A more flexible file model + data file upload

.gitignore

@@ -93,4 +93,6 @@ kubernetes/*.yaml
 itmat-client-old/
 .idea/
 
-target
+target
+
+note

NOTE_CHON

@@ -0,0 +1,9 @@
+fileDownload
+
+fileResolvers
+
+studyResolvers
+
+demoStudy
+
+uploadfiletsx

lerna.json

@@ -5,4 +5,4 @@
     "version": "independent",
     "useWorkspaces": true,
     "npmClient": "yarn"
-}
+}

package.json

@@ -48,6 +48,7 @@
         "eslint-plugin-react": "7.20.3",
         "eslint-plugin-react-hooks": "4.0.8",
         "husky": "4.2.5",
+        "start-server-and-test": "1.11.0",
         "jest-environment-node": "26.1.0",
         "lerna": "3.22.1",
         "typescript": "3.9.7"

packages/itmat-commons/package.json

@@ -20,9 +20,10 @@
         "prepublishOnly": "yarn run build"
     },
     "dependencies": {
-        "graphql": "14.7.0",
+        "graphql": "15.0.0",
         "graphql-tag": "2.10.4",
-        "minio": "7.0.16"
+        "minio": "7.0.16",
+        "uuid": "8.1.0"
     },
     "devDependencies": {
         "@types/express": "4.17.7",

packages/itmat-commons/src/graphql/files.ts

@@ -1,17 +1,46 @@
 import gql from 'graphql-tag';
 
+const file_fragment_without_children = gql`
+    fragment FILE_WITHOUT_CHILDREN on File {
+        id
+        fileName
+        studyId
+        projectId
+        fileType
+        fileSize
+        content
+        description
+        uploadedBy
+        userId
+        dataVersionId
+        patientId
+    }
+`;
+
+// export const CREATE_FILE = gql`
+//     mutation createFile(
+//         $fileName: String!,
+//         $fileType: FileType,
+//         $studyId: String
+//     ) {
+//         createFile(
+//             fileName: $fileName,
+//             fileType: $fileType,
+//             studyId: $studyId
+//         ) {
+//             ...FILE_WITHOUT_CHILDREN
+//         }
+//     }
+//     ${file_fragment_without_children}
+// `;
+
 export const UPLOAD_FILE = gql`
-    mutation uploadFile($studyId: String!, $file: Upload!, $description: String!, $fileLength: Int) {
-        uploadFile(studyId: $studyId, description: $description, file: $file, fileLength: $fileLength) {
-            id
-            fileName
-            studyId
-            projectId
-            fileSize
-            description
-            uploadedBy
+    mutation uploadFile($studyId: String!, $file: Upload!, $description: String, $fileLength: Int, $fileType: FileType) {
+        uploadFile(studyId: $studyId, description: $description, file: $file, fileLength: $fileLength, fileType: $fileType) {
+            ...FILE_WITHOUT_CHILDREN 
         }
     }
+    ${file_fragment_without_children}
 `;
 
 export const DELETE_FILE = gql`
@@ -21,3 +50,42 @@ export const DELETE_FILE = gql`
         }
     }
 `;
+
+// export const GET_FILE_WITHOUT_CHILDREN = gql`
+//     query getFileWithoutChildren($fileId: String!) {
+//         getFile(fileId: $fileId) {
+//             ...FILE_WITHOUT_CHILDREN
+//         }
+//     }
+//     ${file_fragment_without_children}
+// `;
+
+// export const GET_FILE_WITH_CHILDREN = gql`
+//     query getFileWithChildren($fileId: String!) {
+//         getFile(fileId: $fileId) {
+//             childFiles {
+//                 ...FILE_WITHOUT_CHILDREN
+//             }
+//             ...FILE_WITHOUT_CHILDREN
+//         }
+//     }
+//     ${file_fragment_without_children}
+// `;
+
+// export const FETCH_CHILD_FILES = gql`
+//     query fetchChildFiles($dirFileId: String!) {
+//         getFile(fileId: $dirFileId) {
+//             id
+//             childFiles {
+//                 ...FILE_WITHOUT_CHILDREN
+//             }
+//         }
+//     }
+//     ${file_fragment_without_children}
+// `;
+
+// export const CREATE_JOB_FOR_UNZIPPING_FILE = gql`
+//     mutation createJobForUnzippingFile($fileId: String!) {
+//         successful
+//     }
+// `;

packages/itmat-commons/src/graphql/study.ts

@@ -37,7 +37,7 @@ export const GET_STUDY = gql`
                     username
                 }
             }
-            files {
+            files {  # TO_DO: remove in future PR
                 id
                 fileName
                 studyId
@@ -47,6 +47,7 @@ export const GET_STUDY = gql`
                 uploadedBy
             }
             numOfSubjects
+            rootDir
             currentDataVersion
             dataVersions {
                 id

packages/itmat-commons/src/graphql/user.ts

@@ -28,12 +28,12 @@ export const user_fragment = gql`
 `;
 
 export const LOGIN = gql`
-mutation login($username: String!, $password: String!, $totp: String!) {
-  login(username: $username, password: $password, totp: $totp) {
-      ...ALL_FOR_USER
-  }
-}
-${user_fragment}
+    mutation login($username: String!, $password: String!, $totp: String!) {
+        login(username: $username, password: $password, totp: $totp) {
+            ...ALL_FOR_USER
+        }
+    }
+    ${user_fragment}
 `;
 
 export const WHO_AM_I = gql`

packages/itmat-commons/src/models/file/abstract/DirectoryNode.ts

@@ -0,0 +1,103 @@
+import { FileNode } from './FileNode';
+import { fileTypes, fileTypesDirs } from './fileTypes';
+import { IFileMongoEntry } from './mongoEntry';
+import { Collection, FindAndModifyWriteOpResultObject } from 'mongodb';
+
+export class DirectoryNode extends FileNode {
+    private _childFileIds: string[];
+    private _isRoot: boolean;
+
+    constructor(
+        {
+            id,
+            fileName,
+            fileType,
+            uploadedBy,
+            deleted,
+            isRoot = false,
+            childFileIds = []
+        }: {
+            id?: string,
+            fileName: string,
+            fileType: fileTypes,
+            uploadedBy: string,
+            deleted?: number | null,
+            isRoot?: boolean,
+            childFileIds?: string[]
+        }
+    ) {
+        super({ id, fileName, fileType, uploadedBy, deleted });
+        if (!fileTypesDirs.includes(fileType)) {
+            throw new Error(`Cannot instantiate Directory with filetype ${fileType}`);
+        }
+        this._childFileIds = childFileIds;
+        this._isRoot = isRoot;
+    }
+
+    // static validateInstance(entry: IFileMongoEntry): boolean {
+
+    // }
+
+    static makeFromMongoEntry(entry: IFileMongoEntry): DirectoryNode {
+        const { id, fileName, fileType, uploadedBy, deleted, isRoot, childFileIds } = entry;
+        if (!fileTypesDirs.includes(fileType)) {
+            throw new Error('Cannot instantiate FileNode with entry: wrong type.');
+        }
+        if (
+            id === undefined ||
+            fileName === undefined ||
+            fileType === undefined ||
+            uploadedBy === undefined ||
+            deleted === undefined ||
+            isRoot === undefined  ||
+            childFileIds === undefined
+        ) {
+            throw new Error('Cannot instantiate FileNode with entry: missing key.');
+        }
+        return new DirectoryNode({ id, fileName, fileType, uploadedBy, deleted, isRoot, childFileIds });
+    }
+
+    // @override
+    serialiseToMongoObj(): IFileMongoEntry {
+        return ({
+            id: this.id,
+            fileName: this.fileName,
+            studyId: undefined,
+            projectId: undefined,
+            fileType: this.fileType,
+            fileSize: undefined,
+            content: undefined,
+            description: undefined,
+            uploadedBy: this.uploadedBy,
+            isRoot: this._isRoot,
+            patientId: undefined,
+            dataVersionId: undefined,
+            childFileIds: this._childFileIds,
+            deleted: this.deleted
+        });
+    }
+
+
+    // addChildNodeAndUpdateMongo(collection: Collection, file: FileNode): Promise<FindAndModifyWriteOpResultObject<IFileMongoEntry>>{
+    //     // TO_DO
+    //     // this.childFileIds
+    // }
+
+    // @override
+    deleteFileOnMongo(collection: Collection): Promise<FindAndModifyWriteOpResultObject<IFileMongoEntry>> {
+        if (this._isRoot === true) {
+            throw new Error('Cannot delete root directory');
+        }
+        return super.deleteFileOnMongo(collection);
+    }
+
+    get isRoot() { return this._isRoot; }
+    protected get childFileIds() { return this._childFileIds; }
+
+    protected setChildFileIds(value: string[]) { this._childFileIds = value; }
+
+    getChildFiles(collection: Collection): Promise<IFileMongoEntry[]> {
+        return collection.find({ deleted: null, id: { $in: this._childFileIds } }).toArray();
+    }
+
+}

packages/itmat-commons/src/models/file/abstract/FileNode.ts

@@ -0,0 +1,85 @@
+import { v4 as uuid } from 'uuid';
+import { fileTypes } from './fileTypes';
+import { IFileMongoEntry } from './mongoEntry';
+import { Collection, FindAndModifyWriteOpResultObject, InsertOneWriteOpResult, ObjectID } from 'mongodb';
+
+export class FileNode {
+    private readonly _id;
+    private _fileName: string;
+    private readonly _fileType: fileTypes;
+    private readonly _uploadedBy: string;
+    private _deleted: number | null;
+
+    constructor(
+        {
+            id = uuid(),
+            fileName,
+            fileType,
+            uploadedBy,
+            deleted = null
+        }: {
+            id?: string,
+            fileName: string,
+            fileType: fileTypes,
+            uploadedBy: string,
+            deleted?: number | null
+        }
+    ) {
+        this._id = id;
+        this._fileName = fileName;
+        this._fileType = fileType;
+        this._uploadedBy = uploadedBy;
+        this._deleted = deleted;
+    }
+
+    static makeFromMongoEntry(entry: IFileMongoEntry): FileNode {
+        const { id, fileName, fileType, uploadedBy, deleted } = entry;
+        if (
+            id === undefined ||
+            fileName === undefined ||
+            fileType === undefined ||
+            uploadedBy === undefined ||
+            deleted === undefined
+        ) {
+            throw new Error('Cannot instantiate FileNode with entry: missing key.');
+        }
+        return new FileNode({ id, fileName, fileType, uploadedBy, deleted });
+    }
+
+    serialiseToMongoObj(): IFileMongoEntry {
+        return ({
+            id: this._id,
+            fileName: this._fileName,
+            studyId: undefined,
+            projectId: undefined,
+            fileType: this._fileType,
+            fileSize: undefined,
+            description: undefined,
+            content: undefined,
+            uploadedBy: this._uploadedBy,
+            isRoot: undefined,
+            patientId: undefined,
+            dataVersionId: undefined,
+            childFileIds: undefined,
+            deleted: this._deleted
+        });
+    }
+
+    static getFileFromMongo(fileCollection: Collection, query: { id?: string, fileName?: string }): Promise<IFileMongoEntry | null> {
+        return fileCollection.findOne({ ...query, deleted: null });
+    }
+
+    deleteFileOnMongo(fileCollection: Collection): Promise<FindAndModifyWriteOpResultObject<IFileMongoEntry>> {
+        return fileCollection.findOneAndUpdate({ id: this._id, deleted: null, isRoot: { $ne: true } }, { deleted: new Date().valueOf() });
+    }
+
+    uploadFileToMongo(fileCollection: Collection): Promise<InsertOneWriteOpResult<IFileMongoEntry & { _id: ObjectID } >> {
+        return fileCollection.insertOne(this.serialiseToMongoObj());
+    }
+
+    get id() { return this._id; }
+    get fileName() { return this._fileName; }
+    get fileType() { return this._fileType; }
+    get uploadedBy() { return this._uploadedBy; }
+    get deleted() { return this._deleted; }
+}

packages/itmat-commons/src/models/file/abstract/IStudyFileNode.ts

@@ -0,0 +1,3 @@
+export interface IStudyFileNode {
+    readonly studyId: string;
+}

packages/itmat-commons/src/models/file/abstract/IUserPersonalFileNode.ts

@@ -0,0 +1,3 @@
+export interface IUserPersonalFileNode {
+    readonly userId: string;
+}