Update Layout Options

.gitignore

@@ -6,7 +6,7 @@ build.log
 run_app.spec
 clean-up-workspaces.log
 
-# FLASHViewer
+# FLASHApp
 workspaces
 Pipfile
 workspaces-flashtaggerviewer

Dockerfile

@@ -34,9 +34,9 @@ ARG PORT=8501
 ARG GITHUB_TOKEN
 ENV GH_TOKEN=${GITHUB_TOKEN}
 # Streamlit app Gihub user name (to download artifact from).
-ARG GITHUB_USER=t0mdavid-m
+ARG GITHUB_USER=OpenMS
 # Streamlit app Gihub repository name (to download artifact from).
-ARG GITHUB_REPO=FLASHViewer 
+ARG GITHUB_REPO=FLASHApp
 # Name of the zip file containing the windows executable
 ARG ASSET_NAME=OpenMS-App.zip
 

README.md

@@ -1,6 +1,6 @@
-# FLASHViewer
+# FLASHApp
 
-FLASHViewer for visualizing FLASHDeconv's results \
+FLASHApp for visualizing FLASHDeconv's results \
 This app is based on [OpenMS streamlit template project](https://github.com/OpenMS/streamlit-template).
 
 ![Overview](https://github.com/user-attachments/assets/35fe2c24-7dbc-40cd-b8b5-b7504768ade1)
@@ -28,7 +28,7 @@ for more documentation on submodules
 
 ## Build
 
-To build FLASHViewer, you first need to build the `openms-streamlit-vue-component`
+To build FLASHApp, you first need to build the `openms-streamlit-vue-component`
 and copy the build from `./openms-streamlit-vue-component/dist` to 
 `./js-component/dist`.
 
@@ -37,7 +37,7 @@ You then should set streamlit to production in two locations:
 * in `./.streamlit/config.toml` set `developmentMode` to `false`
 * in `./src/components.py` set `_RELEASE` to `True`
 
-These steps should be done before building any version of FLASHViewer.
+These steps should be done before building any version of FLASHApp.
 
 ### Docker
 
@@ -46,14 +46,14 @@ First you need to build an image locally.
 Prerequisite: `src/components.py` has `RELEASE=True` and `dist/` contains a build of the Vue
 component. These should be the settings on the `main` branch.
 
-build image with: `docker build -f Dockerfile --no-cache -t flashviewer:latest --build-arg GITHUB_TOKEN=<your-github-token> .`
+build image with: `docker build -f Dockerfile --no-cache -t flashapp:latest --build-arg GITHUB_TOKEN=<your-github-token> .`
 
 You should see a successful output, but you can check if an image is built with:
 
 `docker image ls`
 
 After it has been built you can run the image with:
 
-`docker run -p 8501:8501 flashviewer:latest`
+`docker run -p 8501:8501 flashapp:latest`
 
 Navigate to `http://localhost:8501` in your browser.

content/FLASHDeconv/FLASHDeconvLayoutManager.py

@@ -1,16 +1,20 @@
+import json
+
 import streamlit as st
+
 from src.common.common import page_setup, v_space, save_params
-import json
+from src.workflow.FileManager import FileManager
+from pathlib import Path
 
 COMPONENT_OPTIONS=[
     'MS1 raw heatmap',
     'MS1 deconvolved heatmap',
     'Scan table',
     'Deconvolved spectrum (Scan table needed)',
-    'Annotated spectrum (Scan table needed)',
+    'Raw spectrum (Scan table needed)',
     'Mass table (Scan table needed)',
     '3D S/N plot (Mass table needed)',
-    'QScore ECDF Plot (report_FDR must be enabled)'
+    'Score Distribution Plot'
     # "Sequence view" and "Internal fragment map" is added when "input_sequence" is submitted
 ]
 
@@ -26,12 +30,37 @@
     # "sequence view" and "internal fragment map" added when "input_sequence" is submitted
 ]
 
+# Setup cache access
+file_manager = FileManager(
+    st.session_state["workspace"],
+    Path(st.session_state['workspace'], 'flashdeconv', 'cache')
+)
+
+def set_layout(layout, side_by_side=False):
+    file_manager.store_data('layout', 'layout', 
+        {
+            'layout': layout,
+            'side_by_side': side_by_side
+        }
+    )
+
+def get_layout():
+    # Check if layout has been set
+    if not file_manager.result_exists('layout', 'layout'):
+        return None
+    # fetch layout from cache
+    layout = file_manager.get_results('layout', 'layout')['layout']
+
+    return layout['layout'], layout['side_by_side'] 
 
 def resetSettingsToDefault(num_of_exp=1):
     st.session_state["layout_setting"] = [[['']]] # 1D: experiment, 2D: row, 3D: column, element=component name
     st.session_state["num_of_experiment_to_show"] = num_of_exp
     for index in range(1, num_of_exp):
         st.session_state.layout_setting.append([['']])
+    if file_manager.result_exists('layout', 'layout'):
+        file_manager.remove_results('layout')
+    st.session_state["edit_mode"] = True
 
 
 def containerForNewComponent(exp_index, row_index, col_index):
@@ -122,33 +151,45 @@ def getTrimmedLayoutSetting():
             trimmed_layout_setting.append(rows)
     return trimmed_layout_setting
 
+def getExpandedLayoutSetting(trimmed_layout_setting):
+    expanded_layout_setting = []
+    for exp in trimmed_layout_setting:
+        rows = []
+        for row in exp:
+            cols = []
+            for col in row:
+                if col:
+                    cols.append(COMPONENT_OPTIONS[COMPONENT_NAMES.index(col)])
+            if cols:
+                rows.append(cols)
+        if rows:
+            expanded_layout_setting.append(rows)
+    return expanded_layout_setting
 
 def handleEditAndSaveButtons():
     # if "Edit" button was clicked,
     if "edit_btn_clicked" in st.session_state and st.session_state["edit_btn_clicked"]:
-        # reset variables based on "saved_layout_setting"
-        st.session_state["num_of_experiment_to_show"] = len(st.session_state["saved_layout_setting"])
+        st.session_state["edit_mode"] = True
+        # reset variables based on saved layout setting
+        st.session_state["num_of_experiment_to_show"] = len(get_layout()[0]) if get_layout() is not None else 1
         st.session_state["layout_setting"] = [[[COMPONENT_OPTIONS[COMPONENT_NAMES.index(col)]
                                                 for col in row if col]
                                                for row in exp if row]
-                                              for exp in st.session_state.saved_layout_setting]
-        # remove saved state, if any
-        del st.session_state["saved_layout_setting"]
+                                              for exp in get_layout()[0]]
 
     # if "Save" button was clicked,
     if "layout_saved" in st.session_state and st.session_state["layout_saved"]:
         got_error = validateSubmittedLayout()
         st.session_state['save_btn_error_message'] = got_error # to show error msg at the end
         if not got_error:
             # get only submitted info from "layout_setting"
-            st.session_state["saved_layout_setting"] = getTrimmedLayoutSetting()
+            set_layout(getTrimmedLayoutSetting(), side_by_side=st.session_state['side_by_side_view'])
+            st.session_state["edit_mode"] = False
 
 
 def handleSettingButtons():
     if "reset_btn_clicked" in st.session_state and st.session_state.reset_btn_clicked:
         resetSettingsToDefault()
-        if "saved_layout_setting" in st.session_state:
-            del st.session_state["saved_layout_setting"]
 
     if "uploaded_json_file" in st.session_state and st.session_state.uploaded_json_file is not None:
         uploaded_layout = json.load(st.session_state.uploaded_json_file)
@@ -179,28 +220,54 @@ def setSequenceView():
 setSequenceView()
 
 # handles "onclick" of buttons
+if st.session_state.get("edit_mode") is None:
+    st.session_state["edit_mode"] = True
 handleSettingButtons()
 handleEditAndSaveButtons()
 
 # initialize setting information
 if "layout_setting" not in st.session_state:
-    resetSettingsToDefault()
+    if get_layout() is not None:
+        # load layout setting from cache
+        st.session_state['layout_setting'] = getExpandedLayoutSetting(get_layout()[0])
+        st.session_state['num_of_experiment_to_show'] = len(st.session_state.layout_setting)
+        st.session_state['side_by_side_view'] = get_layout()[1]
+        st.session_state["edit_mode"] = False
+    else:
+        resetSettingsToDefault()
 # the "num_of_experiment_to_show" changed
 elif "num_of_experiment_to_show" in st.session_state and \
         len(st.session_state.layout_setting) != st.session_state.num_of_experiment_to_show:
     resetSettingsToDefault(st.session_state.num_of_experiment_to_show)
 
 ### title and setting buttons
-c1, c2, c3, c4 = st.columns([6, 1, 1, 1])
+c1, c2, c3, c4, c5 = st.columns([6, 1, 1, 1, 1])
 c1.title("Layout Manager")
 
+# side-by-side view option for 2 experiments
+if 'side_by_side_view' not in st.session_state:
+    st.session_state['side_by_side_view'] = False
+if (
+    ('num_of_experiment_to_show' in st.session_state
+     and st.session_state.num_of_experiment_to_show == 2)
+    or 
+    (not st.session_state.edit_mode
+     and (get_layout() is not None and len(get_layout()[0]) == 2))
+):
+    v_space(1, c2)
+    st.session_state['side_by_side_view'] = c2.checkbox(
+        "Side-by-Side View", value=st.session_state['side_by_side_view'],
+        help="If checked, experiments will be shown side-by-side",
+        disabled=(not st.session_state.edit_mode)
+    )
+
 # Load existing layout setting file
-v_space(1, c2)
-c2.button("Load Setting", key="load_btn_clicked")
+v_space(1, c3)
+c3.button("Load Setting", key="load_btn_clicked")
 
 # Save current layout setting (only after "Saved" button)
-v_space(1, c3)
-c3.download_button(
+v_space(1, c4)
+c4.download_button(
     label="Save Setting",
     data=json.dumps(getTrimmedLayoutSetting()),
     file_name='FLASHViewer_layout_settings.json',
@@ -209,18 +276,18 @@ def setSequenceView():
 )
 
 # Reset settings to default
-v_space(1, c4)
-c4.button("Reset Setting", key="reset_btn_clicked")
+v_space(1, c5)
+c5.button("Reset Setting", key="reset_btn_clicked")
 
 ### space for File Uploader, when "Load Setting" button is clicked
 if "load_btn_clicked" in st.session_state and st.session_state.load_btn_clicked:
     st.file_uploader("Choose a json file", type="json", key="uploaded_json_file")
 
 ### Main part
-if "saved_layout_setting" in st.session_state:
+if (not st.session_state.edit_mode) and (get_layout() is not None):
     # show saved-mode
-    for index_of_experiment in range(len(st.session_state.saved_layout_setting)):
-        layout_info_per_experiment = st.session_state.saved_layout_setting[index_of_experiment]
+    for index_of_experiment in range(len(get_layout()[0])):
+        layout_info_per_experiment = get_layout()[0][index_of_experiment]
         with st.expander("Experiment #%d"%(index_of_experiment+1), expanded=True):
             for row_index, row in enumerate(layout_info_per_experiment):
                 st_cols = st.columns(len(row))
@@ -238,10 +305,8 @@ def setSequenceView():
 
 ### buttons for edit/save
 _, edit_btn_col, save_btn_col = st.columns([9, 1, 1])
-edit_btn_col.button("Edit", key="edit_btn_clicked",
-                    disabled=False if "saved_layout_setting" in st.session_state else True)
-save_btn_col.button("Save", key="layout_saved",
-                    disabled=True if "saved_layout_setting" in st.session_state else False)
+edit_btn_col.button("Edit", key="edit_btn_clicked", disabled=st.session_state.edit_mode)
+save_btn_col.button("Save", key="layout_saved", disabled=(not st.session_state.edit_mode))
 
 ### showing error/success message
 if "save_btn_error_message" in st.session_state and st.session_state.layout_saved:

content/FLASHDeconv/FLASHDeconvViewer.py

@@ -140,8 +140,8 @@ def setSequenceViewInDefaultView():
 
 def select_experiment():
     st.session_state.selected_experiment0 = st.session_state.selected_experiment_dropdown
-    if "saved_layout_setting" in st.session_state and len(st.session_state["saved_layout_setting"]) > 1:
-        for exp_index in range(1, len(st.session_state["saved_layout_setting"])):
+    if len(layout) > 1:
+        for exp_index in range(1, len(layout)):
             if st.session_state[f'selected_experiment_dropdown_{exp_index}'] is None:
                 continue
             st.session_state[f"selected_experiment{exp_index}"] = st.session_state[f'selected_experiment_dropdown_{exp_index}']
@@ -163,6 +163,15 @@ def select_experiment():
 )
 results = file_manager.get_results_list(['deconv_dfs', 'anno_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!')
@@ -171,40 +180,60 @@ def select_experiment():
 # Map names to index
 name_to_index = {n : i for i, n in enumerate(results)}
 
-### for only single experiment on one view
-st.selectbox(
-    "choose experiment", results, 
-    key="selected_experiment_dropdown", 
-    index=name_to_index[st.session_state.selected_experiment0] if 'selected_experiment0' in st.session_state else None,
-    on_change=select_experiment
-)
+if len(layout) == 2 and side_by_side:
+    c1, c2 = st.columns(2)
+    with c1:
+        st.selectbox(
+            "choose experiment", results, 
+            key="selected_experiment_dropdown", 
+            index=name_to_index[st.session_state.selected_experiment0] if 'selected_experiment0' in st.session_state else None,
+            on_change=select_experiment
+        )
+        if 'selected_experiment0' in st.session_state:
+            with st.spinner('Loading component...'):
+                sendDataToJS(st.session_state.selected_experiment0, layout[0])
+    with c2:
+        st.selectbox(
+            "choose experiment", results, 
+            key=f'selected_experiment_dropdown_1',
+            index = name_to_index[st.session_state[f'selected_experiment1']] if f'selected_experiment1' in st.session_state else None,
+            on_change=select_experiment
+        )
+        if f"selected_experiment1" in st.session_state:
+            with st.spinner('Loading component...'):
+                sendDataToJS(st.session_state["selected_experiment1"], layout[1], 'flash_viewer_grid_1')
+
+else:
+    ### for only single experiment on one view
+    st.selectbox(
+        "choose experiment", results, 
+        key="selected_experiment_dropdown", 
+        index=name_to_index[st.session_state.selected_experiment0] if 'selected_experiment0' in st.session_state else None,
+        on_change=select_experiment
+    )
 
-if 'selected_experiment0' in st.session_state:
-    layout_info = DEFAULT_LAYOUT
-    if "saved_layout_setting" in st.session_state:  # when layout manager was used
-        layout_info = st.session_state["saved_layout_setting"][0]
-    with st.spinner('Loading component...'):
-        sendDataToJS(st.session_state.selected_experiment0, layout_info)
 
+    if 'selected_experiment0' in st.session_state:
+        with st.spinner('Loading component...'):
+            sendDataToJS(st.session_state.selected_experiment0, layout[0])
 
-### for multiple experiments on one view
-if "saved_layout_setting" in st.session_state and len(st.session_state["saved_layout_setting"]) > 1:
+    ### for multiple experiments on one view
+    if len(layout) > 1:
 
-    for exp_index, exp_layout in enumerate(st.session_state["saved_layout_setting"]):
-        if exp_index == 0: continue  # skip the first experiment
+        for exp_index, exp_layout in enumerate(layout):
+            if exp_index == 0: continue  # skip the first experiment
 
-        st.divider()  # horizontal line
+            st.divider()  # horizontal line
 
-        st.selectbox(
-            "choose experiment", results, 
-            key=f'selected_experiment_dropdown_{exp_index}',
-            index = name_to_index[st.session_state[f'selected_experiment{exp_index}']] if f'selected_experiment{exp_index}' in st.session_state else None,
-            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}" in st.session_state:
-            layout_info = st.session_state["saved_layout_setting"][exp_index]
-            with st.spinner('Loading component...'):
-                sendDataToJS(st.session_state["selected_experiment%d" % exp_index], layout_info, 'flash_viewer_grid_%d' % exp_index)
+            st.selectbox(
+                "choose experiment", results, 
+                key=f'selected_experiment_dropdown_{exp_index}',
+                index = name_to_index[st.session_state[f'selected_experiment{exp_index}']] if f'selected_experiment{exp_index}' in st.session_state else None,
+                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}" in st.session_state:
+                with st.spinner('Loading component...'):
+                    sendDataToJS(st.session_state["selected_experiment%d" % exp_index], layout[exp_index], 'flash_viewer_grid_%d' % exp_index)
 
 save_params(params)