Merge pull request #372 from AllenInstitute/feature/metadata-editing/…

…create-mms-endpoint-logic

[Large] Create logic for editing metadata

packages/core/components/EditMetadata/ExistingAnnotationPathway.tsx

@@ -1,11 +1,13 @@
 import { IComboBoxOption } from "@fluentui/react";
 import classNames from "classnames";
 import * as React from "react";
+import { useDispatch } from "react-redux";
 
 import MetadataDetails, { ValueCountItem } from "./MetadataDetails";
 import { PrimaryButton, SecondaryButton } from "../Buttons";
 import ComboBox from "../ComboBox";
 import { AnnotationType } from "../../entity/AnnotationFormatter";
+import { interaction } from "../../state";
 
 import styles from "./EditMetadata.module.css";
 
@@ -21,6 +23,7 @@ interface ExistingAnnotationProps {
  * and then entering values for the selected files
  */
 export default function ExistingAnnotationPathway(props: ExistingAnnotationProps) {
+    const dispatch = useDispatch();
     const [newValues, setNewValues] = React.useState<string>();
     const [valueCount, setValueCount] = React.useState<ValueCountItem[]>();
     const [selectedAnnotation, setSelectedAnnotation] = React.useState<string | undefined>();
@@ -68,7 +71,9 @@ export default function ExistingAnnotationPathway(props: ExistingAnnotationProps
     };
 
     function onSubmit() {
-        // TO DO: endpoint logic is in progress on a different branch
+        if (selectedAnnotation && newValues?.trim()) {
+            dispatch(interaction.actions.editFiles({ [selectedAnnotation]: [newValues.trim()] }));
+        }
         props.onDismiss();
     }
 
@@ -94,7 +99,7 @@ export default function ExistingAnnotationPathway(props: ExistingAnnotationProps
                 {valueCount && (
                     <PrimaryButton
                         className={styles.primaryButton}
-                        disabled={!newValues}
+                        disabled={!newValues?.trim()}
                         title=""
                         text="REPLACE"
                         onClick={onSubmit}

packages/core/constants/index.ts

@@ -64,10 +64,10 @@ export enum FESBaseUrl {
 }
 
 export enum MMSBaseUrl {
-    LOCALHOST = "http://localhost:9060",
-    STAGING = "http://stg-aics-api",
-    PRODUCTION = "http://prod-aics-api",
-    TEST = "http://test-aics-api",
+    LOCALHOST = "https://localhost:9060",
+    STAGING = "https://stg-aics.corp.alleninstitute.org",
+    PRODUCTION = "https://aics.corp.alleninstitute.org",
+    TEST = "http://test-aics-mms-api.corp.alleninstitute.org",
 }
 
 export enum LoadBalancerBaseUrl {

packages/core/entity/Annotation/index.ts

@@ -9,6 +9,8 @@ import { AnnotationValue } from "../../services/AnnotationService";
  * Expected JSON structure of an annotation returned from the query service.
  */
 export interface AnnotationResponse {
+    // Undefined when pulled from a non-AICS FMS data source
+    annotationId?: number;
     annotationDisplayName: string;
     annotationName: string;
     description: string;
@@ -70,6 +72,10 @@ export default class Annotation {
         return this.annotation.units;
     }
 
+    public get id(): number | undefined {
+        return this.annotation.annotationId;
+    }
+
     /**
      * Get the annotation this instance represents from a given FmsFile. An annotation on an FmsFile
      * can either be at the "top-level" of the document or it can be within it's "annotations" list.

packages/core/hooks/useFileAccessContextMenu.ts

@@ -136,24 +136,18 @@ export default (filters?: FileFilter[], onDismiss?: () => void) => {
                         ],
                     },
                 },
-                ...(isQueryingAicsFms
-                    ? [
-                          {
-                              key: "edit",
-                              text: "Edit metadata",
-                              title: "Edit metadata of selected files",
-                              disabled: !filters && fileSelection.count() === 0,
-                              iconProps: {
-                                  iconName: "Edit",
-                              },
-                              onClick() {
-                                  dispatch(
-                                      interaction.actions.setVisibleModal(ModalType.EditMetadata)
-                                  );
-                              },
-                          },
-                      ]
-                    : []),
+                {
+                    key: "edit",
+                    text: "Edit metadata",
+                    title: "Edit metadata for selected files",
+                    disabled: !filters && fileSelection.count() === 0,
+                    iconProps: {
+                        iconName: "Edit",
+                    },
+                    onClick() {
+                        dispatch(interaction.actions.setVisibleModal(ModalType.EditMetadata));
+                    },
+                },
                 ...(isQueryingAicsFms && !isOnWeb
                     ? [
                           {

packages/core/services/DatabaseService/index.ts

@@ -53,7 +53,7 @@ export default abstract class DatabaseService {
         _uri: string | File
     ): Promise<void>;
 
-    protected abstract execute(_sql: string): Promise<void>;
+    public abstract execute(_sql: string): Promise<void>;
 
     private static columnTypeToAnnotationType(columnType: string): string {
         switch (columnType) {

packages/core/services/FileService/DatabaseFileService/index.ts

@@ -1,6 +1,11 @@
 import { isEmpty, isNil, uniqueId } from "lodash";
 
-import FileService, { GetFilesRequest, SelectionAggregationResult, Selection } from "..";
+import FileService, {
+    GetFilesRequest,
+    SelectionAggregationResult,
+    Selection,
+    AnnotationNameToValuesMap,
+} from "..";
 import DatabaseService from "../../DatabaseService";
 import DatabaseServiceNoop from "../../DatabaseService/DatabaseServiceNoop";
 import FileDownloadService, { DownloadResolution, DownloadResult } from "../../FileDownloadService";
@@ -184,4 +189,17 @@ export default class DatabaseFileService implements FileService {
             uniqueId()
         );
     }
+
+    public editFile(fileId: string, annotations: AnnotationNameToValuesMap): Promise<void> {
+        const tableName = this.dataSourceNames.sort().join(", ");
+        const columnAssignments = Object.entries(annotations).map(
+            ([name, values]) => `"${name}" = '${values.join(DatabaseService.LIST_DELIMITER)}'`
+        );
+        const sql = `\
+            UPDATE '${tableName}' \
+            SET ${columnAssignments.join(", ")} \
+            WHERE ${DatabaseService.HIDDEN_UID_ANNOTATION} = '${fileId}'; \
+        `;
+        return this.databaseService.execute(sql);
+    }
 }

packages/core/services/FileService/FileServiceNoop.ts

@@ -15,11 +15,11 @@ export default class FileServiceNoop implements FileService {
         return Promise.resolve([]);
     }
 
-    public getFilesAsBuffer(): Promise<Uint8Array> {
-        return Promise.resolve(new Uint8Array());
-    }
-
     public download(): Promise<DownloadResult> {
         return Promise.resolve({ downloadRequestId: "", resolution: DownloadResolution.CANCELLED });
     }
+
+    public editFile(): Promise<void> {
+        return Promise.resolve();
+    }
 }

packages/core/services/FileService/HttpFileService/index.ts

@@ -1,9 +1,15 @@
 import { compact, join, uniqueId } from "lodash";
 
-import FileService, { GetFilesRequest, SelectionAggregationResult, Selection } from "..";
+import FileService, {
+    GetFilesRequest,
+    SelectionAggregationResult,
+    Selection,
+    AnnotationNameToValuesMap,
+} from "..";
 import FileDownloadService, { DownloadResult } from "../../FileDownloadService";
 import FileDownloadServiceNoop from "../../FileDownloadService/FileDownloadServiceNoop";
 import HttpServiceBase, { ConnectionConfig } from "../../HttpServiceBase";
+import Annotation from "../../../entity/Annotation";
 import FileSelection from "../../../entity/FileSelection";
 import FileSet from "../../../entity/FileSet";
 import FileDetail, { FmsFile } from "../../../entity/FileDetail";
@@ -24,6 +30,7 @@ export default class HttpFileService extends HttpServiceBase implements FileServ
     private static readonly ENDPOINT_VERSION = "3.0";
     public static readonly BASE_FILES_URL = `file-explorer-service/${HttpFileService.ENDPOINT_VERSION}/files`;
     public static readonly BASE_FILE_COUNT_URL = `${HttpFileService.BASE_FILES_URL}/count`;
+    public static readonly BASE_FILE_EDIT_URL = `metadata-management-service/1.0/filemetadata`;
     public static readonly BASE_FILE_CACHE_URL = `fss2/${HttpFileService.CACHE_ENDPOINT_VERSION}/file/cache`;
     public static readonly SELECTION_AGGREGATE_URL = `${HttpFileService.BASE_FILES_URL}/selection/aggregate`;
     private static readonly CSV_ENDPOINT_VERSION = "2.0";
@@ -132,6 +139,25 @@ export default class HttpFileService extends HttpServiceBase implements FileServ
         );
     }
 
+    public async editFile(
+        fileId: string,
+        annotationNameToValuesMap: AnnotationNameToValuesMap,
+        annotationNameToAnnotationMap?: Record<string, Annotation>
+    ): Promise<void> {
+        const requestUrl = `${this.metadataManagementServiceBaseURl}/${HttpFileService.BASE_FILE_EDIT_URL}/${fileId}`;
+        const annotations = Object.entries(annotationNameToValuesMap).map(([name, values]) => {
+            const annotationId = annotationNameToAnnotationMap?.[name].id;
+            if (!annotationId) {
+                throw new Error(
+                    `Unable to edit file. Failed to find annotation id for annotation ${name}`
+                );
+            }
+            return { annotationId, values };
+        });
+        const requestBody = JSON.stringify({ customMetadata: { annotations } });
+        await this.put(requestUrl, requestBody);
+    }
+
     /**
      * Cache a list of files to NAS cache (VAST) by sending their IDs to FSS.
      */

packages/core/services/FileService/HttpFileService/test/HttpFileService.test.ts

@@ -2,7 +2,7 @@ import { createMockHttpClient } from "@aics/redux-utils";
 import { expect } from "chai";
 
 import HttpFileService from "..";
-import { FESBaseUrl, LoadBalancerBaseUrl } from "../../../../constants";
+import { FESBaseUrl, LoadBalancerBaseUrl, MMSBaseUrl } from "../../../../constants";
 import FileSelection from "../../../../entity/FileSelection";
 import FileSet from "../../../../entity/FileSet";
 import NumericRange from "../../../../entity/NumericRange";
@@ -11,6 +11,7 @@ import FileDownloadServiceNoop from "../../../FileDownloadService/FileDownloadSe
 describe("HttpFileService", () => {
     const fileExplorerServiceBaseUrl = FESBaseUrl.TEST;
     const loadBalancerBaseUrl = LoadBalancerBaseUrl.TEST;
+    const metadataManagementServiceBaseURl = MMSBaseUrl.TEST;
     const fileIds = ["abc123", "def456", "ghi789", "jkl012"];
     const files = fileIds.map((file_id) => ({
         file_id,
@@ -46,6 +47,34 @@ describe("HttpFileService", () => {
         });
     });
 
+    describe("editFile", () => {
+        const httpClient = createMockHttpClient([
+            {
+                when: () => true,
+                respondWith: {},
+            },
+        ]);
+
+        it("fails if unable to find id of annotation", async () => {
+            // Arrange
+            const httpFileService = new HttpFileService({
+                metadataManagementServiceBaseURl,
+                httpClient,
+                downloadService: new FileDownloadServiceNoop(),
+            });
+
+            // Act / Assert
+            try {
+                await httpFileService.editFile("file_id", { ["Color"]: ["red"] });
+                expect(false, "Expected to throw").to.be.true;
+            } catch (e) {
+                expect((e as Error).message).to.equal(
+                    "Unable to edit file. Failed to find annotation id for annotation Color"
+                );
+            }
+        });
+    });
+
     describe("getAggregateInformation", () => {
         const totalFileSize = 12424114;
         const totalFileCount = 7;

packages/core/services/FileService/index.ts

@@ -1,4 +1,6 @@
+import { AnnotationValue } from "../AnnotationService";
 import { DownloadResult } from "../FileDownloadService";
+import Annotation from "../../entity/Annotation";
 import FileDetail from "../../entity/FileDetail";
 import FileSelection from "../../entity/FileSelection";
 import FileSet from "../../entity/FileSet";
@@ -38,14 +40,23 @@ export interface Selection {
     include?: string[];
 }
 
+export interface AnnotationNameToValuesMap {
+    [name: string]: AnnotationValue[];
+}
+
 export default interface FileService {
     fileExplorerServiceBaseUrl?: string;
     download(
         annotations: string[],
         selections: Selection[],
         format: "csv" | "json" | "parquet"
     ): Promise<DownloadResult>;
-    getCountOfMatchingFiles(fileSet: FileSet): Promise<number>;
+    editFile(
+        fileId: string,
+        annotations: AnnotationNameToValuesMap,
+        annotationNameToAnnotationMap?: Record<string, Annotation>
+    ): Promise<void>;
     getAggregateInformation(fileSelection: FileSelection): Promise<SelectionAggregationResult>;
+    getCountOfMatchingFiles(fileSet: FileSet): Promise<number>;
     getFiles(request: GetFilesRequest): Promise<FileDetail[]>;
 }

packages/core/services/HttpServiceBase/index.ts

@@ -252,6 +252,30 @@ export default class HttpServiceBase {
         return new RestServiceResponse(response.data);
     }
 
+    public async put<T>(url: string, body: string): Promise<RestServiceResponse<T>> {
+        const encodedUrl = HttpServiceBase.encodeURI(url);
+        const config = { headers: { "Content-Type": "application/json" } };
+
+        let response;
+        try {
+            // if this fails, bubble up exception
+            response = await retry.execute(() => this.httpClient.put(encodedUrl, body, config));
+        } catch (err) {
+            // Specific errors about the failure from services will be in this path
+            if (axios.isAxiosError(err) && err?.response?.data?.message) {
+                throw new Error(JSON.stringify(err.response.data.message));
+            }
+            throw err;
+        }
+
+        if (response.status >= 400 || response.data === undefined) {
+            // by default axios will reject if does not satisfy: status >= 200 && status < 300
+            throw new Error(`Request for ${encodedUrl} failed`);
+        }
+
+        return new RestServiceResponse(response.data);
+    }
+
     public async patch<T>(url: string, body: string): Promise<RestServiceResponse<T>> {
         const encodedUrl = HttpServiceBase.encodeURI(url);
         const config = { headers: { "Content-Type": "application/json" } };

packages/core/state/interaction/actions.ts

@@ -4,6 +4,7 @@ import { uniqueId } from "lodash";
 import { ContextMenuItem, PositionReference } from "../../components/ContextMenu";
 import FileFilter from "../../entity/FileFilter";
 import { ModalType } from "../../components/Modal";
+import { AnnotationValue } from "../../services/AnnotationService";
 import { UserSelectedApplication } from "../../services/PersistentConfigService";
 import FileDetail from "../../entity/FileDetail";
 import { Source } from "../../entity/FileExplorerURL";
@@ -265,6 +266,32 @@ export const initializeApp = (payload: { environment: string }) => ({
     payload,
 });
 
+/**
+ * Edit the currently selected files with the given metadata
+ */
+export const EDIT_FILES = makeConstant(STATE_BRANCH_NAME, "edit-files");
+
+export interface EditFilesAction {
+    type: string;
+    payload: {
+        annotations: { [name: string]: AnnotationValue[] };
+        filters?: FileFilter[];
+    };
+}
+
+export function editFiles(
+    annotations: { [name: string]: AnnotationValue[] },
+    filters?: FileFilter[]
+): EditFilesAction {
+    return {
+        type: EDIT_FILES,
+        payload: {
+            annotations,
+            filters,
+        },
+    };
+}
+
 /**
  * PROCESS AND STATUS RELATED ENUMS, INTERFACES, ETC.
  */