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mr-cmr-c
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"id" is a required field in for Parameters and WorkflowSteps
1 parent 02d6dbd commit f28b50d

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2 files changed

+33
-31
lines changed

2 files changed

+33
-31
lines changed

‎cwl_utils/cwl_v1_2_expression_refactor.py‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -715,7 +715,9 @@ def process_workflow_inputs_and_outputs(
715715
source_type_items.append("null")
716716
elif source_type_items != "null":
717717
source_type_items = ["null", source_type_items]
718-
source_type = cwl.CommandInputParameter(type_=source_type_items)
718+
source_type = cwl.CommandInputParameter(
719+
id=None, type_=source_type_items
720+
)
719721
replace_expr_with_etool(
720722
expression,
721723
etool_id,

‎cwl_utils/parser/cwl_v1_2.py‎

Lines changed: 30 additions & 30 deletions
Original file line numberDiff line numberDiff line change
@@ -13750,12 +13750,12 @@ class CommandInputParameter(InputParameter):
1375013750

1375113751
def __init__(
1375213752
self,
13753+
id: Any,
1375313754
type_: Any,
1375413755
label: Optional[Any] = None,
1375513756
secondaryFiles: Optional[Any] = None,
1375613757
streamable: Optional[Any] = None,
1375713758
doc: Optional[Any] = None,
13758-
id: Optional[Any] = None,
1375913759
format: Optional[Any] = None,
1376013760
loadContents: Optional[Any] = None,
1376113761
loadListing: Optional[Any] = None,
@@ -13837,7 +13837,7 @@ def fromDoc(
1383713837
try:
1383813838
id = load_field(
1383913839
_doc.get("id"),
13840-
uri_union_of_None_type_or_strtype_True_False_None_None,
13840+
uri_strtype_True_False_None_None,
1384113841
baseuri,
1384213842
loadingOptions,
1384313843
lc=_doc.get("id")
@@ -13885,7 +13885,7 @@ def fromDoc(
1388513885
if docRoot is not None:
1388613886
id = docRoot
1388713887
else:
13888-
id = "_:" + str(_uuid__.uuid4())
13888+
_errors__.append(ValidationException("missing id"))
1388913889
if not __original_id_is_none:
1389013890
baseuri = cast(str, id)
1389113891
label = None
@@ -14504,12 +14504,12 @@ class CommandOutputParameter(OutputParameter):
1450414504

1450514505
def __init__(
1450614506
self,
14507+
id: Any,
1450714508
type_: Any,
1450814509
label: Optional[Any] = None,
1450914510
secondaryFiles: Optional[Any] = None,
1451014511
streamable: Optional[Any] = None,
1451114512
doc: Optional[Any] = None,
14512-
id: Optional[Any] = None,
1451314513
format: Optional[Any] = None,
1451414514
outputBinding: Optional[Any] = None,
1451514515
extension_fields: Optional[dict[str, Any]] = None,
@@ -14579,7 +14579,7 @@ def fromDoc(
1457914579
try:
1458014580
id = load_field(
1458114581
_doc.get("id"),
14582-
uri_union_of_None_type_or_strtype_True_False_None_None,
14582+
uri_strtype_True_False_None_None,
1458314583
baseuri,
1458414584
loadingOptions,
1458514585
lc=_doc.get("id")
@@ -14627,7 +14627,7 @@ def fromDoc(
1462714627
if docRoot is not None:
1462814628
id = docRoot
1462914629
else:
14630-
id = "_:" + str(_uuid__.uuid4())
14630+
_errors__.append(ValidationException("missing id"))
1463114631
if not __original_id_is_none:
1463214632
baseuri = cast(str, id)
1463314633
label = None
@@ -19322,12 +19322,12 @@ class ExpressionToolOutputParameter(OutputParameter):
1932219322

1932319323
def __init__(
1932419324
self,
19325+
id: Any,
1932519326
type_: Any,
1932619327
label: Optional[Any] = None,
1932719328
secondaryFiles: Optional[Any] = None,
1932819329
streamable: Optional[Any] = None,
1932919330
doc: Optional[Any] = None,
19330-
id: Optional[Any] = None,
1933119331
format: Optional[Any] = None,
1933219332
extension_fields: Optional[dict[str, Any]] = None,
1933319333
loadingOptions: Optional[LoadingOptions] = None,
@@ -19393,7 +19393,7 @@ def fromDoc(
1939319393
try:
1939419394
id = load_field(
1939519395
_doc.get("id"),
19396-
uri_union_of_None_type_or_strtype_True_False_None_None,
19396+
uri_strtype_True_False_None_None,
1939719397
baseuri,
1939819398
loadingOptions,
1939919399
lc=_doc.get("id")
@@ -19441,7 +19441,7 @@ def fromDoc(
1944119441
if docRoot is not None:
1944219442
id = docRoot
1944319443
else:
19444-
id = "_:" + str(_uuid__.uuid4())
19444+
_errors__.append(ValidationException("missing id"))
1944519445
if not __original_id_is_none:
1944619446
baseuri = cast(str, id)
1944719447
label = None
@@ -19827,12 +19827,12 @@ class WorkflowInputParameter(InputParameter):
1982719827

1982819828
def __init__(
1982919829
self,
19830+
id: Any,
1983019831
type_: Any,
1983119832
label: Optional[Any] = None,
1983219833
secondaryFiles: Optional[Any] = None,
1983319834
streamable: Optional[Any] = None,
1983419835
doc: Optional[Any] = None,
19835-
id: Optional[Any] = None,
1983619836
format: Optional[Any] = None,
1983719837
loadContents: Optional[Any] = None,
1983819838
loadListing: Optional[Any] = None,
@@ -19914,7 +19914,7 @@ def fromDoc(
1991419914
try:
1991519915
id = load_field(
1991619916
_doc.get("id"),
19917-
uri_union_of_None_type_or_strtype_True_False_None_None,
19917+
uri_strtype_True_False_None_None,
1991819918
baseuri,
1991919919
loadingOptions,
1992019920
lc=_doc.get("id")
@@ -19962,7 +19962,7 @@ def fromDoc(
1996219962
if docRoot is not None:
1996319963
id = docRoot
1996419964
else:
19965-
id = "_:" + str(_uuid__.uuid4())
19965+
_errors__.append(ValidationException("missing id"))
1996619966
if not __original_id_is_none:
1996719967
baseuri = cast(str, id)
1996819968
label = None
@@ -21312,12 +21312,12 @@ class WorkflowOutputParameter(OutputParameter):
2131221312

2131321313
def __init__(
2131421314
self,
21315+
id: Any,
2131521316
type_: Any,
2131621317
label: Optional[Any] = None,
2131721318
secondaryFiles: Optional[Any] = None,
2131821319
streamable: Optional[Any] = None,
2131921320
doc: Optional[Any] = None,
21320-
id: Optional[Any] = None,
2132121321
format: Optional[Any] = None,
2132221322
outputSource: Optional[Any] = None,
2132321323
linkMerge: Optional[Any] = None,
@@ -21395,7 +21395,7 @@ def fromDoc(
2139521395
try:
2139621396
id = load_field(
2139721397
_doc.get("id"),
21398-
uri_union_of_None_type_or_strtype_True_False_None_None,
21398+
uri_strtype_True_False_None_None,
2139921399
baseuri,
2140021400
loadingOptions,
2140121401
lc=_doc.get("id")
@@ -21443,7 +21443,7 @@ def fromDoc(
2144321443
if docRoot is not None:
2144421444
id = docRoot
2144521445
else:
21446-
id = "_:" + str(_uuid__.uuid4())
21446+
_errors__.append(ValidationException("missing id"))
2144721447
if not __original_id_is_none:
2144821448
baseuri = cast(str, id)
2144921449
label = None
@@ -22111,7 +22111,7 @@ class WorkflowStepInput(Identified, Sink, LoadContents, Labeled):
2211122111

2211222112
def __init__(
2211322113
self,
22114-
id: Optional[Any] = None,
22114+
id: Any,
2211522115
source: Optional[Any] = None,
2211622116
linkMerge: Optional[Any] = None,
2211722117
pickValue: Optional[Any] = None,
@@ -22190,7 +22190,7 @@ def fromDoc(
2219022190
try:
2219122191
id = load_field(
2219222192
_doc.get("id"),
22193-
uri_union_of_None_type_or_strtype_True_False_None_None,
22193+
uri_strtype_True_False_None_None,
2219422194
baseuri,
2219522195
loadingOptions,
2219622196
lc=_doc.get("id")
@@ -22238,7 +22238,7 @@ def fromDoc(
2223822238
if docRoot is not None:
2223922239
id = docRoot
2224022240
else:
22241-
id = "_:" + str(_uuid__.uuid4())
22241+
_errors__.append(ValidationException("missing id"))
2224222242
if not __original_id_is_none:
2224322243
baseuri = cast(str, id)
2224422244
source = None
@@ -22749,7 +22749,7 @@ class WorkflowStepOutput(Identified):
2274922749

2275022750
def __init__(
2275122751
self,
22752-
id: Optional[Any] = None,
22752+
id: Any,
2275322753
extension_fields: Optional[dict[str, Any]] = None,
2275422754
loadingOptions: Optional[LoadingOptions] = None,
2275522755
) -> None:
@@ -22790,7 +22790,7 @@ def fromDoc(
2279022790
try:
2279122791
id = load_field(
2279222792
_doc.get("id"),
22793-
uri_union_of_None_type_or_strtype_True_False_None_None,
22793+
uri_strtype_True_False_None_None,
2279422794
baseuri,
2279522795
loadingOptions,
2279622796
lc=_doc.get("id")
@@ -22838,7 +22838,7 @@ def fromDoc(
2283822838
if docRoot is not None:
2283922839
id = docRoot
2284022840
else:
22841-
id = "_:" + str(_uuid__.uuid4())
22841+
_errors__.append(ValidationException("missing id"))
2284222842
if not __original_id_is_none:
2284322843
baseuri = cast(str, id)
2284422844
extension_fields: dict[str, Any] = {}
@@ -22985,10 +22985,10 @@ class WorkflowStep(Identified, Labeled, Documented):
2298522985

2298622986
def __init__(
2298722987
self,
22988+
id: Any,
2298822989
in_: Any,
2298922990
out: Any,
2299022991
run: Any,
22991-
id: Optional[Any] = None,
2299222992
label: Optional[Any] = None,
2299322993
doc: Optional[Any] = None,
2299422994
requirements: Optional[Any] = None,
@@ -23072,7 +23072,7 @@ def fromDoc(
2307223072
try:
2307323073
id = load_field(
2307423074
_doc.get("id"),
23075-
uri_union_of_None_type_or_strtype_True_False_None_None,
23075+
uri_strtype_True_False_None_None,
2307623076
baseuri,
2307723077
loadingOptions,
2307823078
lc=_doc.get("id")
@@ -23120,7 +23120,7 @@ def fromDoc(
2312023120
if docRoot is not None:
2312123121
id = docRoot
2312223122
else:
23123-
id = "_:" + str(_uuid__.uuid4())
23123+
_errors__.append(ValidationException("missing id"))
2312423124
if not __original_id_is_none:
2312523125
baseuri = cast(str, id)
2312623126
label = None
@@ -24972,12 +24972,12 @@ class OperationInputParameter(InputParameter):
2497224972

2497324973
def __init__(
2497424974
self,
24975+
id: Any,
2497524976
type_: Any,
2497624977
label: Optional[Any] = None,
2497724978
secondaryFiles: Optional[Any] = None,
2497824979
streamable: Optional[Any] = None,
2497924980
doc: Optional[Any] = None,
24980-
id: Optional[Any] = None,
2498124981
format: Optional[Any] = None,
2498224982
loadContents: Optional[Any] = None,
2498324983
loadListing: Optional[Any] = None,
@@ -25055,7 +25055,7 @@ def fromDoc(
2505525055
try:
2505625056
id = load_field(
2505725057
_doc.get("id"),
25058-
uri_union_of_None_type_or_strtype_True_False_None_None,
25058+
uri_strtype_True_False_None_None,
2505925059
baseuri,
2506025060
loadingOptions,
2506125061
lc=_doc.get("id")
@@ -25103,7 +25103,7 @@ def fromDoc(
2510325103
if docRoot is not None:
2510425104
id = docRoot
2510525105
else:
25106-
id = "_:" + str(_uuid__.uuid4())
25106+
_errors__.append(ValidationException("missing id"))
2510725107
if not __original_id_is_none:
2510825108
baseuri = cast(str, id)
2510925109
label = None
@@ -25667,12 +25667,12 @@ class OperationOutputParameter(OutputParameter):
2566725667

2566825668
def __init__(
2566925669
self,
25670+
id: Any,
2567025671
type_: Any,
2567125672
label: Optional[Any] = None,
2567225673
secondaryFiles: Optional[Any] = None,
2567325674
streamable: Optional[Any] = None,
2567425675
doc: Optional[Any] = None,
25675-
id: Optional[Any] = None,
2567625676
format: Optional[Any] = None,
2567725677
extension_fields: Optional[dict[str, Any]] = None,
2567825678
loadingOptions: Optional[LoadingOptions] = None,
@@ -25738,7 +25738,7 @@ def fromDoc(
2573825738
try:
2573925739
id = load_field(
2574025740
_doc.get("id"),
25741-
uri_union_of_None_type_or_strtype_True_False_None_None,
25741+
uri_strtype_True_False_None_None,
2574225742
baseuri,
2574325743
loadingOptions,
2574425744
lc=_doc.get("id")
@@ -25786,7 +25786,7 @@ def fromDoc(
2578625786
if docRoot is not None:
2578725787
id = docRoot
2578825788
else:
25789-
id = "_:" + str(_uuid__.uuid4())
25789+
_errors__.append(ValidationException("missing id"))
2579025790
if not __original_id_is_none:
2579125791
baseuri = cast(str, id)
2579225792
label = None

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