polish spectra library

Author: Arslan-Siraj

content/dia_library.py

@@ -105,6 +105,16 @@ def terminate_subprocess():
       if not selected_mzML_files:
             st.warning("Please select at least one experiment (mzML/raw file) for generating the library.")
       else:
+            if uploaded_file is not None:
+                  uploaded_stem = Path(uploaded_file.name).stem
+
+                  if user_library_name == uploaded_stem:
+                        st.error(
+                              "The library output file name tag cannot be the same as the uploaded library file name. "
+                              "Please choose a different library output file name tag."
+                        )
+                        st.stop()
+
             # Extract base names (without extension) for matching
             mzml_basenames = {os.path.splitext(os.path.basename(f))[0] for f in selected_mzML_files}
 
@@ -234,49 +244,50 @@ def log(msg: str):
 
             #--------------- File Info---------------------
             log("====> mzML file Info with FileInfo OpenMS <====\n")
-
-            FileInfo_exec = os.path.join(os.getcwd(), 'FileInfo')
-            #st.write(selected_mzML_files)
-            for mzml_file in selected_mzML_files:
-                  # Input file: from result-files folder
-                  mzml_path_in = Path(st.session_state.workspace, "mzML-files", mzml_file)
-
-                  # Append current file being processed
-                  log(f"---> Processing mzml file FileInfo: {mzml_file}\n")
-
-                  if os.name == 'nt':
-                        args_FileInfo = [
-                                          FileInfo_exec,
-                                          "-in", str(mzml_path_in)
-                                    ]
-                  else:
-                        args_FileInfo = [
-                                          "FileInfo",
-                                          "-in", str(mzml_path_in)
-                                    ]
-
-                  #st.info(f"Running: {' '.join(args_FileInfo)}")
-
-                  result_FileInfo = subprocess.run(
-                              args_FileInfo,
-                              stdout=subprocess.PIPE,
-                              stderr=subprocess.PIPE,
-                              text=True
-                        )
-
-                  if result_FileInfo.returncode != 0:
-                              console_output.text("FileInfo failed")
-                              st.text(result.stderr)
-                              st.error("FileInfo failed")
-                              st.stop()
-                  else:
-                        log(f"{result_FileInfo.stdout}\n")
-            
-            #-------------------check FileInfo output-----------------
-            if "ion mobility: <none> .. <none>" in result_FileInfo.stdout:
-                  log("\n====> WARNING: No ion mobility information found in mzML files. Please ensure your data contains ion mobility for library generation. <====\n")
-                  st.error("No ion mobility information found in mzML files. Please ensure your data contains ion mobility for library generation.")
-                  st.stop()
+            fileinfo=False
+            if fileinfo:
+                  FileInfo_exec = os.path.join(os.getcwd(), 'FileInfo')
+                  #st.write(selected_mzML_files)
+                  for mzml_file in selected_mzML_files:
+                        # Input file: from result-files folder
+                        mzml_path_in = Path(st.session_state.workspace, "mzML-files", mzml_file)
+
+                        # Append current file being processed
+                        log(f"---> Processing mzml file FileInfo: {mzml_file}\n")
+
+                        if os.name == 'nt':
+                              args_FileInfo = [
+                                                FileInfo_exec,
+                                                "-in", str(mzml_path_in)
+                                          ]
+                        else:
+                              args_FileInfo = [
+                                                "FileInfo",
+                                                "-in", str(mzml_path_in)
+                                          ]
+
+                        #st.info(f"Running: {' '.join(args_FileInfo)}")
+
+                        result_FileInfo = subprocess.run(
+                                    args_FileInfo,
+                                    stdout=subprocess.PIPE,
+                                    stderr=subprocess.PIPE,
+                                    text=True
+                              )
+
+                        if result_FileInfo.returncode != 0:
+                                    console_output.text("FileInfo failed")
+                                    st.text(result.stderr)
+                                    st.error("FileInfo failed")
+                                    st.stop()
+                        else:
+                              log(f"{result_FileInfo.stdout}\n")
+                  
+                  #-------------------check FileInfo output-----------------
+                  if "ion mobility: <none> .. <none>" in result_FileInfo.stdout:
+                        log("\n====> WARNING: No ion mobility information found in mzML files. Please ensure your data contains ion mobility for library generation. <====\n")
+                        st.error("No ion mobility information found in mzML files. Please ensure your data contains ion mobility for library generation.")
+                        st.stop()
 
             #---------------upload the library file from MSFragger---------------------
             if uploaded_file is not None:
@@ -375,8 +386,9 @@ def log(msg: str):
 
     #--------------- Save log file---------------------
     if success_pipline:
+      
       # copy library output folder to result-files for download
-      copy_folder_library_to_results(output_folder_library)
+      copy_folder_library_to_results(output_folder_library, filename_dont_copy=uploaded_file)
 
       # Provide download link
       st.info(f"Preparing download link for library output files ...",  icon="ℹ️")

content/file_upload.py

@@ -53,7 +53,6 @@
         cols = st.columns(3)
         #file uploader submit button
         if cols[1].form_submit_button("Add mzML/raw file to workspace", type="primary"):
-            print(files)
             if not files:
                 st.warning("Upload some files first.")
             else:

content/rescoring.py

@@ -94,7 +94,7 @@
         for f in Path(st.session_state.workspace, "result-files").iterdir()
         if (
             f.name.endswith(".idXML")
-            and not any(x in f.name for x in ["0.0100", "0.1000", "1.0000","RT_feat", "RT_Int_feat", "updated_feat", "_perc_", "_sse_perc_" ])
+            and not any(x in f.name for x in ["0.0100", "0.1000", "1.0000","RT_feat", "RT_Int_feat", "updated_feat", "_perc", "_perc_", "_sse_perc_" ])
         )
     ]
 

src/result_files.py

@@ -487,7 +487,7 @@ def download_folder_library(folder_path: Path | str, link_name: str, zip_name: s
       st.markdown(href, unsafe_allow_html=True)
 
 
-def copy_folder_library_to_results(folder_path: Path | str) -> None:
+def copy_folder_library_to_results(folder_path: Path | str, filename_dont_copy: str) -> None:
     """
     Create a copy of a folder into the results directory.
 
@@ -504,20 +504,35 @@ def copy_folder_library_to_results(folder_path: Path | str) -> None:
     result_dir: Path = Path(st.session_state.workspace, "result-files")
 
     # Copy the folder
-    shutil.copytree(folder_path, result_dir)
-
+    for item in folder_path.iterdir():
+        if item.name != filename_dont_copy.name: 
+            dest = result_dir / item.name
+            if item.is_dir():
+                shutil.copytree(item, dest, dirs_exist_ok=True)
+            else:
+                shutil.copy2(item, dest)
 
+import stat
 def delete_folder_library(folder_path: Path | str) -> None:
     """
-    Delete a folder and its contents.
-
-    Parameters
-    ----------
-    folder_path : Path or str
-        Path to the folder to be deleted.
+    Delete a folder and all of its contents (Linux and Windows safe).
     """
     folder_path = Path(folder_path)
-    if folder_path.is_dir():
-        shutil.rmtree(folder_path)  
+
+    if not folder_path.exists():
+        return
+
+    if not folder_path.is_dir():
+        raise ValueError(f"Provided path is not a directory: {folder_path}")
+
+    def _on_rm_error(func, path, exc_info):
+        # Windows: clear read-only attribute, POSIX: no-op
+        try:
+            Path(path).chmod(stat.S_IWRITE)
+        except Exception:
+            pass
+        func(path)
+
+    shutil.rmtree(folder_path, onerror=_on_rm_error)