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CWL inputs section to schema salad
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@mr-c
mr-c committed Oct 5, 2022
1 parent 0f4459c commit 591bb5f
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Showing 3 changed files with 206 additions and 4 deletions.
5 changes: 5 additions & 0 deletions cwltool/argparser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -312,6 +312,11 @@ def arg_parser() -> argparse.ArgumentParser:
action="store_true",
help="Print input object document dependencies.",
)
printgroup.add_argument(
"--print-input-schema",
action="store_true",
help="Print SALAD schema for the inputs of the document.",
)
printgroup.add_argument(
"--pack",
action="store_true",
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2 changes: 1 addition & 1 deletion cwltool/load_tool.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
import re
import urllib
import uuid
from functools import partial
from typing import (
Any,
Dict,
Expand All @@ -18,7 +19,6 @@
Union,
cast,
)
from functools import partial

from cwl_utils.parser import cwl_v1_2, cwl_v1_2_utils
from ruamel.yaml.comments import CommentedMap, CommentedSeq
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203 changes: 200 additions & 3 deletions cwltool/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -337,6 +337,172 @@ def generate_input_template(tool: Process) -> CWLObjectType:
return template


def generate_input_schema(tool: Process) -> CWLObjectType:
"""Generate a schema-salad schema for the inputs of a given CWL process."""
template: CWLObjectType = {
"saladVersion": "v1.1",
"$base": "https://w3id.org/cwl/cwl#",
"$namespaces": {"cwl": "https://w3id.org/cwl/cwl#"},
"$graph": [
{
"name": "File",
"type": "record",
"fields": [
{
"name": "class",
"type": {
"type": "enum",
"name": "File_class",
"symbols": ["cwl:File"],
},
"jsonldPredicate": {"_id": "@type", "_type": "@vocab"},
},
{
"name": "location",
"type": "string?",
"jsonldPredicate": {"_id": "@type", "_type": "@vocab"},
},
{
"name": "path",
"type": "string?",
"jsonldPredicate": {
"_id": "cwl:path",
"_type": "@id",
},
},
{
"name": "basename",
"type": "string?",
"jsonldPredicate": {
"_id": "cwl:basename",
"_type": "@id",
},
},
{
"name": "dirname",
"type": "string?",
},
{
"name": "nameroot",
"type": "string?",
},
{
"name": "nameext",
"type": "string?",
},
{
"name": "checksum",
"type": "string?",
},
{
"name": "size",
"type": "long?",
},
{
"name": "secondaryFiles",
"type": [
"null",
{"type": "array", "items": ["File", "Directory"]},
],
"jsonldPredicate": {
"_id": "cwl:secondaryFiles",
"secondaryFilesDSL": True,
},
},
{
"name": "format",
"type": "string?",
"jsonldPredicate": {
"_id": "cwl:format",
"_type": "@id",
"identity": True,
},
},
{
"name": "contents",
"type": "string?",
},
],
},
{
"name": "Directory",
"type": "record",
"fields": [
{
"name": "class",
"type": {
"type": "enum",
"name": "Directory_class",
"symbols": ["cwl:Directory"],
},
"jsonldPredicate": {"_id": "@type", "_type": "@vocab"},
},
{
"name": "location",
"type": "string?",
"jsonldPredicate": {"_id": "@type", "_type": "@vocab"},
},
{
"name": "path",
"type": "string?",
"jsonldPredicate": {
"_id": "cwl:path",
"_type": "@id",
},
},
{
"name": "basename",
"type": "string?",
"jsonldPredicate": {
"_id": "cwl:basename",
"_type": "@id",
},
},
{
"name": "listing",
"type": [
"null",
{"type": "array", "items": ["File", "Directory"]},
],
"jsonldPredicate": {
"_id": "cwl:listing",
},
},
],
},
],
}
inputs_record_schema: CWLObjectType = {
"name": "inputs_record_schema",
"type": "record",
"fields": [],
"documentRoot": True,
}
for inp in tool.inputs_record_schema["fields"]:
salad_type: CWLObjectType = {"name": inp["name"], "type": inp["type"]}
if "label" in inp:
salad_type["doc"] = inp["label"]
inputs_record_schema["fields"].append(salad_type)

def rename_cwl_types(item: Any) -> Any:
if isinstance(item, str):
if item == "org.w3id.cwl.cwl.File":
return "cwl:File"
if item == "org.w3id.cwl.cwl.Directory":
return "cwl:Directory"
elif isinstance(item, MutableSequence):
for index, entry in enumerate(item):
item[index] = rename_cwl_types(entry)
elif isinstance(item, MutableMapping):
for key, value in item.items():
item[key] = rename_cwl_types(value)
return item

template["$graph"].append(rename_cwl_types(inputs_record_schema))

return template


def load_job_order(
args: argparse.Namespace,
stdin: IO[Any],
Expand Down Expand Up @@ -757,8 +923,9 @@ def setup_loadingContext(

def make_template(
tool: Process,
stdout: Union[TextIO, StreamWriter] = sys.stdout,
) -> None:
"""Make a template CWL input object for the give Process."""
"""Make a template CWL input object for the given Process."""

def my_represent_none(
self: Any, data: Any
Expand All @@ -775,7 +942,33 @@ def my_represent_none(
yaml.block_seq_indent = 2
yaml.dump(
generate_input_template(tool),
sys.stdout,
stdout,
)


def make_input_schema(
tool: Process,
stdout: Union[TextIO, StreamWriter] = sys.stdout,
) -> None:
"""Make a schema-salad schema for the CWL input object for the given Process."""

def my_represent_none(
self: Any, data: Any
) -> Any: # pylint: disable=unused-argument
"""Force clean representation of 'null'."""
return self.represent_scalar("tag:yaml.org,2002:null", "null")

ruamel.yaml.representer.RoundTripRepresenter.add_representer(
type(None), my_represent_none
)
yaml = YAML()
yaml.default_flow_style = False
yaml.indent = 4
yaml.block_seq_indent = 2
yaml.preserve_quotes = False
yaml.dump(
generate_input_schema(tool),
stdout,
)


Expand Down Expand Up @@ -1166,7 +1359,11 @@ def main(
raise main_missing_exc

if args.make_template:
make_template(tool)
make_template(tool, stdout)
return 0

if args.print_input_schema:
make_input_schema(tool, stdout)
return 0

if args.validate:
Expand Down

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