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fix: ensure that rule inheritance considers the same globals and othe…
…r settings as parent module (#1621)

* fix: ensure that workflow module globals are available for inherited rules.

* inherit from parent modifier

* add missing files

* fix GS bucket names
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johanneskoester committed May 2, 2022
1 parent fc6dfc6 commit 104cab97d9e1a7dda4c9948efa5883d5478d2229
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Showing 10 changed files with 55 additions and 8 deletions.
@@ -131,6 +131,7 @@ class WorkflowModifier:
def __init__(
self,
workflow,
parent_modifier=None,
globals=None,
config=None,
base_snakefile=None,
@@ -146,12 +147,29 @@ def __init__(
replace_wrapper_tag=None,
namespace=None,
):
if parent_modifier is not None:
# init with values from parent modifier
self.base_snakefile = parent_modifier.base_snakefile
self.globals = parent_modifier.globals
self.skip_configfile = parent_modifier.skip_configfile
self.rulename_modifier = parent_modifier.rulename_modifier
self.skip_validation = parent_modifier.skip_validation
self.skip_global_report_caption = parent_modifier.skip_global_report_caption
self.rule_whitelist = parent_modifier.rule_whitelist
self.ruleinfo_overwrite = parent_modifier.ruleinfo_overwrite
self.allow_rule_overwrite = parent_modifier.allow_rule_overwrite
self.path_modifier = parent_modifier.path_modifier
self.replace_wrapper_tag = parent_modifier.replace_wrapper_tag
self.namespace = parent_modifier.namespace
else:
# default settings for globals if not inheriting from parent
self.globals = (
globals if globals is not None else dict(workflow.vanilla_globals)
)

self.workflow = workflow
self.base_snakefile = base_snakefile

self.globals = (
globals if globals is not None else dict(workflow.vanilla_globals)
)
if config is not None:
self.globals["config"] = config

@@ -1933,6 +1933,7 @@ def decorate(maybe_ruleinfo):
ruleinfo = maybe_ruleinfo if not callable(maybe_ruleinfo) else None
with WorkflowModifier(
self,
parent_modifier=self.modifier,
rulename_modifier=get_name_modifier_func(
rules, name_modifier, parent_modifier=self.modifier
),
@@ -1,3 +1,4 @@

from snakemake.utils import min_version

from snakemake import __version__
@@ -27,6 +28,8 @@ onerror:
print(log)




ruleorder: rule2 > rule4

def testin(wildcards):
@@ -57,9 +57,13 @@ def create_google_storage(bucket_name="snakemake-testing"):
return client.create_bucket(bucket_name)


def get_temp_bucket_name():
return "snakemake-testing-%s-bucket" % next(tempfile._get_candidate_names())


@google_credentials
def test_google_lifesciences():
bucket_name = "snakemake-testing-%s" % next(tempfile._get_candidate_names())
bucket_name = get_temp_bucket_name()
create_google_storage(bucket_name)
storage_prefix = "test_google_lifesciences"
workdir = dpath("test_google_lifesciences")
@@ -82,7 +86,7 @@ def test_google_lifesciences():
)
@google_credentials
def test_touch_remote_prefix():
bucket_name = "snakemake-testing-%s-bucket" % next(tempfile._get_candidate_names())
bucket_name = get_temp_bucket_name()
create_google_storage(bucket_name)
storage_prefix = "test_touch_remote_prefix"
workdir = dpath("test_touch_remote_prefix")
@@ -101,7 +105,7 @@ def test_touch_remote_prefix():
@google_credentials
def test_cloud_checkpoints_issue574():
"""see Github issue #574"""
bucket_name = "snakemake-testing-%s" % next(tempfile._get_candidate_names())
bucket_name = get_temp_bucket_name()
create_google_storage(bucket_name)
storage_prefix = "test_cloud_checkpoints_issue574"
workdir = dpath("test_cloud_checkpoints_issue574")
@@ -118,7 +122,7 @@ def test_cloud_checkpoints_issue574():


def test_github_issue1396():
bucket_name = "snakemake-testing-%s" % next(tempfile._get_candidate_names())
bucket_name = get_temp_bucket_name()
create_google_storage(bucket_name)
storage_prefix = "test_github_issue1396"
workdir = dpath("test_github_issue1396")
@@ -135,7 +139,7 @@ def test_github_issue1396():


def test_github_issue1460():
bucket_name = "snakemake-testing-%s" % next(tempfile._get_candidate_names())
bucket_name = get_temp_bucket_name()
create_google_storage(bucket_name)
storage_prefix = "test_github_issue1460"
prefix = "%s/%s" % (bucket_name, storage_prefix)
@@ -0,0 +1 @@
{"version": null, "code": "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", "rule": "b", "input": [], "log": [], "params": [], "shellcmd": "echo test '{}' > foo.txt", "incomplete": false, "starttime": 1651478820.4933672, "endtime": 1651478820.5000339, "job_hash": 8740185748842, "conda_env": null, "container_img_url": null}
@@ -0,0 +1,10 @@
rule a:
output:
"test.out"
shell:
"echo test '{config}' > {output}"


use rule a as b with:
output:
report("foo.txt", caption="caption.rst")
Empty file.
Empty file.
@@ -0,0 +1 @@
test {}
@@ -1614,3 +1614,12 @@ def test_cleanup_metadata_fail():
@skip_on_windows # same on win, no need to test
def test_github_issue1389():
run(dpath("test_github_issue1389"), resources={"foo": 4}, shouldfail=True)


def test_rule_inheritance_globals():
run(
dpath("test_rule_inheritance_globals"),
report="report.html",
targets=["foo.txt"],
check_md5=False,
)

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