Phase 3: Rebuild FLASHApp viewers on OpenMS-Insight via frozen template

.github/workflows/unit-tests.yml

@@ -24,9 +24,24 @@ jobs:
           cache: pip
           cache-dependency-path: requirements.txt
 
+      - name: Set up Node
+        uses: actions/setup-node@v4
+        with:
+          node-version: "21"
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
+          # OpenMS-Insight (Phase-3, 0.1.15) is not on PyPI: build it from the
+          # migration branch (Vue bundle + Python) and install from source so the
+          # requirements.txt pin resolves -- mirrors the Dockerfile insight-build stage.
+          git clone -b claude/kind-heisenberg-u6dVm --single-branch --depth 1 \
+            https://github.com/t0mdavid-m/openms-insight.git /tmp/openms-insight
+          ( cd /tmp/openms-insight/js-component && npm install && npm run build )
+          mkdir -p /tmp/openms-insight/openms_insight/js-component
+          cp -r /tmp/openms-insight/js-component/dist \
+                /tmp/openms-insight/openms_insight/js-component/dist
+          pip install /tmp/openms-insight
           # Pinned runtime deps (pyopenms is needed so ParameterManager imports
           # cleanly at collection time) plus test-only deps. fakeredis backs the
           # QueueManager/WorkflowManager tests, which pytest.importorskip it.

Dockerfile

@@ -80,6 +80,21 @@ RUN mkdir /thirdparty && \
     chmod -R +x /thirdparty
 ENV PATH="/thirdparty/LuciPHOr2:/thirdparty/MSGFPlus:/thirdparty/ThermoRawFileParser:/thirdparty/Comet:/thirdparty/Percolator:/thirdparty/Sage:${PATH}"
 
+# Build the OpenMS-Insight package (Python + Vue bundle) from the migration branch.
+# Insight's Vue dist is gitignored and it has no pip build hook, so build the bundle
+# here and sync it into the package tree; the compile-openms stage pip-installs it.
+FROM node:21 AS insight-build
+ARG INSIGHT_REPO=https://github.com/t0mdavid-m/openms-insight.git
+ARG INSIGHT_BRANCH=claude/kind-heisenberg-u6dVm
+ADD https://api.github.com/repos/t0mdavid-m/openms-insight/git/refs/heads/${INSIGHT_BRANCH} insight-ref.json
+RUN git clone -b ${INSIGHT_BRANCH} --single-branch ${INSIGHT_REPO} /openms-insight
+WORKDIR /openms-insight/js-component
+RUN npm install && npm run build
+RUN mkdir -p /openms-insight/openms_insight/js-component \
+    && rm -rf /openms-insight/openms_insight/js-component/dist \
+    && cp -r /openms-insight/js-component/dist /openms-insight/openms_insight/js-component/dist \
+    && rm -rf /openms-insight/js-component/node_modules
+
 # Build OpenMS and pyOpenMS.
 FROM setup-build-system AS compile-openms
 WORKDIR /
@@ -107,6 +122,10 @@ RUN pip install dist/*.whl
 # Install other dependencies (excluding pyopenms)
 COPY requirements.txt ./requirements.txt 
 RUN grep -Ev '^pyopenms([=<>!~].*)?$' requirements.txt > requirements_cleaned.txt && mv requirements_cleaned.txt requirements.txt
+# OpenMS-Insight: install from the migration branch built in the insight-build stage
+# (with its Vue bundle), before requirements so the pin resolves from source not PyPI.
+COPY --from=insight-build /openms-insight /tmp/openms-insight
+RUN pip install /tmp/openms-insight && rm -rf /tmp/openms-insight
 RUN pip install -r requirements.txt
 
 WORKDIR /
@@ -128,23 +147,9 @@ ENV OPENMS_DATA_PATH="/openms/share/"
 # Remove build directory.
 RUN rm -rf openms-build
 
-# Build JS-component (quick). Placed after the slow OpenMS build so that changes
-# to the Vue component do not invalidate the OpenMS compile cache; its output is
-# copied into the final image in the run-app stage below.
-FROM node:21 AS js-build
-
-# JS Component
-ARG VUE_REPO=https://github.com/t0mdavid-m/openms-streamlit-vue-component.git
-ARG VUE_BRANCH=FVdeploy
-
-ADD https://api.github.com/repos/t0mdavid-m/openms-streamlit-vue-component/git/refs/heads/$VUE_BRANCH version.json
-
-RUN git clone -b ${VUE_BRANCH} --single-branch ${VUE_REPO}
-WORKDIR /openms-streamlit-vue-component
-RUN npm install
-RUN npm run build
-
 # Prepare and run streamlit app.
+# (The legacy local Vue component build stage was removed in the OpenMS-Insight
+# migration -- Insight ships its own Vue bundle via the openms-insight package.)
 FROM compile-openms AS run-app
 
 # Install Redis server for job queue and nginx for load balancing.
@@ -187,9 +192,6 @@ COPY settings.json /app/settings.json
 COPY default-parameters.json /app/default-parameters.json
 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
-
 # 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

@@ -75,6 +75,21 @@ RUN mkdir /thirdparty && \
     chmod -R +x /thirdparty
 ENV PATH="/thirdparty/LuciPHOr2:/thirdparty/MSGFPlus:/thirdparty/ThermoRawFileParser:/thirdparty/Comet:/thirdparty/Percolator:/thirdparty/Sage:${PATH}"
 
+# Build the OpenMS-Insight package (Python + Vue bundle) from the migration branch.
+# Insight's Vue dist is gitignored and it has no pip build hook, so build the bundle
+# here and sync it into the package tree; the compile-openms stage pip-installs it.
+FROM node:21 AS insight-build
+ARG INSIGHT_REPO=https://github.com/t0mdavid-m/openms-insight.git
+ARG INSIGHT_BRANCH=claude/kind-heisenberg-u6dVm
+ADD https://api.github.com/repos/t0mdavid-m/openms-insight/git/refs/heads/${INSIGHT_BRANCH} insight-ref.json
+RUN git clone -b ${INSIGHT_BRANCH} --single-branch ${INSIGHT_REPO} /openms-insight
+WORKDIR /openms-insight/js-component
+RUN npm install && npm run build
+RUN mkdir -p /openms-insight/openms_insight/js-component \
+    && rm -rf /openms-insight/openms_insight/js-component/dist \
+    && cp -r /openms-insight/js-component/dist /openms-insight/openms_insight/js-component/dist \
+    && rm -rf /openms-insight/js-component/node_modules
+
 # Build OpenMS and pyOpenMS.
 FROM setup-build-system AS compile-openms
 WORKDIR /
@@ -102,6 +117,10 @@ RUN pip install dist/*.whl
 # Install other dependencies (excluding pyopenms)
 COPY requirements.txt ./requirements.txt 
 RUN grep -Ev '^pyopenms([=<>!~].*)?$' requirements.txt > requirements_cleaned.txt && mv requirements_cleaned.txt requirements.txt
+# OpenMS-Insight: install from the migration branch built in the insight-build stage
+# (with its Vue bundle), before requirements so the pin resolves from source not PyPI.
+COPY --from=insight-build /openms-insight /tmp/openms-insight
+RUN pip install /tmp/openms-insight && rm -rf /tmp/openms-insight
 RUN pip install -r requirements.txt
 
 WORKDIR /
@@ -123,23 +142,9 @@ ENV OPENMS_DATA_PATH="/openms/share/"
 # Remove build directory.
 RUN rm -rf openms-build
 
-# Build JS-component (quick). Placed after the slow OpenMS build so that changes
-# to the Vue component do not invalidate the OpenMS compile cache; its output is
-# copied into the final image in the run-app stage below.
-FROM node:21 AS js-build
-
-# JS Component
-ARG VUE_REPO=https://github.com/t0mdavid-m/openms-streamlit-vue-component.git
-ARG VUE_BRANCH=FVdeploy
-
-ADD https://api.github.com/repos/t0mdavid-m/openms-streamlit-vue-component/git/refs/heads/$VUE_BRANCH version.json
-
-RUN git clone -b ${VUE_BRANCH} --single-branch ${VUE_REPO}
-WORKDIR /openms-streamlit-vue-component
-RUN npm install
-RUN npm run build
-
 # Prepare and run streamlit app.
+# (The legacy local Vue component build stage was removed in the OpenMS-Insight
+# migration -- Insight ships its own Vue bundle via the openms-insight package.)
 FROM compile-openms AS run-app
 
 # Install Redis server for job queue and nginx for load balancing
@@ -168,9 +173,6 @@ COPY settings.json /app/settings.json
 COPY default-parameters.json /app/default-parameters.json
 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
-
 # 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/FLASHDeconvViewer.py

@@ -2,144 +2,79 @@
 
 from pathlib import Path
 
-from src.common.common import page_setup, save_params
+from src.common.common import page_setup, save_params, show_linked_grid
 from src.workflow.FileManager import FileManager
-from src.render.render import render_grid
-
-DEFAULT_LAYOUT = [['ms1_deconv_heat_map'], ['scan_table', 'mass_table'],
-                  ['anno_spectrum', 'deconv_spectrum'], ['3D_SN_plot']]
-
-def select_experiment():
-    # Map display name back to experiment ID
-    st.session_state.selected_experiment0 = display_name_to_id[st.session_state.selected_experiment_dropdown]
-    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}"] = display_name_to_id[st.session_state[f'selected_experiment_dropdown_{exp_index}']]
-
-def validate_selected_index(file_manager, selected_experiment):
-    results = file_manager.get_results_list(['deconv_dfs', 'anno_dfs'])
-    if selected_experiment in st.session_state:
-        if st.session_state[selected_experiment] in results:
-            # Map experiment ID to display name for the dropdown index
-            exp_id = st.session_state[selected_experiment]
-            display_name = file_manager.get_display_name(exp_id)
-            return display_name_to_index[display_name]
-        else:
-            del st.session_state[selected_experiment]
-    return None
+from src.render.render import make_builders
+from src.render.schema import build_insight_caches
+
+# Default panel layout (one experiment): heatmap on top, scan->mass tables,
+# annotated + deconvolved spectra, then the precursor-signal 3D plot. Cross-links
+# (scan -> mass -> spectrum -> 3D) are carried by the shared StateManager via each
+# component's filters/interactivity.
+DEFAULT_LAYOUT = [
+    ["ms1_deconv_heat_map"],
+    ["scan_table", "mass_table"],
+    ["anno_spectrum", "deconv_spectrum"],
+    ["3D_SN_plot"],
+]
 
 # page initialization
 params = page_setup()
 
-# Get available results
 file_manager = FileManager(
     st.session_state["workspace"],
-    Path(st.session_state['workspace'], 'cache')
+    Path(st.session_state["workspace"], "cache"),
 )
 
-def get_sequence():
-    # Check if layout has been set
-    if not file_manager.result_exists('sequence', 'sequence'):
-        return None
-    # fetch layout from cache
-    sequence = file_manager.get_results('sequence', 'sequence')['sequence']
-
-    return sequence['input_sequence'], sequence['fixed_mod_cysteine'], sequence['fixed_mod_methionine'] 
-
-if get_sequence() is not None:
-    DEFAULT_LAYOUT = DEFAULT_LAYOUT + [['sequence_view']]
-
-results = file_manager.get_results_list(['threedim_SN_plot'])
-
-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
+# Gate: need at least one processed FLASHDeconv result.
+results = file_manager.get_results_list(["threedim_SN_plot"])
 if len(results) == 0:
-    st.error('No results to show yet. Please run a workflow first!')
+    st.error("No results to show yet. Please run a workflow first!")
     st.stop()
 
-# Create display names and mappings
-display_names = [file_manager.get_display_name(exp_id) for exp_id in results]
-display_name_to_id = {file_manager.get_display_name(exp_id): exp_id for exp_id in results}
-display_name_to_index = {n : i for i, n in enumerate(display_names)}
-# Keep backward compatibility mapping for experiment IDs
-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", display_names,
-            key="selected_experiment_dropdown",
-            index=validate_selected_index(file_manager, 'selected_experiment0'),
-            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'
-            )
-    with c2:
-        st.selectbox(
-            "choose experiment", display_names,
-            key=f'selected_experiment_dropdown_1',
-            index=validate_selected_index(file_manager, 'selected_experiment1'),
-            on_change=select_experiment
-        )
-        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'
-                )
+# A global input sequence enables the Sequence View panel (oracle parity).
+has_sequence = file_manager.result_exists("sequence", "sequence")
 
+# Saved layout (trimmed nested list + side_by_side) or the default.
+if file_manager.result_exists("layout", "layout"):
+    saved = file_manager.get_results("layout", "layout")["layout"]
+    layout, side_by_side = saved["layout"], saved["side_by_side"]
 else:
-    ### for only single experiment on one view
-    st.selectbox(
-        "choose experiment", display_names,
-        key="selected_experiment_dropdown",
-        index=validate_selected_index(file_manager, 'selected_experiment0'),
-        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'
+    default = DEFAULT_LAYOUT + [["sequence_view"]] if has_sequence else DEFAULT_LAYOUT
+    layout, side_by_side = [default], False
+
+# Experiments are selected by their stable dataset id; the display name is shown
+# via format_func so duplicate display names can't collapse distinct datasets.
+
+
+def _render_experiment(exp_idx, exp_layout, container):
+    """One experiment selector + its linked grid (tool/data-specific, so in-page)."""
+    with container:
+        # Oracle parity: start blank (nothing selected) and render nothing until the
+        # user picks an experiment -- the old viewer used validate_selected_index
+        # (initially None), which also avoided eagerly building caches on page load.
+        sel = st.selectbox(
+            "choose experiment", results, index=None,
+            format_func=file_manager.get_display_name,
+            placeholder="Choose an experiment", key=f"deconv_exp_{exp_idx}",
         )
+        if sel is None:
+            return
+        ds = sel
+        # Lazily build the Insight tidy caches for this dataset (idempotent).
+        build_insight_caches(file_manager, ds, "flashdeconv")
+        builders = make_builders(file_manager, ds, "flashdeconv")
+        show_linked_grid([exp_layout], builders, tool=f"flashdeconv_{exp_idx}_{ds}")
 
-    ### 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", display_names,
-                key=f'selected_experiment_dropdown_{exp_index}',
-                index=validate_selected_index(file_manager, f'selected_experiment{exp_index}'),
-                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:
-                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
-                )
+if len(layout) == 2 and side_by_side:
+    c1, c2 = st.columns(2)
+    _render_experiment(0, layout[0], c1)
+    _render_experiment(1, layout[1], c2)
+else:
+    for i, exp_layout in enumerate(layout):
+        if i:
+            st.divider()
+        _render_experiment(i, exp_layout, st.container())
 
 save_params(params)