Always format modules.json after writing it

nf_core/lint_utils.py

@@ -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()}"
+ )

nf_core/modules/modules_json.py

@@ -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,
@@ -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
@@ -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?")
@@ -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):
  """
@@ -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")
@@ -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 = [

tests/test_lint_utils.py

@@ -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_synthax_error_file(synthax_error_json, caplog):
+ nf_core.lint_utils.run_prettier_on_file(synthax_error_json)
+ expected_critical_log = "SyntaxError: Unexpected token (1:10)"
+ assert expected_critical_log in caplog.text