Deprecate post sample feature type (#112)

* Replace deprecated methods using FeatureType and SampleType with DimensionType * Remove and mark deprecated methods * Remove unused component * Add back deprecated FeatureType and SampleType methods expected in SharedApi but mark them deprecated * Fix eslint no unused variables error
broadinstitute · Nov 5, 2024 · 77ee6b1 · 77ee6b1
1 parent 5a52e84
commit 77ee6b1
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Showing 14 changed files with 147 additions and 770 deletions.
diff --git a/frontend/packages/@depmap/dataset-manager/src/components/AddDatasetForm.tsx b/frontend/packages/@depmap/dataset-manager/src/components/AddDatasetForm.tsx
diff --git a/frontend/packages/@depmap/dataset-manager/src/components/DatasetForm.tsx b/frontend/packages/@depmap/dataset-manager/src/components/DatasetForm.tsx
@@ -9,11 +9,12 @@ import { tableFormSchema } from "../models/tableDatasetFormSchema";
 import {
   DatasetParams,
   DataType,
-  FeatureType,
   Group,
   InvalidPrioritiesByDataType,
-  SampleType,
   UploadFileResponse,
+  DimensionType,
+  SampleDimensionType,
+  FeatureDimensionType,
 } from "@depmap/types";
 import ChunkedFileUploader from "./ChunkedFileUploader";
 
@@ -60,8 +61,7 @@ interface DatasetFormProps {
   //   clear_state_callback: (isSuccessfulSubmit: boolean) => void
   // ) => void;
   // datasetSubmissionError: string | null;
-  getFeatureTypes: () => Promise<FeatureType[]>;
-  getSampleTypes: () => Promise<SampleType[]>;
+  getDimensionTypes: () => Promise<DimensionType[]>;
   getDataTypesAndPriorities: () => Promise<InvalidPrioritiesByDataType>;
   getGroups: () => Promise<Group[]>;
   uploadFile: (fileArgs: { file: File | Blob }) => Promise<UploadFileResponse>;
@@ -72,8 +72,7 @@ interface DatasetFormProps {
 
 export default function DatasetForm(props: DatasetFormProps) {
   const {
-    getFeatureTypes,
-    getSampleTypes,
+    getDimensionTypes,
     getGroups,
     getDataTypesAndPriorities,
     uploadFile,
@@ -90,10 +89,12 @@ export default function DatasetForm(props: DatasetFormProps) {
   const [fileIds, setFileIds] = useState<string[] | null>(null);
   const [md5Hash, setMD5Hash] = useState<string | null>(null);
 
-  const [featureTypeOptions, setFeatureTypesOptions] = useState<FeatureType[]>(
-    []
-  );
-  const [sampleTypeOptions, setSampleTypesOptions] = useState<SampleType[]>([]);
+  const [featureTypeOptions, setFeatureTypesOptions] = useState<
+    FeatureDimensionType[]
+  >([]);
+  const [sampleTypeOptions, setSampleTypesOptions] = useState<
+    SampleDimensionType[]
+  >([]);
   const [groupOptions, setGroupsOptions] = useState<Group[]>([]);
   const [
     invalidPrioritiesByDataType,
@@ -108,13 +109,11 @@ export default function DatasetForm(props: DatasetFormProps) {
       try {
         const [
           dataTypesPriorities,
-          featureTypes,
-          sampleTypes,
+          dimensionTypes,
           groups,
         ] = await Promise.all([
           getDataTypesAndPriorities(),
-          getFeatureTypes(),
-          getSampleTypes(),
+          getDimensionTypes(),
           getGroups(),
         ]);
 
@@ -123,6 +122,12 @@ export default function DatasetForm(props: DatasetFormProps) {
             name: dType,
           };
         });
+        const sampleTypes: SampleDimensionType[] = [];
+        const featureTypes: FeatureDimensionType[] = [];
+        dimensionTypes.map((dt: FeatureDimensionType | SampleDimensionType) =>
+          dt.axis === "sample" ? sampleTypes.push(dt) : featureTypes.push(dt)
+        );
+
         setInvalidPrioritiesByDataType(dataTypesPriorities);
         setDataTypeOptions(dataTypes);
         setFeatureTypesOptions(featureTypes);
@@ -133,7 +138,7 @@ export default function DatasetForm(props: DatasetFormProps) {
         // setInitFetchError(true);
       }
     })();
-  }, [getFeatureTypes, getSampleTypes, getGroups, getDataTypesAndPriorities]);
+  }, [getDimensionTypes, getGroups, getDataTypesAndPriorities]);
 
   const formComponent = useMemo(() => {
     const onSubmitForm = (formData: { [key: string]: any }) => {
@@ -176,10 +181,12 @@ export default function DatasetForm(props: DatasetFormProps) {
       );
     }
     if (selectedFormat === "table") {
+      const dimensionTypeOptions: DimensionType[] = (featureTypeOptions as DimensionType[]).concat(
+        sampleTypeOptions
+      );
       return (
         <TableDatasetForm
-          featureTypes={featureTypeOptions}
-          sampleTypes={sampleTypeOptions}
+          dimensionTypes={dimensionTypeOptions}
           groups={groupOptions}
           dataTypes={dataTypeOptions}
           invalidDataTypePriorities={invalidPrioritiesByDataType}

diff --git a/frontend/packages/@depmap/dataset-manager/src/components/MatrixDatasetForm.tsx b/frontend/packages/@depmap/dataset-manager/src/components/MatrixDatasetForm.tsx
@@ -13,10 +13,10 @@ import { CustomDatasetMetadata } from "./DatasetMetadataForm";
 import { FormGroup, ControlLabel } from "react-bootstrap";
 import {
   DataType,
-  FeatureType,
+  FeatureDimensionType,
   Group,
   InvalidPrioritiesByDataType,
-  SampleType,
+  SampleDimensionType,
 } from "@depmap/types";
 import { Option, TagInput } from "@depmap/common-components";
 import { ActionMeta, ValueType } from "react-select";
@@ -202,8 +202,8 @@ const uiSchema: UiSchema = {
 };
 
 interface MatrixDatasetFormProps {
-  featureTypes: FeatureType[];
-  sampleTypes: SampleType[];
+  featureTypes: FeatureDimensionType[];
+  sampleTypes: SampleDimensionType[];
   dataTypes: DataType[];
   invalidDataTypePriorities: InvalidPrioritiesByDataType;
   groups: Group[];

diff --git a/frontend/packages/@depmap/dataset-manager/src/components/TableDatasetForm.tsx b/frontend/packages/@depmap/dataset-manager/src/components/TableDatasetForm.tsx
@@ -14,10 +14,9 @@ import { CustomDatasetMetadata } from "./DatasetMetadataForm";
 import { FormGroup, FormControl, ControlLabel } from "react-bootstrap";
 import {
   DataType,
-  FeatureType,
+  DimensionType,
   Group,
   InvalidPrioritiesByDataType,
-  SampleType,
 } from "@depmap/types";
 
 const CustomColumnsMetadata = function (props: FieldProps) {
@@ -138,8 +137,7 @@ function isObject(x: any) {
 }
 
 interface TableDatasetFormProps {
-  featureTypes: FeatureType[];
-  sampleTypes: SampleType[];
+  dimensionTypes: DimensionType[];
   dataTypes: DataType[];
   invalidDataTypePriorities: InvalidPrioritiesByDataType;
   groups: Group[];
@@ -151,8 +149,7 @@ interface TableDatasetFormProps {
 }
 
 export function TableDatasetForm({
-  featureTypes,
-  sampleTypes,
+  dimensionTypes,
   dataTypes,
   invalidDataTypePriorities,
   groups,
@@ -166,7 +163,7 @@ export function TableDatasetForm({
   const [schema, setSchema] = React.useState<RJSFSchema | null>(null);
 
   React.useEffect(() => {
-    const indexOptions = featureTypes.concat(sampleTypes).map((option) => {
+    const indexOptions = dimensionTypes.map((option) => {
       return { title: option.name, const: option.name };
     });
     const dataTypeOptions = dataTypes.map((option) => {
@@ -195,7 +192,7 @@ export function TableDatasetForm({
       },
     };
     setSchema(schemaWithOptions);
-  }, [featureTypes, sampleTypes, dataTypes, groups]);
+  }, [dataTypes, groups, dimensionTypes]);
 
   React.useEffect(() => {
     if (fileIds !== formData.file_ids || md5Hash !== formData.dataset_md5) {

diff --git a/frontend/packages/@depmap/dataset-manager/src/components/index.tsx b/frontend/packages/@depmap/dataset-manager/src/components/index.tsx
@@ -42,10 +42,6 @@ export default function Datasets() {
   } | null>(null);
   const [showMetadataForm, setShowMetadataForm] = useState<boolean>(false);
 
-  // TODO: Remove
-  const getFeatureTypes = useCallback(() => dapi.getFeatureTypes(), [dapi]);
-  const getSampleTypes = useCallback(() => dapi.getSampleTypes(), [dapi]);
-
   const getDimensionTypes = useCallback(() => dapi.getDimensionTypes(), [dapi]);
   const postDimensionType = useCallback(
     (dimTypeArgs: DimensionTypeAddArgs) => dapi.postDimensionType(dimTypeArgs),
@@ -177,8 +173,7 @@ export default function Datasets() {
         formTitle = "Add Dataset";
         datasetFormComponent = (
           <DatasetForm
-            getFeatureTypes={getFeatureTypes}
-            getSampleTypes={getSampleTypes}
+            getDimensionTypes={getDimensionTypes}
             getGroups={getGroups}
             getDataTypesAndPriorities={getDataTypesAndPriorities}
             uploadFile={postFileUpload}
@@ -203,9 +198,8 @@ export default function Datasets() {
     datasetToEdit,
     datasets,
     getDataTypesAndPriorities,
-    getFeatureTypes,
+    getDimensionTypes,
     getGroups,
-    getSampleTypes,
     isEditDatasetMode,
     postDatasetUpload,
     postFileUpload,

diff --git a/frontend/packages/@depmap/dataset-manager/src/stories/AddDatasetForm.stories.tsx b/frontend/packages/@depmap/dataset-manager/src/stories/AddDatasetForm.stories.tsx
diff --git a/frontend/packages/@depmap/dataset-manager/src/stories/DatasetForm.stories.tsx b/frontend/packages/@depmap/dataset-manager/src/stories/DatasetForm.stories.tsx
@@ -1,9 +1,8 @@
 import * as React from "react";
 import {
-  FeatureType,
+  DimensionType,
   Group,
   InvalidPrioritiesByDataType,
-  SampleType,
   UploadFileResponse,
 } from "@depmap/types";
 import DatasetForm from "../components/DatasetForm";
@@ -13,31 +12,28 @@ export default {
   component: DatasetForm,
 };
 
-async function getFeatureTypes(): Promise<FeatureType[]> {
-  const featureTypes = [
+async function getDimensionTypes(): Promise<DimensionType[]> {
+  const dimensionTypes = [
     {
       name: "generic",
+      display_name: "Generic",
       id_column: "label",
-      dataset: null as any,
+      axis: "feature",
     },
     {
       name: "gene",
+      display_name: "Gene",
       id_column: "entrez_id",
-      dataset: null,
+      axis: "feature",
     },
-  ];
-  return featureTypes;
-}
-
-async function getSampleTypes(): Promise<SampleType[]> {
-  const sampleTypes = [
     {
       name: "depmap_model",
+      display_name: "Depmap Model",
       id_column: "depmap_id",
-      dataset: null as any,
+      axis: "sample",
     },
   ];
-  return sampleTypes;
+  return dimensionTypes as DimensionType[];
 }
 
 async function getGroups() {
@@ -72,15 +68,14 @@ async function uploadFile(): Promise<UploadFileResponse> {
   return { file_id: `id-${counter}` };
 }
 
-async function uploadDataset(datasetParams) {
+async function uploadDataset(datasetParams: any) {
   console.log(datasetParams);
 }
 
 export function DatasetFormStory() {
   return (
     <DatasetForm
-      getFeatureTypes={getFeatureTypes}
-      getSampleTypes={getSampleTypes}
+      getDimensionTypes={getDimensionTypes}
       getGroups={getGroups}
       getDataTypesAndPriorities={getDataTypesAndPriorities}
       uploadFile={uploadFile}

diff --git a/frontend/packages/@depmap/types/index.ts b/frontend/packages/@depmap/types/index.ts
@@ -15,6 +15,8 @@ export type {
 
 export type {
   DimensionType,
+  SampleDimensionType,
+  FeatureDimensionType,
   DimensionTypeAddArgs,
   DimensionTypeUpdateArgs,
 } from "./src/DimensionType";

diff --git a/frontend/packages/@depmap/types/src/DimensionType.ts b/frontend/packages/@depmap/types/src/DimensionType.ts
@@ -7,6 +7,14 @@ export interface DimensionType {
   properties_to_index?: string[] | null;
 }
 
+export interface FeatureDimensionType extends DimensionType {
+  axis: "feature";
+}
+
+export interface SampleDimensionType extends DimensionType {
+  axis: "sample";
+}
+
 export interface DimensionTypeAddArgs {
   name: string;
   display_name: string;

diff --git a/frontend/packages/@depmap/types/src/FeatureType.ts b/frontend/packages/@depmap/types/src/FeatureType.ts
@@ -1,3 +1,7 @@
+/**
+ * NOTE: Deprecated Type!! Do not use!
+ */
+
 import { Dataset } from "./Dataset";
 import { AnnotationTypeMap } from "./Metadata";
 

diff --git a/frontend/packages/@depmap/types/src/SampleType.ts b/frontend/packages/@depmap/types/src/SampleType.ts
@@ -1,3 +1,6 @@
+/**
+ * NOTE: Deprecated Type!! Do not use!
+ */
 import { Dataset } from "./Dataset";
 import { AnnotationTypeMap } from "./Metadata";