remove the dynamic load example files

Author: Arslan-Siraj

assets/openms.ico

@@ -73,15 +73,15 @@
     st.session_state["selected-fasta-files"] = params.get("selected-fasta-files", [])
 
 # make sure mzML example files in current session state
-load_example_mzML_files()
+#load_example_mzML_files()
 
 # take mzML files from current session file
 mzML_files_ = [f.name for f in Path(st.session_state.workspace, "mzML-files").iterdir()]
 
 #delete_files(directory = Path(st.session_state.workspace, "mzML-files"), remove_files_end_with = '.raw.mzML')
 
 # make sure fasta example files in current session state
-load_example_fasta_files()
+#load_example_fasta_files()
 
 # take fasta files from current session file
 fasta_files = [f.name for f in Path(st.session_state.workspace,"fasta-files").iterdir()]
@@ -91,6 +91,9 @@
     NuXL_config['enzyme']['restrictions'].remove('Trypsin/P')
     NuXL_config['enzyme']['restrictions'].insert(0, 'Trypsin/P')
 
+mzML_file_path = None
+database_file_path = None
+
 with st.form("fasta-upload", clear_on_submit=False):
 
     # selected mzML file from mzML files list
@@ -248,16 +251,11 @@
                     # Invalid input: Display an error message
                     st.error(f"Invalid XL FDR format: {e} Please provide input in the format [0.01, 0.1, 1.0] or a single float between 0.00 and 1.00.")
 
-    submit_button = st.form_submit_button("Run-analysis", type="primary")
+    submit_button = st.form_submit_button("Run-analysis", type="primary",  disabled=mzML_file_path is None or database_file_path is None)
 
 # out file path
 result_dir: Path = Path(st.session_state.workspace, "result-files")
 
-# create same output file path name as input file path
-mzML_file_name = os.path.basename(mzML_file_path)
-protocol_name = os.path.splitext(mzML_file_name)[0]
-result_path = os.path.join(result_dir, protocol_name + ".idXML")
-
 ##################################### NuXL command (subprocess) ############################
 
 # result dictionary to capture output of subprocess
@@ -288,6 +286,11 @@ def terminate_subprocess():
 
     # with st.spinner("Running analysis... Please wait until analysis done 😑"): #without status/ just spinner button
     with st.status("Running analysis... Please wait until analysis done 😑"):
+       
+        # create same output file path name as input file path
+        mzML_file_name = os.path.basename(mzML_file_path)
+        protocol_name = os.path.splitext(mzML_file_name)[0]
+        result_path = os.path.join(result_dir, protocol_name + ".idXML")
 
         if mzML_file_path.endswith(".raw.mzML"):
             st.warning(f"(.raw.mzML) not supported, please select (.raw) or (.mzML) format",  icon="ℹ️")

content/analyze.py

@@ -55,7 +55,7 @@
                 save_uploaded_mzML(files)
 
     #load example mzML files to current session state
-    load_example_mzML_files()
+    #load_example_mzML_files() 
 
     if any(Path(mzML_dir).iterdir()):
         v_space(2)
@@ -100,7 +100,7 @@
                 save_uploaded_fasta(files)
 
     #load example fasta files to current session state
-    load_example_fasta_files()
+    #load_example_fasta_files()
 
     if any(Path(fasta_dir).iterdir()):
         v_space(2)

content/file_upload.py

@@ -82,7 +82,7 @@
 result_dir: Path = Path(st.session_state.workspace, "result-files")
 
 #make sure load all example result files
-load_example_result_files()
+#load_example_result_files()
 
 session_idXML_files = [
         f.name

content/rescoring.py

@@ -127,7 +127,7 @@ def clean_filename_with_regex(filename):
 with tabs[0]:  
 
     #make sure load all example result files
-    load_example_result_files()
+    #load_example_result_files()
     # take all .idXML files in current session files; .idXML is CSMs 
     session_files = [f.name for f in Path(st.session_state.workspace,"result-files").iterdir() if (f.name.endswith(".idXML") and "_XLs" in f.name)]
     # select box to select .idXML file to see the results
@@ -407,7 +407,7 @@ def clean_filename_with_regex(filename):
 #with "Result files" 
 with tabs[1]:
     #make sure to load all results example files
-    load_example_result_files()
+    #load_example_result_files()
 
     if any(Path(result_dir).iterdir()):
         v_space(2)