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
|
"""Tests of helpful error messages."""
import importlib
from collections.abc import MutableSequence
from pathlib import Path
from typing import Any, Optional, cast
import pytest
from schema_salad import codegen
from schema_salad.avro.schema import Names
from schema_salad.exceptions import ValidationException
from schema_salad.schema import load_schema
from schema_salad.utils import yaml_no_ts
from .util import cwl_file_uri, get_path
def test_error_message1(tmp_path: Path) -> None:
t = "test_schema/test1.cwl"
match = r"""^.*test1\.cwl:2:1:\s+Object\s+`.*test1\.cwl`\s+is\s+not\s+valid\s+because:
\s+\*\s+missing\s+required\s+field\s+`inputs`
\s+\*\s+missing\s+required\s+field\s+`outputs`
\s+\*\s+missing\s+required\s+field\s+`steps`"""
path = get_path("tests/" + t)
assert path.exists()
with pytest.raises(ValidationException, match=match):
load_document_by_uri(tmp_path, path)
def test_error_message2(tmp_path: Path) -> None:
t = "test_schema/test2.cwl"
match = r"""^.*test2\.cwl:2:1:\s+Field\s+`class`\s+contains\s+undefined\s+reference\s+to\s+`file://.+/schema_salad/tests/test_schema/xWorkflow`$"""
path = get_path("tests/" + t)
assert path.exists()
with pytest.raises(ValidationException, match=match):
load_document_by_uri(tmp_path, path)
def test_error_message4(tmp_path: Path) -> None:
t = "test_schema/test4.cwl"
match = r"""^.*test4.cwl:2:1:\s+Object\s+`.*test4.cwl`\s+is\s+not\s+valid\s+because:
.*test4\.cwl:6:1:\s+the\s+`outputs`\s+field\s+is\s+not\s+valid\s+because:
\s+array\s+item\s+is\s+invalid\s+because
.*test4\.cwl:7:3:\s+checking\s+object\s+`.*test4\.cwl#bar`\s+using\s+`WorkflowOutputParameter`
\s+the\s+`type`\s+field\s+is\s+not\s+valid\s+because:
\s+Value\s+`12`\s+is\s+a\s+int,\s+but\s+valid\s+types\s+for\s+this\s+field\s+are\s+\((str|object),\s+(str|object)\)"""
path = get_path("tests/" + t)
assert path.exists()
with pytest.raises(ValidationException, match=match):
load_document_by_uri(tmp_path, path)
def test_error_message5(tmp_path: Path) -> None:
t = "test_schema/test5.cwl"
match = r"""^.*test5\.cwl:2:1:\s+Object\s+`.*test5\.cwl`\s+is\s+not\s+valid\s+because:
.+test5\.cwl:8:1:\s+the\s+`steps`\s+field\s+is\s+not\s+valid\s+because:
.+test5\.cwl:8:9:\s+array\s+item\s+is\s+invalid\s+because
\s+Value\s+is\s+a\s+int,\s+but\s+valid\s+type\s+for\s+this\s+field\s+is\s+an\s+object"""
path = get_path("tests/" + t)
assert path.exists()
with pytest.raises(ValidationException, match=match):
load_document_by_uri(tmp_path, path)
def test_error_message6(tmp_path: Path) -> None:
t = "test_schema/test6.cwl"
match = r"""\*\s+tried\s+`CommandLineTool`\s+but
\s+missing\s+required\s+field\s+`class`
+\*\s+tried\s+`ExpressionTool`\s+but
\s+missing\s+required\s+field\s+`class`
+\*\s+tried\s+`Workflow`\s+but
\s+missing\s+required\s+field\s+`class`"""
path = get_path("tests/" + t)
assert path.exists()
with pytest.raises(ValidationException, match=match):
load_document_by_uri(tmp_path, path)
def test_error_message7(tmp_path: Path) -> None:
t = "test_schema/test7.cwl"
match = r"""^.*test7\.cwl:2:1:\s+Object\s+`.*test7\.cwl`\s+is\s+not\s+valid\s+because:
.*test7\.cwl:8:1:\s+the\s+`steps`\s+field\s+is\s+not\s+valid\s+because:
\s+array\s+item\s+is\s+invalid\s+because
.*test7\.cwl:9:3:\s+checking\s+object\s+`.*test7.cwl#step1`\s+using\s+`WorkflowStep`
\s+\*\s+missing\s+required\s+field\s+`run`
.*test7\.cwl:10:5:\s+\*\s+invalid\s+field\s+`scatter_method`,\s+expected\s+one\s+of:\s+.*\s+.*\s+.*\s+.*\s+.*\s+.*\s+.*\s+.*\s+.*\s+.*$"""
path = get_path("tests/" + t)
assert path.exists()
with pytest.raises(ValidationException, match=match):
load_document_by_uri(tmp_path, path)
def test_error_message8(tmp_path: Path) -> None:
t = "test_schema/test8.cwl"
match = r"""^.*test8.cwl:2:1:\s+Object\s+`.*test8.cwl`\s+is\s+not\s+valid\s+because:
.*test8\.cwl:8:1:\s+the\s+`steps`\s+field\s+is\s+not\s+valid\s+because:
\s+array\s+item\s+is\s+invalid\s+because
.*test8\.cwl:9:3:\s+checking\s+object\s+`.*test8\.cwl#step1`\s+using\s+`WorkflowStep`
\s+\*\s+missing\s+required\s+field\s+`run`
.*test8\.cwl:10:5:\s+\*\s+the\s+`scatterMethod`\s+field\s+is\s+not\s+valid\s+because:
\s+contains\s+undefined\s+reference\s+to\s+`file:///.*/tests/test_schema/abc`$"""
path = get_path("tests/" + t)
assert path.exists()
with pytest.raises(ValidationException, match=match):
load_document_by_uri(tmp_path, path)
def test_error_message9(tmp_path: Path) -> None:
t = "test_schema/test9.cwl"
match = r"""^.*test9.cwl:2:1:\s+Object\s+`.*test9.cwl`\s+is\s+not\s+valid\s+because:
.*test9\.cwl:8:1:\s+the\s+`steps`\s+field\s+is\s+not\s+valid\s+because:
\s+array\s+item\s+is\s+invalid\s+because
.*test9\.cwl:9:3:\s+checking\s+object\s+`.*test9\.cwl#step1`\s+using\s+`WorkflowStep`
\s+\*\s+missing\s+required\s+field\s+`run`
.*test9\.cwl:10:5:\s+\*\s+the\s+`scatterMethod`\s+field\s+is\s+not\s+valid\s+because:
\s+Value\s+`12`\s+is\s+a\s+int,\s+but\s+valid\s+values\s+for\s+this\s+field\s+are\s+\("(dotproduct|nested_crossproduct|flat_crossproduct)",\s+"(dotproduct|nested_crossproduct|flat_crossproduct)",\s+"(dotproduct|nested_crossproduct|flat_crossproduct)"\)"""
path = get_path("tests/" + t)
assert path.exists()
with pytest.raises(ValidationException, match=match):
load_document_by_uri(tmp_path, path)
def test_error_message10(tmp_path: Path) -> None:
t = "test_schema/test10.cwl"
match = r"""^.*test10\.cwl:2:1:\s+Object\s+`.*test10\.cwl`\s+is\s+not\s+valid\s+because:
.*test10\.cwl:8:1:\s+the\s+`steps`\s+field\s+is\s+not\s+valid\s+because:
\s+array\s+item\s+is\s+invalid\s+because
.*test10\.cwl:9:3:\s+checking\s+object\s+`.*test10.cwl#step1`
\s+\*\s+missing\s+required\s+field\s+`run`
.*test10\.cwl:10:5:\s+\*\s+the\s+`scatterMethod`\s+field\s+is\s+not\s+valid\s+because:
\s+Value\s+is\s+a\s+array,\s+but\s+valid\s+types\s+for\s+this\s+field\s+are\s+\("dotproduct|nested_crossproduct|flat_crossproduct",\s+"dotproduct|nested_crossproduct|flat_crossproduct",\s+"dotproduct|nested_crossproduct|flat_crossproduct"\)"""
path = get_path("tests/" + t)
assert path.exists()
with pytest.raises(ValidationException, match=match):
load_document_by_uri(tmp_path, path)
def test_error_message11(tmp_path: Path) -> None:
t = "test_schema/test11.cwl"
match = r"""^.*test11\.cwl:2:1:\s+Object\s+`.*test11.cwl`\s+is\s+not\s+valid\s+because:
.*test11\.cwl:8:1:\s+the\s+`steps`\s+field\s+is\s+not\s+valid\s+because:
\s+array\s+item\s+is\s+invalid\s+because
.*test11\.cwl:9:3:\s+checking\s+object\s+`.*test11\.cwl#step1`\s+using\s+`WorkflowStep`
.*test11\.cwl:10:5:\s+the\s+`run`\s+field\s+is\s+not\s+valid\s+because:\s+contains\s+undefined\s+reference\s+to\s+`file:///.*/tests/test_schema/blub\.cwl`$"""
path = get_path("tests/" + t)
assert path.exists()
with pytest.raises(ValidationException, match=match):
load_document_by_uri(tmp_path, path)
# `loadContents`,\s+`position`,\s+`prefix`,\s+`separate`,\s+`itemSeparator`,\s+`valueFrom`,\s+`shellQuote`
def test_error_message15(tmp_path: Path) -> None:
t = "test_schema/test15.cwl"
match = r"""^.*test15\.cwl:3:1:\s+Object\s+`.*test15\.cwl`\s+is\s+not\s+valid\s+because:
.*test15\.cwl:6:1:\s+the\s+`inputs`\s+field\s+is\s+not\s+valid\s+because:
\s+array\s+item\s+is\s+invalid\s+because
.*test15\.cwl:7:3:\s+checking\s+object\s+`.*test15\.cwl#message`\s+using\s+`CommandInputParameter`
.*test15\.cwl:9:5:\s+the\s+`inputBinding`\s+field\s+is\s+not\s+valid\s+because:
\s+tried\s+`CommandLineBinding`\s+but
.*test15\.cwl:11:7:\s+\*\s+invalid\s+field\s+`invalid_field`,\s+expected\s+one\s+of:\s+`loadContents`,\s+`position`,\s+`prefix`,\s+`separate`,\s+`itemSeparator`,\s+`valueFrom`,\s+`shellQuote`
.*test15\.cwl:12:7:\s+\*\s+invalid\s+field\s+`another_invalid_field`,\s+expected one\s+of:\s+`loadContents`,\s+`position`,\s+`prefix`,\s+`separate`,\s+`itemSeparator`,\s+`valueFrom`,\s+`shellQuote`$"""
path = get_path("tests/" + t)
assert path.exists()
with pytest.raises(ValidationException, match=match):
load_document_by_uri(tmp_path, path)
def load_document_by_uri(tmp_path: Path, path: Path) -> Any:
src_target = tmp_path / "cwl_v1_0.py"
python_codegen(cwl_file_uri, src_target)
spec = importlib.util.spec_from_file_location("cwl_v1_0", src_target)
assert isinstance(spec, importlib.machinery.ModuleSpec)
assert isinstance(spec.loader, importlib.abc.Loader)
temp_cwl_v1_0 = importlib.util.module_from_spec(spec)
spec.loader.exec_module(temp_cwl_v1_0)
cwl_v1_0: Any = temp_cwl_v1_0
path_uri = path.resolve().as_uri()
baseuri = path_uri
loadingOptions = cwl_v1_0.LoadingOptions(fileuri=baseuri)
with open(path) as file:
doc = file.read()
# doc = loadingOptions.fetcher.fetch_text(urllib.parse.unquote(path_uri))
yaml = yaml_no_ts()
doc = yaml.load(doc)
result = cwl_v1_0.load_document_by_yaml(
doc, baseuri, cast(Optional[cwl_v1_0.LoadingOptions], loadingOptions)
)
if isinstance(result, MutableSequence):
lst = []
for r in result:
lst.append(r)
return lst
return result
def python_codegen(
file_uri: str,
target: Path,
parser_info: Optional[str] = None,
package: Optional[str] = None,
) -> None:
document_loader, avsc_names, schema_metadata, metaschema_loader = load_schema(file_uri)
assert isinstance(avsc_names, Names)
schema_raw_doc = metaschema_loader.fetch(file_uri)
schema_doc, schema_metadata = metaschema_loader.resolve_all(schema_raw_doc, file_uri)
codegen.codegen(
"python",
cast(list[dict[str, Any]], schema_doc),
schema_metadata,
document_loader,
target=str(target),
parser_info=parser_info,
package=package,
)
|
