Template updates

.github/workflows/build-windows-executable-app.yaml

@@ -209,7 +209,7 @@ jobs:
         mv python-${{ env.PYTHON_VERSION }} streamlit_exe
         mv run_app.bat streamlit_exe
         cp -r src streamlit_exe
-        cp -r pages streamlit_exe
+        cp -r content streamlit_exe
         cp -r assets streamlit_exe
         cp -r example-data streamlit_exe
         cp -r .streamlit streamlit_exe

Dockerfile

@@ -113,7 +113,7 @@ COPY app.py /app/app.py
 COPY src/ /app/src
 COPY assets/ /app/assets
 COPY example-data/ /app/example-data
-COPY pages/ /app/pages
+COPY content/ /app/pages
 # For streamlit configuration
 COPY .streamlit/config.toml /app/.streamlit/config.toml
 COPY clean-up-workspaces.py /app/clean-up-workspaces.py

Dockerfile_simple

@@ -57,7 +57,7 @@ COPY app.py /app/app.py
 COPY src/ /app/src
 COPY assets/ /app/assets
 COPY example-data/ /app/example-data
-COPY pages/ /app/pages
+COPY content/ /app/pages
 # For streamlit configuration
 COPY .streamlit/config.toml /app/.streamlit/config.toml
 

app.py

@@ -1,87 +1,25 @@
-"""
-Main page for the OpenMS Template App.
-
-This module sets up and displays the Streamlit app for the OpenMS Template App.
-It includes:
-- Setting the app title.
-- Displaying a description.
-- Providing a download button for the Windows version of the app.
-
-Usage:
-Run this script to launch the OpenMS Template App.
-
-Note:
-- If run in local mode, the CAPTCHA control is not applied.
-- If not in local mode, CAPTCHA control is applied to verify the user.
-
-Returns:
-    None
-"""
-
-import sys
-
-from pathlib import Path
 import streamlit as st
+from pathlib import Path
 
-from src.captcha_ import captcha_control
-from src.common import page_setup, save_params
-
-params = page_setup(page="main")
-
-
-def main():
-    """
-    Display main page content.
-    """
-    st.title("OpenMS Streamlit Template App")
-    st.info("""
-This repository contains a template app for OpenMS workflows in a web application using the **streamlit** framework. It serves as a foundation for apps ranging from simple workflows with **pyOpenMS** to complex workflows utilizing **OpenMS TOPP tools** with parallel execution. It includes solutions for handling user data and parameters in workspaces as well as deployment with docker-compose.
-""")
-    st.subheader("Features")
-    st.markdown("""
-- Workspaces for user data with unique shareable IDs
-- Persistent parameters and input files within a workspace
-- Captcha control
-- Packaged executables for Windows
-- framework for workflows with OpenMS TOPP tools
-- Deployment [with docker-compose](https://github.com/OpenMS/streamlit-deployment)
-""")
-    st.subheader("Quick Start")
-    if Path("OpenMS-App.zip").exists():
-        st.markdown("""
-Download the latest version for Windows here by clicking the button below.
-""")
-        with open("OpenMS-App.zip", "rb") as file:
-            st.download_button(
-                label="Download for Windows",
-                data=file,
-                file_name="OpenMS-App.zip",
-                mime="archive/zip",
-                type="primary",
-            )
-        st.markdown("""
-Extract the zip file and run the executable (.exe) file to launch the app. Since every dependency is compressed and packacked the app will take a while to launch (up to one minute).
-""")
-    st.markdown("""
-Check out the documentation for **users** and **developers** is included as pages indicated by the 📖 icon
-
-Try the example pages **📁 mzML file upload**, **👀 visualization** and **example workflows**.
-""")
-    save_params(params)
-
-
-# Check if the script is run in local mode (e.g., "streamlit run app.py local")
-if "local" in sys.argv:
-    # In local mode, run the main function without applying captcha
-    main()
-
-# If not in local mode, assume it's hosted/online mode
-else:
-    # WORK LIKE MULTIPAGE APP
-    if "controllo" not in st.session_state or st.session_state["controllo"] is False:
-        # Apply captcha control to verify the user
-        captcha_control()
-
-    else:
-        # Run the main function
-        main()
+pages = {
+    "OpenMS Web App" : [
+        st.Page(Path("content", "quickstart.py"), title="Quickstart", icon="👋"),
+        st.Page(Path("content", "documentation.py"), title="Documentation", icon="📖"),
+    ],
+    "TOPP Workflow Framework": [
+        st.Page(Path("content", "topp_workflow.py"), title="TOPP Workflow", icon="🚀"),
+    ],
+    "pyOpenMS Workflow" : [
+        st.Page(Path("content", "file_upload.py"), title="File Upload", icon="📂"),
+        st.Page(Path("content", "raw_data_viewer.py"), title="View MS data", icon="👀"),
+        st.Page(Path("content", "run_example_workflow.py"), title="Run Workflow", icon="⚙️"),
+        st.Page(Path("content", "download_section.py"), title="Download Results", icon="⬇️"),
+    ],
+    "Others Topics": [
+        st.Page(Path("content", "simple_workflow.py"), title="Simple Workflow", icon="⚙️"),
+        st.Page(Path("content", "run_subprocess.py"), title="Run Subprocess", icon="🖥️"),
+    ]
+}
+
+pg = st.navigation(pages)
+pg.run()

content/.gitignore

@@ -0,0 +1 @@
+__pycache__/*

content/documentation.py

@@ -0,0 +1,109 @@
+import streamlit as st
+from src.common import page_setup
+from pathlib import Path
+from docs.toppframework import content as topp_framework_content
+
+page_setup()
+
+
+st.title("Documentation")
+
+cols = st.columns(2)
+
+pages = [
+    "User Guide",
+    "Installation",
+    "Developers Guide: How to build app based on this template",
+    "Developers Guide: TOPP Workflow Framework",
+    "Developer Guide: Windows Executables",
+    "Developers Guide: Deployment",
+]
+page = cols[0].selectbox(
+    "**Content**",
+    pages,
+)
+
+#############################################################################################
+# User Guide
+#############################################################################################
+
+if page == pages[0]:
+    with open(Path("docs", "user_guide.md"), "r", encoding="utf-8") as f:
+        content = f.read()
+    st.markdown(content) 
+
+#############################################################################################
+# Installation
+#############################################################################################
+
+if page == pages[1]:
+    if Path("OpenMS-App.zip").exists():
+        st.markdown(
+            """
+Download the latest version for **Windows** here clicking the button below.
+"""
+        )
+        with open("OpenMS-App.zip", "rb") as file:
+            st.download_button(
+                label="Download for Windows",
+                data=file,
+                file_name="OpenMS-App.zip",
+                mime="archive/zip",
+                type="primary",
+            )
+    with open(Path("docs", "installation.md"), "r", encoding="utf-8") as f:
+        content = f.read()
+    st.markdown(content) 
+
+#############################################################################################
+# Developer Overview, how to build app based on Template
+#############################################################################################
+
+if page == pages[2]:
+    with open(Path("docs", "build_app.md"), "r", encoding="utf-8") as f:
+        content = f.read()
+    st.markdown(content) 
+
+#############################################################################################
+# TOPP Workflow Framework
+#############################################################################################
+
+if page == pages[3]:
+    topp_framework_content()
+
+#############################################################################################
+# Windows Executables
+#############################################################################################
+
+if page == pages[4]:
+    st.markdown(
+        """
+## 💻  How to package everything for Windows executables
+
+This guide explains how to package OpenMS apps into Windows executables using two different methods:
+"""
+    )
+
+    tabs = ["**embeddable Python**", "**PyInstaller**"]
+    tabs = st.tabs(tabs)
+
+    # window executable with embeddable python
+    with tabs[0]:
+        with open(Path("docs", "win_exe_with_embed_py.md"), "r", encoding="utf-8") as f:
+            content = f.read()
+        st.markdown(content) 
+
+    # window executable with pyinstaller
+    with tabs[1]:
+        with open(Path("docs", "win_exe_with_pyinstaller.md"), "r", encoding="utf-8") as f:
+            content = f.read()
+        st.markdown(content) 
+
+#############################################################################################
+# Deployment
+#############################################################################################
+
+if page == pages[5]:
+    with open(Path("docs", "deployment.md"), "r", encoding="utf-8") as f:
+        content = f.read()
+    st.markdown(content) 

content/download_section.py

@@ -0,0 +1,72 @@
+import streamlit as st
+
+from pathlib import Path
+import shutil
+
+from src.common import page_setup
+from zipfile import ZipFile, ZIP_DEFLATED
+
+page_setup()
+
+# Define output folder here; all subfolders will be handled as downloadable
+# directories
+output_folder = 'mzML-workflow-results'
+
+
+# Generate full path
+dirpath = Path(st.session_state["workspace"], output_folder)
+
+# Detect downloadable content
+if dirpath.exists():
+    directories = sorted(
+        [entry for entry in dirpath.iterdir() if not entry.is_file()]
+    )
+else:
+    directories = []
+
+# Show error if no content is available for download
+if len(directories) == 0:
+    st.error('No results to show yet. Please run a workflow first!')
+else:
+    # Table Header
+    columns = st.columns(3)
+    columns[0].write('**Run**')
+    columns[1].write('**Download**')
+    columns[2].write('**Delete Result Set**')
+
+    # Table Body
+    for i, directory in enumerate(directories):
+        st.divider()
+        columns = st.columns(3)
+        columns[0].empty().write(directory.name)
+
+        with columns[1]:
+            button_placeholder = st.empty()
+
+            # Show placeholder button before download is prepared
+            clicked = button_placeholder.button('Prepare Download', key=i, use_container_width=True)
+            if clicked:
+                button_placeholder.empty()
+                with st.spinner():
+                    # Create ZIP file
+                    out_zip = Path(dirpath, directory, 'output.zip')
+                    if not out_zip.exists():
+                        with ZipFile(out_zip, 'w', ZIP_DEFLATED) as zip_file:
+                            for output in Path(dirpath, directory).iterdir():
+                                try:
+                                    with open(Path(dirpath, directory, output), 'r') as f:
+                                        zip_file.writestr(output.name, f.read())
+                                except:
+                                    continue
+                    # Show download button after ZIP file was created
+                    with open(out_zip, 'rb') as f:
+                        button_placeholder.download_button(
+                            "Download ⬇️", f, 
+                            file_name = f'{directory}.zip',
+                            use_container_width=True
+                        )
+
+        with columns[2]:
+            if st.button(f"🗑️ {directory.name}", use_container_width=True):
+                shutil.rmtree(directory)
+                st.rerun()

pages/10_📁_File_Upload.py → content/file_upload.py

@@ -3,17 +3,11 @@
 import streamlit as st
 import pandas as pd
 
-from src.captcha_ import captcha_control
 from src.common import page_setup, save_params, v_space, show_table
 from src import fileupload
 
 params = page_setup()
 
-# If run in hosted mode, show captcha as long as it has not been solved
-if "controllo" not in st.session_state or params["controllo"] is False:
-    # Apply captcha by calling the captcha_control function
-    captcha_control()
-
 st.title("File Upload")
 
 tabs = ["File Upload", "Example Data"]