Bug records (#90)

* fixing bug that made two record files or simulation files get the same ID
* change the location where records are mapped in setup and run, and improve the return statement

mdagent/tools/base_tools/simulation_tools/setup_and_run.py

@@ -773,8 +773,7 @@ def create_simulation(self):
                 Sim_id=self.sim_id,
                 term="txt",
             )
-            traj_id = self.path_registry.get_fileid(trajectory_name, FileType.RECORD)
-            log_id = self.path_registry.get_fileid(log_name, FileType.RECORD)
+
             traj_desc = (
                 f"Simulation trajectory for protein {self.pdb_id}"
                 f" and simulation {self.sim_id}"
@@ -801,8 +800,8 @@ def create_simulation(self):
                 )
             )
             self.registry_records = [
-                (traj_id, f"files/records/{trajectory_name}", traj_desc),
-                (log_id, f"files/records/{log_name}", log_desc),
+                ("holder", f"files/records/{trajectory_name}", traj_desc),
+                ("holder", f"files/records/{log_name}", log_desc),
             ]
 
             # TODO add checkpoint too?
@@ -1237,8 +1236,19 @@ def _run(self, **input_args):
                 for record in records:
                     os.rename(record[1].split("/")[-1], f"{record[1]}")
                 for record in records:
+                    record[0] = self.path_registry.get_fileid(  # Step necessary here to
+                        record[1].split("/")[-1],  # avoid id being repeated
+                        FileType.RECORD,
+                    )
                     self.path_registry.map_path(*record)
-            return "Simulation done!"
+            return (
+                "Simulation done! \n Summary: \n"
+                "Record files written to files/records/ with IDs and descriptions: "
+                f"{[(record[0],record[2]) for record in records]}\n"
+                "Standalone script written to files/simulations/ with ID: "
+                f"{sim_id}.\n"
+                f"The initial topology file ID is top_{sim_id} saved in files/pdb/"
+            )
         except Exception as e:
             print(f"An exception was found: {str(e)}.")
             return f"An exception was found trying to write the filenames: {str(e)}."

mdagent/utils/path_registry.py

@@ -205,7 +205,7 @@ def get_fileid(self, file_name: str, type: FileType):
         # Split the filename on underscores
         parts, ending = file_name.split(".")
         parts_list = parts.split("_")
-
+        current_ids = self.list_path_names()
         # Extract the timestamp (assuming it's always in the second to last part)
         timestamp_part = parts_list[-1]
         # Get the last 6 digits of the timestamp
@@ -218,9 +218,19 @@ def get_fileid(self, file_name: str, type: FileType):
             pdb_id = parts_list[0]
             return pdb_id + "_" + timestamp_digits
         if type == FileType.SIMULATION:
-            return "sim" + "_" + timestamp_digits
+            num = 0
+            sim_id = "sim" + f"{num}" + "_" + timestamp_digits
+            while sim_id in current_ids:
+                num += 1
+                sim_id = "sim" + f"{num}" + "_" + timestamp_digits
+            return sim_id
         if type == FileType.RECORD:
-            return "rec" + "_" + timestamp_digits
+            num = 0
+            rec_id = "rec" + f"{num}" + "_" + timestamp_digits
+            while rec_id in current_ids:
+                num += 1
+                rec_id = "rec" + f"{num}" + "_" + timestamp_digits
+            return rec_id
         if type == FileType.SOLVENT:
             return parts + "_" + timestamp_digits