feat(presets): add prisma-2020-db-only (databases & registers only)

src/presets/index.ts

@@ -1,11 +1,13 @@
 import type { FlowDocument, Preset } from "../core/types.js";
 import { stringifyYaml } from "../io/yaml.js";
 import prisma2020 from "./prisma-2020/index.js";
+import prisma2020DbOnly from "./prisma-2020-db-only/index.js";
 import consort2010 from "./consort-2010/index.js";
 import strobe from "./strobe/index.js";
 
 const registry = new Map<string, Preset>();
 registry.set(prisma2020.id, prisma2020);
+registry.set(prisma2020DbOnly.id, prisma2020DbOnly);
 registry.set(consort2010.id, consort2010);
 registry.set(strobe.id, strobe);
 
@@ -46,4 +48,4 @@ export function blankDocumentYaml(presetId: string): string {
   return stringifyYaml(blankDocument(presetId));
 }
 
-export { prisma2020, consort2010, strobe };
+export { prisma2020, prisma2020DbOnly, consort2010, strobe };

src/presets/prisma-2020-db-only/index.ts

@@ -0,0 +1,200 @@
+/**
+ * PRISMA 2020 Flow Diagram preset — databases & registers ONLY variant.
+ *
+ * Follows: Page MJ et al. BMJ 2021;372:n71. https://doi.org/10.1136/bmj.n71
+ * This is the official single-column template for "new systematic reviews
+ * which included searches of databases and registers only" (no websites /
+ * organisations / citation-searching arm). Use this for reviews — including
+ * most diagnostic-test-accuracy (PRISMA-DTA) reviews — whose included studies
+ * all came from database/register searching.
+ */
+
+import type { Preset } from "../../core/types.js";
+
+export const prisma2020DbOnly: Preset = {
+  id: "prisma-2020-db-only",
+  version: "1.0.0",
+  name: "PRISMA 2020 (databases & registers only)",
+  description:
+    "PRISMA 2020 single-column flow diagram for systematic reviews with searches of databases and registers only (no other-methods arm).",
+  citation: {
+    text:
+      "Page MJ, McKenzie JE, Bossuyt PM, et al. The PRISMA 2020 statement: an updated guideline for reporting systematic reviews. BMJ 2021;372:n71.",
+    doi: "10.1136/bmj.n71",
+    url: "https://www.bmj.com/content/372/bmj.n71",
+  },
+
+  grid: {
+    cols: 2,
+    rows: 6,
+    colWidth: 260,
+    rowHeight: 70,
+    colGap: 40,
+    rowGap: 18,
+    padding: 24,
+    sectionLabelWidth: 40,
+  },
+
+  sections: [
+    { id: "identification", label: "Identification", rows: [0, 1] },
+    { id: "screening", label: "Screening", rows: [2, 4] },
+    { id: "included", label: "Included", rows: [5, 5] },
+  ],
+
+  fields: [
+    // Identification – databases & registers
+    { key: "db_records", type: "number", label: "Records identified from databases", required: true, default: 0 },
+    { key: "registry_records", type: "number", label: "Records identified from registers", default: 0 },
+
+    { key: "duplicates_removed", type: "number", label: "Duplicate records removed", default: 0 },
+    { key: "automation_excluded", type: "number", label: "Records marked as ineligible by automation tools", default: 0 },
+    { key: "other_prescreen_removed", type: "number", label: "Records removed for other reasons", default: 0 },
+
+    // Screening
+    { key: "records_screened", type: "number", label: "Records screened", required: true, default: 0 },
+    { key: "records_excluded", type: "number", label: "Records excluded", default: 0 },
+
+    { key: "reports_sought", type: "number", label: "Reports sought for retrieval", default: 0 },
+    { key: "reports_not_retrieved", type: "number", label: "Reports not retrieved", default: 0 },
+
+    { key: "reports_assessed", type: "number", label: "Reports assessed for eligibility", default: 0 },
+    { key: "exclusion_reasons", type: "exclusion_reasons", label: "Reports excluded with reasons", default: [] },
+
+    // Included
+    { key: "studies_included", type: "number", label: "Studies included in review", required: true, default: 0 },
+    { key: "reports_of_included_studies", type: "number", label: "Reports of included studies", default: 0 },
+  ],
+
+  nodes: [
+    // Row 0: Identification
+    {
+      id: "db_sources",
+      kind: "box",
+      cell: { row: 0, col: 0 },
+      template:
+        "Records identified from:\n" +
+        "Databases (n = {{db_records}})\n" +
+        "Registers (n = {{registry_records}})",
+    },
+    {
+      id: "prescreen_removed",
+      kind: "exclusion",
+      cell: { row: 0, col: 1 },
+      template:
+        "Records removed before screening:\n" +
+        "Duplicate records (n = {{duplicates_removed}})\n" +
+        "Records marked as ineligible by automation tools (n = {{automation_excluded}})\n" +
+        "Records removed for other reasons (n = {{other_prescreen_removed}})",
+    },
+
+    // Row 2: Screening
+    {
+      id: "records_screened",
+      kind: "box",
+      cell: { row: 2, col: 0 },
+      template: "Records screened\n(n = {{records_screened}})",
+    },
+    {
+      id: "records_excluded",
+      kind: "exclusion",
+      cell: { row: 2, col: 1 },
+      template: "Records excluded\n(n = {{records_excluded}})",
+    },
+
+    // Row 3: Sought for retrieval
+    {
+      id: "reports_sought",
+      kind: "box",
+      cell: { row: 3, col: 0 },
+      template: "Reports sought for retrieval\n(n = {{reports_sought}})",
+    },
+    {
+      id: "reports_not_retrieved",
+      kind: "exclusion",
+      cell: { row: 3, col: 1 },
+      template: "Reports not retrieved\n(n = {{reports_not_retrieved}})",
+    },
+
+    // Row 4: Assessed for eligibility + excluded-with-reasons
+    {
+      id: "reports_assessed",
+      kind: "box",
+      cell: { row: 4, col: 0 },
+      template: "Reports assessed for eligibility\n(n = {{reports_assessed}})",
+    },
+    {
+      id: "reports_excluded",
+      kind: "exclusion",
+      cell: { row: 4, col: 1 },
+      template:
+        "Reports excluded:\n" +
+        "{{#each exclusion_reasons}}{{reason}} (n = {{n}})\n{{/each}}",
+    },
+
+    // Row 5: Included
+    {
+      id: "included",
+      kind: "box",
+      cell: { row: 5, col: 0, colSpan: 2 },
+      template:
+        "Studies included in review (n = {{studies_included}})\n" +
+        "Reports of included studies (n = {{reports_of_included_studies}})",
+      style: { fill: "#eaf1ff", bold: true },
+    },
+  ],
+
+  edges: [
+    // Main vertical flow (left column).
+    { from: "db_sources", to: "records_screened", fromPort: "s", toPort: "n" },
+    { from: "records_screened", to: "reports_sought", fromPort: "s", toPort: "n" },
+    { from: "reports_sought", to: "reports_assessed", fromPort: "s", toPort: "n" },
+    { from: "reports_assessed", to: "included", fromPort: "s", toPort: "n" },
+
+    // Side branches (to exclusions column).
+    { from: "db_sources", to: "prescreen_removed", fromPort: "e", toPort: "w" },
+    { from: "records_screened", to: "records_excluded", fromPort: "e", toPort: "w" },
+    { from: "reports_sought", to: "reports_not_retrieved", fromPort: "e", toPort: "w" },
+    { from: "reports_assessed", to: "reports_excluded", fromPort: "e", toPort: "w" },
+  ],
+
+  invariants: [
+    {
+      id: "SCREEN_IN",
+      description:
+        "records_screened should equal db_records + registry_records − duplicates_removed − automation_excluded − other_prescreen_removed",
+      lhs: ["records_screened"],
+      rhs: [
+        "db_records",
+        "registry_records",
+        "-duplicates_removed",
+        "-automation_excluded",
+        "-other_prescreen_removed",
+      ],
+      severity: "warning",
+    },
+    {
+      id: "SCREEN_OUT",
+      description: "records_screened should equal records_excluded + reports_sought",
+      lhs: ["records_screened"],
+      rhs: ["records_excluded", "reports_sought"],
+      severity: "warning",
+    },
+    {
+      id: "SOUGHT_OUT",
+      description: "reports_sought should equal reports_not_retrieved + reports_assessed",
+      lhs: ["reports_sought"],
+      rhs: ["reports_not_retrieved", "reports_assessed"],
+      severity: "warning",
+    },
+    {
+      id: "INCLUDED_BALANCE",
+      description:
+        "reports_assessed should equal reports_of_included_studies + Σ exclusion_reasons",
+      lhs: ["reports_assessed"],
+      rhs: ["reports_of_included_studies", "exclusion_reasons"],
+      severity: "warning",
+    },
+  ],
+};
+
+export default prisma2020DbOnly;

test/matrix.test.mjs

@@ -43,9 +43,9 @@ function loadCase(c) {
   return layout(doc, preset);
 }
 
-test("registry exposes prisma-2020, consort-2010, strobe", () => {
+test("registry exposes prisma-2020, prisma-2020-db-only, consort-2010, strobe", () => {
   const ids = listPresets().map((p) => p.id).sort();
-  assert.deepEqual(ids, ["consort-2010", "prisma-2020", "strobe"]);
+  assert.deepEqual(ids, ["consort-2010", "prisma-2020", "prisma-2020-db-only", "strobe"]);
 });
 
 for (const c of CASES) {