Remove using header from MetabRef queries

Author: kheal

corems/molecular_id/search/database_interfaces.py

@@ -92,14 +92,16 @@ def get_header(self):
 
         return header
 
-    def get_query(self, url):
+    def get_query(self, url, use_header=True):
         """
         Request payload from URL according to `get` protocol.
 
         Parameters
         ----------
         url : str
             URL for request.
+        use_header: bool
+            Whether or not the query should include the header
 
         Returns
         -------
@@ -109,7 +111,10 @@ def get_query(self, url):
         """
 
         # Query URL via `get`
-        response = requests.get(url, headers=self.get_header())
+        if use_header:
+            response = requests.get(url, headers=self.get_header())
+        else:
+            response = requests.get(url)
 
         # Check response
         response.raise_for_status()
@@ -352,6 +357,16 @@ def _dict_to_dataclass(self, metabref_lib, data_class):
             if key not in input_dict.keys():
                 input_dict[key] = None
         return data_class(**input_dict)
+    
+    def get_query(self, url, use_header=False):
+        """Overwrites the get_query method on the parent class to default to not use a header
+        
+        Notes
+        -----
+        As of January 2025, the metabref database no longer requires a token and therefore no header is needed
+
+        """
+        return super().get_query(url, use_header)
 
 
 class MetabRefGCInterface(MetabRefInterface):

support_code/nmdc/lipidomics/lipidomics_workflow.py

@@ -408,7 +408,7 @@ def run_lipid_sp_ms1(
         return mz_dict
 
 
-def prep_metadata(mz_dicts, out_dir, token_path):
+def prep_metadata(mz_dicts, out_dir):
     """Prepare metadata for ms2 spectral search
 
     Parameters
@@ -436,9 +436,6 @@ def prep_metadata(mz_dicts, out_dir, token_path):
         metadata["mzs"].update(d)
 
     metabref = MetabRefLCInterface()
-    if token_path is not None:
-        metabref.set_token(token_path)
-    metabref.set_token("tmp_data/thermo_raw_collection/metabref.token")
 
     print("Preparing positive lipid library")
     if metadata["mzs"]["positive"] is not None:
@@ -530,7 +527,6 @@ def run_lipid_workflow(
     file_dir,
     out_dir,
     params_toml,
-    token_path,
     scan_translator=None,
     verbose=True,
     ms1_molecular_search=True,
@@ -546,9 +542,6 @@ def run_lipid_workflow(
         Path to output directory
     params_toml : str or Path
         Path to toml file with parameters
-
-    token_path : str or Path
-        Path to token file for MetabRefLCInterface
     verbose : bool
         Whether to print verbose output
     cores : int
@@ -593,7 +586,7 @@ def run_lipid_workflow(
         pool.close()
         pool.join()
     # Prepare ms2 spectral search space
-    metadata = prep_metadata(mz_dicts, out_dir, token_path)
+    metadata = prep_metadata(mz_dicts, out_dir)
 
     # Run ms2 spectral search and export final results
     if cores == 1 or len(files_list) == 1:
@@ -613,10 +606,9 @@ def run_lipid_workflow(
 if __name__ == "__main__":
     # Set input variables to run
     cores = 1
-    file_dir = Path("/Users/heal742/Library/CloudStorage/OneDrive-PNNL/Documents/_DMS_data/_NMDC/_blanchard_lipidomics")
-    out_dir = Path("tmp_data/_test_241218")
+    file_dir = Path("/Users/heal742/LOCAL/corems_dev/corems/tmp_data/thermo_raw_mini")
+    out_dir = Path("tmp_data/_test_250115")
     params_toml = Path("/Users/heal742/LOCAL/05_NMDC/02_MetaMS/data_processing/configurations/emsl_lipidomics_corems_params.toml")
-    metab_ref_token = Path("tmp_data/thermo_raw_collection/metabref.token")
     verbose = True
     scan_translator = Path("tmp_data/thermo_raw_collection/scan_translator.toml")
 
@@ -631,7 +623,6 @@ def run_lipid_workflow(
         file_dir=file_dir,
         out_dir=out_dir,
         params_toml=params_toml,
-        token_path=metab_ref_token,
         scan_translator=scan_translator,
         verbose=verbose,
         cores=cores,