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Experimental fast validator code path, using cwl-utils #1720

Merged
merged 31 commits into from
Sep 13, 2022
Merged

Experimental fast validator code path, using cwl-utils #1720

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f6d8198
Experimental fast validator code path, using cwl-utils
tetron Aug 26, 2022
b145e3c
Load the schema graph
tetron Aug 27, 2022
3cb3d42
DO NOT MERGE: use cwl-utils from draft PR
mr-c Aug 31, 2022
a5a1b85
improve type hints
mr-c Aug 31, 2022
b00b17e
Fix load_tool typing
tetron Sep 1, 2022
cf846bc
Merge branch 'main' into pa/cwlutil-validator
tetron Sep 1, 2022
3adbcbc
GA: run the conformance tests with the fast validator
mr-c Sep 2, 2022
772a11c
conformance testing: use CWLTOOL_OPTIONS
mr-c Sep 2, 2022
d140151
CWLTOOL_OPTIONS: ignore an empty string
mr-c Sep 2, 2022
80271c4
DO NOT MERGE: container build needs our cwl-util branch
mr-c Sep 2, 2022
8c1c82d
Merge branch 'main' into pa/cwlutil-validator
tetron Sep 2, 2022
09d08d9
Merge branch 'main' into pa/cwlutil-validator
tetron Sep 9, 2022
3d12d6e
Rename --fast-validator to --fast-parser
tetron Sep 9, 2022
3617dd5
mypy & format
tetron Sep 9, 2022
d6226ec
Fix mypy-requirements
tetron Sep 9, 2022
b503d54
Fix github action
tetron Sep 9, 2022
b686e41
use ResolveType
mr-c Sep 9, 2022
833b0d6
Add section to README about --fast-parser
tetron Sep 9, 2022
d64be75
Fast parser expects comment data
tetron Sep 9, 2022
1113260
format
tetron Sep 9, 2022
efa5c44
Update document_loader index to match fast parser
tetron Sep 10, 2022
acaf81c
Fix format
tetron Sep 10, 2022
0584fe8
Make sure everything in $graph gets into the index
tetron Sep 11, 2022
46f53bc
Don't crash update if filename field is missing
tetron Sep 12, 2022
03b2f02
Add loadingContext.skip_resolve_all with note
tetron Sep 12, 2022
7630a51
Fix format
tetron Sep 12, 2022
db08a47
Update README.rst
tetron Sep 13, 2022
1e150ab
conformance tests: report CWLTOOL_OPTIONS
mr-c Sep 13, 2022
f3e14e1
CI: include extra options in coverge classname
mr-c Sep 13, 2022
746033b
Bump cwl-utils version requirement
tetron Sep 13, 2022
2aa44d0
conformance coverage: normalize paths
mr-c Sep 13, 2022
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Fast parser expects comment data
  • Loading branch information
@tetron
tetron committed Sep 9, 2022
commit d64be75af4f73036a570542dd53e0d0a6c10f801
13 changes: 9 additions & 4 deletions cwltool/update.py
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Original file line number Diff line number Diff line change
Expand Up @@ -124,14 +124,19 @@ def fix_inputBinding(t: CWLObjectType) -> None:
upd = upd["$graph"]
for proc in aslist(upd):
proc.setdefault("hints", CommentedSeq())
na = CommentedMap([("class", "NetworkAccess"), ("networkAccess", True)])
na.lc.filename = proc.lc.filename
proc["hints"].insert(
0, CommentedMap([("class", "NetworkAccess"), ("networkAccess", True)])
0, na
)

ll = CommentedMap(
[("class", "LoadListingRequirement"), ("loadListing", "deep_listing")]
)
ll.lc.filename = proc.lc.filename
proc["hints"].insert(
0,
CommentedMap(
[("class", "LoadListingRequirement"), ("loadListing", "deep_listing")]
),
ll,
)
if "cwlVersion" in proc:
del proc["cwlVersion"]
Expand Down