improve docs, factoring, logging and enable labeling in-or-outputs

scripts/assign_noIndex.py

@@ -15,6 +15,11 @@
 
 This is necessary in order for unlabeled samples to pass through a
 LIMS demultiplexing step.
+
+Running the script at the start of a demultiplexing step will unfortunately
+not work as intended, since LIMS performs the demultiplexing magic
+inherent to the step prior to running any EPPs. Running the script on the
+step prior to the demux step will work as intended.
 """
 
 TIMESTAMP: str = dt.now().strftime("%y%m%d_%H%M%S")
@@ -26,30 +31,43 @@ def main(args):
     lims = Lims(BASEURI, USERNAME, PASSWORD)
     process = Process(lims, id=args.pid)
 
-    if args.label == "inputs":
+    # Determine whether to process input or output analytes
+    if args.label == "input":
         arts_list = process.all_inputs()
-    elif args.label == "outputs":
+    elif args.label == "output":
         arts_list = process.all_outputs()
     else:
         raise ValueError(f"Invalid value '{args.label}' for argument 'label'")
 
-    unlabeled_input_arts = [
-        art for art in arts_list if not art.reagent_labels and art.type == "Analyte"
-    ]
+    # Filter for unlabeled analytes
+    unlabeled_analytes = []
+    for analyte in arts_list:
+        if not analyte.type == "Analyte":
+            continue
+        if analyte.reagent_labels:
+            logging.info(
+                f"{args.label.capitalize()} '{analyte.name}' is already labeled ({analyte.reagent_labels}), skipping."
+            )
+            continue
+        unlabeled_analytes.append(analyte)
+    logging.info(f"Found {len(unlabeled_analytes)} unlabeled {args.label} analytes.")
 
     xml_element_noIndex = ET.Element("reagent-label", name="NoIndex")
-    failed_arts = []
-    for art in unlabeled_input_arts:
+    failed_analytes = []
+    for analyte in unlabeled_analytes:
         try:
-            art.root.append(xml_element_noIndex)
-            art.put()
+            analyte.root.append(xml_element_noIndex)
+            analyte.put()
+            logging.info(
+                f"Assigned 'noIndex' reagent label to {args.label} '{analyte.name}'"
+            )
         except Exception as e:
             logging.error(e)
-            failed_arts.append(art)
+            failed_analytes.append(analyte)
 
-    if failed_arts:
+    if failed_analytes:
         logging.error(
-            f"Failed to assign 'noIndex' reagent label to the following artifacts: {', '.join(art.name for art in failed_arts)}"
+            f"Failed to assign 'noIndex' reagent label to the following {args.label}s: {', '.join(art.name for art in failed_analytes)}"
         )
 
 
@@ -58,7 +76,7 @@ def main(args):
     parser = ArgumentParser(description=DESC)
     parser.add_argument("--pid", type=str, help="Lims ID for current Process")
     parser.add_argument("--log", type=str, help="Which log file slot to use")
-    parser.add_argument("--label", type=str, help="Either 'inputs' or 'outputs'")
+    parser.add_argument("--label", type=str, help="Either 'input' or 'output'")
 
     args = parser.parse_args()