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Don't fail linting if md5sum for empty files are found in a stub test #2571

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merged 4 commits into from
Dec 14, 2023
Merged

Don't fail linting if md5sum for empty files are found in a stub test #2571

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2439a4a
Don't fail linting if md5sum for empty files are found in a stub test
mirpedrol Dec 12, 2023
f5e00dd
update changelog
mirpedrol Dec 12, 2023
471107b
add dummy snapshot file content to fix tests
mirpedrol Dec 12, 2023
40ee3b2
Merge branch 'dev' into empty-file-stub
mirpedrol Dec 14, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@
- Correctly pass subworkflow linting test if `COMPONENT.out.versions` is used in the script ([#2448](https://github.com/nf-core/tools/pull/2448))
- Check for spaces in modules container URLs ([#2452](https://github.com/nf-core/tools/issues/2452))
- Correctly ignore `timeline.enabled`, `report.enabled`, `trace.enabled`, `dag.enabled` variables when linting a pipeline. ([#2507](https://github.com/nf-core/tools/pull/2507))
- Don't fail linting if md5sum for empty files are found in a stub test ([#2571](https://github.com/nf-core/tools/pull/2571))

### Modules

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82 changes: 51 additions & 31 deletions nf_core/modules/lint/module_tests.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
"""
Lint the tests of a module in nf-core/modules
"""
import json
import logging
from pathlib import Path

Expand Down Expand Up @@ -52,39 +53,58 @@ def module_tests(_, module: NFCoreComponent):
)
# Validate no empty files
with open(snap_file, "r") as snap_fh:
snap_content = snap_fh.read()
if "d41d8cd98f00b204e9800998ecf8427e" in snap_content:
module.failed.append(
(
"test_snap_md5sum",
"md5sum for empty file found: d41d8cd98f00b204e9800998ecf8427e",
snap_file,
snap_content = json.load(snap_fh)
for test_name in snap_content.keys():
if "d41d8cd98f00b204e9800998ecf8427e" in str(snap_content[test_name]):
if "stub" not in test_name:
module.failed.append(
(
"test_snap_md5sum",
"md5sum for empty file found: d41d8cd98f00b204e9800998ecf8427e",
snap_file,
)
)
else:
module.passed.append(
(
"test_snap_md5sum",
"md5sum for empty file found, but it is a stub test",
snap_file,
)
)
else:
module.passed.append(
(
"test_snap_md5sum",
"no md5sum for empty file found",
snap_file,
)
)
)
else:
module.passed.append(
(
"test_snap_md5sum",
"no md5sum for empty file found",
snap_file,
if "7029066c27ac6f5ef18d660d5741979a" in str(snap_content[test_name]):
if "stub" not in test_name:
module.failed.append(
(
"test_snap_md5sum",
"md5sum for compressed empty file found: 7029066c27ac6f5ef18d660d5741979a",
snap_file,
)
)
else:
module.passed.append(
(
"test_snap_md5sum",
"md5sum for compressed empty file found, but it is a stub test",
snap_file,
)
)
else:
module.passed.append(
(
"test_snap_md5sum",
"no md5sum for compressed empty file found",
snap_file,
)
)
)
if "7029066c27ac6f5ef18d660d5741979a" in snap_content:
module.failed.append(
(
"test_snap_md5sum",
"md5sum for compressed empty file found: 7029066c27ac6f5ef18d660d5741979a",
snap_file,
)
)
else:
module.passed.append(
(
"test_snap_md5sum",
"no md5sum for compressed empty file found",
snap_file,
)
)
else:
module.failed.append(
("test_snapshot_exists", "snapshot file `main.nf.test.snap` does not exist", snap_file)
Expand Down
82 changes: 51 additions & 31 deletions nf_core/subworkflows/lint/subworkflow_tests.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
"""
Lint the tests of a subworkflow in nf-core/modules
"""
import json
import logging
from pathlib import Path

Expand Down Expand Up @@ -59,39 +60,58 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent):
subworkflow.passed.append(("test_snapshot_exists", "test `main.nf.test.snap` exists", snap_file))
# Validate no empty files
with open(snap_file, "r") as snap_fh:
snap_content = snap_fh.read()
if "d41d8cd98f00b204e9800998ecf8427e" in snap_content:
subworkflow.failed.append(
(
"test_snap_md5sum",
"md5sum for empty file found: d41d8cd98f00b204e9800998ecf8427e",
snap_file,
snap_content = json.load(snap_fh)
for test_name in snap_content.keys():
if "d41d8cd98f00b204e9800998ecf8427e" in str(snap_content[test_name]):
if "stub" not in test_name:
subworkflow.failed.append(
(
"test_snap_md5sum",
"md5sum for empty file found: d41d8cd98f00b204e9800998ecf8427e",
snap_file,
)
)
else:
subworkflow.passed.append(
(
"test_snap_md5sum",
"md5sum for empty file found, but it is a stub test",
snap_file,
)
)
else:
subworkflow.passed.append(
(
"test_snap_md5sum",
"no md5sum for empty file found",
snap_file,
)
)
)
else:
subworkflow.passed.append(
(
"test_snap_md5sum",
"no md5sum for empty file found",
snap_file,
if "7029066c27ac6f5ef18d660d5741979a" in str(snap_content[test_name]):
if "stub" not in test_name:
subworkflow.failed.append(
(
"test_snap_md5sum",
"md5sum for compressed empty file found: 7029066c27ac6f5ef18d660d5741979a",
snap_file,
)
)
else:
subworkflow.failed.append(
(
"test_snap_md5sum",
"md5sum for compressed empty file found, but it is a stub test",
snap_file,
)
)
else:
subworkflow.passed.append(
(
"test_snap_md5sum",
"no md5sum for compressed empty file found",
snap_file,
)
)
)
if "7029066c27ac6f5ef18d660d5741979a" in snap_content:
subworkflow.failed.append(
(
"test_snap_md5sum",
"md5sum for compressed empty file found: 7029066c27ac6f5ef18d660d5741979a",
snap_file,
)
)
else:
subworkflow.passed.append(
(
"test_snap_md5sum",
"no md5sum for compressed empty file found",
snap_file,
)
)
else:
subworkflow.failed.append(
("test_snapshot_exists", "test `main.nf.test.snap` does not exist", snap_file)
Expand Down
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