Added support for configurable enum sources, template-only fields, and AMR metadata JSON generation.

CHANGELOG.md

@@ -17,6 +17,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 - Add background execution mode for wrapper [#880](https://github.com/BU-ISCIII/relecov-tools/pull/880)
 - Add weekly SFTP upload report [#881](https://github.com/BU-ISCIII/relecov-tools/pull/881)
+- Added support for configurable enum sources, template-only fields, and AMR metadata JSON generation. [#883](https://github.com/BU-ISCIII/relecov-tools/pull/883)
 
 #### Fixes
 

relecov_tools/assets/schema_utils/amr_metadata.py

@@ -0,0 +1,141 @@
+#!/usr/bin/env python
+import json
+import os
+
+import pandas as pd
+
+SOURCE_SHEET = "amr_gene_list"
+OUTPUT_FILENAME = "amr_genes.json"
+
+
+def load_amr_gene_list(excel_file_path: str) -> pd.DataFrame:
+    """
+    Read the optional amr_gene_list sheet from the input Excel file.
+
+    Args:
+        excel_file_path (str): Path to the schema definition Excel file.
+
+    Returns:
+        pd.DataFrame: AMR gene list data, or an empty DataFrame if the sheet is absent.
+    """
+    try:
+        df = pd.read_excel(
+            excel_file_path,
+            sheet_name=SOURCE_SHEET,
+            na_values=["nan", "N/A", "NA", ""],
+        )
+    except ValueError:
+        return pd.DataFrame()
+
+    if not df.empty:
+        df.columns = [str(column).strip() for column in df.columns]
+        if "Name" in df.columns:
+            df = df[df["Name"].notna()]
+
+    return df
+
+
+def clean_amr_value(value) -> str:
+    """
+    Clean an AMR metadata value for JSON serialization.
+
+    Args:
+        value: Raw value from the amr_gene_list sheet.
+
+    Returns:
+        str: Stripped string value, or an empty string for NA values.
+    """
+    return "" if pd.isna(value) else str(value).strip()
+
+
+def build_amr_genes_json(df: pd.DataFrame, version: str) -> dict:
+    """
+    Build the amr_genes.json content from an amr_gene_list dataframe.
+
+    The output keeps genes and alleles keyed by their formatted Name value. Alleles
+    also include the corresponding gene when gen_for_alleles matches a gene
+    Name_CARD value in the same source sheet.
+
+    Args:
+        df (pd.DataFrame): Data from the amr_gene_list sheet.
+        version (str): Schema version to include in the output JSON.
+
+    Returns:
+        dict: JSON-serializable AMR metadata, or an empty dict if there is no data.
+    """
+    if df.empty:
+        return {}
+
+    if "Category" in df.columns:
+        gene_rows = df[df["Category"].astype(str).str.strip().str.lower() == "gene"]
+    else:
+        gene_rows = pd.DataFrame()
+
+    gene_name_by_card = {
+        clean_amr_value(row.get("Name_CARD")): clean_amr_value(row.get("Name"))
+        for _, row in gene_rows.iterrows()
+        if clean_amr_value(row.get("Name_CARD")) and clean_amr_value(row.get("Name"))
+    }
+
+    terms = {}
+    for _, row in df.iterrows():
+        name = clean_amr_value(row.get("Name"))
+        if not name:
+            continue
+
+        category = clean_amr_value(row.get("Category")).lower()
+        name_card = clean_amr_value(row.get("Name_CARD"))
+        gene_for_alleles = clean_amr_value(row.get("gen_for_alleles"))
+
+        term = {
+            "name_card": name_card,
+            "aro_accession": clean_amr_value(row.get("ARO Accession")),
+            "name": name,
+            "category": category,
+            "classification": clean_amr_value(row.get("Classification")),
+            "description": clean_amr_value(row.get("Description")),
+        }
+
+        if category == "allele":
+            term["allele_name"] = name
+            term["gene_name_card"] = gene_for_alleles
+            term["gene_name"] = gene_name_by_card.get(
+                gene_for_alleles, gene_for_alleles
+            )
+        elif category == "gene":
+            term["gene_name_card"] = name_card
+            term["gene_name"] = name
+
+        terms[name] = term
+
+    return {
+        "version": version,
+        "source_sheet": SOURCE_SHEET,
+        "terms": terms,
+    }
+
+
+def save_amr_genes_json(
+    excel_file_path: str, output_dir: str, version: str
+) -> str | None:
+    """
+    Build and save amr_genes.json from the optional amr_gene_list sheet.
+
+    Args:
+        excel_file_path (str): Path to the schema definition Excel file.
+        output_dir (str): Directory where amr_genes.json should be written.
+        version (str): Schema version to include in the output JSON.
+
+    Returns:
+        str | None: Output path when the file is written, otherwise None.
+    """
+    df = load_amr_gene_list(excel_file_path)
+    amr_genes = build_amr_genes_json(df, version)
+    if not amr_genes:
+        return None
+
+    output_path = os.path.join(output_dir, OUTPUT_FILENAME)
+    with open(output_path, "w", encoding="utf-8") as fh:
+        fh.write(json.dumps(amr_genes, indent=4, ensure_ascii=False))
+
+    return output_path