Merge branch 'release-0.14.1'

Author: stevejpurves

packages/pmc/CHANGELOG.md

@@ -9,6 +9,38 @@
 - 535d5df: Aligning to latest `@curvenote/common`
 - 535d5df: Fixed lint command and applied it
 
+## 0.1.16
+
+### Patch Changes
+
+- 7a83694: Limit the Request New Version transition from certain states
+- f42cdda: Fixes to workflow sync webhook and improvements in Workflow Sync UI to display more error info and indicate how a job was started
+
+## 0.1.15
+
+### Patch Changes
+
+- 7368b9d: Adding a confirmation dialog for PMC Admin inbox actions
+- 7368b9d: Submitters will automatically receive an email when a PMC admin presses "Request New Version"
+
+## 0.1.14
+
+### Patch Changes
+
+- 4c32dda: Made a fix to ensure that inbound submitters files requested emails always cause an auto transition to request new version. Added unit tests.
+- a9b438d: Auto transition from PENDING to send_to_pmc without user interaction
+- a9b438d: Send and email when a new PMC deposit is made
+- a7c978b: Changes to the language around Funding Ids, removing the "grants" from the UI
+- 4a1661e: Moved all emails to templates
+- 05119e8: Simplified breadcrumbs on deposit and preview pages, linking back to Home at the root link.
+- e9a8326: When a deposit is rejected with the message that it should be submited directly by the journal, it will transition to a "No Action Needed" end state
+
+## 0.1.13
+
+### Patch Changes
+
+- 469d8da: Workflow sync will not update certain skipped statuses that are arraved at through workspace interactions e.g. Request New Version or No Action needed, preventing the data form PMC to override these statuses
+
 ## 0.1.0
 
 ### Minor Changes

packages/pmc/package.json

@@ -48,6 +48,10 @@
     "dev": "tsc -w",
     "compile": "tsc --noEmit",
     "format": "prettier --write \"**/*.{ts,tsx,md}\"",
+    "test": "vitest run",
+    "test:unit": "vitest run",
+    "test:watch": "vitest",
+    "test:ci": "vitest run --reporter=verbose",
     "changeset": "changeset",
     "version": "changeset version && npm install"
   },

packages/pmc/src/backend/email/handlers/bulk-submission-parser.server.ts

@@ -19,6 +19,18 @@ export interface PackageResult {
   message?: string;
 }
 
+/** Phrase that indicates the "direct submission only" error from PMC */
+const DIRECT_SUBMISSION_ONLY_PHRASE = 'should be submitted directly to PMC';
+
+/**
+ * Returns true if the error message indicates that the journal requires
+ * direct submission to PMC (bulk submission not accepted).
+ */
+export function isDirectSubmissionOnlyError(message: string | undefined): boolean {
+  if (!message || typeof message !== 'string') return false;
+  return message.toLowerCase().includes(DIRECT_SUBMISSION_ONLY_PHRASE.toLowerCase());
+}
+
 /**
  * Extracts package ID from text using regex patterns
  */

packages/pmc/src/backend/email/handlers/bulk-submission.server.ts

@@ -5,7 +5,11 @@ import type {
   ProcessingResult,
   EmailProcessorConfig,
 } from '../types.server.js';
-import { parseEmailContent, type ParsedEmailResult } from './bulk-submission-parser.server.js';
+import {
+  parseEmailContent,
+  isDirectSubmissionOnlyError,
+  type ParsedEmailResult,
+} from './bulk-submission-parser.server.js';
 import { updateSubmissionMetadataAndStatusIfChanged } from '../email-db.server.js';
 
 /**
@@ -86,8 +90,9 @@ export const bulkSubmissionHandler: InboundEmailHandler = {
       // Process each package independently
       for (const packageResult of parsedResult.packages) {
         try {
-          // Determine the target status based on result type
-          let targetStatus: 'DEPOSIT_CONFIRMED_BY_PMC' | 'DEPOSIT_REJECTED_BY_PMC';
+          // Determine the target status based on result type (errors always go to DEPOSIT_REJECTED_BY_PMC first)
+          type BulkTargetStatus = 'DEPOSIT_CONFIRMED_BY_PMC' | 'DEPOSIT_REJECTED_BY_PMC';
+          let targetStatus: BulkTargetStatus;
           if (packageResult.status === 'success' || packageResult.status === 'warning') {
             targetStatus = 'DEPOSIT_CONFIRMED_BY_PMC';
           } else if (packageResult.status === 'error') {
@@ -96,7 +101,7 @@ export const bulkSubmissionHandler: InboundEmailHandler = {
             throw new Error(`Unknown package status: ${packageResult.status}`);
           }
 
-          // Update metadata and status if changed (skips if already at target status)
+          // First transition: update metadata and status (e.g. to DEPOSIT_REJECTED_BY_PMC for errors)
           await updateSubmissionMetadataAndStatusIfChanged(
             ctx,
             packageResult.packageId,
@@ -106,6 +111,22 @@ export const bulkSubmissionHandler: InboundEmailHandler = {
             'bulk-submission-initial-email',
           );
 
+          // For "direct submission only" errors, make a second transition to NO_ACTION_NEEDED
+          // so we pass through DEPOSIT_REJECTED_BY_PMC and both status changes are recorded as activities
+          if (
+            packageResult.status === 'error' &&
+            isDirectSubmissionOnlyError(packageResult.message)
+          ) {
+            await updateSubmissionMetadataAndStatusIfChanged(
+              ctx,
+              packageResult.packageId,
+              packageResult,
+              messageId,
+              'NO_ACTION_NEEDED',
+              'bulk-submission-initial-email',
+            );
+          }
+
           // TODO: if we are going to send an email to the submitter
           // we would prepare the content and queue it here
 

packages/pmc/src/backend/email/handlers/compose-files-request-email.tsx

@@ -0,0 +1,85 @@
+// eslint-disable-next-line import/no-extraneous-dependencies
+import { describe, it, expect } from 'vitest';
+import { extractManuscriptId } from './email-parsing-utils.server.js';
+
+describe('email-parsing-utils', () => {
+  describe('extractManuscriptId', () => {
+    it.each<{ input: string; expected: string | null; description?: string }>([
+      // NIHMS pattern (checked first)
+      {
+        input: 'NIHMS12345',
+        expected: '12345',
+        description: 'NIHMS prefix with no space',
+      },
+      {
+        input: 'NIHMS 2109555',
+        expected: '2109555',
+        description: 'NIHMS with space before digits',
+      },
+      {
+        input: 'Your submission (NIHMS2109555) has been received',
+        expected: '2109555',
+        description: 'NIHMS in parentheses in sentence',
+      },
+      {
+        input: 'nihms99999',
+        expected: '99999',
+        description: 'lowercase nihms',
+      },
+      // Manuscript ID patterns
+      {
+        input: 'Package ID=191e5fc4eea for Manuscript ID 1502493 was submitted',
+        expected: '1502493',
+        description: '"for Manuscript ID" with numeric ID',
+      },
+      {
+        input: 'Manuscript ID 1502493',
+        expected: '1502493',
+        description: '"Manuscript ID" with numeric ID',
+      },
+      {
+        input: 'Manuscript ID ABC123',
+        expected: 'ABC123',
+        description: '"Manuscript ID" with alphanumeric ID',
+      },
+      {
+        input: 'for Manuscript ID XYZ789',
+        expected: 'XYZ789',
+        description: '"for Manuscript ID" with alphanumeric ID',
+      },
+      {
+        input: 'Manuscript\tID\t12345',
+        expected: '12345',
+        description: 'tab-separated Manuscript ID',
+      },
+      {
+        input: 'Manuscript\nID\n99999',
+        expected: '99999',
+        description: 'newline-separated Manuscript ID',
+      },
+      {
+        input: ' against allergy." (NIHMS2146980) Dear Howard Hughes Medical Institute, The cap',
+        expected: '2146980',
+        description: 'Real-world example from NIHMS files request email',
+      },
+      // No match / edge cases
+      {
+        input: '',
+        expected: null,
+        description: 'empty string',
+      },
+      {
+        input: 'No manuscript or NIHMS here',
+        expected: null,
+        description: 'no matching pattern',
+      },
+      {
+        input: 'Manuscript ID ', // no ID after
+        expected: null,
+        description: 'Manuscript ID with no value',
+      },
+    ])('$description', ({ input, expected }) => {
+      expect(extractManuscriptId(input)).toBe(expected);
+    });
+  });
+});

packages/pmc/src/backend/email/handlers/email-parsing-utils.server.spec.ts

@@ -0,0 +1,122 @@
+// eslint-disable-next-line import/no-extraneous-dependencies
+import { describe, it, expect } from 'vitest';
+import { nihmsFilesRequestHandler } from './nihms-files-request.server.js';
+
+describe('nihms-files-request handler', () => {
+  describe('identify', () => {
+    it.each<{
+      payload: { headers?: { subject?: string }; [key: string]: unknown };
+      expected: boolean;
+      description: string;
+    }>([
+      // Recognized: "please upload" before "to nihms"
+      {
+        payload: {
+          headers: { subject: 'Please upload missing file(s) to NIHMS' },
+        },
+        expected: true,
+        description: 'Real-world example from NIHMS files request email',
+      },
+      {
+        payload: {
+          headers: { subject: 'Please upload missing MDAR Reproducibility Checklist to NIHMS' },
+        },
+        expected: true,
+        description: 'Real-world example from NIHMS files request email',
+      },
+      {
+        payload: {
+          headers: { subject: 'Please upload missing supplementary material to NIHMS' },
+        },
+        expected: true,
+        description: 'Real-world example from NIHMS files request email',
+      },
+      {
+        payload: {
+          headers: { subject: 'Please upload missing figure to NIHMS' },
+        },
+        expected: true,
+        description: 'Real-world example from NIHMS files request email',
+      },
+      {
+        payload: {
+          headers: { subject: 'Please upload missing Tables S1-S30 to NIHMS' },
+        },
+        expected: true,
+        description: 'Real-world example from NIHMS files request email',
+      },
+      {
+        payload: { headers: { subject: 'Please upload additional files to NIHMS' } },
+        expected: true,
+        description: 'subject with "Please upload ... to NIHMS"',
+      },
+      {
+        payload: {
+          headers: { subject: 'Please upload supplementary materials to NIHMS for review' },
+        },
+        expected: true,
+        description: 'subject with extra text after "to NIHMS"',
+      },
+      {
+        payload: {
+          headers: { subject: 'PLEASE UPLOAD files TO NIHMS' },
+        },
+        expected: true,
+        description: 'subject is case-insensitive',
+      },
+      {
+        payload: {
+          envelope: { from: 'other@example.com' },
+          headers: { subject: 'Please upload additional files to NIHMS' },
+        },
+        expected: true,
+        description: 'identifies regardless of envelope/sender',
+      },
+      {
+        payload: {
+          headers: { subject: 'Re: Please upload files to NIHMS' },
+        },
+        expected: true,
+        description: 'subject with Re: prefix still matches',
+      },
+      // Rejected: missing or wrong structure
+      {
+        payload: {},
+        expected: false,
+        description: 'no headers',
+      },
+      {
+        payload: { headers: {} },
+        expected: false,
+        description: 'headers but no subject',
+      },
+      {
+        payload: { headers: { subject: '' } },
+        expected: false,
+        description: 'empty subject',
+      },
+      {
+        payload: { headers: { subject: 'To NIHMS please upload files' } },
+        expected: false,
+        description: '"to nihms" before "please upload"',
+      },
+      {
+        payload: { headers: { subject: 'Please upload something' } },
+        expected: false,
+        description: '"please upload" without "to nihms"',
+      },
+      {
+        payload: { headers: { subject: 'To NIHMS only' } },
+        expected: false,
+        description: '"to nihms" without "please upload"',
+      },
+      {
+        payload: { headers: { subject: 'Unrelated subject line' } },
+        expected: false,
+        description: 'subject with no matching phrases',
+      },
+    ])('$description', ({ payload, expected }) => {
+      expect(nihmsFilesRequestHandler.identify(payload)).toBe(expected);
+    });
+  });
+});