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Merge branch 'dev' into 455
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@NickPhura
NickPhura authored Jan 23, 2024
2 parents 08c0f53 + b42969b commit 0d2b480
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Showing 76 changed files with 3,684 additions and 2,342 deletions.
2 changes: 1 addition & 1 deletion api/package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@
"fast-xml-parser": "~4.1.3",
"fastq": "^1.15.0",
"json-schema-traverse": "^1.0.0",
"jsonpath-plus": "~7.2.0",
"jsonpath-plus": "^8.0.0",
"jsonwebtoken": "~8.5.1",
"jwks-rsa": "~2.0.5",
"knex": "~2.4.2",
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22 changes: 15 additions & 7 deletions api/src/app.ts
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Expand Up @@ -5,9 +5,10 @@ import { OpenAPIV3 } from 'openapi-types';
import swaggerUIExperss from 'swagger-ui-express';
import { defaultPoolConfig, initDBPool } from './database/db';
import { initDBConstants } from './database/db-constants';
import { ensureHTTPError, HTTPErrorType } from './errors/http-error';
import { ensureHTTPError, HTTP400, HTTPErrorType } from './errors/http-error';
import { rootAPIDoc } from './openapi/root-api-doc';
import { authenticateRequest, authenticateRequestOptional } from './request-handlers/security/authentication';
import { scanFileForVirus } from './utils/file-utils';
import { getLogger } from './utils/logger';

const defaultLog = getLogger('app');
Expand Down Expand Up @@ -53,22 +54,29 @@ const openAPIFramework = initialize({
docsPath: '/raw-api-docs', // path to view raw openapi spec
consumesMiddleware: {
'application/json': express.json({ limit: MAX_REQ_BODY_SIZE }),
'multipart/form-data': function (req, res, next) {
'multipart/form-data': async function (req, res, next) {
const multerRequestHandler = multer({
storage: multer.memoryStorage(),
storage: multer.memoryStorage(), // TOOD change to local/PVC storage and stream file uploads to S3?
limits: { fileSize: MAX_UPLOAD_FILE_SIZE }
}).array('media', MAX_UPLOAD_NUM_FILES);

multerRequestHandler(req, res, (error?: any) => {
return multerRequestHandler(req, res, async function (error?: any) {
if (error) {
return next(error);
}

if (req.files && req.files.length) {
const promises = (req.files as Express.Multer.File[]).map(async function (file) {
// Set original request file field to empty string to satisfy OpenAPI validation
// See: https://www.npmjs.com/package/express-openapi#argsconsumesmiddleware
(req.files as Express.Multer.File[]).forEach((file) => (req.body[file.fieldname] = ''));
}
req.body[file.fieldname] = '';

// Scan file for malicious content, if enabled
if (!(await scanFileForVirus(file))) {
throw new HTTP400('Malicious file content detected.', [{ file_name: file.originalname }]);
}
});

await Promise.all(promises);

return next();
});
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2 changes: 1 addition & 1 deletion api/src/database/db-utils.ts
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Expand Up @@ -41,7 +41,7 @@ export const syncErrorWrapper =
*/
const parseError = (error: any) => {
if (error instanceof z.ZodError) {
throw new ApiExecuteSQLError('SQL response failed schema check', [error]);
throw new ApiExecuteSQLError('SQL response failed schema check', [error as Record<string, any>]);
}

if (error.message === 'CONCURRENCY_EXCEPTION') {
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2 changes: 1 addition & 1 deletion api/src/database/db.ts
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Expand Up @@ -392,7 +392,7 @@ export const getDBConnection = function (keycloakToken: object): IDBConnection {

_systemUserId = response?.rows?.[0].api_set_context;
} catch (error) {
throw new ApiExecuteSQLError('Failed to set user context', [error as object]);
throw new ApiExecuteSQLError('Failed to set user context', [error as Record<string, unknown>]);
}
};

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10 changes: 5 additions & 5 deletions api/src/errors/api-error.ts
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Expand Up @@ -6,9 +6,9 @@ export enum ApiErrorType {
}

export class ApiError extends Error {
errors?: (string | object)[];
errors?: (string | Record<string, unknown>)[];

constructor(name: ApiErrorType, message: string, errors?: (string | object)[], stack?: string) {
constructor(name: ApiErrorType, message: string, errors?: (string | Record<string, unknown>)[], stack?: string) {
super(message);

this.name = name;
Expand All @@ -33,7 +33,7 @@ export class ApiError extends Error {
* @extends {ApiError}
*/
export class ApiGeneralError extends ApiError {
constructor(message: string, errors?: (string | object)[]) {
constructor(message: string, errors?: (string | Record<string, unknown>)[]) {
super(ApiErrorType.GENERAL, message, errors);
}
}
Expand All @@ -46,7 +46,7 @@ export class ApiGeneralError extends ApiError {
* @extends {ApiError}
*/
export class ApiUnknownError extends ApiError {
constructor(message: string, errors?: (string | object)[]) {
constructor(message: string, errors?: (string | Record<string, unknown>)[]) {
super(ApiErrorType.UNKNOWN, message, errors);
}
}
Expand All @@ -63,7 +63,7 @@ export class ApiUnknownError extends ApiError {
* @extends {ApiError}
*/
export class ApiExecuteSQLError extends ApiError {
constructor(message: string, errors?: (string | object)[]) {
constructor(message: string, errors?: (string | Record<string, unknown>)[]) {
super(ApiErrorType.EXECUTE_SQL, message, errors);
}
}
22 changes: 14 additions & 8 deletions api/src/errors/http-error.ts
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Expand Up @@ -11,9 +11,15 @@ export enum HTTPErrorType {

export class HTTPError extends Error {
status: number;
errors?: (string | object)[];

constructor(name: HTTPErrorType, status: number, message: string, errors?: (string | object)[], stack?: string) {
errors?: (string | Record<string, unknown>)[];

constructor(
name: HTTPErrorType,
status: number,
message: string,
errors?: (string | Record<string, unknown>)[],
stack?: string
) {
super(message);

this.name = name;
Expand All @@ -38,7 +44,7 @@ export class HTTPError extends Error {
* @extends {HTTPError}
*/
export class HTTP400 extends HTTPError {
constructor(message: string, errors?: (string | object)[]) {
constructor(message: string, errors?: (string | Record<string, unknown>)[]) {
super(HTTPErrorType.BAD_REQUEST, 400, message, errors);
}
}
Expand All @@ -51,7 +57,7 @@ export class HTTP400 extends HTTPError {
* @extends {HTTPError}
*/
export class HTTP401 extends HTTPError {
constructor(message: string, errors?: (string | object)[]) {
constructor(message: string, errors?: (string | Record<string, unknown>)[]) {
super(HTTPErrorType.UNAUTHORIZE, 401, message, errors);
}
}
Expand All @@ -64,7 +70,7 @@ export class HTTP401 extends HTTPError {
* @extends {HTTPError}
*/
export class HTTP403 extends HTTPError {
constructor(message: string, errors?: (string | object)[]) {
constructor(message: string, errors?: (string | Record<string, unknown>)[]) {
super(HTTPErrorType.FORBIDDEN, 403, message, errors);
}
}
Expand All @@ -77,7 +83,7 @@ export class HTTP403 extends HTTPError {
* @extends {HTTPError}
*/
export class HTTP409 extends HTTPError {
constructor(message: string, errors?: (string | object)[]) {
constructor(message: string, errors?: (string | Record<string, unknown>)[]) {
super(HTTPErrorType.CONFLICT, 409, message, errors);
}
}
Expand All @@ -90,7 +96,7 @@ export class HTTP409 extends HTTPError {
* @extends {HTTPError}
*/
export class HTTP500 extends HTTPError {
constructor(message: string, errors?: (string | object)[]) {
constructor(message: string, errors?: (string | Record<string, unknown>)[]) {
super(HTTPErrorType.INTERNAL_SERVER_ERROR, 500, message, errors);
}
}
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51 changes: 15 additions & 36 deletions api/src/openapi/root-api-doc.ts
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Expand Up @@ -143,60 +143,39 @@ export const rootAPIDoc = {
},
SubmissionFeature: {
title: 'BioHub Data Submission Feature',
description:
'The submission feature object is a self-referencing recursive structure designed to support different classes of biotic data, in a hierarchical structure.',
type: 'object',
required: ['id', 'type', 'properties', 'features'],
required: ['type', 'properties', 'child_features'],
properties: {
id: {
title: 'Unique id of the feature',
type: 'string'
title: 'Unique identifer.',
description:
'The unique identifier for the submission feature as supplied by the source system. May not be unique globally or within BioHub.',
type: 'string',
maxLength: 200
},
type: {
title: 'Feature type',
title: 'Feature type.',
description: 'The type of the feature. Must match a supported feature type.',
type: 'string'
},
properties: {
title: 'Feature properties',
title: 'Feature properties.',
description: 'The properties of the feature, which are specific to the feature type.',
type: 'object',
properties: {}
},
features: {
title: 'Feature child features',
child_features: {
title: 'Child features.',
description: 'Child features of the current feature.',
type: 'array',
items: {
$ref: '#/components/schemas/SubmissionFeature'
}
}
},
additionalProperties: false
},
feature: {
type: 'object',
required: ['submission_feature_id', 'submission_id', 'feature_type', 'data', 'parent_submission_feature_id'],
properties: {
submission_feature_id: {
type: 'number'
},
submission_id: {
type: 'number'
},
feature_type: {
type: 'string'
},
data: {
type: 'object'
},
submission_feature_security_ids: {
nullable: true,
type: 'array',
items: {
type: 'number'
}
},
parent_submission_feature_id: {
type: 'number',
nullable: true
}
}
}
}
}
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27 changes: 0 additions & 27 deletions api/src/openapi/schemas/biohub-data-submission.ts
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This file was deleted.

6 changes: 4 additions & 2 deletions api/src/paths/administrative/security/categories.ts
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Expand Up @@ -80,13 +80,15 @@ GET.apiDoc = {
nullable: true
},
update_user: {
type: 'string',
type: 'integer',
minimum: 1,
nullable: true
},
revision_count: {
type: 'integer'
}
}
},
additionalProperties: false
}
}
}
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8 changes: 7 additions & 1 deletion api/src/paths/administrative/security/rules.ts
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Expand Up @@ -46,6 +46,7 @@ GET.apiDoc = {
'description',
'record_effective_date',
'record_end_date',
'security_category_id',
'category_name',
'category_description',
'category_record_effective_date',
Expand All @@ -68,6 +69,10 @@ GET.apiDoc = {
type: 'string',
nullable: true
},
security_category_id: {
type: 'integer',
minimum: 1
},
category_name: {
type: 'string'
},
Expand All @@ -81,7 +86,8 @@ GET.apiDoc = {
type: 'string',
nullable: true
}
}
},
additionalProperties: false
}
}
}
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52 changes: 47 additions & 5 deletions api/src/paths/administrative/security/submission/{submissionId}.ts
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Expand Up @@ -51,18 +51,60 @@ GET.apiDoc = {
type: 'array',
items: {
type: 'object',
required: ['submission_feature_security_id', 'submission_feature_id', 'security_rule_id'],
required: [
'submission_feature_security_id',
'submission_feature_id',
'security_rule_id',
'record_effective_date',
'record_end_date',
'create_date',
'create_user',
'update_date',
'update_user',
'revision_count'
],
properties: {
submission_feature_security_id: {
type: 'integer'
type: 'integer',
minimum: 1
},
submission_feature_id: {
type: 'integer'
type: 'integer',
minimum: 1
},
security_rule_id: {
type: 'integer'
type: 'integer',
minimum: 1
},
record_effective_date: {
type: 'string'
},
record_end_date: {
type: 'string',
nullable: true
},
create_date: {
type: 'string'
},
create_user: {
type: 'integer',
minimum: 1
},
update_date: {
type: 'string',
nullable: true
},
update_user: {
type: 'integer',
minimum: 1,
nullable: true
},
revision_count: {
type: 'integer',
minimum: 0
}
}
},
additionalProperties: false
}
}
}
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