From a71ba9e632cfee4635c42883cf2a9fb0b412d0d0 Mon Sep 17 00:00:00 2001
From: siosonel <siosonel@gmail.com>
Date: Mon, 1 Dec 2025 07:21:29 -0800
Subject: [PATCH 1/9] create cards for ProteinPaint-based analysis tools

---
 config/gen3/analysisTools.json                |  35 ++
 src/features/apps/OncoMatrix.tsx              |   8 +
 src/features/apps/ProteinPaint.tsx            |   8 +
 src/features/proteinpaint/MatrixWrapper.tsx   | 364 ++++++++++++++++++
 .../proteinpaint/ProteinPaintWrapper.tsx      | 239 ++++++++++++
 src/features/proteinpaint/dev.sh              |  31 ++
 src/features/proteinpaint/sjpp-types.tsx      |  56 +++
 7 files changed, 741 insertions(+)
 create mode 100644 src/features/apps/OncoMatrix.tsx
 create mode 100644 src/features/apps/ProteinPaint.tsx
 create mode 100644 src/features/proteinpaint/MatrixWrapper.tsx
 create mode 100644 src/features/proteinpaint/ProteinPaintWrapper.tsx
 create mode 100755 src/features/proteinpaint/dev.sh
 create mode 100644 src/features/proteinpaint/sjpp-types.tsx

diff --git a/config/gen3/analysisTools.json b/config/gen3/analysisTools.json
index 03f00f2..e970cca 100644
--- a/config/gen3/analysisTools.json
+++ b/config/gen3/analysisTools.json
@@ -81,6 +81,41 @@
           "hideCounts" : true,
           "appId" : "CohortComparison",
           "countUnits": "Cases"
+        },
+        {
+          "title": "ProteinPaint",
+          "type": "application",
+          "hasDemo": false,
+          "loginRequired": false,
+          "description": "Visualize mutations in protein-coding genes by consequence type and protein domain.",
+          "icon": "/icons/apps/ProteinPaint.svg",
+          "href": "/?app=ProteinPaint",
+          "appId" : "ProteinPaint",
+          "count": 1000,
+          "countUnits": "Cases"
+        },
+        {
+          "title": "OncoMatrix",
+          "type": "application",
+          "hasDemo": false,
+          "loginRequired": false,
+          "description": "Visualize the top most mutated cases and genes affected by high impact mutations in your cohort.",
+          "icon": "/icons/apps/OncoMatrix.svg",
+          "appId" : "OncoMatrix",
+          "href": "/?app=OncoMatrix",
+          "count": 1000,
+          "countUnits": "Cases"
+        },
+        {
+          "title": "Set Operations",
+          "type": "application",
+          "hasDemo": false,
+          "loginRequired": false,
+          "description": "Display a Venn diagram and compare/contrast your cohorts or sets of the same type.",
+          "icon": "/icons/apps/SetOperations.svg",
+          "href": "/",
+          "count": 1000,
+          "countUnits": "Cases"
         }
       ]
     }
diff --git a/src/features/apps/OncoMatrix.tsx b/src/features/apps/OncoMatrix.tsx
new file mode 100644
index 0000000..c386c45
--- /dev/null
+++ b/src/features/apps/OncoMatrix.tsx
@@ -0,0 +1,8 @@
+import { FC } from "react";
+import { MatrixWrapper } from "../proteinpaint/MatrixWrapper";
+
+const MatrixApp: FC = () => {
+  return <MatrixWrapper chartType="matrix" />;
+};
+
+export default MatrixApp;
diff --git a/src/features/apps/ProteinPaint.tsx b/src/features/apps/ProteinPaint.tsx
new file mode 100644
index 0000000..704010f
--- /dev/null
+++ b/src/features/apps/ProteinPaint.tsx
@@ -0,0 +1,8 @@
+import { FC } from "react";
+import { ProteinPaintWrapper } from "../proteinpaint/ProteinPaintWrapper";
+
+const ProteinPaintApp: FC = () => {
+  return <ProteinPaintWrapper />;
+};
+
+export default ProteinPaintApp;
diff --git a/src/features/proteinpaint/MatrixWrapper.tsx b/src/features/proteinpaint/MatrixWrapper.tsx
new file mode 100644
index 0000000..1203045
--- /dev/null
+++ b/src/features/proteinpaint/MatrixWrapper.tsx
@@ -0,0 +1,364 @@
+import { useRef, useCallback, useState, FC } from "react";
+import { useDeepCompareEffect } from "use-deep-compare";
+import { bindProteinPaint } from "@sjcrh/proteinpaint-client";
+import { useIsDemoApp } from "@/hooks/useIsDemoApp";
+import {
+  useCoreSelector,
+  selectCurrentCohortFilters,
+  convertFilterSetToGqlFilter as buildCohortGqlOperator,
+  FilterSet,
+  //PROTEINPAINT_API,
+  useFetchUserDetailsQuery,
+  useCoreDispatch,
+  // useCreateCaseSetFromValuesMutation,
+  // useGetGenesQuery,
+  Operation,
+  Includes,
+  showModal,
+  hideModal,
+  Modals,
+  selectCurrentModal,
+} from "@gen3/core";
+import { DemoText } from "@/components/tailwindComponents";
+import { LoadingOverlay } from "@mantine/core";
+import {
+  SelectSamples,
+  SelectSamplesCallBackArg,
+  SelectSamplesCallback,
+  RxComponentCallbacks,
+} from "./sjpp-types";
+//import { SaveCohortModal } from "@gff/portal-components";
+//import GeneSetModal from "@/components/Modals/SetModals/GeneSetModal";
+import { isEqual, cloneDeep } from "lodash";
+//import { cohortActionsHooks } from "../cohortBuilder/CohortManager/cohortActionHooks";
+//import { INVALID_COHORT_NAMES } from "../cohortBuilder/utils";
+
+const basepath = 'http://localhost:3000' // PROTEINPAINT_API;
+
+interface PpProps {
+  chartType: "matrix" | "hierCluster";
+  basepath?: string;
+}
+
+export const demoFilter = Object.freeze({
+  op: "in",
+  content: Object.freeze({
+    field: "cases.disease_type",
+    value: Object.freeze(["Gliomas"]),
+  }),
+});
+
+export const MatrixWrapper: FC<PpProps> = (props: PpProps) => {
+  const isDemoMode = useIsDemoApp();
+  // const demoFilter = {
+  //   op: "in",
+  //   content: { field: "cases.disease_type", value: ["Gliomas"] },
+  // };
+  const currentCohort = useCoreSelector(selectCurrentCohortFilters);
+  const filter0 = null // isDemoMode
+    // ? cloneDeep(demoFilter)
+    // : buildCohortGqlOperator(currentCohort);
+  const userDetails = useFetchUserDetailsQuery();
+  const prevData = useRef<any>();
+  const toolApp = useRef<any>();
+  const coreDispatch = useCoreDispatch();
+  const [showSaveCohortModal, setShowSaveCohortModal] = useState(false);
+  const [isLoading, setIsLoading] = useState(false);
+  // const [createSet, response] = useCreateCaseSetFromValuesMutation();
+  // const [newCohortFilters, setNewCohortFilters] =
+  //   useState<FilterSet>(undefined);
+  const [customGeneSetParam, setCustomGeneSetParam] = useState(null);
+  const [lastGeneSetRequestId, setLastGeneSetRequestId] = useState(undefined);
+
+  const dispatch = useCoreDispatch();
+  const modal = useCoreSelector((state) => selectCurrentModal(state));
+
+  const callback = () => {}
+  // useCallback<SelectSamplesCallback>(
+  //   (arg: SelectSamplesCallBackArg) => {
+  //     const cases = arg.samples.map((d) => d["cases.case_id"]);
+  //     if (cases.length > 1) {
+  //       createSet({ values: cases, intent: "portal", set_type: "frozen" });
+  //     } else {
+  //       setNewCohortFilters({
+  //         mode: "and",
+  //         root: {
+  //           "cases.case_id": {
+  //             operator: "includes",
+  //             field: "cases.case_id",
+  //             operands: cases,
+  //           },
+  //         },
+  //       });
+  //       setShowSaveCohortModal(true);
+  //     }
+  //   },
+  //   [createSet],
+  // );
+
+  // a set for the new cohort is created, now show the save cohort modal
+  // useDeepCompareEffect(() => {
+  //   if (response.isSuccess) {
+  //     const filters: FilterSet = {
+  //       mode: "and",
+  //       root: {
+  //         "cases.case_id": {
+  //           operator: "includes",
+  //           field: "cases.case_id",
+  //           operands: [`set_id:${response.data}`],
+  //         },
+  //       },
+  //     };
+  //     setNewCohortFilters(filters);
+  //     setShowSaveCohortModal(true);
+  //   }
+  // }, [response.isSuccess, coreDispatch, response.data]);
+
+  // const genesResponse = useGetGenesQuery(
+  //   {
+  //     request: {
+  //       filters: {
+  //         op: "in",
+  //         content: {
+  //           field: "genes.gene_id",
+  //           value: customGeneSetParam,
+  //         },
+  //       },
+  //       fields: ["gene_id", "symbol"],
+  //       size: 1000,
+  //       //from: currentPage * PAGE_SIZE,
+  //       //sortBy,
+  //     },
+  //     fetchAll: false,
+  //   },
+  //   { skip: !customGeneSetParam?.length },
+  // );
+  // const {
+  //   data: geneDetailData,
+  //   isFetching: isGeneFetching,
+  //   requestId: genesRequestId,
+  // } = genesResponse;
+
+  const showLoadingOverlay = () => setIsLoading(true);
+  const hideLoadingOverlay = () => setIsLoading(false);
+  const matrixCallbacks: RxComponentCallbacks = {
+    "postRender.gdcOncoMatrix": hideLoadingOverlay,
+    "error.gdcOncoMatrix": hideLoadingOverlay,
+  };
+  const appCallbacks: RxComponentCallbacks = {
+    "preDispatch.gdcPlotApp": showLoadingOverlay,
+    "error.gdcPlotApp": hideLoadingOverlay,
+    "postRender.gdcPlotApp": hideLoadingOverlay,
+  };
+  // const genesetCallback = (/*{callback}*/) => {
+  //   dispatch(showModal({ modal: Modals.LocalGeneSetModal }));
+  //   // TODO: pass the gene set to the callback
+  // };
+  const initArgs = getMatrixTrack(
+    props,
+    callback,
+    matrixCallbacks,
+    appCallbacks,
+    //genesetCallback,
+  );
+
+  useDeepCompareEffect(
+    () => {
+      // debounce until one of these is true
+      // otherwise, the userDetails.isFetching changing from false > true > false
+      // could trigger unnecessary, wastefule PP-app state update
+      if (userDetails?.isSuccess === false && userDetails?.isError === false)
+        return;
+      //if (isGeneFetching) return;
+      const data = {
+        filter0: filter0 || null,
+        userData: userDetails?.data,
+        //geneDetailData,
+      };
+      const hasUpdates =
+        (data || prevData.current) && !isEqual(prevData.current, data);
+      if (hasUpdates) prevData.current = data;
+      const rootElem = divRef.current as HTMLElement;
+
+      let updateArgs;
+      if (hasUpdates) {
+        updateArgs = { filter0: data.filter0 };
+        // if (lastGeneSetRequestId != genesRequestId) {
+        //   setLastGeneSetRequestId(genesRequestId);
+        //   updateArgs.genes = geneDetailData.hits.map((h) => ({
+        //     gene: h.symbol,
+        //   }));
+        // }
+
+        // TODO:
+        // showing and hiding the overlay should be triggered by components that may take a while to load/render,
+        // this wrapper code can show the overlay here since it has supplied postRender callbacks above,
+        // but ideally it is the PP-app that triggers both the showing and hiding of the overlay for reliable behavior
+        const toolContainer = rootElem?.parentNode?.parentNode?.parentNode as HTMLElement;
+        toolContainer.style.backgroundColor = "#fff";
+      }
+
+      Object.assign(initArgs, {
+        holder: rootElem,
+        noheader: true,
+        nobox: true,
+        hide_dsHandles: true,
+        filter0: data.filter0,
+      });
+
+      // bindProteinPaint() handles rapid update requests/race condition,
+      // so no need to include debouncing and promise code in this wrapper
+      // TODO: will revert to using runproteinpaint() once these advanced capabilities
+      // are merged into it
+      bindProteinPaint({
+        rootElem,
+        initArgs,
+        updateArgs,
+        isStale() {
+          // new data has replaced this one, will prevent unnecessary render
+          // in case of race condition
+          return prevData.current != data;
+        },
+      })
+        .then?.((_app) => {
+          toolApp.current = _app;
+        })
+        .catch((e) => {
+          // the app should either work or display an error in a red banner within the tool container div,
+          // this uncaught-by-app error is unlikely to happen except for bundling issues that are not detected at build time
+          console.error(e);
+        });
+
+      return () => {
+        if (!toolApp.current) return;
+        const toolName =
+          props.chartType == "hierCluster" ? "GeneExpression" : "OncoMatrix";
+        if (window.location.href.includes(toolName)) return;
+        // cancel unnecessary network requests when this tool app is hidden
+        toolApp.current.triggerAbort();
+      };
+    },
+    // eslint-disable-next-line react-hooks/exhaustive-deps
+    [filter0, userDetails, /*geneDetailData*/],
+  );
+
+  const divRef = useRef<HTMLElement>(null);
+
+  // const updateFilters = (field: string, operation: Operation) => {
+  //   dispatch(hideModal());
+  //   setCustomGeneSetParam((operation as Includes).operands);
+  // };
+  const existingFiltersHook = () => null;
+  return (
+    <div className="relative">
+      {isDemoMode && <DemoText>Demo showing cases with Gliomas.</DemoText>}
+      <div
+        ref={divRef}
+        className="sjpp-wrapper-root-div"
+        //userDetails={userDetails}
+      />
+
+      {/*<SaveCohortModal // Show the modal, create a saved cohort when save button is clicked
+        opened={showSaveCohortModal}
+        onClose={() => setShowSaveCohortModal(false)}
+        filters={newCohortFilters}
+        hooks={cohortActionsHooks}
+        invalidCohortNames={INVALID_COHORT_NAMES}
+      />
+
+      <GeneSetModal
+        opened={modal === Modals.LocalGeneSetModal}
+        modalTitle="Use a previously saved gene set"
+        inputInstructions="Enter one or more gene identifiers in the field below or upload a file to create a gene set."
+        selectSetInstructions="Select one or more sets below to use as an OncoMatrix gene set."
+        updateFilters={updateFilters}
+        existingFiltersHook={existingFiltersHook}
+      />*/}
+
+      <LoadingOverlay
+        data-testid="loading-spinner"
+        visible={isLoading}
+        zIndex={0}
+      />
+    </div>
+  );
+};
+
+interface MatrixArg {
+  holder?: HTMLElement;
+  noheader?: boolean;
+  nobox?: boolean;
+  hide_dsHandles?: boolean;
+  host: string;
+  launchGdcMatrix: boolean;
+  launchGdcHierCluster: boolean;
+  filter0?: any; //FilterSet;
+  opts: MatrixArgOpts;
+  state?: any;
+}
+
+interface MatrixArgOpts {
+  app: MatrixArgOptsApp;
+  matrix?: MatrixArgOptsMatrix;
+  hierCluster?: MatrixArgOptsMatrix;
+}
+
+interface MatrixArgOptsApp {
+  callbacks?: RxComponentCallbacks;
+}
+
+interface MatrixArgOptsMatrix {
+  allow2selectSamples?: SelectSamples;
+  callbacks?: RxComponentCallbacks;
+  customInputs?: {
+    geneset?: {
+      label: string;
+      showInput: () => void;
+    }[];
+  };
+}
+
+function getMatrixTrack(
+  props: PpProps,
+  callback?: SelectSamplesCallback,
+  matrixCallbacks?: RxComponentCallbacks,
+  appCallbacks?: RxComponentCallbacks,
+  //genesetCallback?: () => void,
+): MatrixArg {
+  const arg: MatrixArg = {
+    // host in gdc is just a relative url path,
+    // using the same domain as the GDC portal where PP is embedded
+    host: props.basepath || (basepath as string),
+    launchGdcMatrix: props.chartType == "matrix",
+    launchGdcHierCluster: props.chartType == "hierCluster",
+    opts: {
+      app: {
+        callbacks: appCallbacks,
+      },
+      [props.chartType]: {
+        allow2selectSamples: {
+          buttonText: "Create Cohort",
+          attributes: [
+            {
+              from: "sample",
+              to: "cases.case_id",
+              convert: true,
+            },
+          ],
+          callback,
+        },
+        callbacks: matrixCallbacks,
+        // customInputs: {
+        //   geneset: [
+        //     {
+        //       label: "Load Gene Sets",
+        //       showInput: genesetCallback,
+        //     },
+        //   ],
+        // },
+      },
+    },
+  };
+
+  return arg;
+}
diff --git a/src/features/proteinpaint/ProteinPaintWrapper.tsx b/src/features/proteinpaint/ProteinPaintWrapper.tsx
new file mode 100644
index 0000000..b8c9eb8
--- /dev/null
+++ b/src/features/proteinpaint/ProteinPaintWrapper.tsx
@@ -0,0 +1,239 @@
+import { useRef, useCallback, useState, FC } from "react";
+import { useDeepCompareEffect } from "use-deep-compare";
+import { bindProteinPaint } from "@sjcrh/proteinpaint-client";
+import { useIsDemoApp } from "@/hooks/useIsDemoApp";
+import {
+  useCoreSelector,
+  selectCurrentCohortFilters,
+  FilterSet,
+  //PROTEINPAINT_API,
+  useFetchUserDetailsQuery,
+  useCoreDispatch,
+  convertFilterSetToGqlFilter as buildCohortGqlOperator,
+  //useCreateCaseSetFromValuesMutation,
+} from "@gen3/core";
+import { isEqual, cloneDeep } from "lodash";
+import { DemoText } from "@/components/tailwindComponents";
+// import { SaveCohortModal } from "@gff/portal-components";
+import {
+  SelectSamples,
+  SelectSamplesCallBackArg,
+  SelectSamplesCallback,
+} from "./sjpp-types";
+// import { cohortActionsHooks } from "../cohortBuilder/CohortManager/cohortActionHooks";
+// import { INVALID_COHORT_NAMES } from "../cohortBuilder/utils";
+
+const basepath = 'http://localhost:3000'; //PROTEINPAINT_API;
+
+interface PpProps {
+  basepath?: string;
+  geneId?: string;
+  gene2canonicalisoform?: string;
+  ssm_id?: string;
+  mds3_ssm2canonicalisoform?: mds3_isoform;
+  geneSearch4GDCmds3?: boolean;
+  hardcodeCnvOnly?: boolean;
+}
+
+export const ProteinPaintWrapper: FC<PpProps> = (props: PpProps) => {
+  const isDemoMode = useIsDemoApp();
+  const currentCohort = useCoreSelector(selectCurrentCohortFilters);
+
+  // const cohortFilters = useCoreSelector((state) =>
+  //   isDemoMode ? DEMO_COHORT_FILTERS : selectCurrentCohortFilters(state),
+  // );
+
+  const filter0 = null // isDemoMode ? null : buildCohortGqlOperator(currentCohort);
+  const userDetails = useFetchUserDetailsQuery();
+
+  // to track reusable instance for mds3 skewer track
+  const prevArg = useRef<any>({});
+  const coreDispatch = useCoreDispatch();
+  const [showSaveCohort, setShowSaveCohort] = useState(false);
+  //const [createSet, response] = useCreateCaseSetFromValuesMutation();
+  // const [newCohortFilters, setNewCohortFilters] =
+  //   useState<FilterSet>(undefined);
+
+  const callback = () => {}
+  // useCallback<SelectSamplesCallback>(
+  //   (arg: SelectSamplesCallBackArg) => {
+  //     const cases = arg.samples.map((d) => d["cases.case_id"]);
+  //     if (cases.length > 1) {
+  //       createSet({ values: cases, intent: "portal", set_type: "frozen" });
+  //     } else {
+  //       setNewCohortFilters({
+  //         mode: "and",
+  //         root: {
+  //           "cases.case_id": {
+  //             operator: "includes",
+  //             field: "cases.case_id",
+  //             operands: cases,
+  //           },
+  //         },
+  //       });
+  //       setShowSaveCohort(true);
+  //     }
+  //   },
+  //   [createSet],
+  // );
+
+  // a set for the new cohort is created, now show the save cohort modal
+  // useDeepCompareEffect(() => {
+  //   if (response.isSuccess) {
+  //     const filters: FilterSet = {
+  //       mode: "and",
+  //       root: {
+  //         "cases.case_id": {
+  //           operator: "includes",
+  //           field: "cases.case_id",
+  //           operands: [`set_id:${response.data}`],
+  //         },
+  //       },
+  //     };
+  //     setNewCohortFilters(filters);
+  //     setShowSaveCohort(true);
+  //   }
+  // }, [response.isSuccess, coreDispatch, response.data]);
+
+  useDeepCompareEffect(
+    () => {
+      const rootElem = divRef.current;
+      const data = getLollipopTrack(props, filter0, callback);
+      if (!data) return;
+      if (isDemoMode) {
+        data.geneSymbol = props.hardcodeCnvOnly
+          ? "chr8:127682515-127792250"
+          : "MYC";
+      }
+      // compare the argument to runpp to avoid unnecessary render
+      if ((data || prevArg.current) && isEqual(prevArg.current, data)) return;
+      prevArg.current = data;
+
+      const toolContainer = rootElem?.parentNode?.parentNode?.parentNode as HTMLElement;
+      if (!toolContainer) return
+      toolContainer.style.backgroundColor = "#fff";
+
+      const arg = Object.assign(
+        { holder: rootElem, noheader: true, nobox: true },
+        cloneDeep(data),
+      ) as Mds3Arg;
+
+      // bindProteinPaint() handles rapid update requests/race condition,
+      // so no need to include debouncing and promise code in this wrapper
+      // TODO: will revert to using runproteinpaint() once these advanced capabilities
+      // are merged into it
+      bindProteinPaint({
+        rootElem,
+        initArgs: arg,
+        updateArgs: arg,
+        isStale() {
+          // new data has replaced this one, will prevent unnecessary render
+          // in case of race condition
+          return prevArg.current != data;
+        },
+      });
+    },
+    // eslint-disable-next-line react-hooks/exhaustive-deps
+    [
+      props.gene2canonicalisoform,
+      props.mds3_ssm2canonicalisoform,
+      props.geneSearch4GDCmds3,
+      isDemoMode,
+      filter0,
+      userDetails,
+    ],
+  );
+
+  const divRef = useRef<HTMLElement>(null);
+  const demoText = props.hardcodeCnvOnly
+    ? "Demo showing MYC CNV segments from all GDC cases"
+    : "Demo showing MYC mutations from all GDC cases.";
+  return (
+    <div>
+      {isDemoMode && <DemoText>{demoText}</DemoText>}
+      <div
+        ref={divRef}
+        className="sjpp-wrapper-root-div"
+        //userDetails={userDetails}
+      />
+
+      {/*<SaveCohortModal // Show the modal, create a saved cohort when save button is clicked
+        opened={showSaveCohort}
+        onClose={() => setShowSaveCohort(false)}
+        filters={newCohortFilters}
+        hooks={cohortActionsHooks}
+        invalidCohortNames={INVALID_COHORT_NAMES}
+      />*/}
+    </div>
+  );
+};
+
+interface Mds3Arg {
+  holder?: HTMLElement;
+  noheader?: boolean;
+  nobox?: boolean;
+  hide_dsHandles?: boolean;
+  host: string;
+  gene2canonicalisoform?: string;
+  mds3_ssm2canonicalisoform?: mds3_isoform;
+  geneSearch4GDCmds3?:
+    | boolean
+    | {
+        hardcodeCnvOnly?: boolean;
+      };
+  geneSymbol?: string;
+  tracks?: Track[];
+  filter0?: FilterSet;
+  allow2selectSamples?: SelectSamples;
+}
+
+interface Track {
+  type: string;
+  dslabel: string;
+  filter0: FilterSet;
+  allow2selectSamples?: SelectSamples;
+  hardcodeCnvOnly?: boolean;
+}
+
+interface mds3_isoform {
+  ssm_id: string;
+  dslabel: string;
+}
+
+function getLollipopTrack(
+  props: PpProps,
+  filter0: any,
+  callback: SelectSamplesCallback,
+) {
+  const arg: Mds3Arg = {
+    // host in gdc is just a relative url path,
+    // using the same domain as the GDC portal where PP is embedded
+    host: props.basepath || (basepath as string),
+    geneSearch4GDCmds3: {
+      hardcodeCnvOnly: props.hardcodeCnvOnly,
+    },
+    filter0,
+    allow2selectSamples: {
+      buttonText: "Create Cohort",
+      attributes: [{ from: "sample_id", to: "cases.case_id", convert: true }],
+      callback,
+    },
+  };
+
+  if (props.hardcodeCnvOnly) {
+    arg.geneSearch4GDCmds3 = {
+      hardcodeCnvOnly: true,
+    };
+  } else if (props.geneId) {
+    arg.gene2canonicalisoform = props.geneId;
+  } else if (props.ssm_id) {
+    arg.mds3_ssm2canonicalisoform = {
+      dslabel: "GDC",
+      ssm_id: props.ssm_id,
+    };
+  } else {
+    arg.geneSearch4GDCmds3 = true;
+  }
+
+  return arg;
+}
diff --git a/src/features/proteinpaint/dev.sh b/src/features/proteinpaint/dev.sh
new file mode 100755
index 0000000..8f983ca
--- /dev/null
+++ b/src/features/proteinpaint/dev.sh
@@ -0,0 +1,31 @@
+#!/bin/bash
+
+# run from the gdc-frontend-framework project root folder
+# ./packages/portal-proto/src/features/proteinpaint/dev.sh
+# assumes that the proteinpaint folder is a sibling dir of gff
+if [[ "$1" == "unlink" ]]; then
+	# to test the published client package before submitting a PR with an updated pp-client version
+	npm unlink ../proteinpaint/client
+	npm uninstall @sjcrh/proteinpaint-client --save --workspace=packages/portal-proto
+	npm install @sjcrh/proteinpaint-client --save --save-exact --workspace=packages/portal-proto
+
+else
+	# to test the local PP client code
+	npm link ../proteinpaint/client
+	# An issue with npm link and workspaces: the non-linked @sjcrh/proteinpaint-client package
+	# may be moved to portal-proto/node_modules, creating 2 separate modules of the same package,
+	# must ensure only the linked module is used for bundling so delete
+	rm -rf packages/portal-proto/node_modules/@sjcrh
+	# also not able to do a simpler
+	# `cd packages/portal-proto && npm link path/to/proteinpaint/client`,
+	# where the linked module would be in portal-proto/node_modules instead of the
+	# other way around
+fi
+
+# sometimes the nextjs bundle cache are stale after npm link
+# rm -rf packages/portal-proto/.next
+
+# run the following tab in a separate tab
+# local-ssl-proxy --config ssl-proxy.json --cert localhost.pem --key localhost-key.pem
+# then from the gff dir
+PORT=3333 npm run dev
diff --git a/src/features/proteinpaint/sjpp-types.tsx b/src/features/proteinpaint/sjpp-types.tsx
new file mode 100644
index 0000000..c36a96e
--- /dev/null
+++ b/src/features/proteinpaint/sjpp-types.tsx
@@ -0,0 +1,56 @@
+import { FilterSet } from "@gff/core";
+
+export interface PpApi {
+  update(arg: any): null;
+  staleInstance?: boolean;
+  getState?: () => any;
+}
+
+export type SampleData = {
+  "cases.case_id"?: string;
+};
+
+export interface SelectSamplesCallBackArg {
+  samples: SampleData[];
+  source: string;
+}
+
+export type SelectSamplesCallback = (samples: SelectSamplesCallBackArg) => void;
+
+export type attrMapping = {
+  from: string;
+  to?: string;
+  convert?: boolean;
+};
+
+export interface SelectSamples {
+  buttonText: string;
+  attributes: attrMapping[];
+  callback?: SelectSamplesCallback;
+}
+
+export function getFilters(arg: SelectSamplesCallBackArg): FilterSet {
+  const { samples } = arg;
+  // see comments below about SV-2228
+  const ids = samples.map((d) => d["cases.case_id"]).filter((d) => d && true);
+  return {
+    mode: "and",
+    root: {
+      // see https://jira.opensciencedatacloud.org/browse/SV-2228
+      // per Craig: I suggest always representing cohorts comprised of cases using the cases.case_id filter,
+      // as it is the most general of the case filters. Within an app, you can use any filter needed;
+      // when these become part of the cohort, there is some potential for issues.
+      // NOTE: This is primarily because both the frontend and backends are trying to, in effect,
+      // JOINs across the explore and repository indexes, and there is some additional work needed to work will all filters.
+      "cases.case_id": {
+        operator: "includes",
+        field: "cases.case_id",
+        operands: ids,
+      },
+    },
+  };
+}
+
+export type RxComponentCallbacks = {
+  [eventName: string]: () => void;
+};

From eac760e8f7cc217a03537c28e92889adaccb6459 Mon Sep 17 00:00:00 2001
From: siosonel <siosonel@gmail.com>
Date: Mon, 1 Dec 2025 12:47:23 -0800
Subject: [PATCH 2/9] specify the dslabel='MMRF' argument for
 ProteinPaint-based tools

---
 config/gen3/analysisTools.json                |   2 -
 package-lock.json                             | 183 +++++++++++-------
 package.json                                  |   1 +
 src/features/apps/ProteinPaint.tsx            |   6 +-
 src/features/proteinpaint/MatrixWrapper.tsx   |   4 +
 .../proteinpaint/ProteinPaintWrapper.tsx      |   4 +-
 src/features/proteinpaint/dev.sh              |   8 +-
 7 files changed, 126 insertions(+), 82 deletions(-)

diff --git a/config/gen3/analysisTools.json b/config/gen3/analysisTools.json
index e970cca..526c249 100644
--- a/config/gen3/analysisTools.json
+++ b/config/gen3/analysisTools.json
@@ -89,7 +89,6 @@
           "loginRequired": false,
           "description": "Visualize mutations in protein-coding genes by consequence type and protein domain.",
           "icon": "/icons/apps/ProteinPaint.svg",
-          "href": "/?app=ProteinPaint",
           "appId" : "ProteinPaint",
           "count": 1000,
           "countUnits": "Cases"
@@ -102,7 +101,6 @@
           "description": "Visualize the top most mutated cases and genes affected by high impact mutations in your cohort.",
           "icon": "/icons/apps/OncoMatrix.svg",
           "appId" : "OncoMatrix",
-          "href": "/?app=OncoMatrix",
           "count": 1000,
           "countUnits": "Cases"
         },
diff --git a/package-lock.json b/package-lock.json
index 7f1e454..dacd7ef 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -255,6 +255,7 @@
       "integrity": "sha512-2BCOP7TN8M+gVDj7/ht3hsaO/B/n5oDbiAyyvnRlNOs+u1o+JWNYTQrmpuNp1/Wq2gcFrI01JAW+paEKDMx/CA==",
       "dev": true,
       "license": "MIT",
+      "peer": true,
       "dependencies": {
         "@babel/code-frame": "^7.27.1",
         "@babel/generator": "^7.28.3",
@@ -2275,7 +2276,6 @@
       "resolved": "https://registry.npmjs.org/@codemirror/state/-/state-6.5.2.tgz",
       "integrity": "sha512-FVqsPqtPWKVVL3dPSxy8wEF/ymIEuVzF1PK3VbUgrxXpJUSHQWWZz4JMToquRxnkw+36LTamCZG2iua2Ptq0fA==",
       "license": "MIT",
-      "peer": true,
       "dependencies": {
         "@marijn/find-cluster-break": "^1.0.0"
       }
@@ -2285,7 +2285,6 @@
       "resolved": "https://registry.npmjs.org/@codemirror/view/-/view-6.38.6.tgz",
       "integrity": "sha512-qiS0z1bKs5WOvHIAC0Cybmv4AJSkAXgX5aD6Mqd2epSLlVJsQl8NG23jCVouIgkh4All/mrbdsf2UOLFnJw0tw==",
       "license": "MIT",
-      "peer": true,
       "dependencies": {
         "@codemirror/state": "^6.5.0",
         "crelt": "^1.0.6",
@@ -2401,6 +2400,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": ">=18"
       },
@@ -2442,6 +2442,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": ">=18"
       }
@@ -2578,6 +2579,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       },
@@ -2600,6 +2602,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       }
@@ -2716,6 +2719,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       },
@@ -2738,6 +2742,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       }
@@ -2873,6 +2878,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       },
@@ -2895,6 +2901,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       }
@@ -3010,6 +3017,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       },
@@ -3032,6 +3040,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       }
@@ -3227,6 +3236,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       },
@@ -3249,6 +3259,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       }
@@ -3318,6 +3329,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       },
@@ -3340,6 +3352,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       }
@@ -3517,6 +3530,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       },
@@ -3539,6 +3553,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       }
@@ -3680,6 +3695,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       },
@@ -3702,6 +3718,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       }
@@ -3784,6 +3801,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       },
@@ -3806,6 +3824,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       }
@@ -3914,6 +3933,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       },
@@ -3936,6 +3956,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       }
@@ -4011,6 +4032,7 @@
       "resolved": "https://registry.npmjs.org/@dnd-kit/core/-/core-6.3.1.tgz",
       "integrity": "sha512-xkGBRQQab4RLwgXxoqETICr6S5JlogafbhNsidmrkVv2YRs5MLwpjoF2qpiGjQt8S9AoxtIV603s0GIUpY5eYQ==",
       "license": "MIT",
+      "peer": true,
       "dependencies": {
         "@dnd-kit/accessibility": "^3.1.1",
         "@dnd-kit/utilities": "^3.2.2",
@@ -6535,7 +6557,6 @@
       "integrity": "sha512-kazxw2L9IPuZpQ0mEt9lu9Z98SqR74xcagANmMBU16X0lS23yPc0+S6hGLUz8kVRlomZEs/5S/Zlpqwf5yu6OQ==",
       "dev": true,
       "license": "MIT",
-      "peer": true,
       "dependencies": {
         "@jest/environment": "30.2.0",
         "@jest/fake-timers": "30.2.0",
@@ -6564,7 +6585,6 @@
       "integrity": "sha512-/QPTL7OBJQ5ac09UDRa3EQes4gt1FTEG/8jZ/4v5IVzx+Cv7dLxlVIvfvSVRiiX2drWyXeBjkMSR8hvOWSog5g==",
       "dev": true,
       "license": "MIT",
-      "peer": true,
       "dependencies": {
         "@jest/fake-timers": "30.2.0",
         "@jest/types": "30.2.0",
@@ -6581,7 +6601,6 @@
       "integrity": "sha512-HI3tRLjRxAbBy0VO8dqqm7Hb2mIa8d5bg/NJkyQcOk7V118ObQML8RC5luTF/Zsg4474a+gDvhce7eTnP4GhYw==",
       "dev": true,
       "license": "MIT",
-      "peer": true,
       "dependencies": {
         "@jest/types": "30.2.0",
         "@sinonjs/fake-timers": "^13.0.0",
@@ -6600,7 +6619,6 @@
       "integrity": "sha512-DmdYgtezMkh3cpU8/1uyXakv3tJRcmcXxBOcO0tbaozPwpmh4YMsnWrQm9ZmZMfa5ocbxzbFk6O4bDPEc/iAnA==",
       "dev": true,
       "license": "MIT",
-      "peer": true,
       "dependencies": {
         "@sinclair/typebox": "^0.34.0"
       },
@@ -6614,7 +6632,6 @@
       "integrity": "sha512-H9xg1/sfVvyfU7o3zMfBEjQ1gcsdeTMgqHoYdN79tuLqfTtuu7WckRA1R5whDwOzxaZAeMKTYWqP+WCAi0CHsg==",
       "dev": true,
       "license": "MIT",
-      "peer": true,
       "dependencies": {
         "@jest/pattern": "30.0.1",
         "@jest/schemas": "30.0.5",
@@ -6633,8 +6650,7 @@
       "resolved": "https://registry.npmjs.org/@sinclair/typebox/-/typebox-0.34.41.tgz",
       "integrity": "sha512-6gS8pZzSXdyRHTIqoqSVknxolr1kzfy4/CeDnrzsVz8TTIWUbOBr6gnzOmTYJ3eXQNh4IYHIGi5aIL7sOZ2G/g==",
       "dev": true,
-      "license": "MIT",
-      "peer": true
+      "license": "MIT"
     },
     "node_modules/@jest/environment-jsdom-abstract/node_modules/@sinonjs/fake-timers": {
       "version": "13.0.5",
@@ -6642,7 +6658,6 @@
       "integrity": "sha512-36/hTbH2uaWuGVERyC6da9YwGWnzUZXuPro/F2LfsdOsLnCojz/iSH8MxUt/FD2S5XBSVPhmArFUXcpCQ2Hkiw==",
       "dev": true,
       "license": "BSD-3-Clause",
-      "peer": true,
       "dependencies": {
         "@sinonjs/commons": "^3.0.1"
       }
@@ -7371,15 +7386,13 @@
       "version": "1.2.3",
       "resolved": "https://registry.npmjs.org/@lezer/common/-/common-1.2.3.tgz",
       "integrity": "sha512-w7ojc8ejBqr2REPsWxJjrMFsA/ysDCFICn8zEOR9mrqzOu2amhITYuLD8ag6XZf0CFXDrhKqw7+tW8cX66NaDA==",
-      "license": "MIT",
-      "peer": true
+      "license": "MIT"
     },
     "node_modules/@lezer/highlight": {
       "version": "1.2.1",
       "resolved": "https://registry.npmjs.org/@lezer/highlight/-/highlight-1.2.1.tgz",
       "integrity": "sha512-Z5duk4RN/3zuVO7Jq0pGLJ3qynpxUVsh7IbUbGj88+uV2ApSAn6kWg2au3iJb+0Zi7kKtqffIESgNcRXWZWmSA==",
       "license": "MIT",
-      "peer": true,
       "dependencies": {
         "@lezer/common": "^1.0.0"
       }
@@ -7389,7 +7402,6 @@
       "resolved": "https://registry.npmjs.org/@lezer/lr/-/lr-1.4.2.tgz",
       "integrity": "sha512-pu0K1jCIdnQ12aWNaAVU5bzi7Bd1w54J3ECgANPmYLtQKP0HBj2cE/5coBD66MT10xbtIuUr7tg0Shbsvk0mDA==",
       "license": "MIT",
-      "peer": true,
       "dependencies": {
         "@lezer/common": "^1.0.0"
       }
@@ -7399,6 +7411,7 @@
       "resolved": "https://registry.npmjs.org/@mantine/core/-/core-7.17.8.tgz",
       "integrity": "sha512-42sfdLZSCpsCYmLCjSuntuPcDg3PLbakSmmYfz5Auea8gZYLr+8SS5k647doVu0BRAecqYOytkX2QC5/u/8VHw==",
       "license": "MIT",
+      "peer": true,
       "dependencies": {
         "@floating-ui/react": "^0.26.28",
         "clsx": "^2.1.1",
@@ -7418,6 +7431,7 @@
       "resolved": "https://registry.npmjs.org/@mantine/dates/-/dates-7.17.8.tgz",
       "integrity": "sha512-KYog/YL83PnsMef7EZagpOFq9I2gfnK0eYSzC8YvV9Mb6t/x9InqRssGWVb0GIr+TNILpEkhKoGaSKZNy10Q1g==",
       "license": "MIT",
+      "peer": true,
       "dependencies": {
         "clsx": "^2.1.1"
       },
@@ -7447,6 +7461,7 @@
       "resolved": "https://registry.npmjs.org/@mantine/hooks/-/hooks-7.17.8.tgz",
       "integrity": "sha512-96qygbkTjRhdkzd5HDU8fMziemN/h758/EwrFu7TlWrEP10Vw076u+Ap/sG6OT4RGPZYYoHrTlT+mkCZblWHuw==",
       "license": "MIT",
+      "peer": true,
       "peerDependencies": {
         "react": "^18.x || ^19.x"
       }
@@ -7608,8 +7623,7 @@
       "version": "1.0.2",
       "resolved": "https://registry.npmjs.org/@marijn/find-cluster-break/-/find-cluster-break-1.0.2.tgz",
       "integrity": "sha512-l0h88YhZFyKdXIFNfSWpyjStDjGHwZ/U7iobcK1cQQD8sejsONdQtTVU+1wVN1PBw40PiiHB1vA5S7VTfQiP9g==",
-      "license": "MIT",
-      "peer": true
+      "license": "MIT"
     },
     "node_modules/@mdx-js/loader": {
       "version": "3.1.1",
@@ -8631,6 +8645,7 @@
       "resolved": "https://registry.npmjs.org/@mdx-js/react/-/react-3.1.1.tgz",
       "integrity": "sha512-f++rKLQgUVYDAtECQ6fn/is15GkEH9+nZPM3MS0RcxVqoTfawHvDlSCH7JbMhAM6uJ32v3eXLvLmLvjGu7PTQw==",
       "license": "MIT",
+      "peer": true,
       "dependencies": {
         "@types/mdx": "^2.0.0"
       },
@@ -9055,6 +9070,7 @@
       "resolved": "https://registry.npmjs.org/@opentelemetry/api/-/api-1.9.0.tgz",
       "integrity": "sha512-3giAOQvZiH5F9bMlMiv8+GSPMeqg0dbaeo58/0SlA9sxSqZhnUtxzX9/2FzyhS9sWQf5S0GJE0AKBrFqjpeYcg==",
       "license": "Apache-2.0",
+      "peer": true,
       "engines": {
         "node": ">=8.0.0"
       }
@@ -11158,6 +11174,7 @@
       "integrity": "sha512-8QqtOQT5ACVlmsvKOJNEaWmRPmcojMOzCz4Hs2BGG/toAp/K38LcsMRyLp349glq5AzJbCEeimEoxaX6v/fLrA==",
       "dev": true,
       "license": "MIT",
+      "peer": true,
       "dependencies": {
         "@babel/core": "^7.21.3",
         "@svgr/babel-preset": "8.1.0",
@@ -11267,6 +11284,7 @@
       "dev": true,
       "hasInstallScript": true,
       "license": "Apache-2.0",
+      "peer": true,
       "dependencies": {
         "@swc/counter": "^0.1.3",
         "@swc/types": "^0.1.24"
@@ -11475,18 +11493,6 @@
       "dev": true,
       "license": "Apache-2.0"
     },
-    "node_modules/@swc/helpers": {
-      "version": "0.5.17",
-      "resolved": "https://registry.npmjs.org/@swc/helpers/-/helpers-0.5.17.tgz",
-      "integrity": "sha512-5IKx/Y13RsYd+sauPb2x+U/xZikHjolzfuDgTAl/Tdf3Q8rslRvC19NKDLgAJQ6wsqADk10ntlv08nPFw/gO/A==",
-      "dev": true,
-      "license": "Apache-2.0",
-      "optional": true,
-      "peer": true,
-      "dependencies": {
-        "tslib": "^2.8.0"
-      }
-    },
     "node_modules/@swc/jest": {
       "version": "0.2.39",
       "resolved": "https://registry.npmjs.org/@swc/jest/-/jest-0.2.39.tgz",
@@ -11505,6 +11511,12 @@
         "@swc/core": "*"
       }
     },
+    "node_modules/@swc/nx-darwin-arm64": {
+      "optional": true
+    },
+    "node_modules/@swc/nx-linux-arm64-gnu": {
+      "optional": true
+    },
     "node_modules/@swc/types": {
       "version": "0.1.25",
       "resolved": "https://registry.npmjs.org/@swc/types/-/types-0.1.25.tgz",
@@ -11530,6 +11542,7 @@
       "resolved": "https://registry.npmjs.org/@tabler/icons-react/-/icons-react-3.35.0.tgz",
       "integrity": "sha512-XG7t2DYf3DyHT5jxFNp5xyLVbL4hMJYJhiSdHADzAjLRYfL7AnjlRfiHDHeXxkb2N103rEIvTsBRazxXtAUz2g==",
       "license": "MIT",
+      "peer": true,
       "dependencies": {
         "@tabler/icons": "3.35.0"
       },
@@ -11883,8 +11896,7 @@
       "resolved": "https://registry.npmjs.org/@types/aria-query/-/aria-query-5.0.4.tgz",
       "integrity": "sha512-rfT93uj5s0PRL7EzccGMs3brplhcrghnDoV26NqKhCAS1hVo+WdNsPvE/yb6ilfr5hi2MEk6d5EWJTKdxg8jVw==",
       "dev": true,
-      "license": "MIT",
-      "peer": true
+      "license": "MIT"
     },
     "node_modules/@types/babel__core": {
       "version": "7.20.5",
@@ -12047,6 +12059,7 @@
       "resolved": "https://registry.npmjs.org/@types/eslint/-/eslint-9.6.1.tgz",
       "integrity": "sha512-FXx2pKgId/WyYo2jXw63kk7/+TY7u7AziEJxJAnSFzHlqTAS3Ync6SvgYAN/k4/PQpnnVuzoMuVnByKK2qp0ag==",
       "license": "MIT",
+      "peer": true,
       "dependencies": {
         "@types/estree": "*",
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@@ -12242,7 +12255,6 @@
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       },
@@ -33694,6 +33712,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       }
@@ -33764,6 +33783,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       },
@@ -33786,6 +33806,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       }
@@ -34094,6 +34115,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       },
@@ -34116,6 +34138,7 @@
         }
       ],
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       }
@@ -34650,6 +34673,7 @@
       "resolved": "https://registry.npmjs.org/postcss-selector-parser/-/postcss-selector-parser-6.0.10.tgz",
       "integrity": "sha512-IQ7TZdoaqbT+LCpShg46jnZVlhWD2w6iQYAcYXfHARZ7X1t/UGhhceQDs5X0cGqKvYlHNOuv7Oa1xmb0oQuA3w==",
       "license": "MIT",
+      "peer": true,
       "dependencies": {
         "cssesc": "^3.0.0",
         "util-deprecate": "^1.0.2"
@@ -34703,6 +34727,7 @@
       "integrity": "sha512-I7AIg5boAr5R0FFtJ6rCfD+LFsWHp81dolrFD8S79U9tb8Az2nGrJncnMSnys+bpQJfRUzqs9hnA81OAA3hCuQ==",
       "dev": true,
       "license": "MIT",
+      "peer": true,
       "bin": {
         "prettier": "bin/prettier.cjs"
       },
@@ -34743,7 +34768,6 @@
       "integrity": "sha512-Qb1gy5OrP5+zDf2Bvnzdl3jsTf1qXVMazbvCoKhtKqVs4/YK4ozX4gKQJJVyNe+cajNPn0KoC0MC3FUmaHWEmQ==",
       "dev": true,
       "license": "MIT",
-      "peer": true,
       "dependencies": {
         "ansi-regex": "^5.0.1",
         "ansi-styles": "^5.0.0",
@@ -34759,7 +34783,6 @@
       "integrity": "sha512-Cxwpt2SfTzTtXcfOlzGEee8O+c+MmUgGrNiBcXnuWxuFJHe6a5Hz7qwhwe5OgaSYI0IJvkLqWX1ASG+cJOkEiA==",
       "dev": true,
       "license": "MIT",
-      "peer": true,
       "engines": {
         "node": ">=10"
       },
@@ -34772,8 +34795,7 @@
       "resolved": "https://registry.npmjs.org/react-is/-/react-is-17.0.2.tgz",
       "integrity": "sha512-w2GsyukL62IJnlaff/nRegPQR94C/XXamvMWmSHRJ4y7Ts/4ocGRmTHvOs8PSE6pB3dWOrD/nueuU5sduBsQ4w==",
       "dev": true,
-      "license": "MIT",
-      "peer": true
+      "license": "MIT"
     },
     "node_modules/probe-image-size": {
       "version": "7.2.3",
@@ -35082,6 +35104,7 @@
       "resolved": "https://registry.npmjs.org/react/-/react-18.3.1.tgz",
       "integrity": "sha512-wS+hAgJShR0KhEvPJArfuPVN1+Hz1t0Y6n5jLrGQbkb4urgPE/0Rve+1kMB1v/oWgHgm4WIcV+i7F2pTVj+2iQ==",
       "license": "MIT",
+      "peer": true,
       "dependencies": {
         "loose-envify": "^1.1.0"
       },
@@ -35103,6 +35126,7 @@
       "resolved": "https://registry.npmjs.org/react-cookie/-/react-cookie-7.2.2.tgz",
       "integrity": "sha512-e+hi6axHcw9VODoeVu8WyMWyoosa1pzpyjfvrLdF7CexfU+WSGZdDuRfHa4RJgTpfv3ZjdIpHE14HpYBieHFhg==",
       "license": "MIT",
+      "peer": true,
       "dependencies": {
         "@types/hoist-non-react-statics": "^3.3.5",
         "hoist-non-react-statics": "^3.3.2",
@@ -35162,6 +35186,7 @@
       "resolved": "https://registry.npmjs.org/react-dom/-/react-dom-18.3.1.tgz",
       "integrity": "sha512-5m4nQKp+rZRb09LNH59GM4BxTh9251/ylbKIbpe7TpGxfJ+9kv6BLkLBXIjjspbgbnIBNqlI23tRnTWT0snUIw==",
       "license": "MIT",
+      "peer": true,
       "dependencies": {
         "loose-envify": "^1.1.0",
         "scheduler": "^0.23.2"
@@ -35902,6 +35927,7 @@
       "integrity": "sha512-jCvmsr+1IUSMUyzOkRcvnVbX3ZYC6g9TDrDbFuFmRDq7PD4yaGbLKNQL6k2jnArV8hjYxh7hVhAZB6s9HDGpZA==",
       "dev": true,
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": ">=0.10.0"
       }
@@ -36454,7 +36480,8 @@
       "version": "5.0.1",
       "resolved": "https://registry.npmjs.org/redux/-/redux-5.0.1.tgz",
       "integrity": "sha512-M9/ELqF6fy8FwmkpnF0S3YKOqMyoWJ4+CS5Efg2ct3oY9daQvd/Pc71FpGZsVsbl3Cpb+IIcjBDUnnyBdQbq4w==",
-      "license": "MIT"
+      "license": "MIT",
+      "peer": true
     },
     "node_modules/redux-persist": {
       "version": "6.0.0",
@@ -38788,8 +38815,7 @@
       "resolved": "https://registry.npmjs.org/rrweb-cssom/-/rrweb-cssom-0.8.0.tgz",
       "integrity": "sha512-guoltQEx+9aMf2gDZ0s62EcV8lsXR+0w8915TC3ITdn2YueuNjdAYh/levpU9nFaoChh9RUS5ZdQMrKfVEN9tw==",
       "dev": true,
-      "license": "MIT",
-      "peer": true
+      "license": "MIT"
     },
     "node_modules/rtl-css-js": {
       "version": "1.16.1",
@@ -39030,6 +39056,7 @@
       "resolved": "https://registry.npmjs.org/ajv/-/ajv-8.17.1.tgz",
       "integrity": "sha512-B/gBuNg5SiMTrPkC+A2+cW0RszwxYmn6VYxB/inlBStS5nx6xHIt/ehKRhIMhqusl7a8LjQoZnjCs5vhwxOQ1g==",
       "license": "MIT",
+      "peer": true,
       "dependencies": {
         "fast-deep-equal": "^3.1.3",
         "fast-uri": "^3.0.1",
@@ -39616,6 +39643,7 @@
       "integrity": "sha512-JJkpcmELR8N3uM03OG7Oyi5FiCsfZAjArNANw5aR4L2NFt8vErOi3XA7AgIF7gCyPeDWAmK1NV0IlF3OZnRTtQ==",
       "dev": true,
       "license": "MIT",
+      "peer": true,
       "dependencies": {
         "@storybook/global": "^5.0.0",
         "@testing-library/jest-dom": "^6.6.3",
@@ -40124,8 +40152,7 @@
       "version": "4.1.2",
       "resolved": "https://registry.npmjs.org/style-mod/-/style-mod-4.1.2.tgz",
       "integrity": "sha512-wnD1HyVqpJUI2+eKZ+eo1UwghftP6yuFheBqqe+bWCotBjC2K1YnteJILRMs3SM4V/0dLEW1SC27MWP5y+mwmw==",
-      "license": "MIT",
-      "peer": true
+      "license": "MIT"
     },
     "node_modules/style-to-js": {
       "version": "1.1.18",
@@ -40540,6 +40567,7 @@
       "resolved": "https://registry.npmjs.org/tailwindcss/-/tailwindcss-3.4.18.tgz",
       "integrity": "sha512-6A2rnmW5xZMdw11LYjhcI5846rt9pbLSabY5XPxo+XWdxwZaFEn47Go4NzFiHu9sNNmr/kXivP1vStfvMaK1GQ==",
       "license": "MIT",
+      "peer": true,
       "dependencies": {
         "@alloc/quick-lru": "^5.2.0",
         "arg": "^5.0.2",
@@ -41003,6 +41031,7 @@
       "integrity": "sha512-5gTmgEY/sqK6gFXLIsQNH19lWb4ebPDLA4SdLP7dsWkIXHWlG66oPuVvXSGFPppYZz8ZDZq0dYYrbHfBCVUb1Q==",
       "dev": true,
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": ">=12"
       },
@@ -41277,6 +41306,7 @@
       "integrity": "sha512-f0FFpIdcHgn8zcPSbf1dRevwt047YMnaiJM3u2w2RewrB+fob/zePZcrOyQoLMMO7aBIddLcQIEK5dYjkLnGrQ==",
       "dev": true,
       "license": "MIT",
+      "peer": true,
       "dependencies": {
         "@cspotcode/source-map-support": "^0.8.0",
         "@tsconfig/node10": "^1.0.7",
@@ -41367,7 +41397,8 @@
       "version": "2.8.1",
       "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.8.1.tgz",
       "integrity": "sha512-oJFu94HQb+KVduSUQL7wnpmqnfmLsOA/nAh6b6EH0wCEoK0/mPeXU6c3wKDV83MkOuHPRHtSXKKU99IBazS/2w==",
-      "license": "0BSD"
+      "license": "0BSD",
+      "peer": true
     },
     "node_modules/tty-browserify": {
       "version": "0.0.1",
@@ -41536,6 +41567,7 @@
       "integrity": "sha512-jl1vZzPDinLr9eUt3J/t7V6FgNEw9QjvBPdysz9KfQDD41fQrC2Y4vKQdiaUpFT4bXlb1RHhLpp8wtm6M5TgSw==",
       "devOptional": true,
       "license": "Apache-2.0",
+      "peer": true,
       "bin": {
         "tsc": "bin/tsc",
         "tsserver": "bin/tsserver"
@@ -42895,8 +42927,7 @@
       "version": "2.2.8",
       "resolved": "https://registry.npmjs.org/w3c-keyname/-/w3c-keyname-2.2.8.tgz",
       "integrity": "sha512-dpojBhNsCNN7T82Tm7k26A6G9ML3NkhDsnw9n/eoxSRlVBB4CEtIQ/KTCLI2Fwf3ataSXRhYFkQi3SlnFwPvPQ==",
-      "license": "MIT",
-      "peer": true
+      "license": "MIT"
     },
     "node_modules/w3c-xmlserializer": {
       "version": "5.0.0",
@@ -43091,6 +43122,7 @@
       "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.102.1.tgz",
       "integrity": "sha512-7h/weGm9d/ywQ6qzJ+Xy+r9n/3qgp/thalBbpOi5i223dPXKi04IBtqPN9nTd+jBc7QKfvDbaBnFipYp4sJAUQ==",
       "license": "MIT",
+      "peer": true,
       "dependencies": {
         "@types/eslint-scope": "^3.7.7",
         "@types/estree": "^1.0.8",
@@ -43169,6 +43201,7 @@
       "integrity": "sha512-khZGfAeJx6I8K9zKohEWWYN6KDlVw2DHownoe+6Vtwj1LP9WFgegXnVMSkZ/dBEBtXFwrkkydsaPFlB7f8wU2A==",
       "dev": true,
       "license": "MIT",
+      "peer": true,
       "dependencies": {
         "ansi-html-community": "0.0.8",
         "html-entities": "^2.1.0",
diff --git a/package.json b/package.json
index 836a707..f765e3c 100644
--- a/package.json
+++ b/package.json
@@ -43,6 +43,7 @@
     "@next/mdx": "^15.5.3",
     "@oncojs/survivalplot": "^0.8.3",
     "@react-spring/web": "^9.7.5",
+    "@sjcrh/proteinpaint-client": "2.163.1",
     "cookies-next": "^4.3.0",
     "echarts": "^5.5.1",
     "file-saver": "^2.0.5",
diff --git a/src/features/apps/ProteinPaint.tsx b/src/features/apps/ProteinPaint.tsx
index 704010f..4f678d0 100644
--- a/src/features/apps/ProteinPaint.tsx
+++ b/src/features/apps/ProteinPaint.tsx
@@ -1,7 +1,7 @@
-import { FC } from "react";
-import { ProteinPaintWrapper } from "../proteinpaint/ProteinPaintWrapper";
+import "react";
+import { ProteinPaintWrapper } from "@/features/proteinpaint/ProteinPaintWrapper";
 
-const ProteinPaintApp: FC = () => {
+const ProteinPaintApp = () => {
   return <ProteinPaintWrapper />;
 };
 
diff --git a/src/features/proteinpaint/MatrixWrapper.tsx b/src/features/proteinpaint/MatrixWrapper.tsx
index 1203045..170f890 100644
--- a/src/features/proteinpaint/MatrixWrapper.tsx
+++ b/src/features/proteinpaint/MatrixWrapper.tsx
@@ -285,6 +285,8 @@ export const MatrixWrapper: FC<PpProps> = (props: PpProps) => {
 };
 
 interface MatrixArg {
+  dslabel?: string,
+  genes?: string[],
   holder?: HTMLElement;
   noheader?: boolean;
   nobox?: boolean;
@@ -326,6 +328,8 @@ function getMatrixTrack(
   //genesetCallback?: () => void,
 ): MatrixArg {
   const arg: MatrixArg = {
+    dslabel: 'MMRF',
+    genes: ['MYC', 'MYCN', 'NSD2', 'KRAS'],
     // host in gdc is just a relative url path,
     // using the same domain as the GDC portal where PP is embedded
     host: props.basepath || (basepath as string),
diff --git a/src/features/proteinpaint/ProteinPaintWrapper.tsx b/src/features/proteinpaint/ProteinPaintWrapper.tsx
index b8c9eb8..2f8877f 100644
--- a/src/features/proteinpaint/ProteinPaintWrapper.tsx
+++ b/src/features/proteinpaint/ProteinPaintWrapper.tsx
@@ -169,6 +169,7 @@ export const ProteinPaintWrapper: FC<PpProps> = (props: PpProps) => {
 };
 
 interface Mds3Arg {
+  dslabel?: string;
   holder?: HTMLElement;
   noheader?: boolean;
   nobox?: boolean;
@@ -206,6 +207,7 @@ function getLollipopTrack(
   callback: SelectSamplesCallback,
 ) {
   const arg: Mds3Arg = {
+    dslabel: 'MMRF',
     // host in gdc is just a relative url path,
     // using the same domain as the GDC portal where PP is embedded
     host: props.basepath || (basepath as string),
@@ -228,7 +230,7 @@ function getLollipopTrack(
     arg.gene2canonicalisoform = props.geneId;
   } else if (props.ssm_id) {
     arg.mds3_ssm2canonicalisoform = {
-      dslabel: "GDC",
+      dslabel: "MMRF",
       ssm_id: props.ssm_id,
     };
   } else {
diff --git a/src/features/proteinpaint/dev.sh b/src/features/proteinpaint/dev.sh
index 8f983ca..336d87f 100755
--- a/src/features/proteinpaint/dev.sh
+++ b/src/features/proteinpaint/dev.sh
@@ -28,4 +28,10 @@ fi
 # run the following tab in a separate tab
 # local-ssl-proxy --config ssl-proxy.json --cert localhost.pem --key localhost-key.pem
 # then from the gff dir
-PORT=3333 npm run dev
+PROTEINPAINT_API="http://localhost:3000" PORT=3333 npm run dev
+#
+# OR start close all open Chrome browser windows and in macOS terminal:
+# open -n /Applications/Google\ Chrome.app --args --user-data-dir="/tmp/chrome-dev-session" --disable-web-security
+#
+# TODO: setup and use https://localhost.dev-virtuallab.themmrf.org using local-ssl-proxy
+#

From b7ccefe77d1da905e6ae663a9f6bd2e2d4b974c2 Mon Sep 17 00:00:00 2001
From: siosonel <siosonel@gmail.com>
Date: Tue, 2 Dec 2025 11:02:17 -0600
Subject: [PATCH 3/9] add the PROTEINPAINT_API paths for reverse proxy access
 in env config files

---
 .env.development | 1 +
 .env.production  | 1 +
 2 files changed, 2 insertions(+)

diff --git a/.env.development b/.env.development
index 9f93418..b66e781 100644
--- a/.env.development
+++ b/.env.development
@@ -1 +1,2 @@
 NEXT_PUBLIC_GEN3_COMMONS_NAME=gen3
+NEXT_PUBLIC_PROTEINPAINT_API=/auth/api/custom/proteinpaint
diff --git a/.env.production b/.env.production
index 9f93418..b66e781 100644
--- a/.env.production
+++ b/.env.production
@@ -1 +1,2 @@
 NEXT_PUBLIC_GEN3_COMMONS_NAME=gen3
+NEXT_PUBLIC_PROTEINPAINT_API=/auth/api/custom/proteinpaint

From 0aaf0305f49f2e33dca44073202465377570d5bd Mon Sep 17 00:00:00 2001
From: siosonel <siosonel@gmail.com>
Date: Tue, 2 Dec 2025 12:23:41 -0600
Subject: [PATCH 4/9] update proteinpaint-client version to 2.164.0

---
 package-lock.json | 190 ++++++++++++++++++++--------------------------
 package.json      |   2 +-
 2 files changed, 83 insertions(+), 109 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index dacd7ef..49efdd7 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -30,6 +30,7 @@
         "@next/mdx": "^15.5.3",
         "@oncojs/survivalplot": "^0.8.3",
         "@react-spring/web": "^9.7.5",
+        "@sjcrh/proteinpaint-client": "^2.164.0",
         "cookies-next": "^4.3.0",
         "echarts": "^5.5.1",
         "file-saver": "^2.0.5",
@@ -255,7 +256,6 @@
       "integrity": "sha512-2BCOP7TN8M+gVDj7/ht3hsaO/B/n5oDbiAyyvnRlNOs+u1o+JWNYTQrmpuNp1/Wq2gcFrI01JAW+paEKDMx/CA==",
       "dev": true,
       "license": "MIT",
-      "peer": true,
       "dependencies": {
         "@babel/code-frame": "^7.27.1",
         "@babel/generator": "^7.28.3",
@@ -2276,6 +2276,7 @@
       "resolved": "https://registry.npmjs.org/@codemirror/state/-/state-6.5.2.tgz",
       "integrity": "sha512-FVqsPqtPWKVVL3dPSxy8wEF/ymIEuVzF1PK3VbUgrxXpJUSHQWWZz4JMToquRxnkw+36LTamCZG2iua2Ptq0fA==",
       "license": "MIT",
+      "peer": true,
       "dependencies": {
         "@marijn/find-cluster-break": "^1.0.0"
       }
@@ -2285,6 +2286,7 @@
       "resolved": "https://registry.npmjs.org/@codemirror/view/-/view-6.38.6.tgz",
       "integrity": "sha512-qiS0z1bKs5WOvHIAC0Cybmv4AJSkAXgX5aD6Mqd2epSLlVJsQl8NG23jCVouIgkh4All/mrbdsf2UOLFnJw0tw==",
       "license": "MIT",
+      "peer": true,
       "dependencies": {
         "@codemirror/state": "^6.5.0",
         "crelt": "^1.0.6",
@@ -2400,7 +2402,6 @@
         }
       ],
       "license": "MIT",
-      "peer": true,
       "engines": {
         "node": ">=18"
       },
@@ -2442,7 +2443,6 @@
         }
       ],
       "license": "MIT",
-      "peer": true,
       "engines": {
         "node": ">=18"
       }
@@ -2579,7 +2579,6 @@
         }
       ],
       "license": "MIT",
-      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       },
@@ -2602,7 +2601,6 @@
         }
       ],
       "license": "MIT",
-      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       }
@@ -2719,7 +2717,6 @@
         }
       ],
       "license": "MIT",
-      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       },
@@ -2742,7 +2739,6 @@
         }
       ],
       "license": "MIT",
-      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       }
@@ -2878,7 +2874,6 @@
         }
       ],
       "license": "MIT",
-      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       },
@@ -2901,7 +2896,6 @@
         }
       ],
       "license": "MIT",
-      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       }
@@ -3017,7 +3011,6 @@
         }
       ],
       "license": "MIT",
-      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       },
@@ -3040,7 +3033,6 @@
         }
       ],
       "license": "MIT",
-      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       }
@@ -3236,7 +3228,6 @@
         }
       ],
       "license": "MIT",
-      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       },
@@ -3259,7 +3250,6 @@
         }
       ],
       "license": "MIT",
-      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       }
@@ -3329,7 +3319,6 @@
         }
       ],
       "license": "MIT",
-      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       },
@@ -3352,7 +3341,6 @@
         }
       ],
       "license": "MIT",
-      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       }
@@ -3530,7 +3518,6 @@
         }
       ],
       "license": "MIT",
-      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       },
@@ -3553,7 +3540,6 @@
         }
       ],
       "license": "MIT",
-      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       }
@@ -3695,7 +3681,6 @@
         }
       ],
       "license": "MIT",
-      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       },
@@ -3718,7 +3703,6 @@
         }
       ],
       "license": "MIT",
-      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       }
@@ -3801,7 +3785,6 @@
         }
       ],
       "license": "MIT",
-      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       },
@@ -3824,7 +3807,6 @@
         }
       ],
       "license": "MIT",
-      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       }
@@ -3933,7 +3915,6 @@
         }
       ],
       "license": "MIT",
-      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       },
@@ -3956,7 +3937,6 @@
         }
       ],
       "license": "MIT",
-      "peer": true,
       "engines": {
         "node": "^14 || ^16 || >=18"
       }
@@ -4032,7 +4012,6 @@
       "resolved": "https://registry.npmjs.org/@dnd-kit/core/-/core-6.3.1.tgz",
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       "version": "2.2.8",
       "resolved": "https://registry.npmjs.org/w3c-keyname/-/w3c-keyname-2.2.8.tgz",
       "integrity": "sha512-dpojBhNsCNN7T82Tm7k26A6G9ML3NkhDsnw9n/eoxSRlVBB4CEtIQ/KTCLI2Fwf3ataSXRhYFkQi3SlnFwPvPQ==",
-      "license": "MIT"
+      "license": "MIT",
+      "peer": true
     },
     "node_modules/w3c-xmlserializer": {
       "version": "5.0.0",
@@ -43122,7 +43098,6 @@
       "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.102.1.tgz",
       "integrity": "sha512-7h/weGm9d/ywQ6qzJ+Xy+r9n/3qgp/thalBbpOi5i223dPXKi04IBtqPN9nTd+jBc7QKfvDbaBnFipYp4sJAUQ==",
       "license": "MIT",
-      "peer": true,
       "dependencies": {
         "@types/eslint-scope": "^3.7.7",
         "@types/estree": "^1.0.8",
@@ -43201,7 +43176,6 @@
       "integrity": "sha512-khZGfAeJx6I8K9zKohEWWYN6KDlVw2DHownoe+6Vtwj1LP9WFgegXnVMSkZ/dBEBtXFwrkkydsaPFlB7f8wU2A==",
       "dev": true,
       "license": "MIT",
-      "peer": true,
       "dependencies": {
         "ansi-html-community": "0.0.8",
         "html-entities": "^2.1.0",
diff --git a/package.json b/package.json
index f765e3c..12541b0 100644
--- a/package.json
+++ b/package.json
@@ -43,7 +43,7 @@
     "@next/mdx": "^15.5.3",
     "@oncojs/survivalplot": "^0.8.3",
     "@react-spring/web": "^9.7.5",
-    "@sjcrh/proteinpaint-client": "2.163.1",
+    "@sjcrh/proteinpaint-client": "2.164.0",
     "cookies-next": "^4.3.0",
     "echarts": "^5.5.1",
     "file-saver": "^2.0.5",

From 33d9bde2122543797f1e315aa0de7a36cb907cf3 Mon Sep 17 00:00:00 2001
From: siosonel <siosonel@gmail.com>
Date: Wed, 3 Dec 2025 15:37:37 -0600
Subject: [PATCH 5/9] fix type issues

---
 src/features/proteinpaint/MatrixWrapper.tsx       | 2 +-
 src/features/proteinpaint/ProteinPaintWrapper.tsx | 2 +-
 src/features/proteinpaint/sjpp-types.tsx          | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/features/proteinpaint/MatrixWrapper.tsx b/src/features/proteinpaint/MatrixWrapper.tsx
index 170f890..76ebfad 100644
--- a/src/features/proteinpaint/MatrixWrapper.tsx
+++ b/src/features/proteinpaint/MatrixWrapper.tsx
@@ -1,4 +1,4 @@
-import { useRef, useCallback, useState, FC } from "react";
+import React, { useRef, useCallback, useState, FC } from "react";
 import { useDeepCompareEffect } from "use-deep-compare";
 import { bindProteinPaint } from "@sjcrh/proteinpaint-client";
 import { useIsDemoApp } from "@/hooks/useIsDemoApp";
diff --git a/src/features/proteinpaint/ProteinPaintWrapper.tsx b/src/features/proteinpaint/ProteinPaintWrapper.tsx
index 2f8877f..7c70e79 100644
--- a/src/features/proteinpaint/ProteinPaintWrapper.tsx
+++ b/src/features/proteinpaint/ProteinPaintWrapper.tsx
@@ -1,4 +1,4 @@
-import { useRef, useCallback, useState, FC } from "react";
+import React, { useRef, useCallback, useState, FC } from "react";
 import { useDeepCompareEffect } from "use-deep-compare";
 import { bindProteinPaint } from "@sjcrh/proteinpaint-client";
 import { useIsDemoApp } from "@/hooks/useIsDemoApp";
diff --git a/src/features/proteinpaint/sjpp-types.tsx b/src/features/proteinpaint/sjpp-types.tsx
index c36a96e..e1cd681 100644
--- a/src/features/proteinpaint/sjpp-types.tsx
+++ b/src/features/proteinpaint/sjpp-types.tsx
@@ -1,4 +1,4 @@
-import { FilterSet } from "@gff/core";
+import { FilterSet } from "@gen3/core";
 
 export interface PpApi {
   update(arg: any): null;

From fe99aeeb4ecf65efdd6344a51e491845ceb71994 Mon Sep 17 00:00:00 2001
From: siosonel <siosonel@gmail.com>
Date: Wed, 3 Dec 2025 16:57:21 -0600
Subject: [PATCH 6/9] update proteinpaint-client to 2.164.1; fix more type
 issues related to PP and OncoMatrix tools

---
 package-lock.json                                 | 8 ++++----
 package.json                                      | 2 +-
 src/features/proteinpaint/MatrixWrapper.tsx       | 6 +++---
 src/features/proteinpaint/ProteinPaintWrapper.tsx | 2 +-
 src/features/proteinpaint/sjpp-types.tsx          | 4 ++--
 5 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 49efdd7..9e400dc 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -30,7 +30,7 @@
         "@next/mdx": "^15.5.3",
         "@oncojs/survivalplot": "^0.8.3",
         "@react-spring/web": "^9.7.5",
-        "@sjcrh/proteinpaint-client": "^2.164.0",
+        "@sjcrh/proteinpaint-client": "^2.164.1",
         "cookies-next": "^4.3.0",
         "echarts": "^5.5.1",
         "file-saver": "^2.0.5",
@@ -10563,9 +10563,9 @@
       }
     },
     "node_modules/@sjcrh/proteinpaint-client": {
-      "version": "2.164.0",
-      "resolved": "https://registry.npmjs.org/@sjcrh/proteinpaint-client/-/proteinpaint-client-2.164.0.tgz",
-      "integrity": "sha512-II0+DO6OAmqeEz8slwDesG7no5+FeYJPAu/+fMAFhUwTfK3oWDgqiRXHqsc4Xl0QikziGBfG/1D3+cSKxTEC3w==",
+      "version": "2.164.1",
+      "resolved": "https://registry.npmjs.org/@sjcrh/proteinpaint-client/-/proteinpaint-client-2.164.1.tgz",
+      "integrity": "sha512-Wm9EkdOWZbLTrJteyJ9udTLsWUB+9AVx+vrpG+2xEBdgTnZfF+XgxADqSYspDliGs1254SBRL46e2uiM4za9VA==",
       "license": "SEE LICENSE IN ./LICENSE"
     },
     "node_modules/@standard-schema/spec": {
diff --git a/package.json b/package.json
index 12541b0..3a78a4e 100644
--- a/package.json
+++ b/package.json
@@ -43,7 +43,7 @@
     "@next/mdx": "^15.5.3",
     "@oncojs/survivalplot": "^0.8.3",
     "@react-spring/web": "^9.7.5",
-    "@sjcrh/proteinpaint-client": "2.164.0",
+    "@sjcrh/proteinpaint-client": "^2.164.1",
     "cookies-next": "^4.3.0",
     "echarts": "^5.5.1",
     "file-saver": "^2.0.5",
diff --git a/src/features/proteinpaint/MatrixWrapper.tsx b/src/features/proteinpaint/MatrixWrapper.tsx
index 76ebfad..6fc0401 100644
--- a/src/features/proteinpaint/MatrixWrapper.tsx
+++ b/src/features/proteinpaint/MatrixWrapper.tsx
@@ -220,10 +220,10 @@ export const MatrixWrapper: FC<PpProps> = (props: PpProps) => {
           return prevData.current != data;
         },
       })
-        .then?.((_app) => {
+        .then?.((_app: any) => {
           toolApp.current = _app;
         })
-        .catch((e) => {
+        .catch((e: any) => {
           // the app should either work or display an error in a red banner within the tool container div,
           // this uncaught-by-app error is unlikely to happen except for bundling issues that are not detected at build time
           console.error(e);
@@ -242,7 +242,7 @@ export const MatrixWrapper: FC<PpProps> = (props: PpProps) => {
     [filter0, userDetails, /*geneDetailData*/],
   );
 
-  const divRef = useRef<HTMLElement>(null);
+  const divRef = useRef<HTMLDivElement>(null);
 
   // const updateFilters = (field: string, operation: Operation) => {
   //   dispatch(hideModal());
diff --git a/src/features/proteinpaint/ProteinPaintWrapper.tsx b/src/features/proteinpaint/ProteinPaintWrapper.tsx
index 7c70e79..2a973dd 100644
--- a/src/features/proteinpaint/ProteinPaintWrapper.tsx
+++ b/src/features/proteinpaint/ProteinPaintWrapper.tsx
@@ -144,7 +144,7 @@ export const ProteinPaintWrapper: FC<PpProps> = (props: PpProps) => {
     ],
   );
 
-  const divRef = useRef<HTMLElement>(null);
+  const divRef = useRef<HTMLDivElement>(null);
   const demoText = props.hardcodeCnvOnly
     ? "Demo showing MYC CNV segments from all GDC cases"
     : "Demo showing MYC mutations from all GDC cases.";
diff --git a/src/features/proteinpaint/sjpp-types.tsx b/src/features/proteinpaint/sjpp-types.tsx
index e1cd681..af29376 100644
--- a/src/features/proteinpaint/sjpp-types.tsx
+++ b/src/features/proteinpaint/sjpp-types.tsx
@@ -7,7 +7,7 @@ export interface PpApi {
 }
 
 export type SampleData = {
-  "cases.case_id"?: string;
+  "cases.case_id": string;
 };
 
 export interface SelectSamplesCallBackArg {
@@ -32,7 +32,7 @@ export interface SelectSamples {
 export function getFilters(arg: SelectSamplesCallBackArg): FilterSet {
   const { samples } = arg;
   // see comments below about SV-2228
-  const ids = samples.map((d) => d["cases.case_id"]).filter((d) => d && true);
+  const ids: (string | number)[] = samples.map((d) => d["cases.case_id"]).filter((d) => typeof d === 'string' || typeof d === 'number');
   return {
     mode: "and",
     root: {

From 271fc44326b2a40fea4567a9cf5ef7d4911f65e6 Mon Sep 17 00:00:00 2001
From: siosonel <siosonel@gmail.com>
Date: Wed, 3 Dec 2025 17:12:32 -0600
Subject: [PATCH 7/9] fix the react import in ProteinPaint and OncoMatrix apps

---
 src/features/apps/OncoMatrix.tsx   | 4 ++--
 src/features/apps/ProteinPaint.tsx | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/features/apps/OncoMatrix.tsx b/src/features/apps/OncoMatrix.tsx
index c386c45..e609ae4 100644
--- a/src/features/apps/OncoMatrix.tsx
+++ b/src/features/apps/OncoMatrix.tsx
@@ -1,7 +1,7 @@
-import { FC } from "react";
+import React from "react";
 import { MatrixWrapper } from "../proteinpaint/MatrixWrapper";
 
-const MatrixApp: FC = () => {
+const MatrixApp: React.FC = () => {
   return <MatrixWrapper chartType="matrix" />;
 };
 
diff --git a/src/features/apps/ProteinPaint.tsx b/src/features/apps/ProteinPaint.tsx
index 4f678d0..b326bf0 100644
--- a/src/features/apps/ProteinPaint.tsx
+++ b/src/features/apps/ProteinPaint.tsx
@@ -1,7 +1,7 @@
-import "react";
+import React from "react";
 import { ProteinPaintWrapper } from "@/features/proteinpaint/ProteinPaintWrapper";
 
-const ProteinPaintApp = () => {
+const ProteinPaintApp: React.FC = () => {
   return <ProteinPaintWrapper />;
 };
 

From 111e0fc48adda748d1605b9b2eec5f84c94838ca Mon Sep 17 00:00:00 2001
From: siosonel <siosonel@gmail.com>
Date: Thu, 4 Dec 2025 18:59:42 -0800
Subject: [PATCH 8/9] compute filter0 in PP and OncoMatrix tools

---
 src/features/proteinpaint/MatrixWrapper.tsx   | 32 +++++++++----------
 .../proteinpaint/ProteinPaintWrapper.tsx      | 18 +++++------
 2 files changed, 23 insertions(+), 27 deletions(-)

diff --git a/src/features/proteinpaint/MatrixWrapper.tsx b/src/features/proteinpaint/MatrixWrapper.tsx
index 6fc0401..484f74c 100644
--- a/src/features/proteinpaint/MatrixWrapper.tsx
+++ b/src/features/proteinpaint/MatrixWrapper.tsx
@@ -4,7 +4,6 @@ import { bindProteinPaint } from "@sjcrh/proteinpaint-client";
 import { useIsDemoApp } from "@/hooks/useIsDemoApp";
 import {
   useCoreSelector,
-  selectCurrentCohortFilters,
   convertFilterSetToGqlFilter as buildCohortGqlOperator,
   FilterSet,
   //PROTEINPAINT_API,
@@ -19,6 +18,8 @@ import {
   Modals,
   selectCurrentModal,
 } from "@gen3/core";
+import { joinFilters, selectCurrentCohortCaseFilters } from "@/core/utils";
+import { DEMO_COHORT_FILTERS } from "./constants";
 import { DemoText } from "@/components/tailwindComponents";
 import { LoadingOverlay } from "@mantine/core";
 import {
@@ -32,6 +33,7 @@ import {
 import { isEqual, cloneDeep } from "lodash";
 //import { cohortActionsHooks } from "../cohortBuilder/CohortManager/cohortActionHooks";
 //import { INVALID_COHORT_NAMES } from "../cohortBuilder/utils";
+import { COHORT_FILTER_INDEX } from '@/core';
 
 const basepath = 'http://localhost:3000' // PROTEINPAINT_API;
 
@@ -40,24 +42,20 @@ interface PpProps {
   basepath?: string;
 }
 
-export const demoFilter = Object.freeze({
-  op: "in",
-  content: Object.freeze({
-    field: "cases.disease_type",
-    value: Object.freeze(["Gliomas"]),
-  }),
-});
+// export const demoFilter = Object.freeze({
+//   op: "in",
+//   content: Object.freeze({
+//     field: "cases.disease_type",
+//     value: Object.freeze(["Gliomas"]),
+//   }),
+// });
 
 export const MatrixWrapper: FC<PpProps> = (props: PpProps) => {
   const isDemoMode = useIsDemoApp();
-  // const demoFilter = {
-  //   op: "in",
-  //   content: { field: "cases.disease_type", value: ["Gliomas"] },
-  // };
-  const currentCohort = useCoreSelector(selectCurrentCohortFilters);
-  const filter0 = null // isDemoMode
-    // ? cloneDeep(demoFilter)
-    // : buildCohortGqlOperator(currentCohort);
+  const currentCohort = useCoreSelector((state) =>
+    selectCurrentCohortCaseFilters(state, COHORT_FILTER_INDEX),
+  );
+  const filter0 = isDemoMode ? null : buildCohortGqlOperator(currentCohort);
   const userDetails = useFetchUserDetailsQuery();
   const prevData = useRef<any>();
   const toolApp = useRef<any>();
@@ -251,7 +249,7 @@ export const MatrixWrapper: FC<PpProps> = (props: PpProps) => {
   const existingFiltersHook = () => null;
   return (
     <div className="relative">
-      {isDemoMode && <DemoText>Demo showing cases with Gliomas.</DemoText>}
+      {isDemoMode && <DemoText>Showing cases in demo cohort.</DemoText>}
       <div
         ref={divRef}
         className="sjpp-wrapper-root-div"
diff --git a/src/features/proteinpaint/ProteinPaintWrapper.tsx b/src/features/proteinpaint/ProteinPaintWrapper.tsx
index 2a973dd..8b5d81a 100644
--- a/src/features/proteinpaint/ProteinPaintWrapper.tsx
+++ b/src/features/proteinpaint/ProteinPaintWrapper.tsx
@@ -4,16 +4,16 @@ import { bindProteinPaint } from "@sjcrh/proteinpaint-client";
 import { useIsDemoApp } from "@/hooks/useIsDemoApp";
 import {
   useCoreSelector,
-  selectCurrentCohortFilters,
   FilterSet,
   //PROTEINPAINT_API,
   useFetchUserDetailsQuery,
   useCoreDispatch,
-  convertFilterSetToGqlFilter as buildCohortGqlOperator,
-  //useCreateCaseSetFromValuesMutation,
+  convertFilterSetToGqlFilter as buildCohortGqlOperator
 } from "@gen3/core";
 import { isEqual, cloneDeep } from "lodash";
 import { DemoText } from "@/components/tailwindComponents";
+import { joinFilters, selectCurrentCohortCaseFilters } from "@/core/utils";
+import { DEMO_COHORT_FILTERS } from "./constants";
 // import { SaveCohortModal } from "@gff/portal-components";
 import {
   SelectSamples,
@@ -22,6 +22,7 @@ import {
 } from "./sjpp-types";
 // import { cohortActionsHooks } from "../cohortBuilder/CohortManager/cohortActionHooks";
 // import { INVALID_COHORT_NAMES } from "../cohortBuilder/utils";
+import { COHORT_FILTER_INDEX } from '@/core';
 
 const basepath = 'http://localhost:3000'; //PROTEINPAINT_API;
 
@@ -37,13 +38,10 @@ interface PpProps {
 
 export const ProteinPaintWrapper: FC<PpProps> = (props: PpProps) => {
   const isDemoMode = useIsDemoApp();
-  const currentCohort = useCoreSelector(selectCurrentCohortFilters);
-
-  // const cohortFilters = useCoreSelector((state) =>
-  //   isDemoMode ? DEMO_COHORT_FILTERS : selectCurrentCohortFilters(state),
-  // );
-
-  const filter0 = null // isDemoMode ? null : buildCohortGqlOperator(currentCohort);
+  const currentCohort = useCoreSelector((state) =>
+    selectCurrentCohortCaseFilters(state, COHORT_FILTER_INDEX),
+  );
+  const filter0 = isDemoMode ? null : buildCohortGqlOperator(currentCohort);
   const userDetails = useFetchUserDetailsQuery();
 
   // to track reusable instance for mds3 skewer track

From 41c61ead26aea5b8053b249cd0e83369e8d3f692 Mon Sep 17 00:00:00 2001
From: siosonel <siosonel@gmail.com>
Date: Thu, 4 Dec 2025 19:07:54 -0800
Subject: [PATCH 9/9] track proteinpaint constants

---
 src/features/proteinpaint/constants.ts | 12 ++++++++++++
 1 file changed, 12 insertions(+)
 create mode 100644 src/features/proteinpaint/constants.ts

diff --git a/src/features/proteinpaint/constants.ts b/src/features/proteinpaint/constants.ts
new file mode 100644
index 0000000..9478ba8
--- /dev/null
+++ b/src/features/proteinpaint/constants.ts
@@ -0,0 +1,12 @@
+import { FilterSet } from "@gen3/core";
+
+export const DEMO_COHORT_FILTERS: FilterSet = {
+  mode: "and",
+  root: {
+    "cases.project.project_id": {
+      operator: "includes",
+      field: "cases.project.project_id",
+      operands: ["TCGA-LGG"],
+    },
+  },
+};