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modules_json.py
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modules_json.py
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from pathlib import Path
from nf_core.modules.modules_json import ModulesJson
def modules_json(self):
"""Make sure all modules described in the ``modules.json`` file are actually installed
Every module installed from ``nf-core/modules`` must have an entry in the ``modules.json`` file
with an associated version commit hash.
* Failure: If module entries are found in ``modules.json`` for modules that are not installed
"""
passed = []
warned = []
failed = []
# Load pipeline modules and modules.json
_modules_json = ModulesJson(self.wf_path)
_modules_json.load()
modules_json_dict = _modules_json.modules_json
modules_dir = Path(self.wf_path, "modules")
if _modules_json:
all_modules_passed = True
for repo in modules_json_dict["repos"].keys():
# Check if the modules.json has been updated to keep the
if "modules" not in modules_json_dict["repos"][repo] or not repo.startswith("http"):
failed.append(
"Your `modules.json` file is outdated. "
"It will be automatically generated by running any module command."
)
continue
for dir in modules_json_dict["repos"][repo]["modules"].keys():
for module, module_entry in modules_json_dict["repos"][repo]["modules"][dir].items():
if not Path(modules_dir, dir, module).exists():
failed.append(
f"Entry for `{Path(modules_dir, dir, module)}` found in `modules.json` but module is not installed in "
"pipeline."
)
all_modules_passed = False
if module_entry.get("branch") is None:
failed.append(f"Entry for `{Path(modules_dir, dir, module)}` is missing branch information.")
if module_entry.get("git_sha") is None:
failed.append(f"Entry for `{Path(modules_dir, dir, module)}` is missing version information.")
if all_modules_passed:
passed.append("Only installed modules found in `modules.json`")
else:
warned.append("Could not open `modules.json` file.")
return {"passed": passed, "warned": warned, "failed": failed}