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jmfernandez
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mr-c
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Allow packing Operation records (#1467)
* cwltool now packs `Operation` definitions CWL 1.2 introduced [Operation](https://www.commonwl.org/v1.2/Workflow.html#Operation) in order to model abstract workflow steps, needed to use CWL to describe a workflow which could not exist or be implemented in a different way than CWL. As `cwltool --pack` was ignoring records of class `Operation`, packed workflows were not correct (they did not validate with `cwltool --validate`). The issue was explained at #1466. This commit fixes the issue which arises while packing workflows having `Operation` records. Co-authored-by: Michael R. Crusoe <[email protected]>
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-45
lines changed

6 files changed

+241
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‎MANIFEST.in‎

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@@ -7,6 +7,7 @@ include tests/*
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include tests/tmp1/tmp2/tmp3/.gitkeep
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include tests/tmp4/alpha/*
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include tests/wf/*
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include tests/wf/operation/*
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include tests/override/*
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include tests/checker_wf/*
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include tests/subgraph/*

‎cwltool/pack.py‎

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@@ -251,7 +251,12 @@ def rewrite_id(r: str, mainuri: str) -> None:
251251
if "$schemas" in metadata:
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for s in metadata["$schemas"]:
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schemas.add(s)
254-
if dcr.get("class") not in ("Workflow", "CommandLineTool", "ExpressionTool"):
254+
if dcr.get("class") not in (
255+
"Workflow",
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"CommandLineTool",
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"ExpressionTool",
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"Operation",
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):
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continue
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dc = cast(Dict[str, Any], copy.deepcopy(dcr))
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v = rewrite[r]

‎tests/test_pack.py‎

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@@ -21,57 +21,41 @@
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from .util import get_data, needs_docker
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2323

24-
def test_pack() -> None:
25-
loadingContext, workflowobj, uri = fetch_document(get_data("tests/wf/revsort.cwl"))
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yaml = YAML(typ="safe", pure=True)
27-
28-
with open(get_data("tests/wf/expect_packed.cwl")) as packed_file:
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expect_packed = yaml.load(packed_file)
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packed = cwltool.pack.pack(loadingContext, uri)
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adjustFileObjs(
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packed, partial(make_relative, os.path.abspath(get_data("tests/wf")))
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)
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adjustDirObjs(packed, partial(make_relative, os.path.abspath(get_data("tests/wf"))))
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37-
assert "$schemas" in packed
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packed_schemas = packed["$schemas"]
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assert isinstance(packed_schemas, Sized)
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assert len(packed_schemas) == len(expect_packed["$schemas"])
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del packed["$schemas"]
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del expect_packed["$schemas"]
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44-
assert packed == expect_packed
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46-
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def test_pack_input_named_name() -> None:
48-
loadingContext, workflowobj, uri = fetch_document(
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get_data("tests/wf/trick_revsort.cwl")
50-
)
24+
@pytest.mark.parametrize(
25+
"unpacked,expected",
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[
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("tests/wf/revsort.cwl", "tests/wf/expect_packed.cwl"),
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(
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"tests/wf/operation/operation-single.cwl",
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"tests/wf/operation/expect_operation-single_packed.cwl",
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),
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("tests/wf/trick_revsort.cwl", "tests/wf/expect_trick_packed.cwl"),
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],
34+
)
35+
def test_packing(unpacked: str, expected: str) -> None:
36+
"""Compare expected version reality with various workflows and --pack."""
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loadingContext, workflowobj, uri = fetch_document(get_data(unpacked))
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loadingContext.do_update = False
5239
loadingContext, uri = resolve_and_validate_document(
5340
loadingContext, workflowobj, uri
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)
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loader = loadingContext.loader
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assert loader
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loader.resolve_ref(uri)[0]
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yaml = YAML()
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with open(get_data("tests/wf/expect_trick_packed.cwl")) as packed_file:
61-
expect_packed = yaml.load(packed_file)
6242

6343
packed = cwltool.pack.pack(loadingContext, uri)
64-
adjustFileObjs(
65-
packed, partial(make_relative, os.path.abspath(get_data("tests/wf")))
66-
)
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adjustDirObjs(packed, partial(make_relative, os.path.abspath(get_data("tests/wf"))))
44+
context_dir = os.path.abspath(os.path.dirname(get_data(unpacked)))
45+
adjustFileObjs(packed, partial(make_relative, context_dir))
46+
adjustDirObjs(packed, partial(make_relative, context_dir))
6847

69-
assert "$schemas" in packed
70-
packed_schemas = packed["$schemas"]
71-
assert isinstance(packed_schemas, Sized)
72-
assert len(packed_schemas) == len(expect_packed["$schemas"])
73-
del packed["$schemas"]
74-
del expect_packed["$schemas"]
48+
yaml = YAML(typ="safe", pure=True)
49+
with open(get_data(expected)) as packed_file:
50+
expect_packed = yaml.load(packed_file)
51+
52+
if "$schemas" in expect_packed:
53+
assert "$schemas" in packed
54+
packed_schemas = packed["$schemas"]
55+
assert isinstance(packed_schemas, Sized)
56+
assert len(packed_schemas) == len(expect_packed["$schemas"])
57+
del packed["$schemas"]
58+
del expect_packed["$schemas"]
7559

7660
assert packed == expect_packed
7761

‎tests/wf/operation/abstract-cosifer.cwl‎

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@@ -0,0 +1,25 @@
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class: Operation
2+
cwlVersion: v1.2
3+
4+
requirements:
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DockerRequirement:
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dockerPull: 'tsenit/cosifer:b4d5af45d2fc54b6bff2a9153a8e9054e560302e'
7+
8+
inputs:
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data_matrix:
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type: File
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separator:
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type: string?
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doc: The separator used in the data_matrix file
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index_col:
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type: int?
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gmt_filepath:
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type: File?
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outdir:
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type: string?
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samples_on_rows:
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type: boolean?
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outputs:
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resdir:
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type: Directory

‎tests/wf/operation/expect_operation-single_packed.cwl‎

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@@ -0,0 +1,154 @@
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{
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"$graph": [
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{
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"class": "Operation",
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"requirements": [
6+
{
7+
"dockerPull": "tsenit/cosifer:b4d5af45d2fc54b6bff2a9153a8e9054e560302e",
8+
"class": "DockerRequirement"
9+
}
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],
11+
"inputs": [
12+
{
13+
"type": "File",
14+
"id": "#abstract-cosifer.cwl/data_matrix"
15+
},
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{
17+
"type": [
18+
"null",
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"File"
20+
],
21+
"id": "#abstract-cosifer.cwl/gmt_filepath"
22+
},
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{
24+
"type": [
25+
"null",
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"int"
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],
28+
"id": "#abstract-cosifer.cwl/index_col"
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},
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{
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"type": [
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"null",
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"string"
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],
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"id": "#abstract-cosifer.cwl/outdir"
36+
},
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{
38+
"type": [
39+
"null",
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"boolean"
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],
42+
"id": "#abstract-cosifer.cwl/samples_on_rows"
43+
},
44+
{
45+
"type": [
46+
"null",
47+
"string"
48+
],
49+
"doc": "The separator used in the data_matrix file",
50+
"id": "#abstract-cosifer.cwl/separator"
51+
}
52+
],
53+
"outputs": [
54+
{
55+
"type": "Directory",
56+
"id": "#abstract-cosifer.cwl/resdir"
57+
}
58+
],
59+
"id": "#abstract-cosifer.cwl"
60+
},
61+
{
62+
"class": "Workflow",
63+
"id": "#main",
64+
"label": "abstract-cosifer-workflow",
65+
"inputs": [
66+
{
67+
"type": "File",
68+
"doc": "Gene expression data matrix",
69+
"id": "#data_matrix"
70+
},
71+
{
72+
"type": [
73+
"null",
74+
"File"
75+
],
76+
"doc": "Optional GMT file to perform inference on multiple gene sets",
77+
"id": "#gmt_filepath"
78+
},
79+
{
80+
"type": [
81+
"null",
82+
"int"
83+
],
84+
"doc": "Column index in the data. Defaults to None, a.k.a., no index",
85+
"id": "#index_col"
86+
},
87+
{
88+
"type": "string",
89+
"doc": "Path to the output directory",
90+
"id": "#outdir"
91+
},
92+
{
93+
"type": [
94+
"null",
95+
"boolean"
96+
],
97+
"doc": "Flag that indicates that data contain the samples on rows. Defaults to False.",
98+
"id": "#samples_on_rows"
99+
},
100+
{
101+
"type": [
102+
"null",
103+
"string"
104+
],
105+
"doc": "Separator for the data. Defaults to .",
106+
"id": "#separator"
107+
}
108+
],
109+
"outputs": [
110+
{
111+
"type": "Directory",
112+
"outputSource": "#/abstract_cosifer/resdir",
113+
"id": "#resdir"
114+
}
115+
],
116+
"steps": [
117+
{
118+
"run": "#abstract-cosifer.cwl",
119+
"in": [
120+
{
121+
"source": "#data_matrix",
122+
"id": "#abstract_cosifer/data_matrix"
123+
},
124+
{
125+
"source": "#gmt_filepath",
126+
"id": "#abstract_cosifer/gmt_filepath"
127+
},
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{
129+
"source": "#index_col",
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"id": "#abstract_cosifer/index_col"
131+
},
132+
{
133+
"source": "#outdir",
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"id": "#abstract_cosifer/outdir"
135+
},
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{
137+
"source": "#samples_on_rows",
138+
"id": "#abstract_cosifer/samples_on_rows"
139+
},
140+
{
141+
"source": "#separator",
142+
"id": "#abstract_cosifer/separator"
143+
}
144+
],
145+
"out": [
146+
"#/abstract_cosifer/resdir"
147+
],
148+
"id": "#abstract_cosifer"
149+
}
150+
]
151+
}
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],
153+
"cwlVersion": "v1.2"
154+
}

‎tests/wf/operation/operation-single.cwl‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,27 @@
1+
class: Workflow
2+
cwlVersion: v1.2
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id: abstract_cosifer_workflow
4+
label: abstract-cosifer-workflow
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6+
inputs:
7+
data_matrix: {type: File, doc: "Gene expression data matrix"}
8+
gmt_filepath: {type: "File?", doc: "Optional GMT file to perform inference on multiple gene sets"}
9+
index_col: {type: "int?", doc: "Column index in the data. Defaults to None, a.k.a., no index"}
10+
outdir: {type: string, doc: "Path to the output directory"}
11+
separator: {type: "string?", doc: "Separator for the data. Defaults to ."}
12+
samples_on_rows: {type: "boolean?", doc: "Flag that indicates that data contain the samples on rows. Defaults to False."}
13+
14+
outputs:
15+
resdir: {type: Directory, outputSource: abstract_cosifer/resdir}
16+
17+
steps:
18+
abstract_cosifer:
19+
run: abstract-cosifer.cwl
20+
in:
21+
data_matrix: data_matrix
22+
separator: separator
23+
index_col: index_col
24+
gmt_filepath: gmt_filepath
25+
outdir: outdir
26+
samples_on_rows: samples_on_rows
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out: [resdir]

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