Phase 2: Visit scribe auto-fills GAD-7 / PHQ-9

package.json

@@ -74,7 +74,6 @@
     "node": "^22.18.0 || >=24.2.0"
   },
   "dependencies": {
-    "@huggingface/transformers": "^3.7.1",
     "phenoml": "^17.7.0"
   }
 }

sample-visit-transcript.txt

@@ -0,0 +1,92 @@
+Recommended test transcript — psychiatry visit (GAD-7 / PHQ-9 scribe demo)
+==========================================================================
+
+How to use:
+  Open an encounter → "Note & Tasks" tab → "Screening scribe" section.
+  Paste one of the transcripts below (or dictate it with the mic) and click
+  "Generate screening questionnaires". GAD-7 and PHQ-9 should pre-fill with
+  scored answers that you can review, edit, and save to the encounter.
+
+  Both notes deliberately use PHQ/GAD frequency language ("not at all",
+  "several days", "more than half the days", "nearly every day") so the
+  model can map each symptom to a scored answer option.
+
+  OPTION A — live visit dialogue (clinician + patient).
+  OPTION B — post-visit dictation, spoken by the clinician alone. Use this
+  when the clinician wants to record a summary from memory after the patient
+  has left, rather than transcribing the conversation in real time.
+
+--------------------------------------------------------------------------
+OPTION A — TRANSCRIPT (live visit dialogue)
+--------------------------------------------------------------------------
+
+Clinician: Good morning. Thanks for coming in today. How have things been
+over the last two weeks?
+
+Patient: Honestly, not great. I've been feeling nervous and on edge nearly
+every day. My mind just won't switch off.
+
+Clinician: Tell me more about the worrying.
+
+Patient: I can't stop or control the worrying — it's there nearly every
+day. I worry too much about all kinds of different things, more than half
+the days I'd say. Trouble relaxing is constant, pretty much every day. I've
+been so restless that it's hard to sit still on several days. I get easily
+annoyed or irritable more than half the days. And several days I feel
+afraid, like something awful might happen.
+
+Clinician: That sounds exhausting. How has your mood been?
+
+Patient: Low. I've had little interest or pleasure in doing things nearly
+every day. I feel down, depressed, and hopeless more than half the days.
+
+Clinician: How's your sleep and energy?
+
+Patient: Trouble falling and staying asleep nearly every day, and I'm tired
+with little energy nearly every day too.
+
+Clinician: What about appetite?
+
+Patient: My appetite is poor — that's been happening several days.
+
+Clinician: How do you feel about yourself lately?
+
+Patient: I feel bad about myself, like I'm a failure, more than half the
+days. Concentrating on things like reading or watching TV is hard on
+several days.
+
+Clinician: Have you noticed any change in how you move or speak?
+
+Patient: Not at all, really. No one's mentioned me being slowed down or
+fidgety.
+
+Clinician: I have to ask — any thoughts that you'd be better off dead, or
+of hurting yourself?
+
+Patient: No, not at all. Nothing like that.
+
+Clinician: Thank you for being so open. Let's go through a couple of brief
+screening questionnaires together and talk about next steps.
+
+--------------------------------------------------------------------------
+OPTION B — POST-VISIT DICTATION (clinician, single speaker)
+--------------------------------------------------------------------------
+
+Post-visit note, dictated. This is a 34-year-old patient seen today for a
+follow-up of anxiety and low mood, reporting on the last two weeks.
+
+On the anxiety side: the patient has been feeling nervous, anxious, or on
+edge, and reports being unable to stop or control the
+worrying nearly every day. They describe worrying too much about different
+things more than half the days, with trouble relaxing nearly every day.
+They've been so restless that it's hard to sit still on several days, are
+easily annoyed or irritable more than half the days, and feel afraid as if
+something awful might happen on several days.
+
+On mood: little interest or pleasure in doing things nearly every day, and
+feeling down, depressed, or hopeless more than half the days. Sleep is
+disrupted — trouble falling and staying asleep nearly every day — with
+fatigue and low energy nearly every day. Appetite is poor on several days.
+The patient feels bad about themselves, like a failure, more than half the
+days, and has trouble concentrating on things such as reading or watching
+television on several days. No psychomotor slowing or agitation noted. Denies any thoughts of being better off dead or of self-harm.

src/bots/buildProfile.test.ts

@@ -0,0 +1,113 @@
+// SPDX-FileCopyrightText: Copyright Orangebot, Inc. and Medplum contributors
+// SPDX-License-Identifier: Apache-2.0
+import type { Questionnaire } from '@medplum/fhirtypes';
+import { describe, expect, test } from 'vitest';
+import {
+  buildQuestionnaireResponseProfile,
+  composeExtractionText,
+  getAnswerableItems,
+  profileIdFor,
+  valueTypesFor,
+} from './buildProfile';
+
+const ORDINAL = 'http://hl7.org/fhir/StructureDefinition/ordinalValue';
+
+const questionnaire: Questionnaire = {
+  resourceType: 'Questionnaire',
+  status: 'active',
+  url: 'https://www.medplum.com/questionnaire/gad-7',
+  title: 'GAD-7',
+  item: [
+    {
+      linkId: 'group-1',
+      text: 'Over the last 2 weeks',
+      type: 'group',
+      item: [
+        {
+          linkId: 'gad7-q1',
+          text: 'Feeling nervous',
+          type: 'choice',
+          answerOption: [
+            { valueCoding: { system: 'http://loinc.org', code: 'LA6568-5', display: 'Not at all' }, extension: [{ url: ORDINAL, valueDecimal: 0 }] },
+            { valueCoding: { system: 'http://loinc.org', code: 'LA6569-3', display: 'Several days' }, extension: [{ url: ORDINAL, valueDecimal: 1 }] },
+          ],
+        },
+      ],
+    },
+    { linkId: 'note', text: 'Clinician note', type: 'text' },
+    { linkId: 'display-1', text: 'Instructions', type: 'display' },
+  ],
+};
+
+describe('getAnswerableItems', () => {
+  test('recurses into groups and skips group/display items', () => {
+    const items = getAnswerableItems(questionnaire);
+    expect(items.map((i) => i.linkId)).toEqual(['gad7-q1', 'note']);
+  });
+});
+
+describe('valueTypesFor', () => {
+  test('maps item types to FHIR value[x] types', () => {
+    expect(valueTypesFor({ linkId: 'a', type: 'boolean' })).toEqual(['boolean']);
+    expect(valueTypesFor({ linkId: 'b', type: 'decimal' })).toEqual(['decimal']);
+    expect(valueTypesFor({ linkId: 'c', type: 'text' })).toEqual(['string']);
+    expect(valueTypesFor({ linkId: 'd', type: 'choice', answerOption: [{ valueCoding: { code: 'x' } }] })).toEqual(['Coding']);
+    expect(valueTypesFor({ linkId: 'e', type: 'choice', answerOption: [{ valueString: 'x' }] })).toEqual(['string']);
+  });
+});
+
+describe('profileIdFor', () => {
+  test('is deterministic and content-derived', () => {
+    expect(profileIdFor(questionnaire)).toBe(profileIdFor(questionnaire));
+    expect(profileIdFor(questionnaire)).toMatch(/^qr-gad-7-[0-9a-f]{8}$/);
+  });
+
+  test('changes when the question set changes', () => {
+    const changed: Questionnaire = { ...questionnaire, item: (questionnaire.item ?? []).slice(0, 1) };
+    expect(profileIdFor(changed)).not.toBe(profileIdFor(questionnaire));
+  });
+});
+
+describe('buildQuestionnaireResponseProfile', () => {
+  test('produces a QuestionnaireResponse StructureDefinition with per-question slices', () => {
+    const sd = buildQuestionnaireResponseProfile(questionnaire);
+    expect(sd.resourceType).toBe('StructureDefinition');
+    expect(sd.type).toBe('QuestionnaireResponse');
+    expect(sd.derivation).toBe('constraint');
+    expect(sd.baseDefinition).toBe('http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse');
+    expect(sd.id).toMatch(/^qr-gad-7-/);
+    expect(sd.url).toContain(sd.id as string);
+
+    const elements = sd.snapshot?.element ?? [];
+    // Slicing on item by linkId, rules open.
+    const itemSlice = elements.find((e) => e.id === 'QuestionnaireResponse.item');
+    expect(itemSlice?.slicing?.discriminator?.[0]).toEqual({ type: 'pattern', path: 'linkId' });
+    expect(itemSlice?.slicing?.rules).toBe('open');
+
+    // Fixed linkId for the answerable question slice.
+    const fixedLinkId = elements.find((e) => e.id === 'QuestionnaireResponse.item:gad7-q1.linkId');
+    expect(fixedLinkId?.fixedString).toBe('gad7-q1');
+    expect(fixedLinkId?.min).toBe(1);
+
+    // Constrained answer value type + required binding carrying the allowed codes.
+    const value = elements.find((e) => e.id === 'QuestionnaireResponse.item:gad7-q1.answer.value[x]');
+    expect(value?.type).toEqual([{ code: 'Coding' }]);
+    expect(value?.binding?.strength).toBe('required');
+    expect(value?.binding?.description).toContain('LA6569-3');
+
+    // min:0 everywhere on the slices so nothing is forced.
+    expect(elements.find((e) => e.id === 'QuestionnaireResponse.item:gad7-q1')?.min).toBe(0);
+    expect(value?.min).toBe(0);
+  });
+});
+
+describe('composeExtractionText', () => {
+  test('inlines a compact question key ahead of the transcript', () => {
+    const text = composeExtractionText('patient reports feeling nervous several days', questionnaire);
+    expect(text).toContain('- [gad7-q1] Feeling nervous (choice; allowed codes: LA6568-5=Not at all, LA6569-3=Several days)');
+    expect(text).toContain('patient reports feeling nervous several days');
+    // Only answerable leaves appear in the key.
+    expect(text).not.toContain('[group-1]');
+    expect(text).not.toContain('[display-1]');
+  });
+});