Add more logging output to metadata/add_id component.

CHANGELOG.md

@@ -28,6 +28,8 @@
 
 ## MINOR CHANGES
 
+* `metadata/add_id`: add more runtime logging (PR #663).
+
 * `cluster/leiden`: Bump python to 3.11 and leidenalg to 0.10.0 (PR #645).
 
 * `mapping/htseq_count_to_h5mu` and `multi_star`: update polars and gtfparse (PR #642). 

src/metadata/add_id/script.py

@@ -37,28 +37,41 @@ def make_observation_keys_unique(sample_id: str, sample: MuData) -> None:
     (unique for a sample) to each observation key, the observation key is made
     unique across all samples as well.
     """
-    logger.info('Making observation keys unique across all samples.')
+    logger.info("Making observation keys unique across all "
+                "samples by appending prefix '%s' to the observation names.",
+                sample_id)
     sample.obs.index = f"{sample_id}_" + sample.obs.index
     make_observation_keys_unique_per_mod(sample_id, sample)
+    logger.info("Done making observation keys unique.")
 
 
 def make_observation_keys_unique_per_mod(sample_id: str, sample: MuData) -> None:
     """
     Updating MuData.obs_names is not allowed (it is read-only).
     So the observation keys for each modality has to be updated manually.
     """
-    for mod in sample.mod.values():
+    for mod_name, mod in sample.mod.items():
+        logger.info("Processing modality '%s'", mod_name)
         mod.obs_names = f"{sample_id}_" + mod.obs_names
 
 def main():
+    logger.info("Reading input file '%s'.", par["input"])
     input_data = read_h5mu(par["input"])
+    logger.info("Adding column '%s' to global .obs dataframe, populated with ID '%s'", 
+                par["obs_output"], par["input_id"])
     input_data.obs[par["obs_output"]] = par["input_id"]
-    for mod_data in input_data.mod.values():
+    logger.info("Done adding column to global .obs")
+    for mod_name, mod_data in input_data.mod.items():
+        logger.info("Adding column '%s' to .obs dataframe for modality '%s', "
+                    "populated with ID '%s'", par["obs_output"], mod_name, par["input_id"])
         mod_data.obs[par["obs_output"]] = par["input_id"]
+    logger.info("Done adding per-modality columns.")
     if par["make_observation_keys_unique"]:
         make_observation_keys_unique(par["input_id"], input_data)
-    logger.info("Writing out data to '%s'.", par["output"])
+    logger.info("Writing out data to '%s' with compression '%s'.", 
+                par["output"], par["output_compression"])
     input_data.write_h5mu(par["output"], compression=par["output_compression"])
+    logger.info("Finished")
 
 if __name__ == '__main__':
     main()