Update genesis/api_clients/chembl_api.py

genesis/api_clients/chembl_api.py

@@ -1,91 +1,98 @@
 # genesis/api_clients/chembl_api.py
-import os
 import requests
+import os
 
 CHEMBL_BASE_URL = "https://www.ebi.ac.uk/chembl/api/data"
 
-def _chembl_get(endpoint: str, params: dict = None):
-    """
-    Generic ChEMBL GET request helper.
-    """
-    url = f"{CHEMBL_BASE_URL}/{endpoint}"
-    res = requests.get(url, params=params)
-    res.raise_for_status()
-    return res.json()
-
-
-# -----------------------
-# Drug & Compound Search
-# -----------------------
-def search_drug_by_name(drug_name: str, limit: int = 5):
+def search_drug(drug_name: str, limit: int = 5):
     """
-    Search for a drug/compound by name in ChEMBL.
+    Search ChEMBL for drugs by name.
     """
-    params = {"pref_name__icontains": drug_name, "limit": limit}
-    return _chembl_get("molecule", params)
+    url = f"{CHEMBL_BASE_URL}/molecule/search.json?q={drug_name}&limit={limit}"
+    response = requests.get(url)
+    response.raise_for_status()
+    data = response.json()
+    return [
+        {
+            "molecule_chembl_id": mol.get("molecule_chembl_id"),
+            "pref_name": mol.get("pref_name"),
+            "max_phase": mol.get("max_phase"),
+            "therapeutic_flag": mol.get("therapeutic_flag"),
+            "molecule_type": mol.get("molecule_type"),
+        }
+        for mol in data.get("molecules", [])
+    ]
 
 
 def get_drug_details(chembl_id: str):
     """
-    Retrieve detailed information for a specific ChEMBL compound.
+    Retrieve detailed drug information by ChEMBL ID.
     """
-    return _chembl_get(f"molecule/{chembl_id}")
+    url = f"{CHEMBL_BASE_URL}/molecule/{chembl_id}.json"
+    response = requests.get(url)
+    response.raise_for_status()
+    return response.json()
 
 
-# -----------------------
-# Target & Mechanism
-# -----------------------
-def search_target_by_name(target_name: str, limit: int = 5):
+def get_target_info(chembl_id: str):
     """
-    Search for a biological target (e.g., protein) by name.
+    Get targets for a given drug (by ChEMBL ID).
     """
-    params = {"pref_name__icontains": target_name, "limit": limit}
-    return _chembl_get("target", params)
-
-
-def get_target_details(chembl_target_id: str):
-    """
-    Retrieve target details from ChEMBL.
-    """
-    return _chembl_get(f"target/{chembl_target_id}")
+    url = f"{CHEMBL_BASE_URL}/target.json?molecule_chembl_id={chembl_id}"
+    response = requests.get(url)
+    response.raise_for_status()
+    return response.json().get("targets", [])
 
 
 def get_mechanism_of_action(chembl_id: str):
     """
-    Retrieve the mechanism of action for a given compound.
-    """
-    params = {"molecule_chembl_id": chembl_id}
-    return _chembl_get("mechanism", params)
-
-
-# -----------------------
-# Bioactivity Data
-# -----------------------
-def get_bioactivity_for_target(chembl_target_id: str, limit: int = 10):
-    """
-    Get bioactivity data (IC50, Ki, etc.) for a target.
-    """
-    params = {"target_chembl_id": chembl_target_id, "limit": limit}
-    return _chembl_get("activity", params)
-
-
-def get_bioactivity_for_drug(chembl_id: str, limit: int = 10):
-    """
-    Get bioactivity data for a compound.
-    """
-    params = {"molecule_chembl_id": chembl_id, "limit": limit}
-    return _chembl_get("activity", params)
-
-
-# -----------------------
-# Clinical Candidates
-# -----------------------
-def get_clinical_candidates(drug_name: str):
-    """
-    Find drugs in clinical trials from ChEMBL.
-    """
-    compounds = search_drug_by_name(drug_name, limit=1)
-    if compounds["page_meta"]["total_count"] > 0:
-        chembl_id = compounds["molecules"][0]["molecule_chembl_id"]
-        return get_mechanism_of_action(chembl_id)
-    return None
+    Retrieve mechanism of action for a drug.
+    """
+    url = f"{CHEMBL_BASE_URL}/mechanism.json?molecule_chembl_id={chembl_id}"
+    response = requests.get(url)
+    response.raise_for_status()
+    return [
+        {
+            "mechanism_of_action": m.get("mechanism_of_action"),
+            "target_name": m.get("target_name"),
+            "target_type": m.get("target_type"),
+        }
+        for m in response.json().get("mechanisms", [])
+    ]
+
+
+def get_bioactivity_data(chembl_id: str, limit: int = 10):
+    """
+    Retrieve bioactivity data for a given drug.
+    """
+    url = f"{CHEMBL_BASE_URL}/activity.json?molecule_chembl_id={chembl_id}&limit={limit}"
+    response = requests.get(url)
+    response.raise_for_status()
+    return [
+        {
+            "assay_description": a.get("assay_description"),
+            "standard_type": a.get("standard_type"),
+            "standard_value": a.get("standard_value"),
+            "units": a.get("units"),
+            "activity_comment": a.get("activity_comment"),
+        }
+        for a in response.json().get("activities", [])
+    ]
+
+
+def search_by_target(target_name: str, limit: int = 5):
+    """
+    Search drugs by target name.
+    """
+    url = f"{CHEMBL_BASE_URL}/target/search.json?q={target_name}&limit={limit}"
+    response = requests.get(url)
+    response.raise_for_status()
+    return [
+        {
+            "target_chembl_id": t.get("target_chembl_id"),
+            "pref_name": t.get("pref_name"),
+            "target_type": t.get("target_type"),
+            "organism": t.get("organism"),
+        }
+        for t in response.json().get("targets", [])
+    ]