Add option for deleting the database for a SearcholecularFormulasLC search

Author: kheal

corems/molecular_id/search/molecularFormulaSearch.py

@@ -906,6 +906,10 @@ def __init__(self, lcms_obj, sql_db=None, first_hit=False, find_isotopologues=Tr
         else:
             self.sql_db = sql_db
 
+    def delete_db(self):
+        """Delete the database."""
+        self.sql_db.purge()
+
     def search_spectra_against_candidates(self, mass_spectrum_list, ms_peaks_list, candidate_formulas, ion_type, ion_charge):
         """Search a list of mass spectra against a list of candidate formulas with a given ion type and charge.
 
@@ -977,7 +981,8 @@ def bulk_run_molecular_formula_search(self, mass_spectrum_list, ms_peaks_list, m
 
         # check database for all possible molecular formula combinations based on the setting passed to self.mass_spectrum_obj.molecular_search_settings
         classes = MolecularCombinations(self.sql_db).runworker(
-            self.lcms_obj.parameters.mass_spectrum[mass_spectrum_setting_key].molecular_search
+            self.lcms_obj.parameters.mass_spectrum[mass_spectrum_setting_key].molecular_search,
+            print_time=self.lcms_obj.parameters.mass_spectrum[mass_spectrum_setting_key].molecular_search.verbose_processing
         )
 
         # split the database load to not blowout the memory

support_code/nmdc/lipidomics/lipidomics_workflow.py

@@ -390,8 +390,8 @@ def run_lipid_sp_ms1(
     add_mass_features(myLCMSobj, scan_translator)
     myLCMSobj.remove_unprocessed_data()
     #myLCMSobj.parameters.mass_spectrum['ms1'].molecular_search.verbose_processing = False
-    #if ms1_molecular_search:
-    #    molecular_formula_search(myLCMSobj)
+    if ms1_molecular_search:
+        molecular_formula_search(myLCMSobj)
     export_results(myLCMSobj, out_path=out_path, final=False)
     save_times(myLCMSobj, time_start, out_path)
     if return_mzs:
@@ -613,9 +613,9 @@ def run_lipid_workflow(
 if __name__ == "__main__":
     # Set input variables to run
     cores = 1
-    file_dir = Path("tmp_data/thermo_raw_mini")
-    out_dir = Path("tmp_data/_test_241216")
-    params_toml = Path("tmp_data/EMSL_lipidomics_params.toml")
+    file_dir = Path("/Users/heal742/Library/CloudStorage/OneDrive-PNNL/Documents/_DMS_data/_NMDC/_blanchard_lipidomics")
+    out_dir = Path("tmp_data/_test_241218")
+    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")