Handle json.load() exceptions

CHANGELOG.md

@@ -19,6 +19,8 @@
 ### General
 
 - 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/lint/nextflow_config.py

@@ -146,6 +146,7 @@ def nextflow_config(self):
         "params.singleEnd",
         "params.igenomesIgnore",
         "params.name",
+        "params.enable_conda",
     ]
 
     # Remove field that should be ignored according to the linting config

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/pipeline-template/lib/WorkflowMain.groovy

@@ -75,11 +75,6 @@ class WorkflowMain {
         // Check that a -profile or Nextflow config has been provided to run the pipeline
         NfcoreTemplate.checkConfigProvided(workflow, log)
 
-        // Check that conda channels are set-up correctly
-        if (params.enable_conda) {
-            Utils.checkCondaChannels(log)
-        }
-
         // Check AWS batch settings
         NfcoreTemplate.awsBatch(workflow, params)
 

nf_core/pipeline-template/modules.json

@@ -7,17 +7,17 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     }
                 }

nf_core/pipeline-template/nextflow.config

@@ -41,7 +41,6 @@ params {
     validate_params            = true
     show_hidden_params         = false
     schema_ignore_params       = 'genomes'
-    enable_conda               = false
 {% if nf_core_configs %}
 
     // Config options
@@ -84,7 +83,6 @@ try {
 profiles {
     debug { process.beforeScript = 'echo $HOSTNAME' }
     conda {
-        params.enable_conda    = true
         conda.enabled          = true
         docker.enabled         = false
         singularity.enabled    = false
@@ -93,7 +91,6 @@ profiles {
         charliecloud.enabled   = false
     }
     mamba {
-        params.enable_conda    = true
         conda.enabled          = true
         conda.useMamba         = true
         docker.enabled         = false

nf_core/pipeline-template/nextflow_schema.json

@@ -263,12 +263,6 @@
                     "description": "Show all params when using `--help`",
                     "hidden": true,
                     "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
-                },
-                "enable_conda": {
-                    "type": "boolean",
-                    "description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.",
-                    "hidden": true,
-                    "fa_icon": "fas fa-bacon"
                 }
             }
         }

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/modules/update.py

@@ -303,6 +303,12 @@ def test_update_only_show_differences(self, mock_prompt):
     modules_json = ModulesJson(self.pipeline_dir)
     update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=True)
 
+    # Update modules to a fixed old SHA
+    update_old = ModuleUpdate(
+        self.pipeline_dir, update_all=True, show_diff=False, sha="5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+    )
+    update_old.update()
+
     tmpdir = tempfile.mkdtemp()
     shutil.rmtree(tmpdir)
     shutil.copytree(Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME), tmpdir)
@@ -329,6 +335,12 @@ def test_update_only_show_differences_when_patch(self, mock_prompt):
     modules_json = ModulesJson(self.pipeline_dir)
     update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=True)
 
+    # Update modules to a fixed old SHA
+    update_old = ModuleUpdate(
+        self.pipeline_dir, update_all=True, show_diff=False, sha="5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+    )
+    update_old.update()
+
     # Modify fastqc module, it will have a patch which will be applied during update
     # We modify fastqc because it's one of the modules that can be updated and there's another one before it (custom/dumpsoftwareversions)
     module_path = Path(self.pipeline_dir, "modules", "nf-core", "fastqc")

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