Merge pull request #2124 from mirpedrol/prettier-json-schema

run prettier after dumping a json schema file

CHANGELOG.md

@@ -9,6 +9,7 @@
 ### Linting
 
 - Allow specifying containers in less than three lines ([#2121](https://github.com/nf-core/tools/pull/2121))
+- Run prettier after dumping a json schema file ([#2124](https://github.com/nf-core/tools/pull/2124))
 
 ### Modules
 

nf_core/launch.py

@@ -17,6 +17,7 @@
 
 import nf_core.schema
 import nf_core.utils
+from nf_core.lint_utils import dump_json_with_prettier
 
 log = logging.getLogger(__name__)
 
@@ -700,9 +701,7 @@ def build_command(self):
 
             # Write the user selection to a file and run nextflow with that
             if self.use_params_file:
-                with open(self.params_out, "w") as fp:
-                    json.dump(self.schema_obj.input_params, fp, indent=4)
-                    fp.write("\n")
+                dump_json_with_prettier(self.params_out, self.schema_obj.input_params)
                 self.nextflow_cmd += f' -params-file "{os.path.relpath(self.params_out)}"'
 
             # Call nextflow with a list of command line flags

nf_core/lint_utils.py

@@ -1,3 +1,4 @@
+import json
 import logging
 import subprocess
 from pathlib import Path
@@ -82,3 +83,14 @@ def run_prettier_on_file(file):
                 "There was an error running the prettier pre-commit hook.\n"
                 f"STDOUT: {e.stdout.decode()}\nSTDERR: {e.stderr.decode()}"
             )
+
+
+def dump_json_with_prettier(file_name, file_content):
+    """Dump a JSON file and run prettier on it.
+    Args:
+        file_name (Path | str): A file identifier as a string or pathlib.Path.
+        file_content (dict): Content to dump into the JSON file
+    """
+    with open(file_name, "w") as fh:
+        json.dump(file_content, fh, indent=4)
+    run_prettier_on_file(file_name)

nf_core/modules/modules_json.py

@@ -13,7 +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.lint_utils import dump_json_with_prettier
 from nf_core.modules.modules_repo import (
     NF_CORE_MODULES_NAME,
     NF_CORE_MODULES_REMOTE,
@@ -1023,10 +1023,7 @@ def dump(self):
         """
         # Sort the modules.json
         self.modules_json["repos"] = nf_core.utils.sort_dictionary(self.modules_json["repos"])
-        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)
+        dump_json_with_prettier(self.modules_json_path, self.modules_json)
 
     def resolve_missing_installation(self, missing_installation, component_type):
         missing_but_in_mod_json = [

nf_core/schema.py

@@ -16,6 +16,7 @@
 
 import nf_core.list
 import nf_core.utils
+from nf_core.lint_utils import dump_json_with_prettier
 
 log = logging.getLogger(__name__)
 
@@ -170,9 +171,7 @@ def save_schema(self, suppress_logging=False):
         num_params += sum(len(d.get("properties", {})) for d in self.schema.get("definitions", {}).values())
         if not suppress_logging:
             log.info(f"Writing schema with {num_params} params: '{self.schema_filename}'")
-        with open(self.schema_filename, "w") as fh:
-            json.dump(self.schema, fh, indent=4)
-            fh.write("\n")
+        dump_json_with_prettier(self.schema_filename, self.schema)
 
     def load_input_params(self, params_path):
         """Load a given a path to a parameters file (JSON/YAML)