From 7382f440aa54027ac6fb9556b7147532d4f0e9c4 Mon Sep 17 00:00:00 2001
From: DriesSchaumont <5946712+DriesSchaumont@users.noreply.github.com>
Date: Thu, 18 Jan 2024 13:05:22 +0100
Subject: [PATCH 1/4] Add more logging output to add_id component.

---
 src/metadata/add_id/script.py | 21 +++++++++++++++++----
 1 file changed, 17 insertions(+), 4 deletions(-)

diff --git a/src/metadata/add_id/script.py b/src/metadata/add_id/script.py
index b92e89d8d96..44a4548fc8c 100644
--- a/src/metadata/add_id/script.py
+++ b/src/metadata/add_id/script.py
@@ -37,9 +37,12 @@ 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:
@@ -47,18 +50,28 @@ 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()
\ No newline at end of file

From f1b7801b2399875137d2fb4adac69e25b2f1efe1 Mon Sep 17 00:00:00 2001
From: DriesSchaumont <5946712+DriesSchaumont@users.noreply.github.com>
Date: Thu, 18 Jan 2024 13:06:31 +0100
Subject: [PATCH 2/4] Update CHANGELOG

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3463f434048..508140aedca 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -28,6 +28,8 @@
 
 ## MINOR CHANGES
 
+* `metadata/add_id`: add more runtime logging.
+
 * `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). 

From ac123c488d185e7895e320bac31c6db0d33277fc Mon Sep 17 00:00:00 2001
From: DriesSchaumont <5946712+DriesSchaumont@users.noreply.github.com>
Date: Thu, 18 Jan 2024 13:08:39 +0100
Subject: [PATCH 3/4] Added some quotes

---
 src/metadata/add_id/script.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/metadata/add_id/script.py b/src/metadata/add_id/script.py
index 44a4548fc8c..af8581065e4 100644
--- a/src/metadata/add_id/script.py
+++ b/src/metadata/add_id/script.py
@@ -37,8 +37,8 @@ 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 by appending prefix %s to the observation names.',
+    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)

From d72278401c2c66cb74c4c1aae9a908d39ffce65c Mon Sep 17 00:00:00 2001
From: DriesSchaumont <5946712+DriesSchaumont@users.noreply.github.com>
Date: Thu, 18 Jan 2024 13:10:04 +0100
Subject: [PATCH 4/4] Add PR number to CHANGELOG

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 508140aedca..061393f3be9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -28,7 +28,7 @@
 
 ## MINOR CHANGES
 
-* `metadata/add_id`: add more runtime logging.
+* `metadata/add_id`: add more runtime logging (PR #663).
 
 * `cluster/leiden`: Bump python to 3.11 and leidenalg to 0.10.0 (PR #645).