commands/update_cmd: refactor to use AutoProcess 'sync_project_metadata_file'.

Updates the 'update' command to use the 'sync_project_metadata_file' AutoProcess method to synchronise 'projects.info' with the directories on the filesystem.

Author: pjbriggs

auto_process_ngs/commands/update_cmd.py

@@ -56,54 +56,9 @@ def update(ap, update_paths=True, update_project_metadata=True,
         ap.update_paths()
 
     if update_sync_projects:
-        # Load information from 'projects.info'
-        project_metadata = ap.load_project_metadata(
-            ap.params.project_metadata)
-        # Comment out projects which don't exist on filesystem
-        save_required = False
-        for line in project_metadata:
-            # Iterate through the named projects
-            name = line['Project']
-            if name.startswith('#'):
-                # Commented out, ignore
-                continue
-            # Look for a matching project directory
-            project_dir = os.path.join(ap.analysis_dir, name)
-            if not os.path.exists(project_dir):
-                print(f"Commenting out missing project '{name}'")
-                line['Project'] = f"#{name}"
-                save_required = True
-        if save_required:
-            project_metadata.save()
-        # Add any project directories without entries
-        save_required = False
-        projects = [line['Project'] for line in project_metadata]
-        for project in ap.get_analysis_projects_from_dirs():
-            if project.name.endswith(".bak") \
-                    or project.name.endswith(".orig") \
-                    or project.name.endswith(".tmp"):
-                # Skip directories with extensions indicating they
-                # should be ignored
-                print(f"Not adding entry for unlisted project '{project.name}'")
-                continue
-            elif project.name == "undetermined":
-                # Skip undetermined
-                continue
-            elif project.name not in projects and f"#{project.name}" not in projects:
-                # Add new entry
-                print(f"Adding entry for unlisted project '{project.name}'")
-                project_metadata.add_project(project.name,
-                                             [s.name for s in project.samples],
-                                             user=project.info.user,
-                                             PI=project.info.PI,
-                                             organism=project.info.organism,
-                                             library_type=project.info.library_type,
-                                             sc_platform=project.info.single_cell_platform,
-                                             comments=project.info.comments)
-                save_required = True
-        # Save the updated project metadata if required
-        if save_required:
-            project_metadata.save()
+        # Synchronise projects listed in 'projects.info'
+        # with contents of analysis directory
+        ap.sync_project_metadata_file()
 
     if update_project_metadata:
         # Update project metadata