Update modules install to support version control

nf_core/modules/pipeline_modules.py

@@ -241,6 +241,36 @@ def install(self, module=None):
             self.modules_repo.download_gh_file(dl_filename, api_url)
         log.info("Downloaded {} files to {}".format(len(files), module_dir))
 
+        # Update module.json with new module
+        modules_json_path = os.path.join(self.pipeline_dir, "modules.json")
+        with open(modules_json_path, "r") as fh:
+            modules_json = json.load(fh)
+        try:
+            commit_sha = self.get_module_commit_sha(module)
+        except SystemError as e:
+            log.error(e)
+            log.error(f"Will remove module '{module}'")
+            # Remove the module
+            try:
+                shutil.rmtree(module_dir)
+                # Try cleaning up empty parent if tool/subtool and tool/ is empty
+                if module.count("/") > 0:
+                    parent_dir = os.path.dirname(module_dir)
+                    try:
+                        os.rmdir(parent_dir)
+                    except OSError:
+                        log.debug(f"Parent directory not empty: '{parent_dir}'")
+                    else:
+                        log.debug(f"Deleted orphan tool directory: '{parent_dir}'")
+                return False
+            except OSError as e:
+                log.error("Could not remove module: {}".format(e))
+                return False
+
+        modules_json["modules"][module] = {"git_sha": commit_sha}
+        with open(modules_json_path, "w") as fh:
+            json.dump(modules_json, fh, indent=4)
+
     def update(self, module, force=False):
         log.error("This command is not yet implemented")
         pass
@@ -317,3 +347,43 @@ def has_valid_pipeline(self):
         nf_config = os.path.join(self.pipeline_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.pipeline_dir}'")
+        self.has_modules_file()
+        return True
+
+    def has_modules_file(self):
+        """Checks whether a module.json file has been created and creates one if it is missing"""
+        modules_json_path = os.path.join(self.pipeline_dir, "modules.json")
+        if not os.path.exists(modules_json_path):
+            log.info("Creating missing 'modules.json' file.")
+            pipeline_config = nf_core.utils.fetch_wf_config(self.pipeline_dir)
+            pipeline_name = pipeline_config["manifest.name"]
+            pipeline_url = pipeline_config["manifest.homePage"]
+            modules_json = {"name": pipeline_name.strip("'"), "homePage": pipeline_url.strip("'"), "modules": {}}
+            module_names = [
+                path.replace(f"{self.pipeline_dir}/modules/nf-core/software/", "")
+                for path in glob.glob(f"{self.pipeline_dir}/modules/nf-core/software/*")
+            ]
+            for module_name in module_names:
+                try:
+                    commit_sha = self.get_module_commit_sha(module_name)
+                    modules_json["modules"][module_name] = {"git_sha": commit_sha}
+                except SystemError as e:
+                    log.error(e)
+                    log.error("Will not create 'modules.json' file")
+                    sys.exit(1)
+            modules_json_path = os.path.join(self.pipeline_dir, "modules.json")
+            with open(modules_json_path, "w") as fh:
+                json.dump(modules_json, fh, indent=4)
+
+    def get_module_commit_sha(self, module_name):
+        """Fetches the latests commit SHA for the requested module"""
+        api_url = f'https://api.github.com/repos/nf-core/modules/commits/master?q={{path="software/{module_name}"}}'
+        response = requests.get(api_url, auth=nf_core.utils.github_api_auto_auth())
+        if response.status_code == 200:
+            json_response = response.json()
+            return json_response["sha"]
+        elif response.status_code == 404:
+            log.error(f"Module '{module_name}' not found in 'nf-core/modules/'\n{api_url}")
+            sys.exit(1)
+        else:
+            raise SystemError(f"Unable to fetch commit SHA for module {module_name}")