From 093ed7060975936d7d5a7c9280d61d595ca03ac9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Karatu=C4=9F=20Ozan=20Bircan?= <karatugo@ebi.ac.uk>
Date: Thu, 2 Jan 2025 12:48:52 +0000
Subject: [PATCH] fix: Set SKIPPED status if no sumstat files for yaml gen

---
 sumstats_service/app.py                    | 9 +++++++--
 sumstats_service/config.py                 | 1 +
 sumstats_service/resources/mongo_client.py | 7 +++++--
 3 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/sumstats_service/app.py b/sumstats_service/app.py
index 399fcfe..7e2d634 100644
--- a/sumstats_service/app.py
+++ b/sumstats_service/app.py
@@ -442,8 +442,13 @@ def convert_metadata_to_yaml(gcst_id, **kwargs):
                 additional_info={"exception": str(e)},
             )
         else:
-            logger.info(
-                f"Skipping {gcst_id=} hm: {is_harmonised_included} as it has no files."
+            info = f"Skipping {gcst_id=} hm: {is_harmonised_included} as it has no files."
+            logger.info(info)
+            mdb.insert_or_update_metadata_yaml_request(
+                gcst_id=gcst_id,
+                status=config.MetadataYamlStatus.SKIPPED,
+                is_harmonised=is_harmonised_included,
+                additional_info={"info": info},
             )
 
 
diff --git a/sumstats_service/config.py b/sumstats_service/config.py
index 92e4ea6..748401e 100644
--- a/sumstats_service/config.py
+++ b/sumstats_service/config.py
@@ -227,3 +227,4 @@ class MetadataYamlStatus(Enum):
     IN_PROGRESS = "in-progress"
     COMPLETED = "completed"
     FAILED = "failed"
+    SKIPPED = "skipped"
diff --git a/sumstats_service/resources/mongo_client.py b/sumstats_service/resources/mongo_client.py
index 9b4a731..24896b5 100644
--- a/sumstats_service/resources/mongo_client.py
+++ b/sumstats_service/resources/mongo_client.py
@@ -174,10 +174,13 @@ def insert_or_update_metadata_yaml_request(
         gcst_id,
         status,
         is_harmonised=False,
-        additional_info={},
+        additional_info=None,
         globus_endpoint_id=None,
     ):
 
+        if additional_info is None:
+            additional_info = {}
+
         print(f"adding {gcst_id} with hm: {is_harmonised} to yaml")
 
         update_doc = {
@@ -194,7 +197,7 @@ def insert_or_update_metadata_yaml_request(
 
         # If status is COMPLETED, then reset attempts to 0.
         # Otherwise increment attempts.
-        if status == config.MetadataYamlStatus.COMPLETED:
+        if status == config.MetadataYamlStatus.COMPLETED or status == config.MetadataYamlStatus.SKIPPED:
             update_doc["$set"]["attempts"] = 0
         else:
             update_doc["$inc"] = {"attempts": 1}