test: add tests of multiple result files with mzML loader

massdash/loaders/MzMLDataLoader.py

@@ -31,6 +31,8 @@ def __init__(self, **kwargs):
         super().__init__(**kwargs) 
         self.dataAccess = [MzMLDataAccess(f, 'ondisk', verbose=self.verbose) for f in self.dataFiles]
         self.has_im = np.all([d.has_im for d in self.dataAccess])
+        if self.libraryAccess is None:
+            raise ValueError("If .osw file is not supplied, library file is required for MzMLDataLoader to perform targeted extraction")
 
     def loadTransitionGroups(self, pep_id: str, charge: int, config: TargetedDIAConfig) -> Dict[str, TransitionGroup]:
         '''

test/loaders/__snapshots__/test_ResultsLoader.ambr

@@ -10,6 +10,12 @@
     'test_raw_1',
   ])
 # ---
+# name: test_inferRunNames[dreamdia]
+  list([
+    'test_raw_1',
+    'test_raw_2',
+  ])
+# ---
 # name: test_inferRunNames[openswath]
   list([
     'test_raw_1',
@@ -60,6 +66,24 @@
     }),
   })
 # ---
+# name: test_loadIdentifiedPeptides[dreamdia]
+  dict({
+    'DreamDIA': dict({
+      'test_raw_1.mzML': set({
+        'AGAANIVPNSTGAAK',
+        'DYASIDAAPEER',
+        'IEDQLGEVAQYK',
+        'KVVITAPGGNDVK',
+      }),
+      'test_raw_2.mzML': set({
+        'AGAANIVPNSTGAAK',
+        'DYASIDAAPEER',
+        'IEDQLGEVAQYK',
+        'KVVITAPGGNDVK',
+      }),
+    }),
+  })
+# ---
 # name: test_loadIdentifiedPeptides[openswath]
   dict({
     'OpenSWATH': dict({
@@ -207,6 +231,22 @@
     }),
   })
 # ---
+# name: test_loadIdentifiedProteins[dreamdia]
+  dict({
+    'DreamDIA': dict({
+      'test_raw_1.mzML': set({
+        'Spyo_Exp3652_DDB_SeqID_514830',
+        'Spyo_Exp3652_DDB_SeqID_514851',
+        'Spyo_Exp3652_DDB_SeqID_515131',
+      }),
+      'test_raw_2.mzML': set({
+        'Spyo_Exp3652_DDB_SeqID_514830',
+        'Spyo_Exp3652_DDB_SeqID_514851',
+        'Spyo_Exp3652_DDB_SeqID_515131',
+      }),
+    }),
+  })
+# ---
 # name: test_loadIdentifiedProteins[openswath]
   dict({
     'OpenSWATH': dict({
@@ -242,6 +282,14 @@
     }),
   })
 # ---
+# name: test_loadNumIdentifiedPeptides[dreamdia]
+  dict({
+    'DreamDIA': dict({
+      'test_raw_1.mzML': 4,
+      'test_raw_2.mzML': 4,
+    }),
+  })
+# ---
 # name: test_loadNumIdentifiedPeptides[openswath]
   dict({
     'OpenSWATH': dict({
@@ -296,6 +344,14 @@
     }),
   })
 # ---
+# name: test_loadNumIdentifiedProteins[dreamdia]
+  dict({
+    'DreamDIA': dict({
+      'test_raw_1.mzML': 3,
+      'test_raw_2.mzML': 3,
+    }),
+  })
+# ---
 # name: test_loadNumIdentifiedProteins[openswath]
   dict({
     'OpenSWATH': dict({
@@ -315,6 +371,11 @@
     'DIA-NN',
   ])
 # ---
+# name: test_loadSoftware[dreamdia]
+  list([
+    'DreamDIA',
+  ])
+# ---
 # name: test_loadSoftware[openswath]
   list([
     'OpenSWATH',

test/loaders/test_MzMLDataLoader.py

@@ -24,39 +24,51 @@ def config():
     c.rt_window = 5
     return c
 
-@pytest.fixture
+@pytest.fixture(params=['openswath', 'diann', 'combined'])
 def mzml_data_loader(request):
-    if request.param == 'osw':
+    dataFilesPrefix = f'{TEST_PATH}/test_data/example_dia/raw/'
+    dataFiles = [f"{dataFilesPrefix}/test_raw_1.mzML", f"{dataFilesPrefix}/test_raw_2.mzML"]
+    libFile = None
+
+    if request.param == 'openswath':
         rsltsFile = f'{TEST_PATH}/test_data/example_dia/openswath/osw/test.osw'
+    elif request.param == 'diann':
+        rsltsFile = f'{TEST_PATH}/test_data/example_dia/diann/report/test_diann_report_combined.tsv'
+        libFile = f'{TEST_PATH}/test_data/example_dia/diann/lib/test_1_lib.tsv'
+    elif request.param == 'combined': # note: if two results files are specified, the first one will be used for extraction
+        rsltsFile = [f'{TEST_PATH}/test_data/example_dia/diann/report/test_diann_report_combined.tsv', 
+                     f'{TEST_PATH}/test_data/example_dia/openswath/osw/test.osw']
+    else:
+        raise ValueError(f"Invalid parameter: {request.param}")
 
-        dataFilesPrefix = f'{TEST_PATH}/test_data/example_dia/raw/'
-        dataFiles = [f"{dataFilesPrefix}/test_raw_1.mzML", f"{dataFilesPrefix}/test_raw_2.mzML"]
-        return MzMLDataLoader(rsltsFile=rsltsFile, dataFiles=dataFiles)
+    return MzMLDataLoader(rsltsFile=rsltsFile, dataFiles=dataFiles, libraryFile=libFile, verbose=False, mode='module')
 
+def test_init_error():
+    # if library file is not provided, an error should be raised when only DIA-NN report files are supplied
+    with pytest.raises(ValueError):
+        MzMLDataLoader(rsltsFile=f"{TEST_PATH}/test_data/example_dia/diann/report/test_diann_report_combined.tsv", dataFiles=f'{TEST_PATH}/test_data/example_dia/raw/test_raw_1.mzML', libraryFile=None, verbose=False, mode='module')
 
-'''
-@pytest.mark.parametrize('mzml_data_loader,pep,charge', [('osw', 'AGAANIVPNSTGAAK', 2)], indirect=['mzml_data_loader'])
+@pytest.mark.parametrize('pep,charge', [('DYASIDAAPEER', 2)])
 def test_loadTopTransitionGroupFeatureDf(mzml_data_loader, pep, charge, snapshot_pandas):
     df = mzml_data_loader.loadTopTransitionGroupFeatureDf(pep, charge)
     assert snapshot_pandas == df
 
-@pytest.mark.parametrize('mzml_data_loader,pep,charge', [('osw', 'AGAANIVPNSTGAAK', 2)], indirect=['mzml_data_loader'])
+@pytest.mark.parametrize('pep,charge', [('DYASIDAAPEER', 2)])
 def test_loadTransitionGroupFeaturesDf(mzml_data_loader, pep, charge, snapshot_pandas):
     df = mzml_data_loader.loadTransitionGroupFeaturesDf(pep, charge)
     assert snapshot_pandas == df
-'''
 
-@pytest.mark.parametrize('mzml_data_loader,pep,charge', [('osw', 'AGAANIVPNSTGAAK', 2)], indirect=['mzml_data_loader'])
+@pytest.mark.parametrize('pep,charge', [('DYASIDAAPEER', 2)])
 def test_loadTransitionGroups(mzml_data_loader, config, pep, charge, snapshot_pandas):
     groups = mzml_data_loader.loadTransitionGroups(pep, charge, config)
     assert snapshot_pandas == groups.toPandasDf()
 
-@pytest.mark.parametrize('mzml_data_loader,pep,charge', [('osw', 'AGAANIVPNSTGAAK', 2)], indirect=['mzml_data_loader'])
+@pytest.mark.parametrize('pep,charge', [('DYASIDAAPEER', 2)])
 def test_loadTransitionGroupsDf(mzml_data_loader, config, pep, charge, snapshot_pandas):
     df = mzml_data_loader.loadTransitionGroupsDf(pep, charge, config)
     assert snapshot_pandas == df
 
-@pytest.mark.parametrize('mzml_data_loader,pep,charge', [('osw', 'AGAANIVPNSTGAAK', 2)], indirect=['mzml_data_loader'])
+@pytest.mark.parametrize('pep,charge', [('DYASIDAAPEER', 2)])
 def test_loadFeatureMaps(mzml_data_loader, config, pep, charge, snapshot_pandas):
     feature_maps = mzml_data_loader.loadFeatureMaps(pep, charge, config)
 

test/loaders/test_ResultsLoader.py

@@ -20,6 +20,7 @@ def snapshot_pandas(snapshot):
 
 #f"{TEST_PATH}/test_data/example_dia/dreamdia/test_dreamdia_report.tsv",
     #[f"{TEST_PATH}/test_data/example_dia/diann/report/test_diann_report_combined.tsv", f"{TEST_PATH}/test_data/example_dia/dreamdia/test_dreamdia_report.tsv"]
+    # NOTE: with this PR dreamDIA is not supported
 @pytest.fixture(params=['openswath', 'diann1', 'combined'])
 def resultsLoader(request):
     if request.param == 'openswath':