minor changes for deployment

pages/FileUpload.py

@@ -49,7 +49,8 @@ def showUploadedFilesTable():
 
     # error message if files not exist
     if len(deconv_files) == 0 and len(anno_files) == 0:
-        st.info('No mzML added yet!', icon="ℹ️")
+        #st.info('No mzML added yet!', icon="ℹ️")
+        return
     elif len(deconv_files) == 0:
         st.error("FLASHDeconv deconvolved mzML file is not added yet!")
     elif len(anno_files) == 0:
@@ -108,7 +109,7 @@ def parseUploadedFiles(reparse=False):
     if len(new_deconv_files)==0 and len(new_anno_files)==0 and len(new_tag_files)==0 and len(new_protein_files)==0: # if no newly uploaded files, move on
         return
     elif np.any(np.array([len(new_deconv_files), len(new_anno_files), len(new_protein_files)]) != len(new_tag_files)): # if newly uploaded files doesn't match, write message
-        st.error('Added files are not in pair, so not parsed. \n Here are uploaded ones, but not parsed ones:')
+        st.error('Added files are not in pair, so not parsed. \n Here are added ones, but not parsed ones:')
         # not_parsed = [f.name for f in new_deconv_files] + [f.name for f in new_anno_files]
         not_parsed = new_deconv_files + new_anno_files + new_tag_files + new_protein_files
         for i in not_parsed:

src/Workflow.py

@@ -180,10 +180,8 @@ def execution(self) -> None:
         # Can be done without file manager, however, it ensures everything is correct.
         in_mzMLs = self.file_manager.get_files(self.params["mzML-files"])
         database = self.file_manager.get_files(self.params["fasta-file"])
-        temp_path = self.file_manager._create_results_sub_dir()
+        #temp_path = self.file_manager._create_results_sub_dir()
 
-        # TODO: Dont like
-        base_path = join('..', 'workspaces-streamlit-template', 'default')
         base_path = dirname(self.workflow_dir)
 
         if not exists(join(base_path, 'db-fasta')):
@@ -198,10 +196,10 @@ def execution(self) -> None:
             makedirs(join(base_path, 'proteins-tsv'))
 
         # # Log any messages.
-        self.logger.log(f"Number of input mzML files: {in_mzMLs}")
-        self.logger.log(f"Number of input mzML files: {database}")
+        #self.logger.log(f"Number of input mzML files: {in_mzMLs}")
+        #self.logger.log(f"Number of input mzML files: {database}")
 
-        self.logger.log(self.file_manager.workflow_dir)
+        #self.logger.log(self.file_manager.workflow_dir)
 
 
         uploaded_files = []
@@ -245,7 +243,7 @@ def execution(self) -> None:
                 'FLASHTagger',
                 input_output={
                     'in' : [out_deconv],
-                    'fasta' : [database[0]],
+                    'fasta' : [out_db],
                     'out_tag' :  [out_tag],
                     'out_protein' :  [out_protein]
                 },