Add GC-MS workflow test placeholder

Author: smcolby

tests/test_gcms.py

@@ -1,132 +1,92 @@
-
-__author__ = "Yuri E. Corilo"
-__date__ = "Jul 02, 2019"
 import warnings
+
 warnings.filterwarnings("ignore")
 
+import os
 import sys
-sys.path.append(".")
+from multiprocessing import Pool
 
-import pytest
-from pathlib import Path
-
-from corems.molecular_id.input.nistMSI import ReadNistMSI
+from corems.mass_spectra.calc.GC_RI_Calibration import get_rt_ri_pairs
 from corems.mass_spectra.input.andiNetCDF import ReadAndiNetCDF
 from corems.molecular_id.search.compoundSearch import LowResMassSpectralMatch
-from corems.mass_spectra.calc.GC_RI_Calibration import get_rt_ri_pairs
+from corems.molecular_id.search.database_interfaces import MetabRefGCInterface
+
 
-def start_sql_from_file():
-    
-    ref_lib_path = Path.cwd() / "tests/tests_data/gcms/" / "PNNLMetV20191015.MSL"
-    sql_obj = ReadNistMSI(ref_lib_path).get_sqlLite_obj()
-    return sql_obj
+def start_gcms_metabref_sql(normalize=False, url="sqlite://"):
+    # Initialize MetabRef interface
+    metabref = MetabRefGCInterface()
 
-def test_sql_database():
-    
-    file_location = Path.cwd() / "tests/tests_data/gcms/" / "FAMES_REF.MSL"
+    # Pull contents into SQLite
+    return metabref.get_library(format="sql")
 
-    sqlLite_obj = ReadNistMSI(file_location).get_sqlLite_obj()
 
-    min_max_rt = (18.037, 19.037)
+def start_fames_metabref_sql(normalize=False, url="sqlite://"):
+    # Initialize MetabRef interface
+    metabref = MetabRefGCInterface()
 
-    min_max_ri = (1637.30, 1737.30)
+    # Pull contents into SQLite
+    return metabref.get_fames(format="sql")
 
-    sqlLite_obj.query_min_max_ri((1637.30, 1638.30))
-    sqlLite_obj.query_min_max_rt((17.111, 18.111))
-    sqlLite_obj.query_min_max_ri_and_rt((1637.30, 1638.30),(17.111, 18.111))
 
-def get_gcms(file_path):
-    
-    reader_gcms = ReadAndiNetCDF(file_path)
-	
+def get_gcms(filepath):
+    # Initialize reader
+    reader_gcms = ReadAndiNetCDF(filepath)
+
+    # Run reader
     reader_gcms.run()
-    
+
+    # Get GCMS object
     gcms = reader_gcms.get_gcms_obj()
 
-    #gcms.process_chromatogram()
+    # # Process chromatogram
+    # gcms.process_chromatogram()
 
     return gcms
 
-def get_reference_dict():
 
-    file_path = Path.cwd() / "tests/tests_data/gcms/" / "GCMS_FAMES_01_GCMS-01_20191023.cdf"
-    
-    gcms = get_gcms(file_path)
+def run(args):
+    # Unpack arguments
+    filepath, ref_dict, cal_filepath = args
 
-    sql_obj = start_sql_from_file()
+    # Parse supplied file
+    gcms = get_gcms(filepath)
 
-    if not file_path: return  None
-    
-    else:
-        
-        gcms_ref_obj = get_gcms(file_path)
+    # Process chromatogram
+    gcms.process_chromatogram()
 
-        rt_ri_pairs = get_rt_ri_pairs(gcms_ref_obj, sql_obj)
+    # Calibrate retention index
+    gcms.calibrate_ri(ref_dict, cal_filepath)
 
-        return rt_ri_pairs, file_path
+    # Initialize GCMS refeerence database from MetabRef
+    sql_obj = start_gcms_metabref_sql()
 
-def run(args):
-    
-    file_path, ref_dict, cal_file_path = args
-    
-    gcms = get_gcms(file_path)
-    
-    gcms.calibrate_ri(ref_dict, cal_file_path)
-    
-    gcms.peaks_rt_tic()
-
-    gcms.peaks_rt_tic(json_string=True)
-
-    sql_obj = start_sql_from_file()
+    # Initialize spectral match
     lowResSearch = LowResMassSpectralMatch(gcms, sql_obj=sql_obj)
-    # !!!!!! READ !!!!! use the previous two lines if db/pnnl_lowres_gcms_compounds.sqlite does not exist
-    # and comment the next line
-    #lowResSearch = LowResMassSpectralMatch(gcms)
+
+    # Run spectral match
     lowResSearch.run()
 
     return gcms
 
-def calibrate_and_search(out_put_file_name):
-    
-    import csv
-    
-    ref_dict, cal_file_path = get_reference_dict()
-    
-    if ref_dict:
-        
-        file_path = Path.cwd() / "tests/tests_data/gcms/" / "GCMS_FAMES_01_GCMS-01_20191023.cdf"
-        gcms = run((file_path, ref_dict, cal_file_path))
-        
-        gcms.to_csv(out_put_file_name)
-        gcms.to_excel(out_put_file_name)
-        gcms.to_pandas(out_put_file_name)
-        
-        df = gcms.to_dataframe()
-        json_data = gcms.to_json()
-        
-        #print(json_data)
-
-        gcms.plot_processed_chromatogram()
-
-        gcms.plot_gc_peaks()
-
-        gcms.plot_chromatogram()
-
-        gcms.plot_smoothed_chromatogram()
 
-        gcms.plot_baseline_subtraction()
+def test_gcms_workflow():
+    # # Define paths
+    # filepath = None
+    # calibration_filepath = None
 
-        gcms.plot_detected_baseline()
+    # # Set token
+    # TOKEN_PATH = "metabref.token"
+    # MetabRefGCInterface().set_token(TOKEN_PATH)
 
-        gcms.chromatogram_settings.use_deconvolution = False
-        gcms.process_chromatogram()
-        
+    # # Parse supplied calibration data
+    # gcms_ref_obj = get_gcms(calibration_filepath)
 
-def test_run_gcms_pipeline():
+    # # Build calibration SQLite database from MetabRef
+    # fames_sql_obj = start_fames_metabref_sql()
 
-    out_put_file_name = 'test_gcms'
-    calibrate_and_search(out_put_file_name)
+    # # Determine calibration pairs
+    # rt_ri_pairs = get_rt_ri_pairs(gcms_ref_obj, sql_obj=fames_sql_obj)
 
-if __name__ == "__main__":
-    #test_sql_database()
-    test_run_gcms_pipeline()
+    # # Execute
+    # run((filepath, rt_ri_pairs, calibration_filepath))
+    pass