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Merge pull request #2074 from fabianegli/format-in-modules-json-dump
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Always format modules.json after writing it
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@fabianegli
fabianegli authored Dec 5, 2022
2 parents b9d9682 + c98c5c7 commit f0b6c48
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Showing 3 changed files with 29 additions and 30 deletions.
11 changes: 6 additions & 5 deletions nf_core/lint_utils.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -72,8 +72,9 @@ def run_prettier_on_file(file):
)
except subprocess.CalledProcessError as e:
if ": SyntaxError: " in e.stdout.decode():
raise ValueError(f"Can't format {file} because it has a synthax error.\n{e.stdout.decode()}") from e
raise ValueError(
"There was an error running the prettier pre-commit hook.\n"
f"STDOUT: {e.stdout.decode()}\nSTDERR: {e.stderr.decode()}"
) from e
log.critical(f"Can't format {file} because it has a syntax error.\n{e.stdout.decode()}")
else:
log.warning(
"There was an error running the prettier pre-commit hook.\n"
f"STDOUT: {e.stdout.decode()}\nSTDERR: {e.stderr.decode()}"
)
38 changes: 18 additions & 20 deletions nf_core/modules/modules_json.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@

import nf_core.utils
from nf_core.components.components_utils import get_components_to_install
from nf_core.lint_utils import run_prettier_on_file
from nf_core.modules.modules_repo import (
NF_CORE_MODULES_NAME,
NF_CORE_MODULES_REMOTE,
Expand All @@ -39,6 +40,7 @@ def __init__(self, pipeline_dir):
self.dir = pipeline_dir
self.modules_dir = Path(self.dir, "modules")
self.subworkflows_dir = Path(self.dir, "subworkflows")
self.modules_json_path = Path(self.dir, "modules.json")
self.modules_json = None
self.pipeline_modules = None
self.pipeline_subworkflows = None
Expand All @@ -62,7 +64,7 @@ def create(self):
pipeline_config = nf_core.utils.fetch_wf_config(self.dir)
pipeline_name = pipeline_config.get("manifest.name", "")
pipeline_url = pipeline_config.get("manifest.homePage", "")
modules_json = {"name": pipeline_name.strip("'"), "homePage": pipeline_url.strip("'"), "repos": {}}
new_modules_json = {"name": pipeline_name.strip("'"), "homePage": pipeline_url.strip("'"), "repos": {}}

if not self.modules_dir.exists():
raise UserWarning("Can't find a ./modules directory. Is this a DSL2 pipeline?")
Expand All @@ -74,29 +76,26 @@ def create(self):
repo_module_names = self.get_component_names_from_repo(repos, self.modules_dir)
repo_subworkflow_names = self.get_component_names_from_repo(repos, self.subworkflows_dir)

# Add module/subworkflow info into modules_json
# Add module/subworkflow info
for repo_url, module_names, install_dir in sorted(repo_module_names):
modules_json["repos"][repo_url] = {}
modules_json["repos"][repo_url]["modules"] = {}
modules_json["repos"][repo_url]["modules"][install_dir] = {}
modules_json["repos"][repo_url]["modules"][install_dir] = self.determine_branches_and_shas(
new_modules_json["repos"][repo_url] = {}
new_modules_json["repos"][repo_url]["modules"] = {}
new_modules_json["repos"][repo_url]["modules"][install_dir] = {}
new_modules_json["repos"][repo_url]["modules"][install_dir] = self.determine_branches_and_shas(
"modules", install_dir, repo_url, module_names
)
for repo_url, subworkflow_names, install_dir in sorted(repo_subworkflow_names):
if repo_url not in modules_json["repos"]: # Don't overwrite the repo if it was already added by modules
modules_json["repos"][repo_url] = {}
modules_json["repos"][repo_url]["subworkflows"] = {}
modules_json["repos"][repo_url]["subworkflows"][install_dir] = {}
modules_json["repos"][repo_url]["subworkflows"][install_dir] = self.determine_branches_and_shas(
if repo_url not in new_modules_json["repos"]: # Don't overwrite the repo if it was already added by modules
new_modules_json["repos"][repo_url] = {}
new_modules_json["repos"][repo_url]["subworkflows"] = {}
new_modules_json["repos"][repo_url]["subworkflows"][install_dir] = {}
new_modules_json["repos"][repo_url]["subworkflows"][install_dir] = self.determine_branches_and_shas(
"subworkflows", install_dir, repo_url, subworkflow_names
)

# write the modules.json file and assign it to the object
modules_json_path = Path(self.dir, "modules.json")
with open(modules_json_path, "w") as fh:
json.dump(modules_json, fh, indent=4)
fh.write("\n")
self.modules_json = modules_json
self.modules_json = new_modules_json
self.dump()

def get_component_names_from_repo(self, repos, directory):
"""
Expand Down Expand Up @@ -617,9 +616,8 @@ def load(self):
Raises:
UserWarning: If the modules.json file is not found
"""
modules_json_path = os.path.join(self.dir, "modules.json")
try:
with open(modules_json_path, "r") as fh:
with open(self.modules_json_path, "r") as fh:
self.modules_json = json.load(fh)
except FileNotFoundError:
raise UserWarning("File 'modules.json' is missing")
Expand Down Expand Up @@ -1025,10 +1023,10 @@ def dump(self):
"""
# Sort the modules.json
self.modules_json["repos"] = nf_core.utils.sort_dictionary(self.modules_json["repos"])
modules_json_path = os.path.join(self.dir, "modules.json")
with open(modules_json_path, "w") as fh:
with open(self.modules_json_path, "w") as fh:
json.dump(self.modules_json, fh, indent=4)
fh.write("\n")
run_prettier_on_file(self.modules_json_path)

def resolve_missing_installation(self, missing_installation, component_type):
missing_but_in_mod_json = [
Expand Down
10 changes: 5 additions & 5 deletions tests/test_lint_utils.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ def git_dir_with_json_malformed(temp_git_repo):
return file


@pytest.fixture(name="synthax_error_json")
@pytest.fixture(name="syntax_error_json")
def git_dir_with_json_syntax_error(temp_git_repo):
tmp_git_dir, repo = temp_git_repo
file = tmp_git_dir / "synthax-error.json"
Expand All @@ -59,7 +59,7 @@ def test_run_prettier_on_malformed_file(malformed_json):
assert malformed_json.read_text() == JSON_FORMATTED


def test_run_prettier_on_synthax_error_file(synthax_error_json):
with pytest.raises(ValueError) as exc_info:
nf_core.lint_utils.run_prettier_on_file(synthax_error_json)
assert exc_info.value.args[0].startswith(f"Can't format {synthax_error_json} because it has a synthax error.")
def test_run_prettier_on_syntax_error_file(syntax_error_json, caplog):
nf_core.lint_utils.run_prettier_on_file(syntax_error_json)
expected_critical_log = "SyntaxError: Unexpected token (1:10)"
assert expected_critical_log in caplog.text

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