SIMS-BIOHUB-8

api/src/json-schema/validation-schema.ts

@@ -119,19 +119,24 @@ export const submissionValidationSchema = {
       description: 'The validators that can be applied against a file/sheet within a submission file.',
       anyOf: [
         {
-          $ref: '#/$defs/file_required_columns_validator'
+          $ref: '#/$defs/file_required_columns_validator',
+          description: 'column header validator'
         },
         {
-          $ref: '#/$defs/file_recommended_columns_validator'
+          $ref: '#/$defs/file_recommended_columns_validator',
+          description: 'column header validator'
         },
         {
-          $ref: '#/$defs/file_duplicate_columns_validator'
+          $ref: '#/$defs/file_duplicate_columns_validator',
+          description: 'column header validator'
         },
         {
-          $ref: '#/$defs/file_valid_columns_validator'
+          $ref: '#/$defs/file_valid_columns_validator',
+          description: 'column header validator '
         },
         {
-          $ref: '#/$defs/file_column_unique_validator'
+          $ref: '#/$defs/file_column_unique_validator',
+          description: 'column cell validator '
         }
       ]
     },
@@ -239,7 +244,7 @@ export const submissionValidationSchema = {
       additionalProperties: false
     },
     file_required_columns_validator: {
-      description: 'Validates that this file/sheet contains required columns',
+      description: 'Column header validator that checks whether the file/sheet contains required columns',
       type: 'object',
       properties: {
         file_required_columns_validator: {
@@ -265,7 +270,7 @@ export const submissionValidationSchema = {
       additionalProperties: false
     },
     file_recommended_columns_validator: {
-      description: 'Validates that this file/sheet contains recommended columns',
+      description: 'Column header validator that checks whether the file/sheet contains recommended columns',
       type: 'object',
       properties: {
         file_recommended_columns_validator: {
@@ -291,7 +296,7 @@ export const submissionValidationSchema = {
       additionalProperties: false
     },
     file_duplicate_columns_validator: {
-      description: 'Validates that this file/sheet contains recommended columns',
+      description: 'Column header validator that checks whether this file/sheet contains recommended columns',
       type: 'object',
       properties: {
         file_duplicate_columns_validator: {
@@ -310,7 +315,7 @@ export const submissionValidationSchema = {
       additionalProperties: false
     },
     file_valid_columns_validator: {
-      description: 'Validates that this file/sheet contains only valid (known) columns',
+      description: 'Column header validator that checks whether this file/sheet contains only valid (known) columns',
       type: 'object',
       properties: {
         file_valid_columns_validator: {
@@ -335,7 +340,7 @@ export const submissionValidationSchema = {
       additionalProperties: false
     },
     column_required_validator: {
-      description: 'Validates that this column value is not empty',
+      description: 'Column cell validator that checks that this column value is not empty.',
       type: 'object',
       properties: {
         column_required_validator: {
@@ -452,7 +457,7 @@ export const submissionValidationSchema = {
       additionalProperties: false
     },
     file_column_unique_validator: {
-      description: 'Validates that the column(s) are unique',
+      description: 'Column cell validator the checks that the column(s) are unique',
       type: 'object',
       properties: {
         file_column_unique_validator: {

api/src/paths/project/{projectId}/survey/{surveyId}/observation/submission/get.ts

@@ -242,6 +242,7 @@ export function getOccurrenceSubmission(): RequestHandler {
           SUBMISSION_STATUS_TYPE.SYSTEM_ERROR,
           SUBMISSION_STATUS_TYPE.FAILED_OCCURRENCE_PREPARATION,
           SUBMISSION_STATUS_TYPE.FAILED_VALIDATION,
+          SUBMISSION_STATUS_TYPE.INVALID_MEDIA,
           SUBMISSION_STATUS_TYPE.FAILED_TRANSFORMED,
           SUBMISSION_STATUS_TYPE.FAILED_PROCESSING_OCCURRENCE_DATA,
           SUBMISSION_STATUS_TYPE['AWAITING CURRATION'],

api/src/services/validation-service.test.ts

@@ -1032,7 +1032,7 @@ describe('ValidationService', () => {
       expect(response.media_state.fileErrors).is.empty;
     });
 
-    it('should throw Media is invalid error', async () => {
+    it('should return early if media_state is invalid', async () => {
       const service = mockService();
       const mockMediaState = {
         fileName: 'test file',
@@ -1043,13 +1043,11 @@ describe('ValidationService', () => {
 
       sinon.stub(XLSXCSV.prototype, 'getMediaState').returns(mockMediaState);
 
-      try {
-        await service.validateXLSX(xlsx, parser);
-        expect.fail();
-      } catch (error) {
-        expect(error).to.be.instanceOf(SubmissionError);
-        expect((error as SubmissionError).submissionMessages[0].type).to.be.eql(SUBMISSION_MESSAGE_TYPE.INVALID_MEDIA);
-      }
+      const result = await service.validateXLSX(xlsx, parser);
+
+      expect(result.csv_state).to.be.eql([]);
+      expect(result.media_state.fileName).to.be.eql(mockMediaState.fileName);
+      expect(result.media_state.isValid).to.be.eql(false);
     });
 
     it('should return valid state object with content errors', async () => {

api/src/services/validation-service.ts

@@ -364,8 +364,9 @@ export class ValidationService extends DBService {
     file.validateMedia(parser);
 
     const media_state = file.getMediaState();
+
     if (!media_state.isValid) {
-      throw SubmissionErrorFromMessageType(SUBMISSION_MESSAGE_TYPE.INVALID_MEDIA);
+      return { csv_state: ([] as unknown) as ICsvState[], media_state };
     }
 
     // Run CSV content validations
@@ -401,7 +402,9 @@ export class ValidationService extends DBService {
     const errors: MessageError[] = [];
 
     mediaState.fileErrors?.forEach((fileError) => {
-      errors.push(new MessageError(SUBMISSION_MESSAGE_TYPE.INVALID_MEDIA, `${fileError}`, 'Miscellaneous'));
+      errors.push(
+        new MessageError(SUBMISSION_MESSAGE_TYPE.INVALID_MEDIA, `${fileError}`, SUBMISSION_MESSAGE_TYPE.INVALID_MEDIA)
+      );
     });
 
     csvState?.forEach((csvStateItem) => {
@@ -434,13 +437,13 @@ export class ValidationService extends DBService {
           )
         );
       });
-
-      if (!mediaState.isValid || csvState?.some((item) => !item.isValid)) {
-        // At least 1 error exists, skip remaining steps
-        parseError = true;
-      }
     });
 
+    if (mediaState.fileErrors?.length || csvState?.some((item) => !item.isValid)) {
+      // At least 1 error exists, skip remaining steps
+      parseError = true;
+    }
+
     if (parseError) {
       throw new SubmissionError({ messages: errors });
     }