Stage B/C: OpenMS-Insight viewers for FLASHDeconv & FLASHTnT

Dockerfile

@@ -104,9 +104,12 @@ RUN make -j4 pyopenms
 WORKDIR /openms-build/pyOpenMS
 RUN pip install dist/*.whl
 
-# Install other dependencies (excluding pyopenms)
-COPY requirements.txt ./requirements.txt 
-RUN grep -Ev '^pyopenms([=<>!~].*)?$' requirements.txt > requirements_cleaned.txt && mv requirements_cleaned.txt requirements.txt
+# Install other dependencies (excluding pyopenms and openms-insight).
+# openms-insight is installed from source in the run-app stage instead: the
+# pinned PyPI release does not yet carry the new FLASHApp visualization
+# components, so we build our branch (with its Vue bundle) below.
+COPY requirements.txt ./requirements.txt
+RUN grep -Ev '^(pyopenms|openms-insight)([=<>!~].*)?$' requirements.txt > requirements_cleaned.txt && mv requirements_cleaned.txt requirements.txt
 RUN pip install -r requirements.txt
 
 WORKDIR /
@@ -144,6 +147,31 @@ WORKDIR /openms-streamlit-vue-component
 RUN npm install
 RUN npm run build
 
+# Build the OpenMS-Insight Vue bundle and stage its source tree so the Python
+# package can be installed (with the bundle baked in) in the run-app stage.
+# Like js-build, kept after the slow OpenMS compile so component changes don't
+# invalidate that cache.
+FROM node:21 AS oi-build
+
+# OpenMS-Insight repo/branch providing the new visualization components.
+# Defaults to the migration branch because those components are not yet in the
+# published PyPI release. Override via --build-arg once it is merged/released.
+ARG OPENMS_INSIGHT_REPO=https://github.com/t0mdavid-m/OpenMS-Insight.git
+ARG OPENMS_INSIGHT_BRANCH=claude/flashapp-openms-visualizations-LVv66
+
+# Bust the build cache whenever the branch head moves.
+ADD https://api.github.com/repos/t0mdavid-m/OpenMS-Insight/git/refs/heads/$OPENMS_INSIGHT_BRANCH oi-version.json
+
+RUN git clone -b ${OPENMS_INSIGHT_BRANCH} --single-branch ${OPENMS_INSIGHT_REPO} /openms-insight
+WORKDIR /openms-insight/js-component
+RUN npm install
+RUN npm run build
+# The runtime bridge and the wheel packaging both expect the built bundle at
+# openms_insight/js-component/dist; place it there so the `pip install` in the
+# run-app stage bundles it into site-packages.
+RUN mkdir -p /openms-insight/openms_insight/js-component \
+    && cp -r /openms-insight/js-component/dist /openms-insight/openms_insight/js-component/dist
+
 # Prepare and run streamlit app.
 FROM compile-openms AS run-app
 
@@ -190,6 +218,14 @@ COPY presets.json /app/presets.json
 # Copy the pre-built Vue/JS component (built in the js-build stage above).
 COPY --from=js-build openms-streamlit-vue-component/dist /app/js-component/dist
 
+# Install OpenMS-Insight (our branch build, with its freshly built Vue bundle)
+# into the streamlit env. requirements.txt has openms-insight stripped, so this
+# is the authoritative install and provides the new visualization components.
+# The package ships its Vue bundle at openms_insight/js-component/dist (staged
+# in the oi-build stage), which the runtime bridge loads in production mode.
+COPY --from=oi-build /openms-insight /opt/openms-insight
+RUN mamba run -n streamlit-env pip install /opt/openms-insight
+
 # add cron job to the crontab
 RUN echo "0 3 * * * /root/miniforge3/envs/streamlit-env/bin/python /app/clean-up-workspaces.py >> /app/clean-up-workspaces.log 2>&1" | crontab -
 

Dockerfile.arm

@@ -99,9 +99,12 @@ RUN make -j4 pyopenms
 WORKDIR /openms-build/pyOpenMS
 RUN pip install dist/*.whl
 
-# Install other dependencies (excluding pyopenms)
-COPY requirements.txt ./requirements.txt 
-RUN grep -Ev '^pyopenms([=<>!~].*)?$' requirements.txt > requirements_cleaned.txt && mv requirements_cleaned.txt requirements.txt
+# Install other dependencies (excluding pyopenms and openms-insight). openms-insight
+# is installed from source in the run-app stage: the pinned PyPI release does not
+# yet carry the new FLASHApp visualization components, so we build our branch
+# (with its Vue bundle) below.
+COPY requirements.txt ./requirements.txt
+RUN grep -Ev '^(pyopenms|openms-insight)([=<>!~].*)?$' requirements.txt > requirements_cleaned.txt && mv requirements_cleaned.txt requirements.txt
 RUN pip install -r requirements.txt
 
 WORKDIR /
@@ -139,6 +142,28 @@ WORKDIR /openms-streamlit-vue-component
 RUN npm install
 RUN npm run build
 
+# Build the OpenMS-Insight Vue bundle and stage its source tree so the Python
+# package can be installed (with the bundle baked in) in the run-app stage.
+FROM node:21 AS oi-build
+
+# OpenMS-Insight repo/branch providing the new visualization components. Defaults
+# to the migration branch (its components are not yet in the PyPI release).
+# Override via --build-arg once merged/released.
+ARG OPENMS_INSIGHT_REPO=https://github.com/t0mdavid-m/OpenMS-Insight.git
+ARG OPENMS_INSIGHT_BRANCH=claude/flashapp-openms-visualizations-LVv66
+
+# Bust the build cache whenever the branch head moves.
+ADD https://api.github.com/repos/t0mdavid-m/OpenMS-Insight/git/refs/heads/$OPENMS_INSIGHT_BRANCH oi-version.json
+
+RUN git clone -b ${OPENMS_INSIGHT_BRANCH} --single-branch ${OPENMS_INSIGHT_REPO} /openms-insight
+WORKDIR /openms-insight/js-component
+RUN npm install
+RUN npm run build
+# The runtime bridge and wheel packaging expect the bundle at
+# openms_insight/js-component/dist; place it there so pip install bundles it.
+RUN mkdir -p /openms-insight/openms_insight/js-component \
+    && cp -r /openms-insight/js-component/dist /openms-insight/openms_insight/js-component/dist
+
 # Prepare and run streamlit app.
 FROM compile-openms AS run-app
 
@@ -171,6 +196,14 @@ COPY presets.json /app/presets.json
 # Copy the pre-built Vue/JS component (built in the js-build stage above).
 COPY --from=js-build openms-streamlit-vue-component/dist /app/js-component/dist
 
+# Install OpenMS-Insight (our branch build, with its freshly built Vue bundle)
+# into the streamlit env. requirements.txt has openms-insight stripped, so this
+# is the authoritative install providing the new visualization components. The
+# package ships its Vue bundle at openms_insight/js-component/dist (staged in the
+# oi-build stage), which the runtime bridge loads in production mode.
+COPY --from=oi-build /openms-insight /opt/openms-insight
+RUN mamba run -n streamlit-env pip install /opt/openms-insight
+
 # add cron job to the crontab
 RUN echo "0 3 * * * /root/miniforge3/envs/streamlit-env/bin/python /app/clean-up-workspaces.py >> /app/clean-up-workspaces.log 2>&1" | crontab -
 

content/FLASHDeconv/FLASHDeconvLayoutManager.py

@@ -219,11 +219,13 @@ def handleSettingButtons():
 
 def setSequenceView():
     if get_sequence() is not None:
+        # Parity with the TnT layout: `internal_fragment_map` was dropped because
+        # neither the legacy grid nor the OI viewer renders it (it produces
+        # nothing). Only the sequence view is added on sequence submission.
         global COMPONENT_OPTIONS
-        COMPONENT_OPTIONS = COMPONENT_OPTIONS + ['Sequence view (Mass table needed)',
-                                                 'Internal fragment map (Mass table needed)']
+        COMPONENT_OPTIONS = COMPONENT_OPTIONS + ['Sequence view (Mass table needed)']
         global COMPONENT_NAMES
-        COMPONENT_NAMES = COMPONENT_NAMES + ['sequence_view', 'internal_fragment_map']
+        COMPONENT_NAMES = COMPONENT_NAMES + ['sequence_view']
 
 
 # page initialization

content/FLASHDeconv/FLASHDeconvViewer.py

@@ -4,7 +4,45 @@
 
 from src.common.common import page_setup, save_params
 from src.workflow.FileManager import FileManager
+# Legacy bespoke-grid render path (kept importable until OI integration is verified).
 from src.render.render import render_grid
+# The OpenMS-Insight viewer (Stage B) is imported lazily inside render_panel (see
+# below) so an import failure (e.g. a missing openms-insight install) falls back
+# to the legacy grid instead of breaking the whole page.
+
+
+def _use_oi_viewer():
+    return st.session_state.get("settings", {}).get(
+        "use_openms_insight_viewer", True
+    )
+
+
+def render_panel(experiment_id, layout_info_per_exp, file_manager, identifier,
+                 grid_key, panel_index):
+    """Render one experiment panel via the configured viewer.
+
+    Routes to the new OpenMS-Insight viewer when enabled, else the legacy grid.
+    The OI viewer is imported lazily and guarded so an import failure falls back
+    to the legacy grid rather than breaking the page.
+    """
+    if _use_oi_viewer():
+        try:
+            from content.FLASHDeconv.FLASHDeconvViewerOI import (
+                render_experiment_panel,
+            )
+        except Exception as exc:  # noqa: BLE001 - OI viewer unavailable
+            st.warning(
+                f"OpenMS-Insight viewer unavailable ({exc}); using legacy grid."
+            )
+        else:
+            render_experiment_panel(
+                experiment_id, layout_info_per_exp, file_manager, panel_index
+            )
+            return
+    render_grid(
+        experiment_id, layout_info_per_exp, file_manager,
+        'flashdeconv', identifier, grid_key
+    )
 
 DEFAULT_LAYOUT = [['ms1_deconv_heat_map'], ['scan_table', 'mass_table'],
                   ['anno_spectrum', 'deconv_spectrum'], ['3D_SN_plot']]
@@ -84,9 +122,9 @@ def get_sequence():
             on_change=select_experiment
         )
         if 'selected_experiment0' in st.session_state:
-            render_grid(
-                st.session_state.selected_experiment0, layout[0], file_manager, 
-                'flashdeconv', "selected_experiment0", 'flash_viewer_grid_0'
+            render_panel(
+                st.session_state.selected_experiment0, layout[0], file_manager,
+                "selected_experiment0", 'flash_viewer_grid_0', panel_index=0
             )
     with c2:
         st.selectbox(
@@ -97,10 +135,10 @@ def get_sequence():
         )
         if f"selected_experiment1" in st.session_state:
             with st.spinner('Loading component...'):
-                render_grid(
-                     st.session_state["selected_experiment1"], layout[1], 
-                     file_manager, 'flashdeconv', 'selected_experiment1', 
-                     'flash_viewer_grid_1'
+                render_panel(
+                     st.session_state["selected_experiment1"], layout[1],
+                     file_manager, 'selected_experiment1',
+                     'flash_viewer_grid_1', panel_index=1
                 )
 
 else:
@@ -114,9 +152,9 @@ def get_sequence():
 
 
     if 'selected_experiment0' in st.session_state:
-        render_grid(
-            st.session_state.selected_experiment0, layout[0], file_manager, 
-            'flashdeconv', 'selected_experiment0'
+        render_panel(
+            st.session_state.selected_experiment0, layout[0], file_manager,
+            'selected_experiment0', 'flash_viewer_grid', panel_index=0
         )
 
     ### for multiple experiments on one view
@@ -135,11 +173,11 @@ def get_sequence():
             )
             # 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:
-                render_grid(
-                     st.session_state["selected_experiment%d" % exp_index], 
-                     layout[exp_index], file_manager, 'flashdeconv', 
-                     "selected_experiment%d" % exp_index, 
-                     'flash_viewer_grid_%d' % exp_index
+                render_panel(
+                     st.session_state["selected_experiment%d" % exp_index],
+                     layout[exp_index], file_manager,
+                     "selected_experiment%d" % exp_index,
+                     'flash_viewer_grid_%d' % exp_index, panel_index=exp_index
                 )
 
 save_params(params)