TS Revert (1) (#2402)

* revert all commits to before Typescript migration

* update compat workflow to match latest deps (#2335)

* update compat workflow to match latest deps

* attempt to debug

* attempt to debug

* remove debugging code

* typo

* update deps to match desktop (#2340)

* fix: don't run lint with `--fix` on push tests (#2273)

* fix: don't run lint with `--fix` on push tests

* npx

Co-authored-by: maniarathi <mani.arathi@gmail.com>
Co-authored-by: Madison Dunitz <madison.dunitz@chanzuckerberg.com>

* rename X_approx_distribution to X_approximate_distribution (#2337)

* Correctly handle non-finite numbers in heuristic determination of X distribution (#2342)

* handle non-finites explicitly

* improve and test edge case handling for distribution estimation

* revert debugging changes

* code readability

* clean up type inferencing (#2332)

* unit tests for 64 bit conversion

* clean up type handling

* type inference tests

* more type inference fixes

* use schema to determine user intent for data typing

* stop using deprecated API

* fbs type encoding test

* add missing test

* add more tests

* correctly infer X type for CXG adaptor

* lint

* fix typo

* ts migration

* cleanup from PR review

* lint

* PR review changes

* remove unused packages from client (#2359)

* remove unused packages from client

* add missing peer dep

* fix: disable FE auth testing on compatibility tests (#2377)

* update: release process (#2277)

Co-authored-by: maniarathi <mani.arathi@gmail.com>

* fix: remove spaces in param setup (#2380)

* delete deploy workflow (#2396)

* undo reformatting which now does not pass lint

* fix snapshots which changed due to npm dep changes

* add missing quoting to snapshot

* another snapshot typo fix

* TS Revert (2) - replay PR #2347 and #2354 (#2403)

* replay edits from PR 2347

* TS Revert (3) - replay edits in PR #2327 (#2404)

* replay edits in PR 2327

* TS Revert (4) - replay PR #2355 (#2405)

* replay edits in PR 2355

* add additional babel config

* reformat with new prettier config

Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com>
Co-authored-by: maniarathi <mani.arathi@gmail.com>
Co-authored-by: Madison Dunitz <madison.dunitz@chanzuckerberg.com>

client/src/actions/annotation.js

@@ -0,0 +1,455 @@
+/*
+Action creators for user annotation
+*/
+import difference from "lodash.difference";
+import pako from "pako";
+import * as globals from "../globals";
+import { MatrixFBS, AnnotationsHelpers } from "../util/stateManager";
+
+const { isUserAnnotation } = AnnotationsHelpers;
+
+export const annotationCreateCategoryAction =
+  (newCategoryName, categoryToDuplicate) => async (dispatch, getState) => {
+    /*
+  Add a new user-created category to the obs annotations.
+
+  Arguments:
+    newCategoryName - string name for the category.
+    categoryToDuplicate - obs category to use for initial values, or null.
+  */
+    const { annoMatrix: prevAnnoMatrix, obsCrossfilter: prevObsCrossfilter } =
+      getState();
+    if (!prevAnnoMatrix || !prevObsCrossfilter) return;
+    const { schema } = prevAnnoMatrix;
+
+    /* name must be a string,  non-zero length */
+    if (typeof newCategoryName !== "string" || newCategoryName.length === 0)
+      throw new Error("user annotations require string name");
+
+    /* ensure the name isn't already in use! */
+    if (schema.annotations.obsByName[newCategoryName])
+      throw new Error("name collision on annotation category create");
+
+    let initialValue;
+    let newSchema;
+    let ctor;
+    if (categoryToDuplicate) {
+      /* if we are duplicating a category, retrieve it */
+      const catDupSchema = schema.annotations.obsByName[categoryToDuplicate];
+      const catDupType = catDupSchema?.type;
+      if (catDupType !== "string" && catDupType !== "categorical")
+        throw new Error(
+          "categoryToDuplicate does not exist or has invalid type"
+        );
+
+      const catToDupDf = await prevAnnoMatrix
+        .base()
+        .fetch("obs", categoryToDuplicate);
+      const col = catToDupDf.col(categoryToDuplicate);
+      initialValue = col.asArray();
+      const { categories } = col.summarizeCategorical();
+      // all user-created annotations must have the unassigned category
+      if (!categories.includes(globals.unassignedCategoryLabel)) {
+        categories.push(globals.unassignedCategoryLabel);
+      }
+      ctor = initialValue.constructor;
+      newSchema = {
+        ...catDupSchema,
+        name: newCategoryName,
+        categories,
+        writable: true,
+      };
+    } else {
+      /* else assign to the standard default value */
+      initialValue = globals.unassignedCategoryLabel;
+      ctor = Array;
+      newSchema = {
+        name: newCategoryName,
+        type: "categorical",
+        categories: [globals.unassignedCategoryLabel],
+        writable: true,
+      };
+    }
+
+    const obsCrossfilter = prevObsCrossfilter.addObsColumn(
+      newSchema,
+      ctor,
+      initialValue
+    );
+
+    dispatch({
+      type: "annotation: create category",
+      data: newCategoryName,
+      categoryToDuplicate,
+      annoMatrix: obsCrossfilter.annoMatrix,
+      obsCrossfilter,
+    });
+  };
+
+export const annotationRenameCategoryAction =
+  (oldCategoryName, newCategoryName) => (dispatch, getState) => {
+    /*
+  Rename a user-created annotation category
+  */
+    const { annoMatrix: prevAnnoMatrix, obsCrossfilter: prevObsCrossfilter } =
+      getState();
+    if (!prevAnnoMatrix || !prevObsCrossfilter) return;
+    if (!isUserAnnotation(prevAnnoMatrix, oldCategoryName))
+      throw new Error("not a user annotation");
+
+    /* name must be a string,  non-zero length */
+    if (typeof newCategoryName !== "string" || newCategoryName.length === 0)
+      throw new Error("user annotations require string name");
+
+    if (oldCategoryName === newCategoryName) return;
+
+    const obsCrossfilter = prevObsCrossfilter.renameObsColumn(
+      oldCategoryName,
+      newCategoryName
+    );
+
+    dispatch({
+      type: "annotation: category edited",
+      annoMatrix: obsCrossfilter.annoMatrix,
+      obsCrossfilter,
+      metadataField: oldCategoryName,
+      newCategoryText: newCategoryName,
+      data: newCategoryName,
+    });
+  };
+
+export const annotationDeleteCategoryAction =
+  (categoryName) => (dispatch, getState) => {
+    /*
+  Delete a user-created category
+  */
+    const { annoMatrix: prevAnnoMatrix, obsCrossfilter: prevObsCrossfilter } =
+      getState();
+    if (!prevAnnoMatrix || !prevObsCrossfilter) return;
+    if (!isUserAnnotation(prevAnnoMatrix, categoryName))
+      throw new Error("not a user annotation");
+
+    const obsCrossfilter = prevObsCrossfilter.dropObsColumn(categoryName);
+    dispatch({
+      type: "annotation: delete category",
+      annoMatrix: obsCrossfilter.annoMatrix,
+      obsCrossfilter,
+      metadataField: categoryName,
+    });
+  };
+
+export const annotationCreateLabelInCategory =
+  (categoryName, labelName, assignSelected) => async (dispatch, getState) => {
+    /*
+  Add a new label to a user-defined category.  If assignSelected is true, assign
+  the label to all currently selected cells.
+  */
+    const { annoMatrix: prevAnnoMatrix, obsCrossfilter: prevObsCrossfilter } =
+      getState();
+    if (!prevAnnoMatrix || !prevObsCrossfilter) return;
+    if (!isUserAnnotation(prevAnnoMatrix, categoryName))
+      throw new Error("not a user annotation");
+
+    let obsCrossfilter = prevObsCrossfilter.addObsAnnoCategory(
+      categoryName,
+      labelName
+    );
+    if (assignSelected) {
+      obsCrossfilter = await obsCrossfilter.setObsColumnValues(
+        categoryName,
+        prevObsCrossfilter.allSelectedLabels(),
+        labelName
+      );
+    }
+
+    dispatch({
+      type: "annotation: add new label to category",
+      annoMatrix: obsCrossfilter.annoMatrix,
+      obsCrossfilter,
+      metadataField: categoryName,
+      newLabelText: labelName,
+      assignSelectedCells: assignSelected,
+    });
+  };
+
+export const annotationDeleteLabelFromCategory =
+  (categoryName, labelName) => async (dispatch, getState) => {
+    /*
+  delete a label from a user-defined category
+  */
+    const { annoMatrix: prevAnnoMatrix, obsCrossfilter: prevObsCrossfilter } =
+      getState();
+    if (!prevAnnoMatrix || !prevObsCrossfilter) return;
+    if (!isUserAnnotation(prevAnnoMatrix, categoryName))
+      throw new Error("not a user annotation");
+
+    const obsCrossfilter = await prevObsCrossfilter.removeObsAnnoCategory(
+      categoryName,
+      labelName,
+      globals.unassignedCategoryLabel
+    );
+
+    dispatch({
+      type: "annotation: delete label",
+      metadataField: categoryName,
+      label: labelName,
+      annoMatrix: obsCrossfilter.annoMatrix,
+      obsCrossfilter,
+    });
+  };
+
+export const annotationRenameLabelInCategory =
+  (categoryName, oldLabelName, newLabelName) => async (dispatch, getState) => {
+    /*
+  label name change
+  */
+    const { annoMatrix: prevAnnoMatrix, obsCrossfilter: prevObsCrossfilter } =
+      getState();
+    if (!prevAnnoMatrix || !prevObsCrossfilter) return;
+    if (!isUserAnnotation(prevAnnoMatrix, categoryName))
+      throw new Error("not a user annotation");
+
+    let obsCrossfilter = await prevObsCrossfilter.resetObsColumnValues(
+      categoryName,
+      oldLabelName,
+      newLabelName
+    );
+    obsCrossfilter = await obsCrossfilter.removeObsAnnoCategory(
+      categoryName,
+      oldLabelName,
+      globals.unassignedCategoryLabel
+    );
+
+    dispatch({
+      type: "annotation: label edited",
+      editedLabel: newLabelName,
+      metadataField: categoryName,
+      label: oldLabelName,
+      annoMatrix: obsCrossfilter.annoMatrix,
+      obsCrossfilter,
+    });
+  };
+
+export const annotationLabelCurrentSelection =
+  (categoryName, labelName) => async (dispatch, getState) => {
+    /*
+  set the label on all currently selected
+  */
+    const { annoMatrix: prevAnnoMatrix, obsCrossfilter: prevObsCrossfilter } =
+      getState();
+    if (!prevAnnoMatrix || !prevObsCrossfilter) return;
+    if (!isUserAnnotation(prevAnnoMatrix, categoryName))
+      throw new Error("not a user annotation");
+
+    const obsCrossfilter = await prevObsCrossfilter.setObsColumnValues(
+      categoryName,
+      prevObsCrossfilter.allSelectedLabels(),
+      labelName
+    );
+
+    dispatch({
+      type: "annotation: label current cell selection",
+      metadataField: categoryName,
+      label: labelName,
+      obsCrossfilter,
+      annoMatrix: obsCrossfilter.annoMatrix,
+    });
+  };
+
+function writableAnnotations(annoMatrix) {
+  return annoMatrix.schema.annotations.obs.columns
+    .filter((s) => s.writable)
+    .map((s) => s.name);
+}
+
+export const needToSaveObsAnnotations = (annoMatrix, lastSavedAnnoMatrix) => {
+  /*
+  Return true if there are LIKELY user-defined annotation modifications between the two
+  annoMatrices.  Technically not an action creator, but intimately intertwined
+  with the save process.
+
+  Two conditions will trigger a need to save:
+    * the collection of user-defined columns have changed
+    * the contents of the user-defined columns have change
+  */
+
+  annoMatrix = annoMatrix.base();
+
+  // if the annoMatrix hasn't changed, we are guaranteed no changes to the matrix schema or contents.
+  if (annoMatrix === lastSavedAnnoMatrix) return false;
+
+  // if the schema has changed, we need to save
+  const currentWritable = writableAnnotations(annoMatrix);
+  if (difference(currentWritable, writableAnnotations(lastSavedAnnoMatrix))) {
+    return true;
+  }
+
+  // no schema changes; check for change in contents
+  return currentWritable.some(
+    (col) => annoMatrix.col(col) !== lastSavedAnnoMatrix.col(col)
+  );
+};
+
+export const saveObsAnnotationsAction = () => async (dispatch, getState) => {
+  /*
+  Save the user-created obs annotations IF any have changed.
+  */
+  const state = getState();
+  const { annotations, autosave } = state;
+  const { dataCollectionNameIsReadOnly, dataCollectionName } = annotations;
+  const { lastSavedAnnoMatrix, saveInProgress } = autosave;
+
+  const annoMatrix = state.annoMatrix.base();
+
+  if (saveInProgress || annoMatrix === lastSavedAnnoMatrix) return;
+  if (!needToSaveObsAnnotations(annoMatrix, lastSavedAnnoMatrix)) {
+    dispatch({
+      type: "writable obs annotations - save complete",
+      lastSavedAnnoMatrix: annoMatrix,
+    });
+    return;
+  }
+
+  /*
+  Else, we really do need to save
+  */
+
+  dispatch({
+    type: "writable obs annotations - save started",
+  });
+
+  const df = await annoMatrix.fetch("obs", writableAnnotations(annoMatrix));
+  const matrix = MatrixFBS.encodeMatrixFBS(df);
+  const compressedMatrix = pako.deflate(matrix);
+  try {
+    const queryString =
+      !dataCollectionNameIsReadOnly && !!dataCollectionName
+        ? `?annotation-collection-name=${encodeURIComponent(
+            dataCollectionName
+          )}`
+        : "";
+    const res = await fetch(
+      `${globals.API.prefix}${globals.API.version}annotations/obs${queryString}`,
+      {
+        method: "PUT",
+        body: compressedMatrix,
+        headers: new Headers({
+          "Content-Type": "application/octet-stream",
+        }),
+        credentials: "include",
+      }
+    );
+    if (res.ok) {
+      dispatch({
+        type: "writable obs annotations - save complete",
+        lastSavedAnnoMatrix: annoMatrix,
+      });
+    } else {
+      dispatch({
+        type: "writable obs annotations - save error",
+        message: `HTTP error ${res.status} - ${res.statusText}`,
+        res,
+      });
+    }
+  } catch (error) {
+    dispatch({
+      type: "writable obs annotations - save error",
+      message: error.toString(),
+      error,
+    });
+  }
+};
+
+export const saveGenesetsAction = () => async (dispatch, getState) => {
+  const state = getState();
+
+  // bail if gene sets not available, or in readonly mode.
+  const { config } = state;
+  const { lastTid, genesets } = state.genesets;
+
+  const genesetsAreAvailable =
+    config?.parameters?.annotations_genesets ?? false;
+  const genesetsReadonly =
+    config?.parameters?.annotations_genesets_readonly ?? true;
+  if (!genesetsAreAvailable || genesetsReadonly) {
+    // our non-save was completed!
+    return dispatch({
+      type: "autosave: genesets complete",
+      lastSavedGenesets: genesets,
+    });
+  }
+
+  dispatch({
+    type: "autosave: genesets started",
+  });
+
+  /* Create the JSON OTA data structure */
+  const tid = (lastTid ?? 0) + 1;
+  const genesetsOTA = [];
+  for (const [name, gs] of genesets) {
+    const genes = [];
+    for (const g of gs.genes.values()) {
+      genes.push({
+        gene_symbol: g.geneSymbol,
+        gene_description: g.geneDescription,
+      });
+    }
+    genesetsOTA.push({
+      geneset_name: name,
+      geneset_description: gs.genesetDescription,
+      genes,
+    });
+  }
+  const ota = {
+    tid,
+    genesets: genesetsOTA,
+  };
+
+  /* Save to server */
+  try {
+    const { dataCollectionNameIsReadOnly, dataCollectionName } =
+      state.annotations;
+    const queryString =
+      !dataCollectionNameIsReadOnly && !!dataCollectionName
+        ? `?annotation-collection-name=${encodeURIComponent(
+            dataCollectionName
+          )}`
+        : "";
+
+    const res = await fetch(
+      `${globals.API.prefix}${globals.API.version}genesets${queryString}`,
+      {
+        method: "PUT",
+        headers: new Headers({
+          Accept: "application/json",
+          "Content-Type": "application/json",
+        }),
+        body: JSON.stringify(ota),
+        credentials: "include",
+      }
+    );
+    if (!res.ok) {
+      return dispatch({
+        type: "autosave: genesets error",
+        message: `HTTP error ${res.status} - ${res.statusText}`,
+        res,
+      });
+    }
+    return Promise.all([
+      dispatch({
+        type: "autosave: genesets complete",
+        lastSavedGenesets: genesets,
+      }),
+      dispatch({
+        type: "geneset: set tid",
+        tid,
+      }),
+    ]);
+  } catch (error) {
+    return dispatch({
+      type: "autosave: genesets error",
+      message: error.toString(),
+      error,
+    });
+  }
+};

client/src/actions/annotation.ts

@@ -1,530 +0,0 @@
-/*
-Action creators for user annotation
-*/
-import difference from "lodash.difference";
-import pako from "pako";
-import * as globals from "../globals";
-import { MatrixFBS, AnnotationsHelpers } from "../util/stateManager";
-
-const { isUserAnnotation } = AnnotationsHelpers;
-
-export const annotationCreateCategoryAction = (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  newCategoryName: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  categoryToDuplicate: any
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-) => async (dispatch: any, getState: any) => {
-  /*
-  Add a new user-created category to the obs annotations.
-
-  Arguments:
-    newCategoryName - string name for the category.
-    categoryToDuplicate - obs category to use for initial values, or null.
-  */
-  const {
-    annoMatrix: prevAnnoMatrix,
-    obsCrossfilter: prevObsCrossfilter,
-  } = getState();
-  if (!prevAnnoMatrix || !prevObsCrossfilter) return;
-  const { schema } = prevAnnoMatrix;
-
-  /* name must be a string,  non-zero length */
-  if (typeof newCategoryName !== "string" || newCategoryName.length === 0)
-    throw new Error("user annotations require string name");
-
-  /* ensure the name isn't already in use! */
-  if (schema.annotations.obsByName[newCategoryName])
-    throw new Error("name collision on annotation category create");
-
-  let initialValue;
-  let newSchema;
-  let ctor;
-  if (categoryToDuplicate) {
-    /* if we are duplicating a category, retrieve it */
-    const catDupSchema = schema.annotations.obsByName[categoryToDuplicate];
-    const catDupType = catDupSchema?.type;
-    if (catDupType !== "string" && catDupType !== "categorical")
-      throw new Error("categoryToDuplicate does not exist or has invalid type");
-
-    const catToDupDf = await prevAnnoMatrix
-      .base()
-      .fetch("obs", categoryToDuplicate);
-    const col = catToDupDf.col(categoryToDuplicate);
-    initialValue = col.asArray();
-    const { categories } = col.summarizeCategorical();
-    // all user-created annotations must have the unassigned category
-    if (!categories.includes(globals.unassignedCategoryLabel)) {
-      categories.push(globals.unassignedCategoryLabel);
-    }
-    ctor = initialValue.constructor;
-    newSchema = {
-      ...catDupSchema,
-      name: newCategoryName,
-      categories,
-      writable: true,
-    };
-  } else {
-    /* else assign to the standard default value */
-    initialValue = globals.unassignedCategoryLabel;
-    ctor = Array;
-    newSchema = {
-      name: newCategoryName,
-      type: "categorical",
-      categories: [globals.unassignedCategoryLabel],
-      writable: true,
-    };
-  }
-
-  const obsCrossfilter = prevObsCrossfilter.addObsColumn(
-    newSchema,
-    ctor,
-    initialValue
-  );
-
-  dispatch({
-    type: "annotation: create category",
-    data: newCategoryName,
-    categoryToDuplicate,
-    annoMatrix: obsCrossfilter.annoMatrix,
-    obsCrossfilter,
-  });
-};
-
-export const annotationRenameCategoryAction = (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  oldCategoryName: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  newCategoryName: any
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-) => (dispatch: any, getState: any) => {
-  /*
-  Rename a user-created annotation category
-  */
-  const {
-    annoMatrix: prevAnnoMatrix,
-    obsCrossfilter: prevObsCrossfilter,
-  } = getState();
-  if (!prevAnnoMatrix || !prevObsCrossfilter) return;
-  if (!isUserAnnotation(prevAnnoMatrix, oldCategoryName))
-    throw new Error("not a user annotation");
-
-  /* name must be a string,  non-zero length */
-  if (typeof newCategoryName !== "string" || newCategoryName.length === 0)
-    throw new Error("user annotations require string name");
-
-  if (oldCategoryName === newCategoryName) return;
-
-  const obsCrossfilter = prevObsCrossfilter.renameObsColumn(
-    oldCategoryName,
-    newCategoryName
-  );
-
-  dispatch({
-    type: "annotation: category edited",
-    annoMatrix: obsCrossfilter.annoMatrix,
-    obsCrossfilter,
-    metadataField: oldCategoryName,
-    newCategoryText: newCategoryName,
-    data: newCategoryName,
-  });
-};
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const annotationDeleteCategoryAction = (categoryName: any) => (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  dispatch: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  getState: any
-) => {
-  /*
-  Delete a user-created category
-  */
-  const {
-    annoMatrix: prevAnnoMatrix,
-    obsCrossfilter: prevObsCrossfilter,
-  } = getState();
-  if (!prevAnnoMatrix || !prevObsCrossfilter) return;
-  if (!isUserAnnotation(prevAnnoMatrix, categoryName))
-    throw new Error("not a user annotation");
-
-  const obsCrossfilter = prevObsCrossfilter.dropObsColumn(categoryName);
-  dispatch({
-    type: "annotation: delete category",
-    annoMatrix: obsCrossfilter.annoMatrix,
-    obsCrossfilter,
-    metadataField: categoryName,
-  });
-};
-
-export const annotationCreateLabelInCategory = (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  categoryName: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  labelName: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  assignSelected: any // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-) => async (dispatch: any, getState: any) => {
-  /*
-  Add a new label to a user-defined category.  If assignSelected is true, assign
-  the label to all currently selected cells.
-  */
-  const {
-    annoMatrix: prevAnnoMatrix,
-    obsCrossfilter: prevObsCrossfilter,
-  } = getState();
-  if (!prevAnnoMatrix || !prevObsCrossfilter) return;
-  if (!isUserAnnotation(prevAnnoMatrix, categoryName))
-    throw new Error("not a user annotation");
-
-  let obsCrossfilter = prevObsCrossfilter.addObsAnnoCategory(
-    categoryName,
-    labelName
-  );
-  if (assignSelected) {
-    obsCrossfilter = await obsCrossfilter.setObsColumnValues(
-      categoryName,
-      prevObsCrossfilter.allSelectedLabels(),
-      labelName
-    );
-  }
-
-  dispatch({
-    type: "annotation: add new label to category",
-    annoMatrix: obsCrossfilter.annoMatrix,
-    obsCrossfilter,
-    metadataField: categoryName,
-    newLabelText: labelName,
-    assignSelectedCells: assignSelected,
-  });
-};
-
-export const annotationDeleteLabelFromCategory = (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  categoryName: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  labelName: any // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-) => async (dispatch: any, getState: any) => {
-  /*
-  delete a label from a user-defined category
-  */
-  const {
-    annoMatrix: prevAnnoMatrix,
-    obsCrossfilter: prevObsCrossfilter,
-  } = getState();
-  if (!prevAnnoMatrix || !prevObsCrossfilter) return;
-  if (!isUserAnnotation(prevAnnoMatrix, categoryName))
-    throw new Error("not a user annotation");
-
-  const obsCrossfilter = await prevObsCrossfilter.removeObsAnnoCategory(
-    categoryName,
-    labelName,
-    globals.unassignedCategoryLabel
-  );
-
-  dispatch({
-    type: "annotation: delete label",
-    metadataField: categoryName,
-    label: labelName,
-    annoMatrix: obsCrossfilter.annoMatrix,
-    obsCrossfilter,
-  });
-};
-
-export const annotationRenameLabelInCategory = (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  categoryName: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  oldLabelName: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  newLabelName: any
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-) => async (dispatch: any, getState: any) => {
-  /*
-  label name change
-  */
-  const {
-    annoMatrix: prevAnnoMatrix,
-    obsCrossfilter: prevObsCrossfilter,
-  } = getState();
-  if (!prevAnnoMatrix || !prevObsCrossfilter) return;
-  if (!isUserAnnotation(prevAnnoMatrix, categoryName))
-    throw new Error("not a user annotation");
-
-  let obsCrossfilter = await prevObsCrossfilter.resetObsColumnValues(
-    categoryName,
-    oldLabelName,
-    newLabelName
-  );
-  obsCrossfilter = await obsCrossfilter.removeObsAnnoCategory(
-    categoryName,
-    oldLabelName,
-    globals.unassignedCategoryLabel
-  );
-
-  dispatch({
-    type: "annotation: label edited",
-    editedLabel: newLabelName,
-    metadataField: categoryName,
-    label: oldLabelName,
-    annoMatrix: obsCrossfilter.annoMatrix,
-    obsCrossfilter,
-  });
-};
-
-export const annotationLabelCurrentSelection = (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  categoryName: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  labelName: any
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-) => async (dispatch: any, getState: any) => {
-  /*
-  set the label on all currently selected
-  */
-  const {
-    annoMatrix: prevAnnoMatrix,
-    obsCrossfilter: prevObsCrossfilter,
-  } = getState();
-  if (!prevAnnoMatrix || !prevObsCrossfilter) return;
-  if (!isUserAnnotation(prevAnnoMatrix, categoryName))
-    throw new Error("not a user annotation");
-
-  const obsCrossfilter = await prevObsCrossfilter.setObsColumnValues(
-    categoryName,
-    prevObsCrossfilter.allSelectedLabels(),
-    labelName
-  );
-
-  dispatch({
-    type: "annotation: label current cell selection",
-    metadataField: categoryName,
-    label: labelName,
-    obsCrossfilter,
-    annoMatrix: obsCrossfilter.annoMatrix,
-  });
-};
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-function writableAnnotations(annoMatrix: any) {
-  return (
-    annoMatrix.schema.annotations.obs.columns
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      .filter((s: any) => s.writable)
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      .map((s: any) => s.name)
-  );
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-export const needToSaveObsAnnotations = (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  annoMatrix: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  lastSavedAnnoMatrix: any
-) => {
-  /*
-  Return true if there are LIKELY user-defined annotation modifications between the two
-  annoMatrices.  Technically not an action creator, but intimately intertwined
-  with the save process.
-
-  Two conditions will trigger a need to save:
-    * the collection of user-defined columns have changed
-    * the contents of the user-defined columns have change
-  */
-
-  annoMatrix = annoMatrix.base();
-
-  // if the annoMatrix hasn't changed, we are guaranteed no changes to the matrix schema or contents.
-  if (annoMatrix === lastSavedAnnoMatrix) return false;
-
-  // if the schema has changed, we need to save
-  const currentWritable = writableAnnotations(annoMatrix);
-  if (difference(currentWritable, writableAnnotations(lastSavedAnnoMatrix))) {
-    return true;
-  }
-
-  // no schema changes; check for change in contents
-  return currentWritable.some(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    (col: any) => annoMatrix.col(col) !== lastSavedAnnoMatrix.col(col)
-  );
-};
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-export const saveObsAnnotationsAction = () => async (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  dispatch: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  getState: any
-) => {
-  /*
-  Save the user-created obs annotations IF any have changed.
-  */
-  const state = getState();
-  const { annotations, autosave } = state;
-  const { dataCollectionNameIsReadOnly, dataCollectionName } = annotations;
-  const { lastSavedAnnoMatrix, saveInProgress } = autosave;
-
-  const annoMatrix = state.annoMatrix.base();
-
-  if (saveInProgress || annoMatrix === lastSavedAnnoMatrix) return;
-  if (!needToSaveObsAnnotations(annoMatrix, lastSavedAnnoMatrix)) {
-    dispatch({
-      type: "writable obs annotations - save complete",
-      lastSavedAnnoMatrix: annoMatrix,
-    });
-    return;
-  }
-
-  /*
-  Else, we really do need to save
-  */
-
-  dispatch({
-    type: "writable obs annotations - save started",
-  });
-
-  const df = await annoMatrix.fetch("obs", writableAnnotations(annoMatrix));
-  const matrix = MatrixFBS.encodeMatrixFBS(df);
-  const compressedMatrix = pako.deflate(matrix);
-  try {
-    const queryString =
-      !dataCollectionNameIsReadOnly && !!dataCollectionName
-        ? `?annotation-collection-name=${encodeURIComponent(
-            dataCollectionName
-          )}`
-        : "";
-    const res = await fetch(
-      `${globals.API.prefix}${globals.API.version}annotations/obs${queryString}`,
-      {
-        method: "PUT",
-        body: compressedMatrix,
-        headers: new Headers({
-          "Content-Type": "application/octet-stream",
-        }),
-        credentials: "include",
-      }
-    );
-    if (res.ok) {
-      dispatch({
-        type: "writable obs annotations - save complete",
-        lastSavedAnnoMatrix: annoMatrix,
-      });
-    } else {
-      dispatch({
-        type: "writable obs annotations - save error",
-        message: `HTTP error ${res.status} - ${res.statusText}`,
-        res,
-      });
-    }
-  } catch (error) {
-    dispatch({
-      type: "writable obs annotations - save error",
-      message: error.toString(),
-      error,
-    });
-  }
-};
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-export const saveGenesetsAction = () => async (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  dispatch: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  getState: any
-) => {
-  const state = getState();
-
-  // bail if gene sets not available, or in readonly mode.
-  const { config } = state;
-  const { lastTid, genesets } = state.genesets;
-
-  const genesetsAreAvailable =
-    config?.parameters?.annotations_genesets ?? false;
-  const genesetsReadonly =
-    config?.parameters?.annotations_genesets_readonly ?? true;
-  if (!genesetsAreAvailable || genesetsReadonly) {
-    // our non-save was completed!
-    return dispatch({
-      type: "autosave: genesets complete",
-      lastSavedGenesets: genesets,
-    });
-  }
-
-  dispatch({
-    type: "autosave: genesets started",
-  });
-
-  /* Create the JSON OTA data structure */
-  const tid = (lastTid ?? 0) + 1;
-  const genesetsOTA = [];
-  for (const [name, gs] of genesets) {
-    const genes = [];
-    for (const g of gs.genes.values()) {
-      genes.push({
-        gene_symbol: g.geneSymbol,
-        gene_description: g.geneDescription,
-      });
-    }
-    genesetsOTA.push({
-      geneset_name: name,
-      geneset_description: gs.genesetDescription,
-      genes,
-    });
-  }
-  const ota = {
-    tid,
-    genesets: genesetsOTA,
-  };
-
-  /* Save to server */
-  try {
-    const {
-      dataCollectionNameIsReadOnly,
-      dataCollectionName,
-    } = state.annotations;
-    const queryString =
-      !dataCollectionNameIsReadOnly && !!dataCollectionName
-        ? `?annotation-collection-name=${encodeURIComponent(
-            dataCollectionName
-          )}`
-        : "";
-
-    const res = await fetch(
-      `${globals.API.prefix}${globals.API.version}genesets${queryString}`,
-      {
-        method: "PUT",
-        headers: new Headers({
-          Accept: "application/json",
-          "Content-Type": "application/json",
-        }),
-        body: JSON.stringify(ota),
-        credentials: "include",
-      }
-    );
-    if (!res.ok) {
-      return dispatch({
-        type: "autosave: genesets error",
-        message: `HTTP error ${res.status} - ${res.statusText}`,
-        res,
-      });
-    }
-    return await Promise.all([
-      dispatch({
-        type: "autosave: genesets complete",
-        lastSavedGenesets: genesets,
-      }),
-      dispatch({
-        type: "geneset: set tid",
-        tid,
-      }),
-    ]);
-  } catch (error) {
-    return dispatch({
-      type: "autosave: genesets error",
-      message: error.toString(),
-      error,
-    });
-  }
-};

client/src/actions/embedding.js

@@ -0,0 +1,47 @@
+/*
+action creators related to embeddings choice
+*/
+
+import { AnnoMatrixObsCrossfilter } from "../annoMatrix";
+import { _setEmbeddingSubset } from "../util/stateManager/viewStackHelpers";
+
+export async function _switchEmbedding(
+  prevAnnoMatrix,
+  prevCrossfilter,
+  newEmbeddingName
+) {
+  /*
+  DRY helper used by embedding action creators
+  */
+  const base = prevAnnoMatrix.base();
+  const embeddingDf = await base.fetch("emb", newEmbeddingName);
+  const annoMatrix = _setEmbeddingSubset(prevAnnoMatrix, embeddingDf);
+  const obsCrossfilter = await new AnnoMatrixObsCrossfilter(
+    annoMatrix,
+    prevCrossfilter.obsCrossfilter
+  ).select("emb", newEmbeddingName, {
+    mode: "all",
+  });
+  return [annoMatrix, obsCrossfilter];
+}
+
+export const layoutChoiceAction =
+  (newLayoutChoice) => async (dispatch, getState) => {
+    /*
+  On layout choice, make sure we have selected all on the previous layout, AND the new
+  layout.
+  */
+    const { annoMatrix: prevAnnoMatrix, obsCrossfilter: prevCrossfilter } =
+      getState();
+    const [annoMatrix, obsCrossfilter] = await _switchEmbedding(
+      prevAnnoMatrix,
+      prevCrossfilter,
+      newLayoutChoice
+    );
+    dispatch({
+      type: "set layout choice",
+      layoutChoice: newLayoutChoice,
+      obsCrossfilter,
+      annoMatrix,
+    });
+  };

client/src/actions/embedding.ts

@@ -1,60 +0,0 @@
-/*
-action creators related to embeddings choice
-*/
-
-import { Action, ActionCreator } from "redux";
-import { ThunkAction } from "redux-thunk";
-import { AnnoMatrixObsCrossfilter } from "../annoMatrix";
-import type { AppDispatch, RootState } from "../reducers";
-import { _setEmbeddingSubset } from "../util/stateManager/viewStackHelpers";
-import { Field } from "../common/types/schema";
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-export async function _switchEmbedding(
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  prevAnnoMatrix: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  prevCrossfilter: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  newEmbeddingName: any
-) {
-  /*
-  DRY helper used by embedding action creators
-  */
-  const base = prevAnnoMatrix.base();
-  const embeddingDf = await base.fetch("emb", newEmbeddingName);
-  const annoMatrix = _setEmbeddingSubset(prevAnnoMatrix, embeddingDf);
-  const obsCrossfilter = await new AnnoMatrixObsCrossfilter(
-    annoMatrix,
-    prevCrossfilter.obsCrossfilter
-  ).select(Field.emb, newEmbeddingName, {
-    mode: "all",
-  });
-  return [annoMatrix, obsCrossfilter];
-}
-
-export const layoutChoiceAction: ActionCreator<
-  ThunkAction<Promise<void>, RootState, never, Action<"set layout choice">>
-> =
-  (newLayoutChoice: string) =>
-  async (dispatch: AppDispatch, getState: () => RootState): Promise<void> => {
-    /*
-  On layout choice, make sure we have selected all on the previous layout, AND the new
-  layout.
-  */
-  const {
-    annoMatrix: prevAnnoMatrix,
-    obsCrossfilter: prevCrossfilter,
-  } = getState();
-  const [annoMatrix, obsCrossfilter] = await _switchEmbedding(
-    prevAnnoMatrix,
-    prevCrossfilter,
-    newLayoutChoice
-  );
-  dispatch({
-    type: "set layout choice",
-    layoutChoice: newLayoutChoice,
-    obsCrossfilter,
-    annoMatrix,
-  });
-};

client/src/actions/geneset.js

@@ -21,45 +21,34 @@ The behavior manifest in these action creators:
 Note that crossfilter indices are lazy created, as needed.
 */
 
-import { Dataframe } from "../util/dataframe";
-
-export const genesetDelete =
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  (genesetName: any) => (dispatch: any, getState: any) => {
-    const state = getState();
-    const { genesets } = state;
-    const gs = genesets?.genesets?.get(genesetName) ?? {};
-    const geneSymbols = Array.from(gs.genes.keys());
-    const obsCrossfilter = dropGeneset(
-      dispatch,
-      state,
-      genesetName,
-      geneSymbols
-    );
-    if (genesetName === state.colors.colorAccessor) {
-      dispatch({
-        type: "reset colorscale",
-      });
-    }
+export const genesetDelete = (genesetName) => (dispatch, getState) => {
+  const state = getState();
+  const { genesets } = state;
+  const gs = genesets?.genesets?.get(genesetName) ?? {};
+  const geneSymbols = Array.from(gs.genes.keys());
+  const obsCrossfilter = dropGeneset(dispatch, state, genesetName, geneSymbols);
+  if (genesetName === state.colors.colorAccessor) {
     dispatch({
-      type: "geneset: delete",
-      genesetName,
-      obsCrossfilter,
-      annoMatrix: obsCrossfilter.annoMatrix,
+      type: "reset colorscale",
     });
-  };
+  }
+  dispatch({
+    type: "geneset: delete",
+    genesetName,
+    obsCrossfilter,
+    annoMatrix: obsCrossfilter.annoMatrix,
+  });
+};
 
 export const genesetAddGenes =
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  (genesetName: any, genes: any) => async (dispatch: any, getState: any) => {
+  (genesetName, genes) => async (dispatch, getState) => {
     const state = getState();
     const { obsCrossfilter: prevObsCrossfilter, annoMatrix } = state;
     const { schema } = annoMatrix;
     const varIndex = schema.annotations.var.index;
-    const df: Dataframe = await annoMatrix.fetch("var", varIndex);
+    const df = await annoMatrix.fetch("var", varIndex);
     const geneNames = df.col(varIndex).asArray();
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    genes = genes.reduce((acc: any, gene: any) => {
+    genes = genes.reduce((acc, gene) => {
       if (geneNames.indexOf(gene.geneSymbol) === -1) {
         postUserErrorToast(
           `${gene.geneSymbol} doesn't appear to be a valid gene name.`
@@ -88,8 +77,7 @@ export const genesetAddGenes =
   };
 
 export const genesetDeleteGenes =
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  (genesetName: any, geneSymbols: any) => (dispatch: any, getState: any) => {
+  (genesetName, geneSymbols) => (dispatch, getState) => {
     const state = getState();
     const obsCrossfilter = dropGeneset(
       dispatch,
@@ -110,14 +98,7 @@ export const genesetDeleteGenes =
 Private
 */
 
-function dropGenesetSummaryDimension(
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  obsCrossfilter: any,
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  state: any,
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  genesetName: any
-) {
+function dropGenesetSummaryDimension(obsCrossfilter, state, genesetName) {
   const { annoMatrix, genesets } = state;
   const varIndex = annoMatrix.schema.annotations?.var?.index;
   const gs = genesets?.genesets?.get(genesetName) ?? {};
@@ -133,8 +114,7 @@ function dropGenesetSummaryDimension(
   return obsCrossfilter.dropDimension("X", query);
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-function dropGeneDimension(obsCrossfilter: any, state: any, gene: any) {
+function dropGeneDimension(obsCrossfilter, state, gene) {
   const { annoMatrix } = state;
   const varIndex = annoMatrix.schema.annotations?.var?.index;
   const query = {
@@ -147,21 +127,10 @@ function dropGeneDimension(obsCrossfilter: any, state: any, gene: any) {
   return obsCrossfilter.dropDimension("X", query);
 }
 
-function dropGeneset(
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  dispatch: any,
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  state: any,
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  genesetName: any,
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  geneSymbols: any
-) {
+function dropGeneset(dispatch, state, genesetName, geneSymbols) {
   const { obsCrossfilter: prevObsCrossfilter } = state;
   const obsCrossfilter = geneSymbols.reduce(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    (crossfilter: any, gene: any) =>
-      dropGeneDimension(crossfilter, state, gene),
+    (crossfilter, gene) => dropGeneDimension(crossfilter, state, gene),
     dropGenesetSummaryDimension(prevObsCrossfilter, state, genesetName)
   );
   dispatch({
@@ -169,8 +138,7 @@ function dropGeneset(
     continuousNamespace: { isGeneSetSummary: true },
     selection: genesetName,
   });
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  geneSymbols.forEach((g: any) =>
+  geneSymbols.forEach((g) =>
     dispatch({
       type: "continuous metadata histogram cancel",
       continuousNamespace: { isUserDefined: true },

client/src/actions/index.js

@@ -1,4 +1,3 @@
-import type { Config } from "../globals";
 import * as globals from "../globals";
 import { AnnoMatrixLoader, AnnoMatrixObsCrossfilter } from "../annoMatrix";
 import {
@@ -12,12 +11,8 @@ import * as annoActions from "./annotation";
 import * as viewActions from "./viewStack";
 import * as embActions from "./embedding";
 import * as genesetActions from "./geneset";
-import { AppDispatch, RootState } from "../reducers";
-import { EmbeddingSchema, Schema } from "../common/types/schema";
-import { UserInfoPayload } from "../reducers/userInfo";
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-function setGlobalConfig(config: any) {
+function setGlobalConfig(config) {
   /**
    * Set any global run-time config not _exclusively_ managed by the config reducer.
    * This should only set fields defined in globals.globalConfig.
@@ -30,8 +25,7 @@ function setGlobalConfig(config: any) {
 /*
 return promise fetching user-configured colors
 */
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-async function userColorsFetchAndLoad(dispatch: any) {
+async function userColorsFetchAndLoad(dispatch) {
   return fetchJson("colors").then((response) =>
     dispatch({
       type: "universe: user color load success",
@@ -40,38 +34,36 @@ async function userColorsFetchAndLoad(dispatch: any) {
   );
 }
 
-async function schemaFetch(): Promise<{ schema: Schema }> {
-  return fetchJson<{ schema: Schema }>("schema");
+async function schemaFetch() {
+  return fetchJson("schema");
 }
 
-async function configFetch(dispatch: AppDispatch): Promise<Config> {
-  const response = await fetchJson<{ config: globals.Config }>("config");
-  const config = { ...globals.configDefaults, ...response.config };
+async function configFetch(dispatch) {
+  return fetchJson("config").then((response) => {
+    const config = { ...globals.configDefaults, ...response.config };
 
-  setGlobalConfig(config);
+    setGlobalConfig(config);
 
-  dispatch({
-    type: "configuration load complete",
-    config,
+    dispatch({
+      type: "configuration load complete",
+      config,
+    });
+    return config;
   });
-  return config;
 }
 
-async function userInfoFetch(dispatch: AppDispatch): Promise<UserInfoPayload> {
-  return fetchJson<{ userinfo: UserInfoPayload }>("userinfo").then(
-    (response) => {
-      const { userinfo: userInfo } = response || {};
-      dispatch({
-        type: "userInfo load complete",
-        userInfo,
-      });
-      return userInfo;
-    }
-  );
+async function userInfoFetch(dispatch) {
+  return fetchJson("userinfo").then((response) => {
+    const { userinfo: userInfo } = response || {};
+    dispatch({
+      type: "userInfo load complete",
+      userInfo,
+    });
+    return userInfo;
+  });
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-async function genesetsFetch(dispatch: any, config: any) {
+async function genesetsFetch(dispatch, config) {
   /* request genesets ONLY if the backend supports the feature */
   const defaultResponse = {
     genesets: [],
@@ -92,32 +84,26 @@ async function genesetsFetch(dispatch: any, config: any) {
   }
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-function prefetchEmbeddings(annoMatrix: any) {
+function prefetchEmbeddings(annoMatrix) {
   /*
   prefetch requests for all embeddings
   */
   const { schema } = annoMatrix;
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  const available = schema.layout.obs.map((v: any) => v.name);
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  available.forEach((embName: any) => annoMatrix.prefetch("emb", embName));
+  const available = schema.layout.obs.map((v) => v.name);
+  available.forEach((embName) => annoMatrix.prefetch("emb", embName));
 }
 
 /*
 Application bootstrap
 */
-const doInitialDataLoad = (): ((
-  dispatch: AppDispatch,
-  getState: () => RootState
-) => void) =>
-  catchErrorsWrap(async (dispatch: AppDispatch) => {
+const doInitialDataLoad = () =>
+  catchErrorsWrap(async (dispatch) => {
     dispatch({ type: "initial data load start" });
 
     try {
       const [config, schema] = await Promise.all([
         configFetch(dispatch),
-        schemaFetch(),
+        schemaFetch(dispatch),
         userColorsFetchAndLoad(dispatch),
         userInfoFetch(dispatch),
       ]);
@@ -140,7 +126,7 @@ const doInitialDataLoad = (): ((
       const layoutSchema = schema?.schema?.layout?.obs ?? [];
       if (
         defaultEmbedding &&
-        layoutSchema.some((s: EmbeddingSchema) => s.name === defaultEmbedding)
+        layoutSchema.some((s) => s.name === defaultEmbedding)
       ) {
         dispatch(embActions.layoutChoiceAction(defaultEmbedding));
       }
@@ -149,25 +135,21 @@ const doInitialDataLoad = (): ((
     }
   }, true);
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-function requestSingleGeneExpressionCountsForColoringPOST(gene: any) {
+function requestSingleGeneExpressionCountsForColoringPOST(gene) {
   return {
     type: "color by expression",
     gene,
   };
 }
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-const requestUserDefinedGene = (gene: any) => ({
+const requestUserDefinedGene = (gene) => ({
   type: "request user defined gene success",
-
   data: {
     genes: [gene],
   },
 });
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-const dispatchDiffExpErrors = (dispatch: any, response: any) => {
+const dispatchDiffExpErrors = (dispatch, response) => {
   switch (response.status) {
     case 403:
       dispatchNetworkErrorMessageToUser(
@@ -191,16 +173,8 @@ const dispatchDiffExpErrors = (dispatch: any, response: any) => {
 };
 
 const requestDifferentialExpression =
-  (
-    // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-    set1: any,
-    // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-    set2: any,
-    num_genes = 50
-    // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  ) =>
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  async (dispatch: any, getState: any) => {
+  (set1, set2, num_genes = 50) =>
+  async (dispatch, getState) => {
     dispatch({ type: "request differential expression started" });
     try {
       /*
@@ -248,9 +222,7 @@ const requestDifferentialExpression =
       const varIndex = await annoMatrix.fetch("var", varIndexName);
       const diffexpLists = { negative: [], positive: [] };
       for (const polarity of Object.keys(diffexpLists)) {
-        // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-        diffexpLists[polarity] = response[polarity].map((v: any) => [
+        diffexpLists[polarity] = response[polarity].map((v) => [
           varIndex.at(v[0], varIndexName),
           ...v.slice(1),
         ]);
@@ -269,10 +241,10 @@ const requestDifferentialExpression =
     }
   };
 
-function fetchJson<T>(pathAndQuery: string): Promise<T> {
-  return doJsonRequest<T>(
+function fetchJson(pathAndQuery) {
+  return doJsonRequest(
     `${globals.API.prefix}${globals.API.version}${pathAndQuery}`
-  ) as Promise<T>;
+  );
 }
 
 export default {

client/src/actions/selection.js

@@ -0,0 +1,192 @@
+/*
+Action creators for selection 
+*/
+export const selectContinuousMetadataAction =
+  (type, query, range, oldProps = {}) =>
+  async (dispatch, getState) => {
+    const { obsCrossfilter: prevObsCrossfilter } = getState();
+
+    const selection = range
+      ? {
+          mode: "range",
+          lo: range[0],
+          hi: range[1],
+          inclusive: true, // [lo, hi] incluisve selection
+        }
+      : { mode: "all" };
+
+    const obsCrossfilter = await prevObsCrossfilter.select(...query, selection);
+
+    dispatch({
+      type,
+      obsCrossfilter,
+      range,
+      ...oldProps,
+    });
+  };
+
+export const selectCategoricalMetadataAction =
+  (
+    type, // action type
+    metadataField, // annotation category name
+    labels,
+    label, // the label being selected/deselected
+    isSelected, // bool
+    oldProps = {}
+  ) =>
+  async (dispatch, getState) => {
+    const { obsCrossfilter: prevObsCrossfilter, categoricalSelection } =
+      getState();
+
+    const labelSelectionState = new Map(categoricalSelection[metadataField]);
+    labels.forEach(
+      (l) => labelSelectionState.has(l) || labelSelectionState.set(l, true)
+    );
+    labelSelectionState.set(label, isSelected);
+
+    const values = Array.from(labelSelectionState.keys()).filter((k) =>
+      labelSelectionState.get(k)
+    );
+    const selection = {
+      mode: "exact",
+      values,
+    };
+    const obsCrossfilter = await prevObsCrossfilter.select(
+      "obs",
+      metadataField,
+      selection
+    );
+
+    dispatch({
+      type,
+      obsCrossfilter,
+      metadataField,
+      labelSelectionState,
+      ...oldProps,
+    });
+  };
+
+export const selectCategoricalAllMetadataAction =
+  (
+    type, // action type
+    metadataField, // annotation category name
+    labels,
+    isSelected, // bool, select all or none
+    oldProps = {}
+  ) =>
+  async (dispatch, getState) => {
+    const { obsCrossfilter: prevObsCrossfilter, categoricalSelection } =
+      getState();
+
+    const labelSelectionState = new Map(categoricalSelection[metadataField]);
+    labels.forEach((label) => labelSelectionState.set(label, isSelected));
+
+    const selection = { mode: isSelected ? "all" : "none" };
+    const obsCrossfilter = await prevObsCrossfilter.select(
+      "obs",
+      metadataField,
+      selection
+    );
+
+    dispatch({
+      type,
+      obsCrossfilter,
+      metadataField,
+      labelSelectionState,
+      ...oldProps,
+    });
+  };
+
+/**
+ ** Graph selection-related actions
+ **/
+
+export const graphBrushStartAction = () =>
+  /* no change to crossfilter until a change fires */
+  ({ type: "graph brush start" });
+
+const _graphBrushWithinRectAction =
+  (type, embName, brushCoords) => async (dispatch, getState) => {
+    const { obsCrossfilter: prevObsCrossfilter } = getState();
+
+    const selection = { mode: "within-rect", ...brushCoords };
+    const obsCrossfilter = await prevObsCrossfilter.select(
+      "emb",
+      embName,
+      selection
+    );
+
+    dispatch({
+      type,
+      obsCrossfilter,
+      brushCoords,
+    });
+  };
+
+const _graphAllAction = (type, embName) => async (dispatch, getState) => {
+  const { obsCrossfilter: prevObsCrossfilter } = getState();
+
+  const obsCrossfilter = await prevObsCrossfilter.select("emb", embName, {
+    mode: "all",
+  });
+
+  dispatch({
+    type,
+    obsCrossfilter,
+  });
+};
+
+export const graphBrushChangeAction = (embName, brushCoords) =>
+  _graphBrushWithinRectAction("graph brush change", embName, brushCoords);
+
+export const graphBrushEndAction = (embName, brushCoords) =>
+  _graphBrushWithinRectAction("graph brush end", embName, brushCoords);
+
+export const graphBrushCancelAction = (embName) =>
+  _graphAllAction("graph brush cancel", embName);
+export const graphBrushDeselectAction = (embName) =>
+  _graphAllAction("graph brush deselect", embName);
+
+export const graphLassoStartAction = () =>
+  /* no change to crossfilter until a change fires */
+  ({ type: "graph lasso start" });
+
+export const graphLassoCancelAction = (embName) =>
+  _graphAllAction("graph lasso cancel", embName);
+
+export const graphLassoDeselectAction = (embName) =>
+  _graphAllAction("graph lasso cancel", embName);
+
+export const graphLassoEndAction =
+  (embName, polygon) => async (dispatch, getState) => {
+    const { obsCrossfilter: prevObsCrossfilter } = getState();
+
+    const selection = {
+      mode: "within-polygon",
+      polygon,
+    };
+    const obsCrossfilter = await prevObsCrossfilter.select(
+      "emb",
+      embName,
+      selection
+    );
+
+    dispatch({
+      type: "graph lasso end",
+      obsCrossfilter,
+      polygon,
+    });
+  };
+
+/*
+Differential expression set selection
+*/
+export const setCellSetFromSelection = (cellSetId) => (dispatch, getState) => {
+  const { obsCrossfilter } = getState();
+  const selected = obsCrossfilter.allSelectedLabels();
+
+  dispatch({
+    type: `store current cell selection as differential set ${cellSetId}`,
+    data: selected.length > 0 ? selected : null,
+  });
+};

client/src/actions/selection.ts

@@ -1,248 +0,0 @@
-/*
-Action creators for selection 
-*/
-export const selectContinuousMetadataAction = (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  type: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  query: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  range: any,
-  oldProps = {} // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-) => async (dispatch: any, getState: any) => {
-  const { obsCrossfilter: prevObsCrossfilter } = getState();
-
-  const selection = range
-    ? {
-        mode: "range",
-        lo: range[0],
-        hi: range[1],
-        inclusive: true, // [lo, hi] incluisve selection
-      }
-    : { mode: "all" };
-
-  const obsCrossfilter = await prevObsCrossfilter.select(...query, selection);
-
-  dispatch({
-    type,
-    obsCrossfilter,
-    range,
-    ...oldProps,
-  });
-};
-
-export const selectCategoricalMetadataAction = (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  type: any, // action type
-  // annotation category name
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  metadataField: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  labels: any,
-  // the label being selected/deselected
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  label: any,
-  // bool
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  isSelected: any,
-  oldProps = {}
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-) => async (dispatch: any, getState: any) => {
-  const {
-    obsCrossfilter: prevObsCrossfilter,
-    categoricalSelection,
-  } = getState();
-
-  const labelSelectionState = new Map(categoricalSelection[metadataField]);
-  labels.forEach(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    (l: any) => labelSelectionState.has(l) || labelSelectionState.set(l, true)
-  );
-  labelSelectionState.set(label, isSelected);
-
-  const values = Array.from(labelSelectionState.keys()).filter((k) =>
-    labelSelectionState.get(k)
-  );
-  const selection = {
-    mode: "exact",
-    values,
-  };
-  const obsCrossfilter = await prevObsCrossfilter.select(
-    "obs",
-    metadataField,
-    selection
-  );
-
-  dispatch({
-    type,
-    obsCrossfilter,
-    metadataField,
-    labelSelectionState,
-    ...oldProps,
-  });
-};
-
-export const selectCategoricalAllMetadataAction = (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  type: any, // action type
-  // annotation category name
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  metadataField: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  labels: any,
-  // bool, select all or none
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  isSelected: any,
-  oldProps = {}
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-) => async (dispatch: any, getState: any) => {
-  const {
-    obsCrossfilter: prevObsCrossfilter,
-    categoricalSelection,
-  } = getState();
-
-  const labelSelectionState = new Map(categoricalSelection[metadataField]);
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  labels.forEach((label: any) => labelSelectionState.set(label, isSelected));
-
-  const selection = { mode: isSelected ? "all" : "none" };
-  const obsCrossfilter = await prevObsCrossfilter.select(
-    "obs",
-    metadataField,
-    selection
-  );
-
-  dispatch({
-    type,
-    obsCrossfilter,
-    metadataField,
-    labelSelectionState,
-    ...oldProps,
-  });
-};
-
-/**
- ** Graph selection-related actions
- **/
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-export const graphBrushStartAction = () =>
-  /* no change to crossfilter until a change fires */
-  ({ type: "graph brush start" });
-
-const _graphBrushWithinRectAction = (
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  type: any,
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  embName: any,
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  brushCoords: any
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-) => async (dispatch: any, getState: any) => {
-  const { obsCrossfilter: prevObsCrossfilter } = getState();
-
-  const selection = { mode: "within-rect", ...brushCoords };
-  const obsCrossfilter = await prevObsCrossfilter.select(
-    "emb",
-    embName,
-    selection
-  );
-
-  dispatch({
-    type,
-    obsCrossfilter,
-    brushCoords,
-  });
-};
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-const _graphAllAction = (type: any, embName: any) => async (
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  dispatch: any,
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  getState: any
-) => {
-  const { obsCrossfilter: prevObsCrossfilter } = getState();
-
-  const obsCrossfilter = await prevObsCrossfilter.select("emb", embName, {
-    mode: "all",
-  });
-
-  dispatch({
-    type,
-    obsCrossfilter,
-  });
-};
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const graphBrushChangeAction = (embName: any, brushCoords: any) =>
-  _graphBrushWithinRectAction("graph brush change", embName, brushCoords);
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const graphBrushEndAction = (embName: any, brushCoords: any) =>
-  _graphBrushWithinRectAction("graph brush end", embName, brushCoords);
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const graphBrushCancelAction = (embName: any) =>
-  _graphAllAction("graph brush cancel", embName);
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const graphBrushDeselectAction = (embName: any) =>
-  _graphAllAction("graph brush deselect", embName);
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-export const graphLassoStartAction = () =>
-  /* no change to crossfilter until a change fires */
-  ({ type: "graph lasso start" });
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const graphLassoCancelAction = (embName: any) =>
-  _graphAllAction("graph lasso cancel", embName);
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const graphLassoDeselectAction = (embName: any) =>
-  _graphAllAction("graph lasso cancel", embName);
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const graphLassoEndAction = (embName: any, polygon: any) => async (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  dispatch: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  getState: any
-) => {
-  const { obsCrossfilter: prevObsCrossfilter } = getState();
-
-  const selection = {
-    mode: "within-polygon",
-    polygon,
-  };
-  const obsCrossfilter = await prevObsCrossfilter.select(
-    "emb",
-    embName,
-    selection
-  );
-
-  dispatch({
-    type: "graph lasso end",
-    obsCrossfilter,
-    polygon,
-  });
-};
-
-/*
-Differential expression set selection
-*/
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const setCellSetFromSelection = (cellSetId: any) => (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  dispatch: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  getState: any
-) => {
-  const { obsCrossfilter } = getState();
-  const selected = obsCrossfilter.allSelectedLabels();
-
-  dispatch({
-    type: `store current cell selection as differential set ${cellSetId}`,
-    data: selected.length > 0 ? selected : null,
-  });
-};

client/src/actions/viewStack.js

@@ -18,13 +18,7 @@ import {
   _userResetSubsetAnnoMatrix,
 } from "../util/stateManager/viewStackHelpers";
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const clipAction = (min: any, max: any) => (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  dispatch: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  getState: any
-) => {
+export const clipAction = (min, max) => (dispatch, getState) => {
   /*
   apply a clip to the current annoMatrix.  By convention, the clip
   view is ALWAYS the top view.
@@ -40,8 +34,7 @@ export const clipAction = (min: any, max: any) => (
   });
 };
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const subsetAction = () => (dispatch: any, getState: any) => {
+export const subsetAction = () => (dispatch, getState) => {
   /*
   Subset the annoMatrix to the current crossfilter selection by pushing a 
   subset view.
@@ -49,10 +42,8 @@ export const subsetAction = () => (dispatch: any, getState: any) => {
   By convention, a clip view is ALWAYS the top view, so if present, pop
   off and re-apply
   */
-  const {
-    annoMatrix: prevAnnoMatrix,
-    obsCrossfilter: prevObsCrossfilter,
-  } = getState();
+  const { annoMatrix: prevAnnoMatrix, obsCrossfilter: prevObsCrossfilter } =
+    getState();
   const annoMatrix = _userSubsetAnnoMatrix(
     prevAnnoMatrix,
     prevObsCrossfilter.allSelectedMask()
@@ -65,8 +56,7 @@ export const subsetAction = () => (dispatch: any, getState: any) => {
   });
 };
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const resetSubsetAction = () => (dispatch: any, getState: any) => {
+export const resetSubsetAction = () => (dispatch, getState) => {
   /*
   Reset the annoMatrix to all data.  Because we may have multiple views
   stacked, we pop them all.  By convention, any clip transformation will