Update app.py

app.py

@@ -8,17 +8,39 @@ from tools.final_answer import FinalAnswerTool
 from Gradio_UI import GradioUI
 
 # Below is an example of a tool that does nothing. Amaze us with your creativity !
-Tool Name: diseaseGeneExtractor, Description: Retrieve disease genes., Arguments: a: str, b: str, Outputs: str
 
 @tool
-def retrieve_disease_genes(arg1:str, arg2:str)-> str: #it's import to specify the return type
-    #Keep this format for the description / args / args description but feel free to modify the tool
-    """A tool that retrieves genes associated with a given disease.
-    Args:
-        arg1: the name of the disease
-        arg2: the type of data source
-    """
-    return {list}
+def resolve_gene(query: str) -> dict:
+    """Return HGNC symbol, Ensembl ID, canonical coords (GRCh37/38), synonyms."""
+
+@tool
+def resolve_variant(query: str, assembly: str) -> dict:
+    """Return rsID, position, liftover if needed, nearest genes."""
+
+@tool
+def query_gwas_associations(
+    gene_id: str | None = None, rsid: str | None = None,
+    region: tuple | None = None, trait_efo: str | None = None,
+    pval_max: float = 5e-8
+) -> list[dict]:
+    """GWAS Catalog hits with study metadata."""
+
+@tool
+def query_finemap_and_ld(rsid: str, ancestry: str) -> dict:
+    """Credible set, PP, LD partners via OTG + LDlink."""
+
+@tool
+def annotate_variant(rsid: str) -> dict:
+    """VEP consequence, gnomAD AF."""
+
+@tool
+def enrich_traits_with_efo(trait_labels: list[str]) -> list[dict]:
+    """Map to EFO terms and parents for grouping."""
+
+@tool
+def collate_and_rank(records: list[dict]) -> dict:
+    """Merge, score, aggregate, and return final payload with provenance."""
+
 
 @tool
 def get_current_time_in_timezone(timezone: str) -> str:
@@ -57,7 +79,7 @@ with open("prompts.yaml", 'r') as stream:
     
 agent = CodeAgent(
     model=model,
-    tools=[final_answer], ## add your tools here (don't remove final answer)
+    tools=[resolve_gene, resolve_variant, query_gwas_associations, query_finemap_and_ld, , annotate_variant, enrich_traits_with_efo, collate_and_rank, final_answer], ## add your tools here (don't remove final answer)
     max_steps=6,
     verbosity_level=1,
     grammar=None,