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Use existing location if a secondary file has one. #1380

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Use existing location if a secondary file has one. #1380

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4a15ac8
Use existing location if a secondary file has one.
DailyDreaming Nov 30, 2020
bf2aa5d
fake change to force TravisCI to run
mr-c Dec 3, 2020
0434297
Address mypy.
DailyDreaming Dec 7, 2020
25d526e
Cruft.
DailyDreaming Dec 7, 2020
1e5897e
Black.
DailyDreaming Dec 7, 2020
f40a017
Attempt to trigger tests.
DailyDreaming Dec 7, 2020
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52 changes: 44 additions & 8 deletions cwltool/builder.py
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Original file line number Diff line number Diff line change
@@ -1,11 +1,13 @@
import copy
import logging
import math
import os
from typing import (
IO,
Any,
Callable,
Dict,
Iterable,
List,
MutableMapping,
MutableSequence,
Expand Down Expand Up @@ -423,13 +425,47 @@ def _capture_files(f: CWLObjectType) -> CWLObjectType:

if isinstance(sfname, str):
d_location = cast(str, datum["location"])
if "/" in d_location:
sf_location = (
d_location[0 : d_location.rindex("/") + 1]
+ sfname
)
else:
sf_location = d_location + sfname
sf_location = None
if (
isinstance(datum, MutableMapping)
and "secondaryFiles" in datum
):
if isinstance(datum["secondaryFiles"], Iterable):
for existing_processed_secondaryfile in datum[
"secondaryFiles"
]:
if isinstance(
existing_processed_secondaryfile,
MutableMapping,
):
existing_processed_location = existing_processed_secondaryfile.get(
"location"
)
if (
existing_processed_location
and isinstance(
existing_processed_location, str
)
):
if (
os.path.basename(
existing_processed_location
)
== sfname
):
# the secondary file has already been processed;
# use established location
sf_location = existing_processed_secondaryfile[
"location"
]
if not sf_location:
if "/" in d_location:
sf_location = (
d_location[0 : d_location.rindex("/") + 1]
+ sfname
)
else:
sf_location = f'{d_location}{sfname}'
sfbasename = sfname
elif isinstance(sfname, MutableMapping):
sf_location = sfname["location"]
Expand Down Expand Up @@ -472,7 +508,7 @@ def addsf(
sfname,
)
elif discover_secondaryFiles and self.fs_access.exists(
sf_location
cast(str, sf_location)
):
addsf(
cast(
Expand Down