Merge pull request #185 from achalbajpai/upstream-fresh-branch

feat: automatically load example data in pyOpenMS workflow

Author: t0mdavid-m

content/file_upload.py

@@ -3,14 +3,27 @@
 import streamlit as st
 import pandas as pd
 
-from src.common.common import page_setup, save_params, v_space, show_table, TK_AVAILABLE, tk_directory_dialog
+from src.common.common import (
+    page_setup,
+    save_params,
+    v_space,
+    show_table,
+    TK_AVAILABLE,
+    tk_directory_dialog,
+)
 from src import fileupload
 
 params = page_setup()
 
 st.title("File Upload")
 
-tabs = ["File Upload", "Example Data"]
+# Check if there are any files in the workspace
+mzML_dir = Path(st.session_state.workspace, "mzML-files")
+if not any(Path(mzML_dir).iterdir()):
+    # No files present, load example data
+    fileupload.load_example_mzML_files()
+
+tabs = ["File Upload"]
 if st.session_state.location == "local":
     tabs.append("Files from local folder")
 
@@ -28,55 +41,74 @@
             else:
                 st.warning("Select files first.")
 
-# Example mzML files
-with tabs[1]:
-    st.markdown("Short information text on example data.")
-    cols = st.columns(3)
-    if cols[1].button("Load Example Data", type="primary"):
-        fileupload.load_example_mzML_files()
-
 # Local file upload option: via directory path
 if st.session_state.location == "local":
-    with tabs[2]:
+    with tabs[1]:
         st_cols = st.columns([0.05, 0.95], gap="small")
         with st_cols[0]:
             st.write("\n")
             st.write("\n")
-            dialog_button = st.button("📁", key='local_browse', help="Browse for your local directory with MS data.", disabled=not TK_AVAILABLE)
+            dialog_button = st.button(
+                "📁",
+                key="local_browse",
+                help="Browse for your local directory with MS data.",
+                disabled=not TK_AVAILABLE,
+            )
             if dialog_button:
-                st.session_state["local_dir"] = tk_directory_dialog("Select directory with your MS data", st.session_state["previous_dir"])
+                st.session_state["local_dir"] = tk_directory_dialog(
+                    "Select directory with your MS data",
+                    st.session_state["previous_dir"],
+                )
                 st.session_state["previous_dir"] = st.session_state["local_dir"]
         with st_cols[1]:
             # with st.form("local-file-upload"):
-            local_mzML_dir = st.text_input("path to folder with mzML files", value=st.session_state["local_dir"])
+            local_mzML_dir = st.text_input(
+                "path to folder with mzML files", value=st.session_state["local_dir"]
+            )
         # raw string for file paths
         local_mzML_dir = rf"{local_mzML_dir}"
         cols = st.columns([0.65, 0.3, 0.4, 0.25], gap="small")
-        copy_button = cols[1].button("Copy files to workspace", type="primary", disabled=(local_mzML_dir == ""))
-        use_copy = cols[2].checkbox("Make a copy of files", key="local_browse-copy_files", value=True, help="Create a copy of files in workspace.")
+        copy_button = cols[1].button(
+            "Copy files to workspace", type="primary", disabled=(local_mzML_dir == "")
+        )
+        use_copy = cols[2].checkbox(
+            "Make a copy of files",
+            key="local_browse-copy_files",
+            value=True,
+            help="Create a copy of files in workspace.",
+        )
         if not use_copy:
-                st.warning(
-        "**Warning**: You have deselected the `Make a copy of files` option. "
-        "This **_assumes you know what you are doing_**. "
-        "This means that the original files will be used instead. "
-    )
+            st.warning(
+                "**Warning**: You have deselected the `Make a copy of files` option. "
+                "This **_assumes you know what you are doing_**. "
+                "This means that the original files will be used instead. "
+            )
         if copy_button:
             fileupload.copy_local_mzML_files_from_directory(local_mzML_dir, use_copy)
 
-mzML_dir = Path(st.session_state.workspace, "mzML-files")
 if any(Path(mzML_dir).iterdir()):
     v_space(2)
     # Display all mzML files currently in workspace
-    df = pd.DataFrame({"file name": [f.name for f in Path(mzML_dir).iterdir() if "external_files.txt" not in f.name]})
-    
+    df = pd.DataFrame(
+        {
+            "file name": [
+                f.name
+                for f in Path(mzML_dir).iterdir()
+                if "external_files.txt" not in f.name
+            ]
+        }
+    )
+
     # Check if local files are available
     external_files = Path(mzML_dir, "external_files.txt")
     if external_files.exists():
         with open(external_files, "r") as f_handle:
             external_files = f_handle.readlines()
             external_files = [f.strip() for f in external_files]
-            df = pd.concat([df, pd.DataFrame({"file name": external_files})], ignore_index=True)
-    
+            df = pd.concat(
+                [df, pd.DataFrame({"file name": external_files})], ignore_index=True
+            )
+
     st.markdown("##### mzML files in current workspace:")
     show_table(df)
     v_space(1)