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fix: failure to properly apply default remote prefix in combination w…
…ith the unpack marker (#1448)

* fix: failure to properly apply default remote prefix in combination with the unpack marker

* only in case of from_callable
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johanneskoester committed Mar 1, 2022
1 parent dd27209 commit 82666f1b2b043f0a8de739d7027aba66eccdaee3
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Showing 4 changed files with 41 additions and 6 deletions.
@@ -787,8 +787,6 @@ def _apply_wildcards(
groupid=groupid,
**aux_params
)
if apply_path_modifier and not incomplete:
item = self.apply_path_modifier(item, property=property)

if is_unpack and not incomplete:
if not allow_unpack:
@@ -808,14 +806,14 @@ def _apply_wildcards(
)
# Allow streamlined code with/without unpack
if isinstance(item, list):
pairs = zip([None] * len(item), item)
pairs = zip([None] * len(item), item, [_is_callable] * len(item))
else:
assert isinstance(item, dict)
pairs = item.items()
pairs = [(name, item, _is_callable) for name, item in item.items()]
else:
pairs = [(name, item)]
pairs = [(name, item, _is_callable)]

for name, item in pairs:
for name, item, from_callable in pairs:
is_iterable = True
if not_iterable(item) or no_flattening:
item = [item]
@@ -829,6 +827,10 @@ def _apply_wildcards(
raise WorkflowError(
"Function did not return str or list " "of str.", rule=self
)

if from_callable and apply_path_modifier and not incomplete:
item_ = self.apply_path_modifier(item_, property=property)

concrete = concretize(item_, wildcards, _is_callable)
newitems.append(concrete)
if mapping is not None:
@@ -0,0 +1,16 @@
def get_files(wildcards):
files_1 = expand("file_{i}", i=list(range(1, 5)))
files_2 = expand("file_{i}", i=list(range(5, 9)))
return {"files_1": files_1, "files_2": files_2}


rule all:
input:
unpack(get_files),


rule make_files:
output:
expand("file_{i}", i=list(range(1, 9))),
shell:
"touch {output}"
Empty file.
@@ -109,3 +109,20 @@ def test_cloud_checkpoints_issue574():
)
finally:
cleanup_google_storage(storage_prefix, bucket_name)


def test_github_issue1396():
bucket_name = "snakemake-testing-%s" % next(tempfile._get_candidate_names())
create_google_storage(bucket_name)
storage_prefix = "test_github_issue1396"
workdir = dpath("test_github_issue1396")
try:
run(
workdir,
default_remote_prefix="%s/%s" % (bucket_name, storage_prefix),
google_lifesciences=True,
google_lifesciences_cache=False,
dryrun=True,
)
finally:
cleanup_google_storage(storage_prefix, bucket_name)

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