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Tweak handling of empty files when generating the test YAML #1442

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Mar 14, 2022
Merged

Tweak handling of empty files when generating the test YAML #1442

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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,9 @@
* Added `--conda-package-version` flag for specifying version of conda package in `nf-core modules create`. ([#1238](https://github.com/nf-core/tools/issues/1238))
* Add option of writing diffs to file in `nf-core modules update` using either interactive prompts or the new `--diff-file` flag.
* Fixed edge case where module names that were substrings of other modules caused both to be installed ([#1380](https://github.com/nf-core/tools/issues/1380))
* Tweak handling of empty files when generating the test YAML ([#1376](https://github.com/nf-core/tools/issues/1376))
* Fail linting if a md5sum for an empty file is found (instead of a warning)
* Don't skip the md5 when generating a test file if an empty file is found (so that linting fails and can be manually checked)

## [v2.2 - Lead Liger](https://github.com/nf-core/tools/releases/tag/2.2) - [2021-12-14]

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4 changes: 2 additions & 2 deletions nf_core/modules/lint/module_tests.py
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Expand Up @@ -55,15 +55,15 @@ def module_tests(module_lint_object, module):
# Look for md5sums of empty files
for tfile in test.get("files", []):
if tfile.get("md5sum") == "d41d8cd98f00b204e9800998ecf8427e":
module.warned.append(
module.failed.append(
(
"test_yml_md5sum",
"md5sum for empty file found: d41d8cd98f00b204e9800998ecf8427e",
module.test_yml,
)
)
if tfile.get("md5sum") == "7029066c27ac6f5ef18d660d5741979a":
module.warned.append(
module.failed.append(
(
"test_yml_md5sum",
"md5sum for compressed empty file found: 7029066c27ac6f5ef18d660d5741979a",
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10 changes: 6 additions & 4 deletions nf_core/modules/test_yml_builder.py
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Expand Up @@ -232,10 +232,12 @@ def create_test_file_dict(self, results_dir, is_repeat=False):
# Check that this isn't an empty file
if self.check_if_empty_file(elem):
if not is_repeat:
self.errors.append(f"Empty file, skipping md5sum: '{os.path.basename(elem)}'")
else:
elem_md5 = self._md5(elem)
test_file["md5sum"] = elem_md5
self.errors.append(f"Empty file found! '{os.path.basename(elem)}'")
# Add the md5 anyway, linting should fail later and can be manually removed if needed.
# Originally we skipped this if empty, but then it's too easy to miss the warning.
# Equally, if a file is legitimately empty we don't want to prevent this from working.
elem_md5 = self._md5(elem)
test_file["md5sum"] = elem_md5
# Switch out the results directory path with the expected 'output' directory
test_file["path"] = elem.replace(results_dir, "output")
test_files.append(test_file)
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