Merge branch 'main' into main

Author: definitelynotchirag

.github/workflows/ci.yml

@@ -0,0 +1,27 @@
+name: continuous-integration
+
+on: [push]
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        # Requirements file generated with python=3.11 
+        python-version: ["3.11"]
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt # test with requirements file so can easily bump with dependabot
+        pip install pytest
+    - name: Test
+      run: |
+        python -m pytest test_gui.py 

.github/workflows/workflow-tests.yml

@@ -23,3 +23,6 @@ jobs:
     - name: Running test cases
       run: |
         pytest test.py
+    - name: Running GUI tests
+      run: |
+        pytest test_gui.py

.gitignore

@@ -9,4 +9,5 @@ get-pip.py
 run_app.bat
 python*
 **/__pycache__/
-gdpr_consent/node_modules/
+gdpr_consent/node_modules/
+*~

README.md

@@ -18,6 +18,11 @@ This repository contains a template app for OpenMS workflows in a web applicatio
 
 Documentation for **users** and **developers** is included as pages in [this template app](https://abi-services.cs.uni-tuebingen.de/streamlit-template/), indicated by the 📖 icon.
 
+## Citation
+
+Please cite:
+Müller, T. D., Siraj, A., et al. OpenMS WebApps: Building User-Friendly Solutions for MS Analysis. Journal of Proteome Research (2025). [https://doi.org/10.1021/acs.jproteome.4c00872](https://doi.org/10.1021/acs.jproteome.4c00872)
+
 ## References
 
 - Pfeuffer, J., Bielow, C., Wein, S. et al. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat Methods 21, 365–367 (2024). [https://doi.org/10.1038/s41592-024-02197-7](https://doi.org/10.1038/s41592-024-02197-7)

settings.json

@@ -13,5 +13,6 @@
         }
     },
     "online_deployment": false,
-    "is_workspace_enabled": true
+    "is_workspace_enabled": true,
+    "test": true
 }

src/common/common.py

@@ -242,6 +242,17 @@ def page_setup(page: str = "") -> dict[str, Any]:
 
     captcha_control()  
 
+    # If run in hosted mode, show captcha as long as it has not been solved
+    #if not "local" in sys.argv:
+    #    if "controllo" not in st.session_state:
+    #        # Apply captcha by calling the captcha_control function
+    #        captcha_control()
+    
+    # If run in hosted mode, show captcha as long as it has not been solved
+    if 'controllo' not in st.session_state or ("controllo" in params.keys() and params["controllo"] == False):
+        # Apply captcha by calling the captcha_control function
+        captcha_control()  
+
     return params
 
 
@@ -395,11 +406,16 @@ def get_current_chunk(df, chunk_size, chunk_index):
     )
 
     rows = event["selection"]["rows"]
-    if not rows:
+    
+    if st.session_state.settings['test']: # is a test App, return first row as selected
+        return 1
+    elif not rows:
         return None
-    # Calculate the index based on the current page and chunk size
-    base_index = (page - 1) * chunk_size
-    return base_index + rows[0]
+    else:
+        # Calculate the index based on the current page and chunk size
+        base_index = (page - 1) * chunk_size
+        print(base_index)
+        return base_index + rows[0]
 
 
 

src/workflow/StreamlitUI.py

@@ -1114,11 +1114,13 @@ def export_parameters_markdown(self):
             version = result.stderr.split("Version: ")[1].split("-")[0]
 
         markdown.append(
-            f"""Data was processed using **{st.session_state.settings['app-name']}** ([{url}]({url})), a web application based on the OpenMS WebApps framework.
-OpenMS ([https://www.openms.de](https://www.openms.de)) is a free and open-source software for LC-MS data analysis [1].
+            f"""Data was processed using **{st.session_state.settings['app-name']}** ([{url}]({url})), a web application based on the OpenMS WebApps framework [1].
+OpenMS ([https://www.openms.de](https://www.openms.de)) is a free and open-source software for LC-MS data analysis [2].
 The workflow includes the **OpenMS {version}** TOPP tools {tools} as well as Python scripts. Non-default parameters are listed in the supplementary section below.
 
-[1] Sachsenberg, Timo, et al. "OpenMS 3 expands the frontiers of open-source computational mass spectrometry." (2023).
+[1] Müller, Tom David, et al. "OpenMS WebApps: Building User-Friendly Solutions for MS Analysis." (2025) [https://doi.org/10.1021/acs.jproteome.4c00872](https://doi.org/10.1021/acs.jproteome.4c00872).
+\\
+[2] Pfeuffer, Julianus, et al. "OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data." (2024) [https://doi.org/10.1038/s41592-024-02197-7](https://doi.org/10.1038/s41592-024-02197-7).
 """
         )
         markdown.append(self.non_default_params_summary())

test_gui.py

@@ -0,0 +1,108 @@
+from streamlit.testing.v1 import AppTest
+import pytest
+from src import fileupload
+import json
+from pathlib import Path
+import shutil
+
+@pytest.fixture
+def launch(request):
+    test = AppTest.from_file(request.param)
+
+    ## Initialize session state ##
+    with open("settings.json", "r") as f:
+        test.session_state.settings = json.load(f)
+    test.session_state.settings['test'] = True 
+    test.secrets['workspace'] = 'test'
+    return test
+
+
+
+# Test launching of all pages
+@pytest.mark.parametrize('launch', (
+                       #"content/quickstart.py", # NOTE: this page does not work due to streamlit.errors.StreamlitPageNotFoundError error
+                       "content/documentation.py",
+                       "content/topp_workflow_file_upload.py",
+                       "content/topp_workflow_parameter.py",
+                       "content/topp_workflow_execution.py",
+                       "content/topp_workflow_results.py",
+                       "content/file_upload.py",
+                       "content/raw_data_viewer.py",
+                       "content/run_example_workflow.py",
+                       "content/download_section.py",
+                       "content/simple_workflow.py",
+                       "content/run_subprocess.py"), indirect=True)
+def test_launch(launch):
+    launch.run()
+    assert not launch.exception
+
+
+
+########### PAGE SPECIFIC TESTS ############
+@pytest.mark.parametrize('launch,selection', [("content/documentation.py", 'User Guide'),
+                                              ("content/documentation.py", 'Installation'),
+                                              ("content/documentation.py", 'Developers Guide: How to build app based on this template'),
+                                              ("content/documentation.py", 'Developers Guide: TOPP Workflow Framework'),
+                                              ("content/documentation.py", 'Developer Guide: Windows Executables'),
+                                              ("content/documentation.py", 'Developers Guide: Deployment')], indirect=['launch'])
+def test_documentation(launch, selection):
+    launch.run()
+    launch.selectbox[0].select(selection).run()
+    assert not launch.exception
+
+
+@pytest.mark.parametrize('launch', ["content/file_upload.py"], indirect=True)
+def test_file_upload_load_example(launch):
+    launch.run()
+    for i in launch.tabs:
+        if i.label == "Example Data":
+            i.button[0].click().run()
+            assert not launch.exception
+
+
+# NOTE: All tabs are automatically checked
+@pytest.mark.parametrize('launch,example', [("content/raw_data_viewer.py", 'Blank.mzML'),
+                                            ("content/raw_data_viewer.py", 'Treatment.mzML'),
+                                            ("content/raw_data_viewer.py", 'Pool.mzML'),
+                                            ("content/raw_data_viewer.py", 'Control.mzML')], indirect=['launch'])
+def test_view_raw_ms_data(launch, example):
+    launch.run()
+
+    ## Load Example file, based on implementation of fileupload.load_example_mzML_files() ###
+    mzML_dir = Path(launch.session_state.workspace, "mzML-files")
+
+    # Copy files from example-data/mzML to workspace mzML directory, add to selected files
+    for f in Path("example-data", "mzML").glob("*.mzML"):
+        shutil.copy(f, mzML_dir)
+    launch.run()
+
+    ## TODO: Figure out a way to select a spectrum to be displayed 
+    launch.selectbox[0].select(example).run()
+    assert not launch.exception
+
+
+@pytest.mark.parametrize('launch,example', [("content/run_example_workflow.py", ['Blank']),
+                                            ("content/run_example_workflow.py", ['Treatment']),
+                                            ("content/run_example_workflow.py", ['Pool']),
+                                            ("content/run_example_workflow.py", ['Control']),
+                                            ("content/run_example_workflow.py", ['Control', 'Blank'])], indirect=['launch'])
+def test_run_workflow(launch, example):
+    launch.run()
+    ## Load Example file, based on implementation of fileupload.load_example_mzML_files() ###
+    mzML_dir = Path(launch.session_state.workspace, "mzML-files")
+
+    # Copy files from example-data/mzML to workspace mzML directory, add to selected files
+    for f in Path("example-data", "mzML").glob("*.mzML"):
+        shutil.copy(f, mzML_dir)
+    launch.run()
+
+    ## Select experiments to process 
+    for e in example:
+        launch.multiselect[0].select(e)
+    
+    launch.run()
+    assert not launch.exception
+    
+    # Press the "Run Workflow" button
+    launch.button[1].click().run(timeout=60)
+    assert not launch.exception