Add FLASHIda Support

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

@@ -313,6 +313,7 @@ jobs:
         cp -r src streamlit_exe
         cp -r content streamlit_exe
         cp -r assets streamlit_exe
+        cp -r scripts streamlit_exe
         cp -r static streamlit_exe
         cp -r example-data streamlit_exe
         cp openms-bin/*.dll streamlit_exe

.streamlit/config.toml

@@ -6,7 +6,7 @@ developmentMode = false
 
 [server]
 maxUploadSize =  2000 #MB
-port = 8501 # should be same as configured in deployment repo
+port = 8502 # should be same as configured in deployment repo
 
 [theme]
 # The preset Streamlit theme that your custom theme inherits from. One of "light" or "dark".

app.py

@@ -35,5 +35,15 @@
         ],
     }
 
+    with open('settings.json', 'r') as f:
+        settings = json.load(f)
+    if settings['enable_flashida']:
+        pages["🧠 FLASHIda"] = ([
+            st.Page(Path("content", "FLASHIda", "FLASHIdaWorkflow.py"), title="Workflow", icon="⚙️"),
+            st.Page(Path("content", "FLASHIda", "FLASHIdaViewer.py"), title="Viewer", icon="👀"),
+            st.Page(Path("content", "FLASHIda", "FLASHIdaSimulatorWorkflow.py"), title="Simulator", icon="⚙️"),
+            st.Page(Path("content", "FLASHIda", "FLASHIdaSimulatorViewer.py"), title="Viewer", icon="👀"),
+        ])
+
     pg = st.navigation(pages, expanded=True)
     pg.run()

content/FLASHIda/FLASHIdaSimulatorViewer.py

@@ -0,0 +1,126 @@
+import streamlit as st
+
+from pathlib import Path
+
+from src.common.common import page_setup, save_params
+from src.workflow.FileManager import FileManager
+from src.render.render import render_grid
+
+DEFAULT_LAYOUT = [['ms1_deconv_heat_map']]
+
+def select_experiment():
+    st.session_state.selected_experiment0_ida = st.session_state.selected_experiment_dropdown_ida
+    print(st.session_state.selected_experiment0_ida)
+    if len(layout) > 1:
+        for exp_index in range(1, len(layout)):
+            if st.session_state[f'selected_experiment_dropdown_{exp_index}_ida'] is None:
+                continue
+            st.session_state[f"selected_experiment{exp_index}_ida"] = st.session_state[f'selected_experiment_dropdown_{exp_index}_ida']
+
+def validate_selected_index(file_manager, selected_experiment):
+    results = file_manager.get_results_list(['simulation_dfs'])
+    if selected_experiment in st.session_state:
+        if st.session_state[selected_experiment] in results:
+            return name_to_index[st.session_state[selected_experiment]]
+        else:
+            del st.session_state[selected_experiment]
+    return None
+
+# page initialization
+params = page_setup()
+
+# Get available results
+file_manager = FileManager(
+    st.session_state["workspace"],
+    Path(st.session_state['workspace'], 'flashidasimulator', 'cache')
+)
+
+results = file_manager.get_results_list(['simulation_dfs'])
+
+if file_manager.result_exists('layout', 'layout'):
+    layout = file_manager.get_results('layout', 'layout')['layout']
+    side_by_side = layout['side_by_side']
+    layout = layout['layout']
+
+else:
+    layout = [DEFAULT_LAYOUT]
+    side_by_side = False
+
+### if no input file is given, show blank page
+if len(results) == 0:
+    st.error('No results to show yet. Please run a workflow first!')
+    st.stop()
+
+# Map names to index
+name_to_index = {n : i for i, n in enumerate(results)}
+
+if len(layout) == 2 and side_by_side:
+    c1, c2 = st.columns(2)
+    with c1:
+        st.selectbox(
+            "choose experiment", results, 
+            key="selected_experiment_dropdown_ida", 
+            index=validate_selected_index(file_manager, 'selected_experiment0_ida'),
+            on_change=select_experiment
+        )
+        if 'selected_experiment0_ida' in st.session_state:
+            render_grid(
+                st.session_state.selected_experiment0_ida, layout[0], file_manager, 
+                'flashidasimulator', "selected_experiment0_ida", 'flash_viewer_grid_0_ida'
+            )
+    with c2:
+        st.selectbox(
+            "choose experiment", results, 
+            key=f'selected_experiment_dropdown_1_ida',
+            index=validate_selected_index(file_manager, 'selected_experiment1_ida'),
+            on_change=select_experiment
+        )
+        if f"selected_experiment1_ida" in st.session_state:
+            with st.spinner('Loading component...'):
+                render_grid(
+                     st.session_state["selected_experiment1_ida"], layout[1], 
+                     file_manager, 'flashidasimulator', 'selected_experiment1_ida', 
+                     'flash_viewer_grid_1_ida'
+                )
+
+else:
+    ### for only single experiment on one view
+    st.selectbox(
+        "choose experiment", results, 
+        key="selected_experiment_dropdown_ida", 
+        index=validate_selected_index(file_manager, 'selected_experiment0_ida'),
+        on_change=select_experiment
+    )
+
+
+    if 'selected_experiment0_ida' in st.session_state:
+        print('Lets go!')
+        render_grid(
+            st.session_state.selected_experiment0_ida, layout[0], file_manager, 
+            'flashidasimulator', 'selected_experiment0_ida'
+        )
+
+    ### for multiple experiments on one view
+    if len(layout) > 1:
+
+        for exp_index, exp_layout in enumerate(layout):
+            if exp_index == 0: continue  # skip the first experiment
+
+            st.divider()  # horizontal line
+
+            st.selectbox(
+                "choose experiment", results, 
+                key=f'selected_experiment_dropdown_{exp_index}_ida',
+                index=validate_selected_index(file_manager, f'selected_experiment{exp_index}_ida'),
+                on_change=select_experiment
+            )
+            # if #experiment input files are less than #layouts, all the pre-selection will be the first experiment
+            if f"selected_experiment{exp_index}_ida" in st.session_state:
+                render_grid(
+                     st.session_state["selected_experiment%d_ida" % exp_index], 
+                     layout[exp_index], file_manager, 'flashidasimulator', 
+                     "selected_experiment%d_ida" % exp_index, 
+                     'flash_viewer_grid_%d_ida' % exp_index
+                )
+
+save_params(params)

content/FLASHIda/FLASHIdaSimulatorWorkflow.py

@@ -0,0 +1,21 @@
+import streamlit as st
+
+from src.Workflow import IdaSimulatorWorkflow
+from src.common.common import page_setup
+
+
+params = page_setup()
+
+wf = IdaSimulatorWorkflow()
+
+st.title('FLASHIda - Intelligent Data Acquisition')
+
+t = st.tabs(["📁 **File Upload**", "⚙️ **Configure**", "🚀 **Run**"])
+with t[0]:
+    wf.show_file_upload_section()
+
+with t[1]:
+    wf.show_parameter_section()
+
+with t[2]:
+    wf.show_execution_section()

content/FLASHIda/FLASHIdaViewer.py

@@ -0,0 +1,119 @@
+import streamlit as st
+
+from pathlib import Path
+
+from src.common.common import page_setup, save_params
+from src.workflow.FileManager import FileManager
+from src.render.render import render_grid
+
+
+DEFAULT_LAYOUT = [
+    ['ms2_table'], 
+    ['combined_spectrum'], 
+    ['anno_spectrum', 'deconv_spectrum']
+]
+
+
+
+def select_experiment():
+    st.session_state.selected_experiment0_ida = st.session_state.selected_experiment_dropdown_ida
+    if len(layout) > 1:
+        for exp_index in range(1, len(layout)):
+            if st.session_state[f'selected_experiment_dropdown_{exp_index}_ida'] is None:
+                continue
+            st.session_state[f"selected_experiment{exp_index}_ida"] = st.session_state[f'selected_experiment_dropdown_{exp_index}_ida']
+
+def validate_selected_index(file_manager, selected_experiment):
+    results = file_manager.get_results_list(
+        ['deconv_dfs', 'anno_dfs', 'ms2_dfs']
+    )
+    if selected_experiment in st.session_state:
+        if st.session_state[selected_experiment] in results:
+            return name_to_index[st.session_state[selected_experiment]]
+        else:
+            del st.session_state[selected_experiment]
+    return None
+
+# page initialization
+params = page_setup("IdaViewer")
+
+# Get available results
+file_manager = FileManager(
+    st.session_state["workspace"],
+    Path(st.session_state['workspace'], 'flashida', 'cache')
+)
+results = file_manager.get_results_list(
+    ['deconv_dfs', 'anno_dfs', 'ms2_dfs']
+)
+
+if file_manager.result_exists('layout', 'layout'):
+    layout = file_manager.get_results('layout', 'layout')['layout']
+    side_by_side = layout['side_by_side']
+    layout = layout['layout']
+
+else:
+    layout = [DEFAULT_LAYOUT]
+    side_by_side = False
+
+### if no input file is given, show blank page
+if len(results) == 0:
+    st.error('No results to show yet. Please run a workflow first!')
+    st.stop()
+
+# Map names to index
+name_to_index = {n : i for i, n in enumerate(results)}
+
+if len(layout) == 2 and side_by_side:
+    c1, c2 = st.columns(2)
+    with c1:
+        st.selectbox(
+            "choose experiment", results, 
+            key="selected_experiment_dropdown_ida", 
+            index=validate_selected_index(file_manager, 'selected_experiment0_ida'),
+            on_change=select_experiment
+        )
+        if 'selected_experiment0_ida' in st.session_state:
+            render_grid(st.session_state.selected_experiment0_ida, layout[0], file_manager, 'flashida', 'selected_experiment0_ida')
+    with c2:
+        st.selectbox(
+            "choose experiment", results, 
+            key=f'selected_experiment_dropdown_1_ida',
+            index=validate_selected_index(file_manager, 'selected_experiment1_ida'),
+            on_change=select_experiment
+        )
+        if f"selected_experiment1_ida" in st.session_state:
+            render_grid(st.session_state.selected_experiment1_ida, layout[1], file_manager, 'flashida', 'selected_experiment1_ida', 'flash_viewer_grid_1')
+
+
+else:
+    ### for only single experiment on one view
+    st.selectbox(
+        "choose experiment", results, 
+        key="selected_experiment_dropdown_ida", 
+        index=validate_selected_index(file_manager, 'selected_experiment0_ida'),
+        on_change=select_experiment
+    )
+
+    if 'selected_experiment0_ida' in st.session_state:
+        render_grid(st.session_state.selected_experiment0_ida, layout[0], file_manager, 'flashida', 'selected_experiment0_ida')
+
+    ### for multiple experiments on one view
+    if len(layout) > 1:
+
+        for exp_index, exp_layout in enumerate(layout):
+            if exp_index == 0: continue  # skip the first experiment
+
+            st.divider() # horizontal line
+
+            st.selectbox(
+                "choose experiment", results, 
+                key=f'selected_experiment_dropdown_{exp_index}_ida',
+                index=validate_selected_index(file_manager, f'selected_experiment{exp_index}_ida'),
+                on_change=select_experiment
+            )
+
+            # if #experiment input files are less than #layouts, all the pre-selection will be the first experiment
+            if f"selected_experiment{exp_index}_ida" in st.session_state:
+                render_grid(st.session_state["selected_experiment%d_ida" % exp_index], layout[exp_index], file_manager, 'flashida', f"selected_experiment{exp_index}_ida", 'flash_viewer_grid_%d' % exp_index)
+
+save_params(params)