BHBC-1962-1963: Validation refactoring and error handling

api/src/app.ts

@@ -4,7 +4,7 @@ import multer from 'multer';
 import { OpenAPIV3 } from 'openapi-types';
 import swaggerUIExperss from 'swagger-ui-express';
 import { defaultPoolConfig, initDBPool } from './database/db';
-import { ensureHTTPError, HTTPErrorType } from './errors/custom-error';
+import { ensureHTTPError, HTTPErrorType } from './errors/http-error';
 import { rootAPIDoc } from './openapi/root-api-doc';
 import { authenticateRequest } from './request-handlers/security/authentication';
 import { getLogger } from './utils/logger';
@@ -88,6 +88,11 @@ const openAPIFramework = initialize({
   // If `next` is not included express will silently skip calling the `errorMiddleware` entirely.
   // eslint-disable-next-line @typescript-eslint/no-unused-vars
   errorMiddleware: function (error, req, res, next) {
+    if (res.headersSent) {
+      // response has already been sent
+      return;
+    }
+
     // Ensure all errors (intentionally thrown or not) are in the same format as specified by the schema
     const httpError = ensureHTTPError(error);
 

api/src/constants/database.ts

@@ -7,7 +7,8 @@
 export enum SYSTEM_IDENTITY_SOURCE {
   DATABASE = 'DATABASE',
   IDIR = 'IDIR',
-  BCEID = 'BCEID'
+  BCEID = 'BCEID',
+  SYSTEM = 'SYSTEM'
 }
 
 export enum SCHEMAS {

api/src/constants/status.ts

@@ -27,5 +27,43 @@ export enum SUBMISSION_STATUS_TYPE {
   'AWAITING CURRATION' = 'Awaiting Curration',
   'REJECTED' = 'Rejected',
   'ON HOLD' = 'On Hold',
-  'SYSTEM_ERROR' = 'System Error'
+  'SYSTEM_ERROR' = 'System Error',
+
+  //Failure
+  'FAILED_OCCURRENCE_PREPARATION' = 'Failed to prepare submission',
+  'INVALID_MEDIA' = 'Media is not valid',
+  'FAILED_VALIDATION' = 'Failed to validate',
+  'FAILED_TRANSFORMED' = 'Failed to transform',
+  'FAILED_PROCESSING_OCCURRENCE_DATA' = 'Failed to process occurrence data'
+}
+
+export enum SUBMISSION_MESSAGE_TYPE {
+  //message types that match the submission_message_type table
+  'DUPLICATE_HEADER' = 'Duplicate header',
+  'UNKNOWN_HEADER' = 'Unknown Header',
+  'MISSING_REQUIRED_HEADER' = 'Missing Required Header',
+  'MISSING_RECOMMENDED_HEADER' = 'Missing Recommended Header',
+  'MISCELLANEOUS' = 'Miscellaneous',
+  'MISSING_REQUIRED_FIELD' = 'Missing Required Field',
+  'UNEXPECTED_FORMAT' = 'Unexpected Format',
+  'OUT_OF_RANGE' = 'Out of Range',
+  'INVALID_VALUE' = 'Invalid Value',
+  'MISSING_VALIDATION_SCHEMA' = 'Missing Validation Schema',
+  'FAILED_GET_OCCURRENCE' = 'Failed to Get Occurrence Submission',
+  'FAILED_GET_FILE_FROM_S3' = 'Failed to get file from S3',
+  'FAILED_UPLOAD_FILE_TO_S3' = 'Failed to upload file to S3',
+  'FAILED_PARSE_SUBMISSION' = 'Failed to parse submission',
+  'FAILED_PREP_DWC_ARCHIVE' = 'Failed to prep DarwinCore Archive',
+  'FAILED_PREP_XLSX' = 'Failed to prep XLSX',
+  'FAILED_PERSIST_PARSE_ERRORS' = 'Failed to persist parse errors',
+  'FAILED_GET_VALIDATION_RULES' = 'Failed to get validation rules',
+  'FAILED_GET_TRANSFORMATION_RULES' = 'Failed to get transformation rules',
+  'FAILED_PERSIST_TRANSFORMATION_RESULTS' = 'Failed to persist transformation results',
+  'FAILED_TRANSFORM_XLSX' = 'Failed to transform XLSX',
+  'FAILED_VALIDATE_DWC_ARCHIVE' = 'Failed to validate DarwinCore Archive',
+  'FAILED_PERSIST_VALIDATION_RESULTS' = 'Failed to persist validation results',
+  'FAILED_UPDATE_OCCURRENCE_SUBMISSION' = 'Failed to update occurrence submission',
+  'FAILED_TO_GET_TRANSFORM_SCHEMA' = 'Unable to get transform schema for submission',
+  'INVALID_MEDIA' = 'Media is invalid',
+  'UNSUPPORTED_FILE_TYPE' = 'File submitted is not a supported type'
 }

api/src/database/db.test.ts

@@ -4,7 +4,7 @@ import * as pg from 'pg';
 import Sinon from 'sinon';
 import SQL from 'sql-template-strings';
 import { SYSTEM_IDENTITY_SOURCE } from '../constants/database';
-import { HTTPError } from '../errors/custom-error';
+import { HTTPError } from '../errors/http-error';
 import { setSystemUserContextSQL } from '../queries/database/user-context-queries';
 import * as db from './db';
 import { getAPIUserDBConnection, getDBConnection, getDBPool, getKnex, IDBConnection, initDBPool } from './db';

api/src/database/db.ts

@@ -1,7 +1,7 @@
 import knex, { Knex } from 'knex';
 import * as pg from 'pg';
 import { SQLStatement } from 'sql-template-strings';
-import { ApiExecuteSQLError, ApiGeneralError } from '../errors/custom-error';
+import { ApiExecuteSQLError, ApiGeneralError } from '../errors/api-error';
 import { queries } from '../queries/queries';
 import { getUserIdentifier, getUserIdentitySource } from '../utils/keycloak-utils';
 import { getLogger } from '../utils/logger';

api/src/errors/api-error.test.ts

@@ -0,0 +1,25 @@
+import { expect } from 'chai';
+import { describe } from 'mocha';
+import { ApiErrorType, ApiExecuteSQLError, ApiGeneralError, ApiUnknownError } from './api-error';
+
+describe('ApiError', () => {
+  describe('No error value provided', () => {
+    let message: string;
+
+    before(() => {
+      message = 'response message';
+    });
+
+    it('Creates Api General error', function () {
+      expect(new ApiGeneralError(message).name).to.equal(ApiErrorType.GENERAL);
+    });
+
+    it('Creates Api Unknown error', function () {
+      expect(new ApiUnknownError(message).name).to.equal(ApiErrorType.UNKNOWN);
+    });
+
+    it('Creates Api execute SQL error', function () {
+      expect(new ApiExecuteSQLError(message).name).to.equal(ApiErrorType.EXECUTE_SQL);
+    });
+  });
+});

api/src/errors/api-error.ts

@@ -0,0 +1,82 @@
+export enum ApiErrorType {
+  BUILD_SQL = 'Error constructing SQL query',
+  EXECUTE_SQL = 'Error executing SQL query',
+  GENERAL = 'Error',
+  UNKNOWN = 'Unknown Error'
+}
+
+export class ApiError extends Error {
+  errors?: (string | object)[];
+
+  constructor(name: ApiErrorType, message: string, errors?: (string | object)[], stack?: string) {
+    super(message);
+
+    this.name = name;
+    this.errors = errors || [];
+    this.stack = stack;
+
+    if (stack) {
+      this.stack = stack;
+    }
+
+    if (!this.stack) {
+      Error.captureStackTrace(this);
+    }
+  }
+}
+
+/**
+ * Api encountered an error.
+ *
+ * @export
+ * @class ApiGeneralError
+ * @extends {ApiError}
+ */
+export class ApiGeneralError extends ApiError {
+  constructor(message: string, errors?: (string | object)[]) {
+    super(ApiErrorType.GENERAL, message, errors);
+  }
+}
+
+/**
+ * API encountered an unknown/unexpected error.
+ *
+ * @export
+ * @class ApiUnknownError
+ * @extends {ApiError}
+ */
+export class ApiUnknownError extends ApiError {
+  constructor(message: string, errors?: (string | object)[]) {
+    super(ApiErrorType.UNKNOWN, message, errors);
+  }
+}
+
+/**
+ * API executed a query against the database, but the response was missing data, or indicated the query failed.
+ *
+ * Examples:
+ * - A query to select rows that are expected to exist returns with `rows=[]`.
+ * - A query to insert a new record returns with `rowCount=0` indicating no new row was added.
+ *
+ * @export
+ * @class ApiExecuteSQLError
+ * @extends {ApiError}
+ */
+export class ApiExecuteSQLError extends ApiError {
+  constructor(message: string, errors?: (string | object)[]) {
+    super(ApiErrorType.EXECUTE_SQL, message, errors);
+  }
+}
+
+/**
+ * API failed to build SQL a query.
+ *
+ * @export
+ * @class ApiBuildSQLError
+ * @extends {ApiError}
+ */
+export class ApiBuildSQLError extends ApiError {
+  constructor(message: string, errors?: (string | object)[]) {
+    super(ApiErrorType.BUILD_SQL, message, errors);
+  }
+}

api/src/errors/custom-error.test.ts → api/src/errors/http-error.test.ts

@@ -1,47 +1,8 @@
 import { expect } from 'chai';
 import { describe } from 'mocha';
 import { DatabaseError } from 'pg';
-import {
-  ApiBuildSQLError,
-  ApiError,
-  ApiErrorType,
-  ApiExecuteSQLError,
-  ApiGeneralError,
-  ApiUnknownError,
-  ensureHTTPError,
-  HTTP400,
-  HTTP401,
-  HTTP403,
-  HTTP409,
-  HTTP500,
-  HTTPError
-} from './custom-error';
-
-describe('ApiError', () => {
-  describe('No error value provided', () => {
-    let message: string;
-
-    before(() => {
-      message = 'response message';
-    });
-
-    it('Creates Api General error', function () {
-      expect(new ApiGeneralError(message).name).to.equal(ApiErrorType.GENERAL);
-    });
-
-    it('Creates Api Unknown error', function () {
-      expect(new ApiUnknownError(message).name).to.equal(ApiErrorType.UNKNOWN);
-    });
-
-    it('Creates Api build SQL error', function () {
-      expect(new ApiBuildSQLError(message).name).to.equal(ApiErrorType.BUILD_SQL);
-    });
-
-    it('Creates Api execute SQL error', function () {
-      expect(new ApiExecuteSQLError(message).name).to.equal(ApiErrorType.EXECUTE_SQL);
-    });
-  });
-});
+import { ApiError, ApiErrorType } from './api-error';
+import { ensureHTTPError, HTTP400, HTTP401, HTTP403, HTTP409, HTTP500, HTTPError } from './http-error';
 
 describe('HTTPError', () => {
   describe('No error value provided', () => {

api/src/errors/custom-error.ts → api/src/errors/http-error.ts

@@ -1,87 +1,5 @@
 import { DatabaseError } from 'pg';
-
-export enum ApiErrorType {
-  BUILD_SQL = 'Error constructing SQL query',
-  EXECUTE_SQL = 'Error executing SQL query',
-  GENERAL = 'Error',
-  UNKNOWN = 'Unknown Error'
-}
-
-export class ApiError extends Error {
-  errors?: (string | object)[];
-
-  constructor(name: ApiErrorType, message: string, errors?: (string | object)[], stack?: string) {
-    super(message);
-
-    this.name = name;
-    this.errors = errors || [];
-    this.stack = stack;
-
-    if (stack) {
-      this.stack = stack;
-    }
-
-    if (!this.stack) {
-      Error.captureStackTrace(this);
-    }
-  }
-}
-
-/**
- * Api encountered an error.
- *
- * @export
- * @class ApiGeneralError
- * @extends {ApiError}
- */
-export class ApiGeneralError extends ApiError {
-  constructor(message: string, errors?: (string | object)[]) {
-    super(ApiErrorType.GENERAL, message, errors);
-  }
-}
-
-/**
- * API encountered an unknown/unexpected error.
- *
- * @export
- * @class ApiUnknownError
- * @extends {ApiError}
- */
-export class ApiUnknownError extends ApiError {
-  constructor(message: string, errors?: (string | object)[]) {
-    super(ApiErrorType.UNKNOWN, message, errors);
-  }
-}
-
-/**
- * API failed to build SQL a query.
- *
- * @export
- * @class ApiBuildSQLError
- * @extends {ApiError}
- */
-export class ApiBuildSQLError extends ApiError {
-  constructor(message: string, errors?: (string | object)[]) {
-    super(ApiErrorType.BUILD_SQL, message, errors);
-  }
-}
-
-/**
- * API executed a query against the database, but the response was missing data, or indicated the query failed.
- *
- * Examples:
- * - A query to select rows that are expected to exist returns with `rows=[]`.
- * - A query to insert a new record returns with `rowCount=0` indicating no new row was added.
- *
- * @export
- * @class ApiExecuteSQLError
- * @extends {ApiError}
- */
-export class ApiExecuteSQLError extends ApiError {
-  constructor(message: string, errors?: (string | object)[]) {
-    super(ApiErrorType.EXECUTE_SQL, message, errors);
-  }
-}
+import { ApiError } from './api-error';
 
 export enum HTTPErrorType {
   BAD_REQUEST = 'Bad Request',