Give better suggestion when modules.json file is out-of-date.

CHANGELOG.md

@@ -72,6 +72,7 @@
 - Fix misc. issues with `--branch` and `--base-path` ([#1726](https://github.com/nf-core/tools/issues/1726))
 - Add `branch` field to module entries in `modules.json` to record what branch a module was installed from ([#1728](https://github.com/nf-core/tools/issues/1728))
 - Fix unbound variable issues and minor refactoring [#1742](https://github.com/nf-core/tools/pull/1742/)
+- Recreate modules.json file instead of complaining about incorrectly formatted file. ([#1741](https://github.com/nf-core/tools/pull/1741)
 
 ## [v2.4.1 - Cobolt Koala Patch](https://github.com/nf-core/tools/releases/tag/2.4) - [2022-05-16]
 

nf_core/lint/__init__.py

@@ -86,8 +86,9 @@ def run_linting(
     # Create the modules lint object
     module_lint_obj = nf_core.modules.lint.ModuleLint(pipeline_dir)
 
-    # Verify that the pipeline is correctly configured
+    # Verify that the pipeline is correctly configured and has  a modules.json file
     module_lint_obj.has_valid_directory()
+    module_lint_obj.has_modules_file()
 
     # Run only the tests we want
     if key:

nf_core/modules/list.py

@@ -93,7 +93,7 @@ def pattern_msg(keywords):
                     repo_modules = repo_entry.get("modules")
                     if repo_modules is None:
                         raise UserWarning(
-                            "You 'modules.json' file is not up to date. Please remove it and rerun the command"
+                            "You 'modules.json' file is not up to date. You can fix it by running 'nf-core modules update'."
                         )
                     module_entry = repo_modules.get(module)
 

nf_core/modules/modules_command.py

@@ -62,7 +62,6 @@ def has_valid_directory(self):
         nf_config = os.path.join(self.dir, "nextflow.config")
         if not os.path.exists(main_nf) and not os.path.exists(nf_config):
             raise UserWarning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.dir}'")
-        self.has_modules_file()
         return True
 
     def has_modules_file(self):

nf_core/modules/modules_json.py

@@ -74,11 +74,12 @@ def create(self):
             modules_json["repos"][repo_name]["modules"] = self.determine_module_branches_and_shas(
                 repo_name, remote_url, base_path, module_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
 
     def get_pipeline_module_repositories(self, modules_dir, repos=None):
         """
@@ -354,7 +355,7 @@ def unsynced_modules(self):
                     if "git_sha" not in modules[module] or "branch" not in modules[module]:
                         raise UserWarning(
                             "The 'modules.json' file is not up to date. "
-                            "Please reinstall it by removing it and rerunning the command."
+                            "You can fix it by running 'nf-core modules update'."
                         )
                     missing_installation[module_repo_name]["modules"].pop(module)
                     if len(missing_installation[module_repo_name]["modules"]) == 0:
@@ -368,7 +369,7 @@ def unsynced_modules(self):
     def has_git_url_and_base_path(self):
         """
         Check that that all repo entries in the modules.json
-        has a git url and a base_path
+        have a git url and a base_path
 
         Returns:
             (bool): True if they are found for all repos, False otherwise
@@ -430,12 +431,13 @@ def check_up_to_date(self):
         If a module is installed but the entry in 'modules.json' is missing we iterate through
         the commit log in the remote to try to determine the SHA.
         """
-        self.load()
-        if not self.has_git_url_and_base_path():
-            raise UserWarning(
-                "The 'modules.json' file is not up to date. "
-                "Please reinstall it by removing it and rerunning the command."
-            )
+        try:
+            self.load()
+            if not self.has_git_url_and_base_path():
+                raise KeyError
+        except (UserWarning, KeyError):
+            log.info("The 'modules.json' file is not up to date. Recreating the 'module.json' file.")
+            self.create()
 
         missing_from_modules_json, missing_installation = self.unsynced_modules()
 

nf_core/modules/remove.py

@@ -28,8 +28,9 @@ def remove(self, module):
             log.error("You cannot remove a module in a clone of nf-core/modules")
             return False
 
-        # Check whether pipelines is valid
+        # Check whether pipeline is valid and with a modules.json file
         self.has_valid_directory()
+        self.has_modules_file()
 
         repo_name = self.modules_repo.fullname
         if module is None:

tests/modules/modules_json.py

@@ -1,3 +1,4 @@
+import copy
 import json
 import os
 import shutil
@@ -176,3 +177,18 @@ def test_mod_json_dump(self):
     with open(mod_json_path, "r") as f:
         mod_json_new = json.load(f)
     assert mod_json == mod_json_new
+
+
+def test_mod_json_with_missing_base_path_fail(self):
+    # Load module.json and remove the base_path entry
+    mod_json_obj = ModulesJson(self.pipeline_dir)
+    mod_json_orig = mod_json_obj.get_modules_json()
+    mod_json = copy.deepcopy(mod_json_orig)
+    mod_json["repos"]["nf-core/modules"].pop("base_path")
+    # save the altered module.json and load it again to check if it will fix itself
+    mod_json_obj.modules_json = mod_json
+    mod_json_obj.dump()
+    mod_json_obj_new = ModulesJson(self.pipeline_dir)
+    mod_json_obj_new.check_up_to_date()
+    mod_json_new = mod_json_obj_new.get_modules_json()
+    assert mod_json_orig == mod_json_new

tests/test_modules.py

@@ -142,6 +142,7 @@ def test_modulesrepo_class(self):
         test_mod_json_up_to_date_module_removed,
         test_mod_json_up_to_date_reinstall_fails,
         test_mod_json_update,
+        test_mod_json_with_missing_base_path_fail,
     )
     from .modules.patch import (
         test_create_patch_change,