From 62c4b649b85f7e4e135f5465e4e8d65fd52791a3 Mon Sep 17 00:00:00 2001
From: Jakub Dylag <jjd1c23@soton.ac.uk>
Date: Thu, 3 Apr 2025 04:01:56 +0100
Subject: [PATCH] (fix) Add metadata dict values for each concept set
---
acmc/phen.py | 30 +++++++++++++++++++++++++++++-
1 file changed, 29 insertions(+), 1 deletion(-)
diff --git a/acmc/phen.py b/acmc/phen.py
index 3c2232d..647f0f2 100644
--- a/acmc/phen.py
+++ b/acmc/phen.py
@@ -142,10 +142,11 @@ CONFIG_SCHEMA = {
"type": "dict",
"schema": {"divide_col": {"type": "string"}},
},
+
},
- # "metadata": {"type": "dict", "required": True},
},
},
+ "metadata": {"type": "dict", "required": False},
},
},
},
@@ -820,6 +821,10 @@ def _map_target_code_type(phen_path: Path, phenotype: dict, target_code_type: st
# Process each folder in codes section
for files in phenotype["concept_sets"]:
concept_set_name = files["name"]
+ if "metadata" in files:
+ concept_set_metadata = files["metadata"]
+ else:
+ concept_set_metadata = {}
for concept_set in files["files"]:
_logger.debug(f"--- {concept_set} ---")
@@ -874,6 +879,10 @@ def _map_target_code_type(phen_path: Path, phenotype: dict, target_code_type: st
target_code_type=target_code_type,
concept_name=concept_set_name,
)
+ trans_out = add_metadata(
+ codes=trans_out,
+ metadata=concept_set_metadata
+ )
out = pd.concat([out, trans_out])
else:
source_df = df[source_column_names]
@@ -882,6 +891,10 @@ def _map_target_code_type(phen_path: Path, phenotype: dict, target_code_type: st
target_code_type=target_code_type,
concept_name=concept_set_name,
)
+ trans_out = add_metadata(
+ codes=trans_out,
+ metadata=concept_set_metadata
+ )
out = pd.concat([out, trans_out])
if len(code_errors) > 0:
@@ -977,6 +990,21 @@ def _map_target_code_type(phen_path: Path, phenotype: dict, target_code_type: st
_logger.info(f"Phenotype processed target code type {target_code_type}")
+# Add metadata dict to each row of Df codes
+def add_metadata(
+ codes: pd.DataFrame, metadata: dict
+) -> pd.DataFrame:
+ """Add concept set metadata, stored as a dictionary, to each concept row"""
+
+ for meta_name, meta_value in metadata.items():
+ codes[meta_name] = meta_value
+ _logger.debug(
+ f"Adding metadata for concept set: metadata name {meta_name}, metadata value {meta_value}"
+ )
+
+ return codes
+
+
def _generate_version_tag(
repo: git.Repo, increment: str = DEFAULT_VERSION_INC, use_v_prefix: bool = False
) -> str:
--
GitLab