1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
|
import json
from typing import Any
import pytest
import schema_salad.metaschema as cg_metaschema
from schema_salad.exceptions import ValidationException
from schema_salad.utils import yaml_no_ts
from .matcher import JsonDiffMatcher
from .util import get_data_uri, get_path
def test_load() -> None:
doc = {
"type": "record",
"fields": [{"name": "hello", "doc": "Hello test case", "type": "string"}],
}
rs = cg_metaschema.RecordSchema.fromDoc(
doc, "http://example.com/", cg_metaschema.LoadingOptions(no_link_check=True)
)
assert "record" == rs.type_
assert rs.fields and "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_err() -> None:
doc = {"doc": "Hello test case", "type": "string"}
with pytest.raises(ValidationException):
cg_metaschema.RecordField.fromDoc(doc, "", cg_metaschema.LoadingOptions())
def test_include() -> None:
doc = {"name": "hello", "doc": [{"$include": "hello.txt"}], "type": "documentation"}
path_uri = get_data_uri("tests") + "/_"
rf = cg_metaschema.Documentation.fromDoc(
doc,
"http://example.com/",
cg_metaschema.LoadingOptions(fileuri=path_uri, no_link_check=True),
)
assert "http://example.com/#hello" == rf.name
assert ["hello world!\n"] == rf.doc
assert "documentation" == rf.type_
assert {
"name": "http://example.com/#hello",
"doc": ["hello world!\n"],
"type": "documentation",
} == rf.save()
def test_import() -> None:
doc = {"type": "record", "fields": [{"$import": "hellofield.yml"}]}
lead = get_data_uri("tests")
rs = cg_metaschema.RecordSchema.fromDoc(
doc, "http://example.com/", cg_metaschema.LoadingOptions(fileuri=lead + "/_")
)
assert "record" == rs.type_
assert rs.fields and 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_import2() -> None:
path_uri = get_data_uri("tests/docimp/d1.yml")
rs = cg_metaschema.load_document(path_uri, "", cg_metaschema.LoadingOptions())
path2_uri = get_data_uri("tests/docimp/d1.yml")
assert [
{
"doc": [
"*Hello*",
"hello 2",
"*dee dee dee five*",
"hello 3",
"hello 4",
"*dee dee dee five*",
"hello 5",
],
"type": "documentation",
"name": path2_uri + "#Semantic_Annotations_for_Linked_Avro_Data",
}
] == [r.save() for r in rs]
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() -> None:
doc = {
"type": "record",
"fields": {"hello": {"doc": "Hello test case", "type": "string"}},
}
rs = cg_metaschema.RecordSchema.fromDoc(
doc, "http://example.com/", cg_metaschema.LoadingOptions(no_link_check=True)
)
assert "record" == rs.type_
assert rs.fields and "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_idmap2() -> None:
doc = {"type": "record", "fields": {"hello": "string"}}
rs = cg_metaschema.RecordSchema.fromDoc(
doc, "http://example.com/", cg_metaschema.LoadingOptions(no_link_check=True)
)
assert "record" == rs.type_
assert rs.fields and "http://example.com/#hello" == rs.fields[0].name
assert rs.fields[0].doc is None
assert "string" == rs.fields[0].type_
assert {
"type": "record",
"fields": [{"name": "http://example.com/#hello", "type": "string"}],
} == rs.save()
def test_load_pt() -> None:
path_uri = get_data_uri("tests/pt.yml")
doc = cg_metaschema.load_document(
path_uri, "", cg_metaschema.LoadingOptions(no_link_check=True)
)
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_shortname() -> None:
"""Test shortname() function."""
assert cg_metaschema.shortname("http://example.com/foo") == "foo"
assert cg_metaschema.shortname("http://example.com/#bar") == "bar"
assert cg_metaschema.shortname("http://example.com/foo/bar") == "bar"
assert cg_metaschema.shortname("http://example.com/foo#bar") == "bar"
assert cg_metaschema.shortname("http://example.com/#foo/bar") == "bar"
assert cg_metaschema.shortname("http://example.com/foo#bar/baz") == "baz"
@pytest.fixture
def metaschema_pre() -> Any:
"""Prep-parsed schema for testing."""
with get_path("tests/metaschema-pre.yml").open() as f:
pre = json.load(f)
return pre
def test_load_metaschema(metaschema_pre: Any) -> None:
path_uri = get_data_uri("metaschema/metaschema.yml")
doc = cg_metaschema.load_document(
path_uri,
"",
cg_metaschema.LoadingOptions(no_link_check=True),
)
saved = [d.save(relative_uris=False) for d in doc]
# with open(get_data("tests/metaschema-pre.yml"), "w") as fh
# json.dump(saved, fh, indent=4)
assert saved == JsonDiffMatcher(metaschema_pre)
def test_load_by_yaml_metaschema(metaschema_pre: Any) -> None:
path = get_path("metaschema/metaschema.yml")
with path.open() as path_handle:
yaml = yaml_no_ts()
yaml_doc = yaml.load(path_handle)
doc = cg_metaschema.load_document_by_yaml(
yaml_doc,
path.as_uri(),
None,
)
saved = [d.save(relative_uris=False) for d in doc]
assert saved == JsonDiffMatcher(metaschema_pre)
def test_load_cwlschema() -> None:
path_uri = get_data_uri("tests/test_schema/CommonWorkflowLanguage.yml")
doc = cg_metaschema.load_document(
path_uri,
"",
cg_metaschema.LoadingOptions(no_link_check=True),
)
path2 = get_path("tests/cwl-pre.yml")
saved = [d.save(relative_uris=False) for d in doc]
# with path2.open("w") as f:
# json.dump(saved, f, indent=2)
with path2.open() as f:
pre = json.load(f)
assert saved == JsonDiffMatcher(pre)
|
