)
saved = [d.save(relative_uris=False) for d in doc]
self.assertEqual(saved, JsonDiffMatcher(pre))
def test_load_cwlschema():
doc = cg_metaschema.load_document(
file_uri(get_data("tests/test_schema/CommonWorkflowLanguage.yml")),
"",
cg_metaschema.LoadingOptions(),
)
with open(get_data("tests/cwl-pre.yml")) as f:
pre = json.load(f)
saved = [d.save(relative_uris=False) for d in doc]
assert saved == JsonDiffMatcher(pre)
def test_load_pt():
doc = cg_metaschema.load_document(file_uri(get_data("tests/pt.yml")), "",
cg_metaschema.LoadingOptions())
assert [
"https://w3id.org/cwl/salad#null",
"http://www.w3.org/2001/XMLSchema#boolean",
"http://www.w3.org/2001/XMLSchema#int",
"http://www.w3.org/2001/XMLSchema#long",
"http://www.w3.org/2001/XMLSchema#float",
"http://www.w3.org/2001/XMLSchema#double",
"http://www.w3.org/2001/XMLSchema#string",
] == doc.symbols
def test_load_pt(self):
doc = cg_metaschema.load_document(file_uri(get_data("tests/pt.yml")),
"", cg_metaschema.LoadingOptions())
self.assertEqual([
'https://w3id.org/cwl/salad#null',
'http://www.w3.org/2001/XMLSchema#boolean',
'http://www.w3.org/2001/XMLSchema#int',
'http://www.w3.org/2001/XMLSchema#long',
'http://www.w3.org/2001/XMLSchema#float',
'http://www.w3.org/2001/XMLSchema#double',
'http://www.w3.org/2001/XMLSchema#string'
], doc.symbols)
def test_err2(self):
doc = {
"type":
"rucord",
"fields": [{
"name": "hello",
"doc": "Hello test case",
"type": "string"
}]
}
with self.assertRaises(cg_metaschema.ValidationException):
rs = cg_metaschema.RecordSchema(doc, "",
cg_metaschema.LoadingOptions())
def test_load_metaschema() -> None:
path = get_data("metaschema/metaschema.yml")
assert path
doc = cg_metaschema.load_document(
file_uri(path),
"",
cg_metaschema.LoadingOptions(),
)
path2 = get_data("tests/metaschema-pre.yml")
assert path2
with open(path2) as f:
pre = json.load(f)
saved = [d.save(relative_uris=False) for d in doc]
assert saved == JsonDiffMatcher(pre)
def test_import2(self):
rs = cg_metaschema.load_document(
file_uri(get_data("tests/docimp/d1.yml")), "",
cg_metaschema.LoadingOptions())
self.assertEqual([{
'doc': [
u'*Hello*', 'hello 2', u'*dee dee dee five*', 'hello 3',
'hello 4', u'*dee dee dee five*', 'hello 5'
],
'type':
'documentation',
'name':
file_uri(get_data("tests/docimp/d1.yml")) +
"#Semantic_Annotations_for_Linked_Avro_Data"
}], [r.save() for r in rs])
def test_include() -> None:
doc = {"name": "hello", "doc": [{"$include": "hello.txt"}], "type": "documentation"}
path = get_data("tests/_")
assert path
rf = cg_metaschema.Documentation.fromDoc(
doc,
"http://example.com/",
cg_metaschema.LoadingOptions(fileuri=file_uri(path)),
)
assert "http://example.com/#hello" == rf.name
assert ["hello world!\n"] == rf.doc
assert "documentation" == rf.type
assert {
"name": "http://example.com/#hello",
"doc": ["hello world!\n"],
"type": "documentation",
} == rf.save()
def test_import2():
rs = cg_metaschema.load_document(file_uri(get_data("tests/docimp/d1.yml")),
"", cg_metaschema.LoadingOptions())
assert [{
"doc": [
"*Hello*",
"hello 2",
"*dee dee dee five*",
"hello 3",
"hello 4",
"*dee dee dee five*",
"hello 5",
],
"type":
"documentation",
"name":
file_uri(get_data("tests/docimp/d1.yml")) +
"#Semantic_Annotations_for_Linked_Avro_Data",
}] == [r.save() for r in rs]
def test_import():
doc = {"type": "record", "fields": [{"$import": "hellofield.yml"}]}
lead = file_uri(os.path.normpath(get_data("tests")))
rs = cg_metaschema.RecordSchema.fromDoc(
doc, "http://example.com/",
cg_metaschema.LoadingOptions(fileuri=lead + "/_"))
assert "record" == rs.type
assert lead + "/hellofield.yml#hello" == rs.fields[0].name
assert "hello world!\n" == rs.fields[0].doc
assert "string" == rs.fields[0].type
assert {
"type":
"record",
"fields": [{
"name": lead + "/hellofield.yml#hello",
"doc": "hello world!\n",
"type": "string",
}],
} == rs.save()
def test_import(self):
doc = {"type": "record", "fields": [{"$import": "hellofield.yml"}]}
lead = file_uri(os.path.normpath(get_data("tests")))
rs = cg_metaschema.RecordSchema(
doc, "http://example.com/",
cg_metaschema.LoadingOptions(fileuri=lead + "/_"))
self.assertEqual("record", rs.type)
self.assertEqual(lead + "/hellofield.yml#hello", rs.fields[0].name)
self.assertEqual("hello world!\n", rs.fields[0].doc)
self.assertEqual("string", rs.fields[0].type)
self.assertEqual(
{
"type":
"record",
"fields": [{
"name": lead + "/hellofield.yml#hello",
"doc": "hello world!\n",
"type": "string"
}]
}, rs.save())
def test_include(self):
doc = {
"name": "hello",
"doc": [{
"$include": "hello.txt"
}],
"type": "documentation"
}
rf = cg_metaschema.Documentation(
doc, "http://example.com/",
cg_metaschema.LoadingOptions(
fileuri=file_uri(get_data("tests/_"))))
self.assertEqual("http://example.com/#hello", rf.name)
self.assertEqual(["hello world!\n"], rf.doc)
self.assertEqual("documentation", rf.type)
self.assertEqual(
{
"name": "http://example.com/#hello",
"doc": ["hello world!\n"],
"type": "documentation"
}, rf.save())
def test_err() -> None:
doc = {"doc": "Hello test case", "type": "string"}
with pytest.raises(ValidationException):
cg_metaschema.RecordField.fromDoc(doc, "",
cg_metaschema.LoadingOptions())
def test_err(self):
doc = {"doc": "Hello test case", "type": "string"}
with self.assertRaises(cg_metaschema.ValidationException):
rf = cg_metaschema.RecordField(doc, "",
cg_metaschema.LoadingOptions())
