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mr-cmr-c
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secfiles DSL fix & refresh from 1.2.1_proposed
1 parent 5debdbc commit 99b4c66

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2 files changed

+26
-52
lines changed

2 files changed

+26
-52
lines changed

‎cwl_utils/parser/cwl_v1_1.py‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -2,13 +2,13 @@
22
# This file was autogenerated using schema-salad-tool --codegen=python
33
# The code itself is released under the Apache 2.0 license and the help text is
44
# subject to the license of the original schema.
5-
from abc import ABC, abstractmethod
65
import copy
76
import os
87
import pathlib
98
import re
109
import tempfile
1110
import uuid as _uuid__ # pylint: disable=unused-import # noqa: F401
11+
from abc import ABC, abstractmethod
1212
from io import StringIO
1313
from typing import (
1414
Any,
@@ -337,6 +337,7 @@ def load(self, doc, baseuri, loadingOptions, docRoot=None):
337337
d
338338
)
339339
)
340+
r.append(new_dict)
340341

341342
else:
342343
raise ValidationException(
@@ -360,6 +361,7 @@ def load(self, doc, baseuri, loadingOptions, docRoot=None):
360361
doc
361362
)
362363
)
364+
r.append(new_dict)
363365

364366
elif isinstance(doc, str):
365367
if doc.endswith("?"):

‎cwl_utils/parser/cwl_v1_2.py‎

Lines changed: 23 additions & 51 deletions
Original file line numberDiff line numberDiff line change
@@ -2,13 +2,13 @@
22
# This file was autogenerated using schema-salad-tool --codegen=python
33
# The code itself is released under the Apache 2.0 license and the help text is
44
# subject to the license of the original schema.
5-
from abc import ABC, abstractmethod
65
import copy
76
import os
87
import pathlib
98
import re
109
import tempfile
1110
import uuid as _uuid__ # pylint: disable=unused-import # noqa: F401
11+
from abc import ABC, abstractmethod
1212
from io import StringIO
1313
from typing import (
1414
Any,
@@ -337,6 +337,7 @@ def load(self, doc, baseuri, loadingOptions, docRoot=None):
337337
d
338338
)
339339
)
340+
r.append(new_dict)
340341

341342
else:
342343
raise ValidationException(
@@ -360,6 +361,7 @@ def load(self, doc, baseuri, loadingOptions, docRoot=None):
360361
doc
361362
)
362363
)
364+
r.append(new_dict)
363365

364366
elif isinstance(doc, str):
365367
if doc.endswith("?"):
@@ -1112,7 +1114,7 @@ def fromDoc(
11121114
try:
11131115
items = load_field(
11141116
_doc.get("items"),
1115-
uri_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_False_True_2,
1117+
typedsl_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_2,
11161118
baseuri,
11171119
loadingOptions,
11181120
)
@@ -1174,9 +1176,9 @@ def save(
11741176
for ef in self.extension_fields:
11751177
r[prefix_url(ef, self.loadingOptions.vocab)] = self.extension_fields[ef]
11761178
if self.items is not None:
1177-
u = save_relative_uri(self.items, base_url, False, 2, relative_uris)
1178-
if u:
1179-
r["items"] = u
1179+
r["items"] = save(
1180+
self.items, top=False, base_url=base_url, relative_uris=relative_uris
1181+
)
11801182
if self.type is not None:
11811183
r["type"] = save(
11821184
self.type, top=False, base_url=base_url, relative_uris=relative_uris
@@ -2811,7 +2813,7 @@ def fromDoc(
28112813
try:
28122814
items = load_field(
28132815
_doc.get("items"),
2814-
uri_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype_False_True_2,
2816+
typedsl_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype_2,
28152817
baseuri,
28162818
loadingOptions,
28172819
)
@@ -2916,9 +2918,9 @@ def save(
29162918
if u:
29172919
r["name"] = u
29182920
if self.items is not None:
2919-
u = save_relative_uri(self.items, self.name, False, 2, relative_uris)
2920-
if u:
2921-
r["items"] = u
2921+
r["items"] = save(
2922+
self.items, top=False, base_url=self.name, relative_uris=relative_uris
2923+
)
29222924
if self.type is not None:
29232925
r["type"] = save(
29242926
self.type, top=False, base_url=self.name, relative_uris=relative_uris
@@ -3679,7 +3681,7 @@ def fromDoc(
36793681
try:
36803682
items = load_field(
36813683
_doc.get("items"),
3682-
uri_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype_False_True_2,
3684+
typedsl_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype_2,
36833685
baseuri,
36843686
loadingOptions,
36853687
)
@@ -3784,9 +3786,9 @@ def save(
37843786
if u:
37853787
r["name"] = u
37863788
if self.items is not None:
3787-
u = save_relative_uri(self.items, self.name, False, 2, relative_uris)
3788-
if u:
3789-
r["items"] = u
3789+
r["items"] = save(
3790+
self.items, top=False, base_url=self.name, relative_uris=relative_uris
3791+
)
37903792
if self.type is not None:
37913793
r["type"] = save(
37923794
self.type, top=False, base_url=self.name, relative_uris=relative_uris
@@ -5966,7 +5968,7 @@ def fromDoc(
59665968
try:
59675969
items = load_field(
59685970
_doc.get("items"),
5969-
uri_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_False_True_2,
5971+
typedsl_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_2,
59705972
baseuri,
59715973
loadingOptions,
59725974
)
@@ -6092,9 +6094,9 @@ def save(
60926094
if u:
60936095
r["name"] = u
60946096
if self.items is not None:
6095-
u = save_relative_uri(self.items, self.name, False, 2, relative_uris)
6096-
if u:
6097-
r["items"] = u
6097+
r["items"] = save(
6098+
self.items, top=False, base_url=self.name, relative_uris=relative_uris
6099+
)
60986100
if self.type is not None:
60996101
r["type"] = save(
61006102
self.type, top=False, base_url=self.name, relative_uris=relative_uris
@@ -6905,7 +6907,7 @@ def fromDoc(
69056907
try:
69066908
items = load_field(
69076909
_doc.get("items"),
6908-
uri_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_False_True_2,
6910+
typedsl_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_2,
69096911
baseuri,
69106912
loadingOptions,
69116913
)
@@ -7012,9 +7014,9 @@ def save(
70127014
if u:
70137015
r["name"] = u
70147016
if self.items is not None:
7015-
u = save_relative_uri(self.items, self.name, False, 2, relative_uris)
7016-
if u:
7017-
r["items"] = u
7017+
r["items"] = save(
7018+
self.items, top=False, base_url=self.name, relative_uris=relative_uris
7019+
)
70187020
if self.type is not None:
70197021
r["type"] = save(
70207022
self.type, top=False, base_url=self.name, relative_uris=relative_uris
@@ -14699,12 +14701,6 @@ def save(
1469914701
typedsl_enum_d961d79c225752b9fadb617367615ab176b47d77Loader_2 = _TypeDSLLoader(
1470014702
enum_d961d79c225752b9fadb617367615ab176b47d77Loader, 2
1470114703
)
14702-
uri_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_False_True_2 = _URILoader(
14703-
union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype,
14704-
False,
14705-
True,
14706-
2,
14707-
)
1470814704
enum_d062602be0b4b8fd33e69e29a841317b6ab665bcLoader = _EnumLoader(("array",))
1470914705
typedsl_enum_d062602be0b4b8fd33e69e29a841317b6ab665bcLoader_2 = _TypeDSLLoader(
1471014706
enum_d062602be0b4b8fd33e69e29a841317b6ab665bcLoader, 2
@@ -14834,12 +14830,6 @@ def save(
1483414830
idmap_fields_union_of_None_type_or_array_of_InputRecordFieldLoader = _IdMapLoader(
1483514831
union_of_None_type_or_array_of_InputRecordFieldLoader, "name", "type"
1483614832
)
14837-
uri_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype_False_True_2 = _URILoader(
14838-
union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype,
14839-
False,
14840-
True,
14841-
2,
14842-
)
1484314833
union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype = _UnionLoader(
1484414834
(
1484514835
CWLTypeLoader,
@@ -14876,12 +14866,6 @@ def save(
1487614866
idmap_fields_union_of_None_type_or_array_of_OutputRecordFieldLoader = _IdMapLoader(
1487714867
union_of_None_type_or_array_of_OutputRecordFieldLoader, "name", "type"
1487814868
)
14879-
uri_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype_False_True_2 = _URILoader(
14880-
union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype,
14881-
False,
14882-
True,
14883-
2,
14884-
)
1488514869
union_of_None_type_or_Any_type = _UnionLoader(
1488614870
(
1488714871
None_type,
@@ -15082,12 +15066,6 @@ def save(
1508215066
union_of_None_type_or_array_of_CommandInputRecordFieldLoader, "name", "type"
1508315067
)
1508415068
)
15085-
uri_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_False_True_2 = _URILoader(
15086-
union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype,
15087-
False,
15088-
True,
15089-
2,
15090-
)
1509115069
union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype = _UnionLoader(
1509215070
(
1509315071
CWLTypeLoader,
@@ -15132,12 +15110,6 @@ def save(
1513215110
union_of_None_type_or_array_of_CommandOutputRecordFieldLoader, "name", "type"
1513315111
)
1513415112
)
15135-
uri_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_False_True_2 = _URILoader(
15136-
union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype,
15137-
False,
15138-
True,
15139-
2,
15140-
)
1514115113
union_of_CWLTypeLoader_or_stdinLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype = _UnionLoader(
1514215114
(
1514315115
CWLTypeLoader,

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