Merge branch 'dev' into dist/streamlit_deployment

Author: jcharkow

massdash/loaders/access/OSWDataAccess.py

@@ -670,7 +670,7 @@ def getTransitionGroupFeaturesDf(self, run_basename_wo_ext: str, fullpeptidename
         return features[self.columns]
 
     def getTopTransitionGroupFeatureDf(self, run_basename_wo_ext: str, fullpeptidename: str, charge: int) -> pd.DataFrame:
-        columns = ['filename', 'leftBoundary', 'rightBoundary', 'areaIntensity', 'qvalue', 'consensusApex', 'consensusApexIntensity', 'sequence', 'precursor_charge', 'software']
+        columns = self.columns #['filename', 'leftBoundary', 'rightBoundary', 'areaIntensity', 'qvalue', 'consensusApex', 'consensusApexIntensity', 'sequence', 'precursor_charge', 'software']
         run_id = self._runIDFromRunName(run_basename_wo_ext)
         precursor_id = self.getPrecursorIDFromPeptideAndCharge(fullpeptidename, charge)
 
@@ -681,7 +681,7 @@ def getTopTransitionGroupFeatureDf(self, run_basename_wo_ext: str, fullpeptidena
 
         features['sequence'] = fullpeptidename
         features['precursor_charge'] = charge
-        return features[['leftBoundary', 'rightBoundary', 'areaIntensity', 'qvalue', 'consensusApex', 'consensusApexIntensity', 'sequence', 'precursor_charge', 'software']]
+        return features[self.columns]
 
     def getTransitionGroupFeatures(self, run_basename_wo_ext: str, fullpeptidename: str, charge: int) -> List[TransitionGroupFeature]:
         run_id = self._runIDFromRunName(run_basename_wo_ext)

massdash/ui/FileInputRawDataUISettings.py

@@ -52,6 +52,9 @@ def create_ui(self, transition_list_file_path: str=None, raw_file_path: str=None
         st.sidebar.subheader("Input Raw file")
         self.raw_file_path_input = st.sidebar.text_input("Enter file path", raw_file_path, key='raw_data_file_path', help="Path to the raw file (*.mzML)")
 
+        st.sidebar.subheader("Input Feature file")
+        self.feature_file_path = st.sidebar.text_input("Enter file path", feature_file_path, key='raw_data_feature_file_path', help="Path to the feature file (*.osw / *.tsv)")
+
     def get_mzml_files(self, threads: int=1):
         """
         Given a path to a directory or a file, returns a list of full file paths to *.mzML files in the directory or the file itself.