Add command line interface to viewer

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

@@ -80,7 +80,7 @@ jobs:
     - name: Create .bat file
       run: |
         echo '@echo off' > ${{ env.APP_NAME }}.bat
-        echo 'setlocal EnableDelayedExpansion' > ${{ env.APP_NAME }}.bat
+        echo 'setlocal EnableDelayedExpansion' >> ${{ env.APP_NAME }}.bat
         echo '' >> ${{ env.APP_NAME }}.bat
         echo 'REM Set OpenMS data path for TOPP tools' >> ${{ env.APP_NAME }}.bat
         echo 'set OPENMS_DATA_PATH=%~dp0share\OpenMS' >> ${{ env.APP_NAME }}.bat
@@ -96,7 +96,8 @@ jobs:
         echo 'REM Create credentials.toml with empty email to disable email prompt' >> ${{ env.APP_NAME }}.bat
         echo 'copy /Y ".streamlit\credentials.toml" "%USERPROFILE%\.streamlit\credentials.toml" > nul' >> ${{ env.APP_NAME }}.bat
         echo '' >> ${{ env.APP_NAME }}.bat
-        echo 'start /min .\python-${{ env.PYTHON_VERSION }}\python -m streamlit run app.py local' >> ${{ env.APP_NAME }}.bat
+        echo 'REM Launch using CLI with any passed arguments (supports: toppview-lite file.mzML)' >> ${{ env.APP_NAME }}.bat
+        echo '.\python-${{ env.PYTHON_VERSION }}\python cli.py %*' >> ${{ env.APP_NAME }}.bat
 
     - name: Create All-in-one executable folder
       run: |
@@ -110,6 +111,7 @@ jobs:
         cp -r example-data streamlit_exe
         cp -r .streamlit streamlit_exe
         cp app.py streamlit_exe
+        cp cli.py streamlit_exe
         cp settings.json streamlit_exe
         cp default-parameters.json streamlit_exe
         cp ${{ env.APP_NAME }}.bat streamlit_exe
@@ -124,6 +126,14 @@ jobs:
         1. Navigate to the installation directory.
         2. Double-click on the file: ${{ env.APP_NAME }}.bat or ${{ env.APP_NAME }} shortcut.
 
+        Command Line Usage:
+        - Open a file directly: ${{ env.APP_NAME }}.bat path/to/file.mzML
+        - Check server status:  ${{ env.APP_NAME }}.bat --status
+        - Stop background server: ${{ env.APP_NAME }}.bat --stop
+
+        The application runs a background server for fast file loading.
+        After the first startup, opening new files is nearly instant.
+
         Additional Information:
         - If multiple Streamlit apps are running, you can change the port in the .streamlit/config.toml file.
           Example:
@@ -195,6 +205,7 @@ jobs:
               <ComponentRef Id="CreateAppFolder" />
               <ComponentRef Id="DesktopShortcutComponent" />
               <ComponentRef Id="InstallDirShortcutComponent" />
+              <ComponentRef Id="FileAssociationComponent" />
             </Feature>
 
             <!-- Create shortcut for running app on desktop -->
@@ -209,6 +220,16 @@ jobs:
               <RegistryValue Root="HKCU" Key="Software\\OpenMS\\${{ env.APP_NAME }}" Name="InstallFolderShortcut" Type="integer" Value="1" KeyPath="yes" />
             </Component>
 
+            <!-- File association for .mzML files -->
+            <Component Id="FileAssociationComponent" Guid="d4e5f6a7-b8c9-0d1e-2f3a-4b5c6d7e8f90" Directory="AppSubFolder">
+              <RegistryValue Root="HKCU" Key="Software\\OpenMS\\${{ env.APP_NAME }}" Name="FileAssociation" Type="integer" Value="1" KeyPath="yes" />
+              <ProgId Id="TOPPViewLite.mzML" Description="mzML Mass Spectrometry File" Icon="AppIcon">
+                <Extension Id="mzML" ContentType="application/x-mzml">
+                  <Verb Id="open" Command="Open with ${{ env.APP_NAME }}" TargetFile="[AppSubFolder]${{ env.APP_NAME }}.bat" Argument="&quot;%1&quot;" />
+                </Extension>
+              </ProgId>
+            </Component>
+
             <!-- Provide icon here; it should exist in the SourceDir folder -->
             <Icon Id="AppIcon" SourceFile="SourceDir/openms.ico" />
 

app.py

@@ -9,11 +9,19 @@
             st.session_state.settings = json.load(f)
 
 if __name__ == '__main__':
+    # Check if a file is being loaded via CLI (load_file query parameter)
+    # If so, redirect directly to the viewer page
+    load_file = st.query_params.get("load_file")
+    if load_file:
+        default_page = Path("content", "viewer.py")
+    else:
+        default_page = Path("content", "welcome.py")
+
     pages = {
         str(st.session_state.settings["app-name"]): [
-            st.Page(Path("content", "welcome.py"), title="Welcome", icon="👋", default=True),
+            st.Page(Path("content", "welcome.py"), title="Welcome", icon="👋", default=(not load_file)),
             st.Page(Path("content", "upload.py"), title="Upload", icon="📂"),
-            st.Page(Path("content", "viewer.py"), title="Viewer", icon="👀"),
+            st.Page(Path("content", "viewer.py"), title="Viewer", icon="👀", default=bool(load_file)),
         ],
     }