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drop pack.py in favor of cwl_utils.pack #1730

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drop pack.py in favor of cwl_utils.pack #1730

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8af88ce
drop pack.py in favor of cwl_utils.pack
mr-c Sep 2, 2022
cbc0a69
sync the changes in packing format
mr-c Sep 2, 2022
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17 changes: 5 additions & 12 deletions cwltool/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@
import coloredlogs
import pkg_resources # part of setuptools
import ruamel.yaml
from cwl_utils.pack import pack
from ruamel.yaml.comments import CommentedMap, CommentedSeq
from ruamel.yaml.main import YAML
from schema_salad.exceptions import ValidationException
Expand Down Expand Up @@ -68,7 +69,6 @@
from .loghandler import _logger, configure_logging, defaultStreamHandler
from .mpi import MpiConfig
from .mutation import MutationManager
from .pack import pack
from .process import (
CWL_IANA,
Process,
Expand Down Expand Up @@ -629,16 +629,11 @@ def loadref(base: str, uri: str) -> Union[CommentedMap, CommentedSeq, str, None]


def print_pack(
loadingContext: LoadingContext,
uri: str,
) -> str:
"""Return a CWL serialization of the CWL document in JSON."""
packed = pack(loadingContext, uri)
if len(cast(Sized, packed["$graph"])) > 1:
return json_dumps(packed, indent=4, default=str)
return json_dumps(
cast(MutableSequence[CWLObjectType], packed["$graph"])[0], indent=4, default=str
)
packed = pack(uri)
return json_dumps(packed, indent=4, default=str)


def supported_cwl_versions(enable_dev: bool) -> List[str]:
Expand Down Expand Up @@ -1127,14 +1122,12 @@ def main(
processobj, metadata = loadingContext.loader.resolve_ref(uri)
processobj = cast(Union[CommentedMap, CommentedSeq], processobj)
if args.pack:
print(print_pack(loadingContext, uri), file=stdout)
print(print_pack(uri), file=stdout)
return 0

if args.provenance and runtimeContext.research_obj:
# Can't really be combined with args.pack at same time
runtimeContext.research_obj.packed_workflow(
print_pack(loadingContext, uri)
)
runtimeContext.research_obj.packed_workflow(print_pack(uri))

if args.print_pre:
print(
Expand Down
323 changes: 0 additions & 323 deletions cwltool/pack.py
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1 change: 0 additions & 1 deletion setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,6 @@
# "cwltool/__main__.py",
"cwltool/main.py",
"cwltool/mutation.py",
"cwltool/pack.py",
# "cwltool/pathmapper.py", # class PathMapper needs to be subclassable
"cwltool/process.py",
"cwltool/procgenerator.py",
Expand Down
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