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10827 static checker (#321)
* Add static checker for source and sink types * Propagate line numbers so that static checker output has proper source lines. Add checking for missing input parameters and unknown output parameters. * Try to initialize all workflow steps before reporting validation errors. * Print notice when scattering over empty input. * Move early exit for validation after making tool objects to get benefits of static checking.
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8 files changed

+589
-31
lines changed

8 files changed

+589
-31
lines changed

‎cwltool/main.py

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -683,9 +683,6 @@ def main(argsl=None, # type: List[str]
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preprocess_only=args.print_pre or args.pack,
684684
fetcher_constructor=fetcher_constructor)
685685

686-
if args.validate:
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return 0
688-
689686
if args.pack:
690687
stdout.write(print_pack(document_loader, processobj, uri, metadata))
691688
return 0
@@ -697,6 +694,9 @@ def main(argsl=None, # type: List[str]
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tool = make_tool(document_loader, avsc_names, metadata, uri,
698695
makeTool, vars(args))
699696

697+
if args.validate:
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return 0
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700700
if args.print_rdf:
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printrdf(tool, document_loader.ctx, args.rdf_serializer, stdout)
702702
return 0

‎cwltool/workflow.py

Lines changed: 216 additions & 27 deletions
Large diffs are not rendered by default.

‎tests/checker_wf/broken-wf.cwl

Lines changed: 72 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,72 @@
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class: Workflow
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cwlVersion: v1.0
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requirements:
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ScatterFeatureRequirement: {}
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MultipleInputFeatureRequirement: {}
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StepInputExpressionRequirement: {}
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inputs:
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letters0:
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type: [string, int]
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default: "a0"
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letters1:
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type: string[]
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default: ["a1", "b1"]
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letters2:
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type: [string, int]
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default: "a2"
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letters3:
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type: string[]
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default: ["a3", "b3"]
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letters4:
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type: int
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default: 4
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letters5:
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type: string[]
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default: ["a5", "b5", "c5"]
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outputs:
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all:
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type: File[]
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outputSource: cat/txt
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steps:
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echo_v:
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run: echo.cwl
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in:
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echo_in: {}
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out: [txt]
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echo_w:
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run: echo.cwl
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in:
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echo_in: letters0
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out: [txt]
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echo_x:
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run: echo.cwl
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scatter: echo_in
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in:
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echo_in:
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source: [letters1, letters2]
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linkMerge: merge_nested
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out: [txt]
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echo_y:
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run: echo.cwl
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scatter: echo_in
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in:
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echo_in:
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source: [letters3, letters4]
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linkMerge: merge_flattened
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out: [txt]
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echo_z:
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run: echo.cwl
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in:
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echo_in:
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source: letters5
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valueFrom: "special value parsed in valueFrom"
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out: [txt]
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cat:
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run: cat.cwl
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in:
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cat_in:
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source: [echo_w/txt, echo_x/txt, echo_y/txt, echo_z/txt, letters0]
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linkMerge: merge_flattened
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out: [txt]

‎tests/checker_wf/broken-wf2.cwl

Lines changed: 71 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,71 @@
1+
class: Workflow
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cwlVersion: v1.0
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requirements:
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ScatterFeatureRequirement: {}
5+
MultipleInputFeatureRequirement: {}
6+
StepInputExpressionRequirement: {}
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inputs:
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letters0:
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type: [string, int]
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default: "a0"
11+
letters1:
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type: string[]
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default: ["a1", "b1"]
14+
letters2:
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type: [string, int]
16+
default: "a2"
17+
letters3:
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type: string[]
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default: ["a3", "b3"]
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letters4:
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type: int
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default: 4
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letters5:
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type: string[]
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default: ["a5", "b5", "c5"]
26+
27+
outputs:
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all:
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type: File[]
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outputSource: cat/txt
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steps:
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echo_v:
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run: echo.cwl
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in: {}
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out: [txt]
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echo_w:
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run: echo.cwl
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in:
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echo_in: letters0
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out: [txt, other]
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echo_x:
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run: echo.cwl
44+
scatter: echo_in
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in:
46+
echo_in:
47+
source: [letters1, letters2]
48+
linkMerge: merge_nested
49+
out: [txt]
50+
echo_y:
51+
run: echo.cwl
52+
scatter: echo_in
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in:
54+
echo_in:
55+
source: [letters3, letters4]
56+
linkMerge: merge_flattened
57+
out: [txt]
58+
echo_z:
59+
run: echo.cwl
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in:
61+
echo_in:
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source: letters5
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valueFrom: "special value parsed in valueFrom"
64+
out: [txt]
65+
cat:
66+
run: cat.cwl
67+
in:
68+
cat_in:
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source: [echo_w/txt, echo_x/txt, echo_y/txt, echo_z/txt, letters0]
70+
linkMerge: merge_flattened
71+
out: [txt]

‎tests/checker_wf/cat.cwl

Lines changed: 11 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,11 @@
1+
cwlVersion: v1.0
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class: CommandLineTool
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baseCommand: cat
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inputs:
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cat_in:
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type: File[]
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inputBinding: {}
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stdout: all.txt
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outputs:
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txt:
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type: stdout

‎tests/checker_wf/echo.cwl

Lines changed: 13 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,13 @@
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cwlVersion: v1.0
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class: CommandLineTool
3+
baseCommand: echo
4+
inputs:
5+
echo_in:
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type:
7+
- string
8+
- string[]
9+
inputBinding: {}
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stdout: out.txt
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outputs:
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txt:
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type: stdout

‎tests/checker_wf/functional-wf.cwl

Lines changed: 67 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,67 @@
1+
class: Workflow
2+
cwlVersion: v1.0
3+
requirements:
4+
ScatterFeatureRequirement: {}
5+
MultipleInputFeatureRequirement: {}
6+
StepInputExpressionRequirement: {}
7+
inputs:
8+
letters0:
9+
type: [string, int]
10+
default: "a0"
11+
letters1:
12+
type: string[]
13+
default: ["a1", "b1"]
14+
letters2:
15+
type: [string, int]
16+
default: "a2"
17+
letters3:
18+
type: string[]
19+
default: ["a3", "b3"]
20+
letters4:
21+
type: string
22+
default: "a4"
23+
letters5:
24+
type: string[]
25+
default: ["a5", "b5", "c5"]
26+
27+
outputs:
28+
all:
29+
type: File
30+
outputSource: cat/txt
31+
32+
steps:
33+
echo_w:
34+
run: echo.cwl
35+
in:
36+
echo_in: letters0
37+
out: [txt]
38+
echo_x:
39+
run: echo.cwl
40+
scatter: echo_in
41+
in:
42+
echo_in:
43+
source: [letters1, letters2]
44+
linkMerge: merge_nested
45+
out: [txt]
46+
echo_y:
47+
run: echo.cwl
48+
scatter: echo_in
49+
in:
50+
echo_in:
51+
source: [letters3, letters4]
52+
linkMerge: merge_flattened
53+
out: [txt]
54+
echo_z:
55+
run: echo.cwl
56+
in:
57+
echo_in:
58+
source: letters5
59+
valueFrom: "special value parsed in valueFrom"
60+
out: [txt]
61+
cat:
62+
run: cat.cwl
63+
in:
64+
cat_in:
65+
source: [echo_w/txt, echo_x/txt, echo_y/txt, echo_z/txt]
66+
linkMerge: merge_flattened
67+
out: [txt]

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