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Feat/add properties #2609

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Feat/add properties #2609

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62e7db8
fix: Fix the permission issue and the ui with widescreen resolution
wsy19961129 Oct 7, 2024
cd13c11
feat: Allow adding metadata of uploading data
wsy19961129 Oct 22, 2024
23a0539
chore: Update dependencies
fguitton Oct 14, 2024
19af50c
perf: Boost the performance of uploading large files
wsy19961129 Oct 29, 2024
a993693
fix: Fix lint
wsy19961129 Oct 29, 2024
d5e6403
feat: Remove button
YFMao15 Oct 30, 2024
3de3662
feat: Remove cloud pattern
YFMao15 Oct 30, 2024
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8 changes: 4 additions & 4 deletions jest.config.ts
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
import { getJestProjects } from '@nx/jest';
import { getJestProjectsAsync } from '@nx/jest';

export default {
projects: getJestProjects()
};
export default async () => ({
projects: await getJestProjectsAsync()
});
83 changes: 43 additions & 40 deletions package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -28,23 +28,25 @@
"format-fix": "nx format --all"
},
"devDependencies": {
"@babel/core": "^7.25.2",
"@babel/preset-react": "^7.24.7",
"@nx/esbuild": "19.8.0",
"@nx/eslint": "19.8.0",
"@nx/eslint-plugin": "19.8.0",
"@nx/express": "19.8.0",
"@nx/jest": "19.8.0",
"@nx/js": "19.8.0",
"@nx/node": "19.8.0",
"@nx/react": "19.8.0",
"@nx/web": "19.8.0",
"@nx/webpack": "19.8.0",
"@nx/workspace": "19.8.0",
"@babel/core": "^7.25.8",
"@babel/preset-react": "^7.25.7",
"@commitlint/config-conventional": "^18.6.3",
"@commitlint/config-nx-scopes": "^18.6.1",
"@nx/esbuild": "20.0.0",
"@nx/eslint": "20.0.0",
"@nx/eslint-plugin": "20.0.0",
"@nx/express": "20.0.0",
"@nx/jest": "20.0.0",
"@nx/js": "20.0.0",
"@nx/node": "20.0.0",
"@nx/react": "20.0.0",
"@nx/web": "20.0.0",
"@nx/webpack": "20.0.0",
"@nx/workspace": "20.0.0",
"@pmmmwh/react-refresh-webpack-plugin": "^0.5.15",
"@svgr/webpack": "8.1.0",
"@swc/cli": "0.4.0",
"@swc/core": "1.7.26",
"@swc/core": "1.7.35",
"@swc/jest": "0.2.36",
"@testing-library/react": "16.0.1",
"@types/bcrypt": "5.0.2",
Expand All @@ -56,52 +58,52 @@
"@types/jest": "29.5.13",
"@types/json2csv": "5.0.7",
"@types/jsonwebtoken": "9.0.7",
"@types/node": "^22.5.5",
"@types/node": "^22.7.5",
"@types/nodemailer": "6.4.16",
"@types/passport": "1.0.16",
"@types/qrcode": "1.5.5",
"@types/react": "18.3.8",
"@types/react-dom": "18.3.0",
"@types/react": "18.3.11",
"@types/react-dom": "18.3.1",
"@types/react-highlight-words": "0.20.0",
"@types/supertest": "6.0.2",
"@types/tmp": "0.2.6",
"@types/uuid": "10.0.0",
"@types/webpack-env": "1.18.5",
"@typescript-eslint/eslint-plugin": "8.6.0",
"@typescript-eslint/parser": "8.6.0",
"@typescript-eslint/eslint-plugin": "8.8.1",
"@typescript-eslint/parser": "8.8.1",
"commitlint": "^18.6.1",
"esbuild": "^0.24.0",
"eslint": "8.57.1",
"eslint-config-prettier": "9.1.0",
"eslint-plugin-import": "2.30.0",
"eslint-plugin-import": "2.31.0",
"eslint-plugin-jsonc": "2.16.0",
"eslint-plugin-jsx-a11y": "6.10.0",
"eslint-plugin-react": "7.36.1",
"eslint-plugin-react-hooks": "4.6.2",
"eslint-plugin-react": "7.37.1",
"eslint-plugin-react-hooks": "5.0.0",
"get-port": "7.1.0",
"git-rev-sync": "3.0.2",
"husky": "^9.1.6",
"jest": "29.7.0",
"jest-environment-jsdom": "29.7.0",
"mongodb-memory-server": "10.0.1",
"nx": "19.8.0",
"mongodb-memory-server": "10.1.2",
"nx": "20.0.0",
"prettier": "^3.3.3",
"react-refresh": "^0.14.2",
"supertest": "7.0.0",
"swc-loader": "0.2.6",
"ts-essentials": "10.0.2",
"ts-jest": "29.2.5",
"ts-node": "10.9.2",
"typescript": "5.6.2",
"typescript": "5.6.3",
"url-loader": "^4.1.1",
"webpack": "^5.94.0",
"webpack": "^5.95.0",
"webpack-merge": "^6.0.1"
},
"dependencies": {
"@ant-design/icons": "5.5.1",
"@apollo/client": "3.11.8",
"@apollo/server": "4.11.0",
"@commitlint/config-conventional": "^18.6.3",
"@commitlint/config-nx-scopes": "^18.6.1",
"@ideafast/idgen": "0.1.1",
"@ideafast/idgen": "0.2.1",
"@simplewebauthn/browser": "^10.0.0",
"@simplewebauthn/server": "^10.0.1",
"@nivo/calendar": "0.87.0",
Expand All @@ -116,24 +118,22 @@
"@trpc/react-query": "10.45.2",
"@trpc/server": "10.45.2",
"JSONStream": "1.3.5",
"antd": "5.21.0",
"antd": "5.21.4",
"antd-img-crop": "4.23.0",
"apollo-upload-client": "18.0.1",
"axios": "1.7.7",
"bcrypt": "5.1.1",
"commitlint": "^18.6.1",
"connect-mongo": "5.1.0",
"connect-timeout": "1.9.0",
"core-js": "^3.38.1",
"cors": "2.8.5",
"csv-parse": "5.5.6",
"dayjs": "1.11.13",
"deepmerge": "4.3.1",
"esbuild": "^0.24.0",
"export-from-json": "1.7.4",
"express": "^4.21.0",
"express-rate-limit": "7.4.0",
"express-session": "1.18.0",
"express": "^4.21.1",
"express-rate-limit": "7.4.1",
"express-session": "1.18.1",
"fs-extra": "11.2.0",
"graphql": "16.9.0",
"graphql-scalars": "1.23.0",
Expand All @@ -143,7 +143,7 @@
"graphql-upload-minimal": "1.6.1",
"graphql-ws": "5.16.0",
"hi-base32": "0.5.1",
"http-proxy-middleware": "3.0.2",
"http-proxy-middleware": "3.0.3",
"https-browserify": "1.0.0",
"json-bigint-patch": "0.0.8",
"jsonwebtoken": "9.0.2",
Expand All @@ -158,14 +158,14 @@
"passport": "0.7.0",
"path-browserify": "1.0.1",
"qrcode": "1.5.4",
"rc-picker": "4.6.14",
"rc-picker": "4.6.15",
"react": "18.3.1",
"react-csv": "2.2.2",
"react-dom": "18.3.1",
"react-dropzone": "14.2.3",
"react-dropzone": "14.2.9",
"react-helmet-async": "2.0.5",
"react-highlight-words": "0.20.0",
"react-router-dom": "6.26.2",
"react-router-dom": "6.27.0",
"react-spinners": "0.14.1",
"regenerator-runtime": "0.14.1",
"sanitize-filename": "1.6.3",
Expand All @@ -183,9 +183,12 @@
"**/@jest/create-cache-key-function": "^29",
"**/@jest/reporters": "^29",
"**/@jest/test-result": "^29",
"**/@types/express": "^4",
"**/@types/express-serve-static-core": "^4",
"**/dicer": "^0.3.1",
"**/jest-config": "^29",
"**/jest-resolve": "^29",
"**/jest-util": "^29",
"**/pretty-format": "^29"
}
}
}
2 changes: 1 addition & 1 deletion packages/itmat-apis/src/graphql/resolvers/userResolvers.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ export class UserResolvers {

async validateResetPassword(_parent, args: { token: string, encryptedEmail: string }) {
try {
return await this.userCore.validateResetPassword(args.token, args.encryptedEmail);
return await this.userCore.validateResetPassword(args.encryptedEmail, args.token);
} catch (e) {
return GraphQLErrorDecroator(e as CoreError);
}
Expand Down
8 changes: 5 additions & 3 deletions packages/itmat-apis/src/trpc/dataProcedure.ts
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Expand Up @@ -41,7 +41,8 @@ const CreateFieldInputSchema = z.object({
unit: z.optional(z.string()),
comments: z.optional(z.string()),
verifier: z.optional(z.array(z.array(ZValueVerifier))),
properties: z.optional(z.array(ZFieldProperty))
properties: z.optional(z.array(ZFieldProperty)),
metadata: z.optional(z.record(z.string(), z.unknown()))
});

const EditFieldInputSchema = CreateFieldInputSchema;
Expand Down Expand Up @@ -108,7 +109,8 @@ export class DataRouter {
unit: opts.input.unit,
comments: opts.input.comments,
verifier: opts.input.verifier,
properties: opts.input.properties
properties: opts.input.properties,
metadata: opts.input.metadata
});
}),
/**
Expand Down Expand Up @@ -288,7 +290,7 @@ export class DataRouter {
*/
getFiles: this.baseProcedure.input(z.object({
studyId: z.string(),
versionId: z.optional(z.string()),
versionId: z.optional(z.union([z.string(), z.null(), z.array(z.union([z.string(), z.null()]))])),
fieldIds: z.optional(z.array(z.string())),
readable: z.optional(z.boolean()),
useCache: z.optional(z.boolean()),
Expand Down
60 changes: 57 additions & 3 deletions packages/itmat-cores/src/coreFunc/dataCore.ts
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Expand Up @@ -43,6 +43,7 @@ interface CreateFieldInput {
comments?: string;
verifier?: ValueVerifierInput[][];
properties?: IFieldProperty[];
metadata?: Record<string, unknown>;
}

type EditFieldInput = CreateFieldInput;
Expand Down Expand Up @@ -255,7 +256,7 @@ export class DataCore {
deletedTime: null,
deletedUser: null
},
metadata: {}
metadata: fieldInput.metadata ?? {}
};

await this.db.collections.field_dictionary_collection.insertOne(fieldEntry);
Expand Down Expand Up @@ -1301,16 +1302,19 @@ export class DataCore {
permissionArr.push(obj);
}
if (permissionArr.length === 0) {
return [];
continue;
}
roleArr.push({ $or: permissionArr });
}

if (roleArr.length === 0) {
return [];
}

const availableFields = (await this.getStudyFields(requester, studyId, dataVersions)).reduce((a, c) => {
a[c.fieldId] = c;
return a;
}, {});

const availableFieldIds = Object.keys(availableFields);
const refactoredFieldIds = fieldIds ?? Object.keys(availableFields);
const queryField = async (fieldId: string) => {
Expand Down Expand Up @@ -1340,6 +1344,10 @@ export class DataCore {
}
}, {
$replaceRoot: { newRoot: '$latestDocument' }
}, {
$match: {
'life.deletedTime': null
}
}, {
$project: {
_id: 0, // Exclude the _id field
Expand Down Expand Up @@ -1536,6 +1544,52 @@ export class DataCore {
}
}

public async uploadFileDataWithFileEntry(requester: IUserWithoutToken | undefined, studyId: string, fieldId: string, fileEntry: IFile, properties?: string) {
if (!requester) {
throw new CoreError(
enumCoreErrors.NOT_LOGGED_IN,
enumCoreErrors.NOT_LOGGED_IN
);
}
const roles = await this.permissionCore.getRolesOfUser(requester, requester.id, studyId);
if (roles.length === 0) {
throw new CoreError(
enumCoreErrors.NO_PERMISSION_ERROR,
enumCoreErrors.NO_PERMISSION_ERROR
);
}
const study = await this.db.collections.studies_collection.findOne({ 'id': studyId, 'life.deletedTime': null });
if (!study) {
throw new CoreError(
enumCoreErrors.CLIENT_ACTION_ON_NON_EXISTENT_ENTRY,
'Study does not exist.'
);
}
try {
const parsedProperties = properties ? JSON.parse(properties) : {};
const dataInput: IDataInput[] = [{
fieldId: fieldId,
value: fileEntry.id,
properties: parsedProperties
}];
const res = await this.uploadData(requester, studyId, dataInput);
if (!res[0].successful) {
throw new CoreError(
enumCoreErrors.CLIENT_MALFORMED_INPUT,
res[0].description ?? 'Failed to upload file.'
);
}
// invalidate the cache
await this.db.collections.cache_collection.updateMany({ 'keys.studyId': studyId, 'keys.query': 'getStudyFiles' }, { $set: { status: enumCacheStatus.OUTDATED } });
return fileEntry;
} catch (error) {
throw new CoreError(
enumCoreErrors.CLIENT_MALFORMED_INPUT,
`${(error as Error).message}`
);
}
}

/**
* Get the summary of a study.
* Admins can study managers can access this function.
Expand Down
26 changes: 12 additions & 14 deletions packages/itmat-cores/src/coreFunc/permissionCore.ts
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Expand Up @@ -95,35 +95,33 @@ export class PermissionCore {
*/
public async checkFieldOrDataPermission(user: IUserWithoutToken, studyId: string, entry: Partial<IField> | Partial<IData>, permission: enumDataAtomicPermissions) {
const roles = await this.getRolesOfUser(user, user.id, studyId);
let tag = true;
const tags: boolean[] = [];
for (const role of roles) {
let tag = true;
const dataPermissions = role.dataPermissions;
for (const dataPermission of dataPermissions) {
for (const field of dataPermission.fields) {
if (!(new RegExp(field).test(String(entry.fieldId)))) {
tag = false;
}
if (dataPermission.fields.every(field => !(new RegExp(field).test(String(entry.fieldId))))) {
tag = false;
}
if ('value' in entry && dataPermission.dataProperties) {
if (entry.properties) {
for (const property in dataPermission.dataProperties) {
for (const prop of dataPermission.dataProperties[property]) {
if (!(new RegExp(prop).test(String(entry.properties[property])))) {
tag = false;
}
if (dataPermission.dataProperties[property].every(prop => !(new RegExp(prop).test(String(entry.properties?.[property]))))) {
tag = false;
}
}
}
}
if (!permissionString[permission].includes(dataPermission.permission)) {
tag = false;
}
if (tag) {
return true;
}
}
tags.push(tag);
}
if (tags.every(tag => tag === false)) {
return false;
}
return false;
return true;
}

/**
Expand Down Expand Up @@ -269,4 +267,4 @@ export class PermissionCore {

return makeGenericResponse(roleId, true, undefined, 'Role deleted successfully.');
}
}
}
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