Rename 'process' method to 'launch' across core and realms

lib/base/abstract_project.py

@@ -33,19 +33,14 @@ def __init__(self, doc: Any, yggdrasil_db_manager: Any) -> None:
         self.yggdrasil_db_manager: Any = yggdrasil_db_manager
 
     @abstractmethod
-    def pre_process(self) -> None:
-        """Handle preliminary processing specific to the realm's requirements."""
-        pass
-
-    @abstractmethod
-    async def process(self) -> None:
+    async def launch(self) -> None:
         """Define the main processing logic for the project.
 
         This method should be implemented by each project class to define how the processing
         of the document unfolds.
 
         Note:
-            Since processing might involve asynchronous operations (e.g., submitting and monitoring jobs),
+            Since its course might involve asynchronous operations (e.g., submitting and monitoring jobs),
             this method is defined as asynchronous.
         """
         pass

lib/realms/smartseq3/smartseq3.py

@@ -151,10 +151,8 @@ def ensure_project_directory(self):
             logging.error(f"Failed to create project directory: {e}")
             return None
 
-    async def process(self):
-        """
-        Process the SmartSeq3 project by handling its samples.
-        """
+    async def launch(self):
+        """Launch the SmartSeq3 Realm to handle its samples."""
         self.status = "processing"
         logging.info(
             f"Processing SmartSeq3 project {self.project_info['project_name']}"
@@ -212,15 +210,6 @@ def _generate_ngi_report(self):
         else:
             logging.error("Failed to generate the NGI report.")
 
-    def pre_process(self, doc):
-        """
-        Pre-process method placeholder.
-
-        Args:
-            doc (dict): Document to pre-process.
-        """
-        pass
-
     def create_slurm_job(self, sample):
         """
         Placeholder for creating a Slurm job on the project level.

lib/realms/tenx/tenx_project.py

@@ -397,12 +397,8 @@ def extract_samples(self) -> List[TenXRunSample]:
         run_samples = self.create_run_samples(grouped_lab_samples)
         return run_samples
 
-    def pre_process(self) -> None:
-        """Perform any pre-processing steps required before processing the project."""
-        pass
-
-    async def process(self):
-        """Process the TenX project by handling its samples."""
+    async def launch(self):
+        """Launch the TenX Realm to handle its samples."""
         logging.info(f"Processing TenX project {self.project_info['project_name']}")
         self.status = "processing"
 

ygg-mule.py

@@ -71,7 +71,7 @@ def process_document(doc_id):
             if RealmClass:
                 realm = RealmClass(document, ydm)
                 if realm.proceed:
-                    asyncio.run(realm.process())
+                    asyncio.run(realm.launch())
                     logging.info("Processing complete.")
                 else:
                     logging.info(

ygg_trunk.py

@@ -56,13 +56,12 @@ async def process_couchdb_changes():
                         RealmClass = Ygg.load_realm_class(module_loc)
 
                         if RealmClass:
-                            # Call the module's process function
+                            # Call the module's launch function
                             realm = RealmClass(data, ydm)
                             if realm.proceed:
-                                task = asyncio.create_task(realm.process())
+                                task = asyncio.create_task(realm.launch())
                                 tasks.append(task)
                                 # print(f"Tasks ({realm.project_info['project_id']}): {tasks}")
-                                # module.process(data)
                             else:
                                 logging.info(
                                     f"Skipping task creation due to missing required information. {data.get('project_id')}"