Merge pull request #2134 from mirpedrol/handle-json-exception

Handle json.load() exceptions

CHANGELOG.md

@@ -20,6 +20,7 @@
 
 - Only check that a pipeline name doesn't contain dashes if the name is provided by prompt of `--name`. Don't check if a template file is used. ([#2123](https://github.com/nf-core/tools/pull/2123))
 - Deprecate `--enable_conda` parameter. Use `conda.enable` instead ([#2131](https://github.com/nf-core/tools/pull/2131))
+- Handle `json.load()` exceptions ([#2134](https://github.com/nf-core/tools/pull/2134))
 
 ## [v2.7.1 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.1) - [2022-12-08]
 

nf_core/modules/modules_json.py

@@ -618,7 +618,11 @@ def load(self):
         """
         try:
             with open(self.modules_json_path, "r") as fh:
-                self.modules_json = json.load(fh)
+                try:
+                    self.modules_json = json.load(fh)
+                except json.JSONDecodeError as e:
+                    raise UserWarning(f"Unable to load JSON file '{self.modules_json_path}' due to error {e}")
+
         except FileNotFoundError:
             raise UserWarning("File 'modules.json' is missing")
 

nf_core/schema.py

@@ -182,7 +182,10 @@ def load_input_params(self, params_path):
         # First, try to load as JSON
         try:
             with open(params_path, "r") as fh:
-                params = json.load(fh)
+                try:
+                    params = json.load(fh)
+                except json.JSONDecodeError as e:
+                    raise UserWarning(f"Unable to load JSON file '{params_path}' due to error {e}")
                 self.input_params.update(params)
             log.debug(f"Loaded JSON input params: {params_path}")
         except Exception as json_e:

nf_core/utils.py

@@ -248,7 +248,10 @@ def fetch_wf_config(wf_path, cache_config=True):
         if os.path.isfile(cache_path):
             log.debug(f"Found a config cache, loading: {cache_path}")
             with open(cache_path, "r") as fh:
-                config = json.load(fh)
+                try:
+                    config = json.load(fh)
+                except json.JSONDecodeError as e:
+                    raise UserWarning(f"Unable to load JSON file '{cache_path}' due to error {e}")
             return config
     log.debug("No config cache found")
 

tests/modules/modules_json.py

@@ -18,7 +18,10 @@ def test_get_modules_json(self):
     """Checks that the get_modules_json function returns the correct result"""
     mod_json_path = os.path.join(self.pipeline_dir, "modules.json")
     with open(mod_json_path, "r") as fh:
-        mod_json_sb = json.load(fh)
+        try:
+            mod_json_sb = json.load(fh)
+        except json.JSONDecodeError as e:
+            raise UserWarning(f"Unable to load JSON file '{mod_json_path}' due to error {e}")
 
     mod_json_obj = ModulesJson(self.pipeline_dir)
     mod_json = mod_json_obj.get_modules_json()
@@ -212,7 +215,10 @@ def test_mod_json_dump(self):
 
     # Check that the dump function writes the correct content
     with open(mod_json_path, "r") as f:
-        mod_json_new = json.load(f)
+        try:
+            mod_json_new = json.load(f)
+        except json.JSONDecodeError as e:
+            raise UserWarning(f"Unable to load JSON file '{mod_json_path}' due to error {e}")
     assert mod_json == mod_json_new
 
 

tests/test_launch.py

@@ -327,7 +327,11 @@ def test_build_command_params(self):
         )
         # Check saved parameters file
         with open(self.nf_params_fn, "r") as fh:
-            saved_json = json.load(fh)
+            try:
+                saved_json = json.load(fh)
+            except json.JSONDecodeError as e:
+                raise UserWarning(f"Unable to load JSON file '{self.nf_params_fn}' due to error {e}")
+
         assert saved_json == {"input": "custom_input"}
 
     def test_build_command_params_cl(self):

tests/test_lint.py

@@ -134,7 +134,10 @@ def test_json_output(self, tmp_dir):
 
         # Load created JSON file and check its contents
         with open(json_fn, "r") as fh:
-            saved_json = json.load(fh)
+            try:
+                saved_json = json.load(fh)
+            except json.JSONDecodeError as e:
+                raise UserWarning(f"Unable to load JSON file '{json_fn}' due to error {e}")
         assert saved_json["num_tests_pass"] > 0
         assert saved_json["num_tests_warned"] > 0
         assert saved_json["num_tests_ignored"] == 0