helixlife-expert-cli 0.1.0

package/cli/dist/modules/meta/plot-params.js.map

@@ -0,0 +1 @@
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package/cli/dist/modules/meta/prisma-flow-docx.d.ts

@@ -0,0 +1,23 @@
+export interface PrismaFlowData {
+    pubmed_retrieval_count: number;
+    registers_count: number;
+    duplicate_count: number;
+    automation_excluded_count: number;
+    other_exclusion_count: number;
+    screened_count: number;
+    tiab_excluded_count: number;
+    reports_sought_count: number;
+    reports_not_retrieved_count: number;
+    fulltext_count: number;
+    wrong_population_count: number;
+    wrong_intervention_count: number;
+    wrong_comparator_count: number;
+    wrong_study_design_count: number;
+    wrong_outcomes_count: number;
+    irrelevant_count: number;
+    included_count: number;
+    included_reports_count: number;
+    prisma_text?: string;
+}
+export declare function buildPrismaFlowDocx(data: PrismaFlowData): Promise<Buffer>;
+//# sourceMappingURL=prisma-flow-docx.d.ts.map

package/cli/dist/modules/meta/prisma-flow-docx.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"prisma-flow-docx.d.ts","sourceRoot":"","sources":["../../../src/modules/meta/prisma-flow-docx.ts"],"names":[],"mappings":"AAgBA,MAAM,WAAW,cAAc;IAC7B,sBAAsB,EAAE,MAAM,CAAC;IAC/B,eAAe,EAAE,MAAM,CAAC;IACxB,eAAe,EAAE,MAAM,CAAC;IACxB,yBAAyB,EAAE,MAAM,CAAC;IAClC,qBAAqB,EAAE,MAAM,CAAC;IAC9B,cAAc,EAAE,MAAM,CAAC;IACvB,mBAAmB,EAAE,MAAM,CAAC;IAC5B,oBAAoB,EAAE,MAAM,CAAC;IAC7B,2BAA2B,EAAE,MAAM,CAAC;IACpC,cAAc,EAAE,MAAM,CAAC;IACvB,sBAAsB,EAAE,MAAM,CAAC;IAC/B,wBAAwB,EAAE,MAAM,CAAC;IACjC,sBAAsB,EAAE,MAAM,CAAC;IAC/B,wBAAwB,EAAE,MAAM,CAAC;IACjC,oBAAoB,EAAE,MAAM,CAAC;IAC7B,gBAAgB,EAAE,MAAM,CAAC;IACzB,cAAc,EAAE,MAAM,CAAC;IACvB,sBAAsB,EAAE,MAAM,CAAC;IAC/B,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB;AA+ND,wBAAsB,mBAAmB,CAAC,IAAI,EAAE,cAAc,GAAG,OAAO,CAAC,MAAM,CAAC,CAqI/E"}

package/cli/dist/modules/meta/prisma-flow-docx.js

@@ -0,0 +1,302 @@
+import { Resvg } from "@resvg/resvg-js";
+import { AlignmentType, Document, HorizontalPositionRelativeFrom, ImageRun, Packer, Paragraph, TextRun, TextWrappingType, UnderlineType, VerticalAnchor, VerticalPositionRelativeFrom, WpsShapeRun, } from "docx";
+const PT_TO_EMU = 12700;
+const PT_TO_PX = 4 / 3;
+const FONT = "Arial";
+const FS = 18;
+const FS_SIDEBAR = 16;
+const FS_TITLE = 20;
+const FS_HEADER = 18;
+const FS_FOOTER = FS;
+const COLOR = {
+    text: "1C1F21",
+    title: "61666D",
+    boxBorder: "1C1F21",
+    yellow: "FFC000",
+    blue: "9DC3E6",
+    footer: "61666D",
+    footerMuted: "93999F",
+    primary: "9747FF",
+    white: "FFFFFF",
+};
+const SIDEBAR_X = 40;
+const SIDEBAR_W = 24;
+const CONTENT_X = 72;
+const LEFT_W = 195;
+const ARROW_GAP = 30;
+const RIGHT_X = CONTENT_X + LEFT_W + ARROW_GAP;
+const RIGHT_W = 240;
+const CONTENT_W = LEFT_W + ARROW_GAP + RIGHT_W;
+const BAR_TOP = 68;
+const BAR_H = 26;
+const ID_TOP = 106;
+const ID_LEFT_H = 92;
+const ID_RIGHT_H = 92;
+const S1_TOP = 222;
+const S2_TOP = 290;
+const S3_TOP = 358;
+const ROW_H = 44;
+const BIG_H = 136;
+const INCLUDED_TOP = 426;
+const INCLUDED_H = 68;
+const LEFT_CX = CONTENT_X + LEFT_W / 2;
+let drawingId = 1;
+function nextDrawingProperties(kind) {
+    const id = String(drawingId++);
+    return { id, name: `PRISMA ${kind} ${id}` };
+}
+function textRun(text, options) {
+    return new TextRun({
+        text,
+        font: FONT,
+        size: options?.size ?? FS,
+        bold: options?.bold,
+        italics: options?.italic,
+        color: options?.color ?? COLOR.text,
+    });
+}
+function linkRun(text) {
+    return new TextRun({
+        text,
+        font: FONT,
+        size: FS_FOOTER,
+        bold: true,
+        color: COLOR.primary,
+        underline: { type: UnderlineType.SINGLE, color: COLOR.primary },
+    });
+}
+function paragraph(runs, alignment = AlignmentType.LEFT) {
+    return new Paragraph({
+        children: runs,
+        alignment,
+        spacing: { before: 0, after: 0, line: 276 },
+    });
+}
+function createBox(x, y, width, height, paragraphs, options) {
+    return new WpsShapeRun({
+        type: "wps",
+        altText: nextDrawingProperties("shape"),
+        children: paragraphs,
+        transformation: {
+            width: Math.round(width * PT_TO_PX),
+            height: Math.round(height * PT_TO_PX),
+        },
+        floating: {
+            horizontalPosition: {
+                relative: HorizontalPositionRelativeFrom.PAGE,
+                offset: Math.round(x * PT_TO_EMU),
+            },
+            verticalPosition: {
+                relative: VerticalPositionRelativeFrom.PAGE,
+                offset: Math.round(y * PT_TO_EMU),
+            },
+            allowOverlap: true,
+            wrap: { type: TextWrappingType.NONE },
+        },
+        outline: {
+            type: "solidFill",
+            solidFillType: "rgb",
+            value: options?.borderColor ?? COLOR.boxBorder,
+            width: options?.borderWidth ?? 9525,
+        },
+        solidFill: { type: "rgb", value: options?.fill ?? COLOR.white },
+        bodyProperties: {
+            margins: { top: 91440, bottom: 91440, left: 91440, right: 91440 },
+            noAutoFit: true,
+        },
+    });
+}
+function createSidebar(x, y, visualWidth, visualHeight, label) {
+    const centerX = x + visualWidth / 2;
+    const centerY = y + visualHeight / 2;
+    const actualWidth = visualHeight;
+    const actualHeight = visualWidth;
+    return new WpsShapeRun({
+        type: "wps",
+        altText: nextDrawingProperties("shape"),
+        children: [
+            new Paragraph({
+                children: [textRun(label, { bold: true, size: FS_SIDEBAR })],
+                alignment: AlignmentType.CENTER,
+                spacing: { before: 0, after: 0 },
+            }),
+        ],
+        transformation: {
+            width: Math.round(actualWidth * PT_TO_PX),
+            height: Math.round(actualHeight * PT_TO_PX),
+            rotation: 270,
+        },
+        floating: {
+            horizontalPosition: {
+                relative: HorizontalPositionRelativeFrom.PAGE,
+                offset: Math.round((centerX - actualWidth / 2) * PT_TO_EMU),
+            },
+            verticalPosition: {
+                relative: VerticalPositionRelativeFrom.PAGE,
+                offset: Math.round((centerY - actualHeight / 2) * PT_TO_EMU),
+            },
+            allowOverlap: true,
+            wrap: { type: TextWrappingType.NONE },
+        },
+        outline: {
+            type: "solidFill",
+            solidFillType: "rgb",
+            value: COLOR.blue,
+            width: 0,
+        },
+        solidFill: { type: "rgb", value: COLOR.blue },
+        bodyProperties: {
+            margins: { top: 0, bottom: 0, left: 0, right: 0 },
+            verticalAnchor: VerticalAnchor.CENTER,
+            noAutoFit: true,
+        },
+    });
+}
+function arrowPng(direction, length) {
+    const isDown = direction === "down";
+    const width = isDown ? 24 : length * 2;
+    const height = isDown ? length * 2 : 24;
+    const line = isDown
+        ? `<line x1="12" y1="0" x2="12" y2="${height - 10}"/><polygon points="12,${height} 4,${height - 14} 20,${height - 14}"/>`
+        : `<line x1="0" y1="12" x2="${width - 10}" y2="12"/><polygon points="${width},12 ${width - 14},4 ${width - 14},20"/>`;
+    const svg = `<svg xmlns="http://www.w3.org/2000/svg" width="${width}" height="${height}" viewBox="0 0 ${width} ${height}"><g stroke="#101828" fill="#101828" stroke-width="2.4">${line}</g></svg>`;
+    return Buffer.from(new Resvg(svg).render().asPng());
+}
+function arrowImage(direction, x, y, length) {
+    const isDown = direction === "down";
+    return new ImageRun({
+        type: "png",
+        altText: nextDrawingProperties("arrow"),
+        data: arrowPng(direction, length),
+        transformation: {
+            width: isDown ? 12 : length,
+            height: isDown ? length : 12,
+        },
+        floating: {
+            horizontalPosition: {
+                relative: HorizontalPositionRelativeFrom.PAGE,
+                offset: Math.round(x * PT_TO_EMU),
+            },
+            verticalPosition: {
+                relative: VerticalPositionRelativeFrom.PAGE,
+                offset: Math.round(y * PT_TO_EMU),
+            },
+            allowOverlap: true,
+            behindDocument: false,
+            wrap: { type: TextWrappingType.NONE },
+        },
+    });
+}
+export async function buildPrismaFlowDocx(data) {
+    const value = (field) => String(data[field] ?? "");
+    const box = (x, y, width, height, lines) => createBox(x, y, width, height, lines.map((line) => paragraph(line)));
+    const countLine = (field) => [
+        textRun("(n = "),
+        textRun(value(field)),
+        textRun(")"),
+    ];
+    const yellowBar = createBox(CONTENT_X, BAR_TOP, CONTENT_W, BAR_H, [paragraph([textRun("Identification of studies via databases and registers", { bold: true, size: FS_HEADER })], AlignmentType.CENTER)], { fill: COLOR.yellow, borderColor: COLOR.yellow, borderWidth: 0 });
+    const sidebarId = createSidebar(SIDEBAR_X, ID_TOP, SIDEBAR_W, ID_RIGHT_H, "Identification");
+    const sidebarScreen = createSidebar(SIDEBAR_X, S1_TOP, SIDEBAR_W, S3_TOP + ROW_H - S1_TOP, "Screening");
+    const sidebarIncluded = createSidebar(SIDEBAR_X, INCLUDED_TOP, SIDEBAR_W, INCLUDED_H, "Included");
+    const idLeft = box(CONTENT_X, ID_TOP, LEFT_W, ID_LEFT_H, [
+        [textRun("Records identified from*:")],
+        [textRun("    Databases (n = "), textRun(value("pubmed_retrieval_count")), textRun(")")],
+        [textRun("    Registers (n = "), textRun(value("registers_count")), textRun(")")],
+    ]);
+    const idRight = box(RIGHT_X, ID_TOP, RIGHT_W, ID_RIGHT_H, [
+        [textRun("Records removed "), textRun("before", { italic: true }), textRun(" screening:")],
+        [textRun("    Duplicate records removed (n = "), textRun(value("duplicate_count")), textRun(")")],
+        [textRun("    Records marked as ineligible by automation tools (n = "), textRun(value("automation_excluded_count")), textRun(")")],
+        [textRun("    Records removed for other reasons (n = "), textRun(value("other_exclusion_count")), textRun(")")],
+    ]);
+    const s1Left = box(CONTENT_X, S1_TOP, LEFT_W, ROW_H, [[textRun("Records screened")], countLine("screened_count")]);
+    const s1Right = box(RIGHT_X, S1_TOP, RIGHT_W, ROW_H, [[textRun("Records excluded**")], countLine("tiab_excluded_count")]);
+    const s2Left = box(CONTENT_X, S2_TOP, LEFT_W, ROW_H, [[textRun("Reports sought for retrieval")], countLine("reports_sought_count")]);
+    const s2Right = box(RIGHT_X, S2_TOP, RIGHT_W, ROW_H, [[textRun("Reports not retrieved")], countLine("reports_not_retrieved_count")]);
+    const s3Left = box(CONTENT_X, S3_TOP, LEFT_W, ROW_H, [[textRun("Reports assessed for eligibility")], countLine("fulltext_count")]);
+    const bigRight = box(RIGHT_X, S3_TOP, RIGHT_W, BIG_H, [
+        [textRun("Reports excluded:")],
+        [textRun("    Inappropriate population (n = "), textRun(value("wrong_population_count")), textRun(")")],
+        [textRun("    Inappropriate intervention (n = "), textRun(value("wrong_intervention_count")), textRun(")")],
+        [textRun("    Inappropriate comparator (n = "), textRun(value("wrong_comparator_count")), textRun(")")],
+        [textRun("    Inappropriate study design (n = "), textRun(value("wrong_study_design_count")), textRun(")")],
+        [textRun("    Inappropriate outcome (n = "), textRun(value("wrong_outcomes_count")), textRun(")")],
+        [textRun("    Irrelevant (n = "), textRun(value("irrelevant_count")), textRun(")")],
+        [textRun("    etc.")],
+    ]);
+    const included = box(CONTENT_X, INCLUDED_TOP, LEFT_W, INCLUDED_H, [
+        [textRun("Studies included in review")],
+        countLine("included_count"),
+        [textRun("Reports of included studies")],
+        countLine("included_reports_count"),
+    ]);
+    const rightLength = Math.round(ARROW_GAP * PT_TO_PX);
+    const rightX = CONTENT_X + LEFT_W;
+    const downX = LEFT_CX - 6;
+    const shapes = new Paragraph({
+        children: [
+            yellowBar,
+            sidebarId,
+            sidebarScreen,
+            sidebarIncluded,
+            idLeft,
+            idRight,
+            s1Left,
+            s1Right,
+            s2Left,
+            s2Right,
+            s3Left,
+            bigRight,
+            included,
+            arrowImage("right", rightX, ID_TOP + ID_LEFT_H / 2 - 6, rightLength),
+            arrowImage("right", rightX, S1_TOP + ROW_H / 2 - 6, rightLength),
+            arrowImage("right", rightX, S2_TOP + ROW_H / 2 - 6, rightLength),
+            arrowImage("right", rightX, S3_TOP + ROW_H / 2 - 6, rightLength),
+            arrowImage("down", downX, ID_TOP + ID_LEFT_H, Math.round((S1_TOP - ID_TOP - ID_LEFT_H) * PT_TO_PX)),
+            arrowImage("down", downX, S1_TOP + ROW_H, Math.round((S2_TOP - S1_TOP - ROW_H) * PT_TO_PX)),
+            arrowImage("down", downX, S2_TOP + ROW_H, Math.round((S3_TOP - S2_TOP - ROW_H) * PT_TO_PX)),
+            arrowImage("down", downX, S3_TOP + ROW_H, Math.round((INCLUDED_TOP - S3_TOP - ROW_H) * PT_TO_PX)),
+        ],
+    });
+    const title = (text, before, after) => new Paragraph({
+        children: [textRun(text, { bold: true, size: FS_TITLE, color: COLOR.title })],
+        alignment: AlignmentType.CENTER,
+        spacing: { before, after },
+    });
+    const spacer = new Paragraph({
+        children: [],
+        spacing: { before: Math.round((INCLUDED_TOP + INCLUDED_H - 30) * 20), after: 100 },
+    });
+    const footer = [
+        "*Consider, if feasible to do so, reporting the number of records identified from each database or register searched (rather than the total number across all databases/registers).",
+        "**If automation tools were used, indicate how many records were excluded by a human and how many were excluded by automation tools.",
+        "Source: Page MJ, et al. BMJ 2021;372:n71. doi: 10.1136/bmj.n71.",
+    ].map((note, index) => new Paragraph({
+        children: [textRun(note, { size: FS_FOOTER, bold: true, color: index < 2 ? COLOR.footer : COLOR.footerMuted })],
+        spacing: { before: index === 2 ? 160 : 40, after: 40 },
+    }));
+    footer.push(new Paragraph({
+        children: [
+            textRun("This work is licensed under CC BY 4.0. To view a copy of this license, visit ", { size: FS_FOOTER, bold: true, color: COLOR.footerMuted }),
+            linkRun("https://creativecommons.org/licenses/by/4.0"),
+        ],
+        spacing: { before: 40, after: 40 },
+    }));
+    const doc = new Document({
+        sections: [
+            {
+                properties: { page: { margin: { top: 400, right: 400, bottom: 400, left: 400 } } },
+                children: [
+                    title("PRISMA 2020 flow diagram for new systematic reviews which included", 200, 0),
+                    title("searches of databases and registers only", 0, 200),
+                    shapes,
+                    spacer,
+                    ...footer,
+                ],
+            },
+        ],
+    });
+    return Buffer.from(await Packer.toBuffer(doc));
+}
+//# sourceMappingURL=prisma-flow-docx.js.map

package/cli/dist/modules/meta/prisma-flow-docx.js.map

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package/cli/dist/modules/meta/retrieve.d.ts

@@ -0,0 +1,113 @@
+import { type OutputFormat } from "../../core/index.js";
+import type { MetaWorkflowNode } from "./types.js";
+export interface MetaRetrieveBaseOptions {
+    workflowId: string;
+    format?: OutputFormat;
+    configPath?: string;
+}
+export interface CreateRetrieveExpressionOptions extends MetaRetrieveBaseOptions {
+    picosNodeId?: string;
+}
+export interface SaveRetrieveExpressionOptions extends MetaRetrieveBaseOptions {
+    expressionJson?: string;
+    expressionFile?: string;
+    nodeId?: string;
+}
+export interface CheckRetrieveExpressionOptions extends MetaRetrieveBaseOptions {
+    nodeId?: string;
+}
+export interface GetRetrieveExpressionOptions extends MetaRetrieveBaseOptions {
+    nodeId?: string;
+}
+export interface RerunRetrieveExpressionOptions extends MetaRetrieveBaseOptions {
+    nodeId?: string;
+}
+export interface CreateRetrieveLiteratureOptions extends MetaRetrieveBaseOptions {
+    expressionJson?: string;
+    expressionFile?: string;
+}
+export interface ListRetrieveLiteratureOptions extends MetaRetrieveBaseOptions {
+    nodeId?: string;
+    page?: number;
+    limit?: number;
+    sort?: string;
+    order?: "asc" | "desc";
+    publicationType?: string[];
+}
+export interface AddRetrieveLiteratureOptions extends MetaRetrieveBaseOptions {
+    literatureJson?: string;
+    literatureFile?: string;
+    nodeId?: string;
+}
+export interface MetaRetrieveStepResult {
+    runnerId: string;
+    nodeId: string;
+    nodeType: string;
+    status: string;
+    input: Record<string, unknown>;
+    output: unknown;
+    displayOutput?: Record<string, unknown>;
+    displayInstruction?: string;
+    expressionMarkdown?: string;
+    /** 检索结果唯一展示源（9 列 Markdown 表） */
+    tableMarkdown?: string;
+    total?: number;
+    page?: number;
+    limit?: number;
+    node: MetaWorkflowNode;
+}
+export interface MetaRetrieveSaveResult {
+    runnerId: string;
+    nodeId: string;
+    input?: Record<string, unknown>;
+    data: unknown;
+    displayInstruction?: string;
+    /** 检索结果唯一展示源（9 列 Markdown 表） */
+    tableMarkdown?: string;
+    total?: number;
+    page?: number;
+    limit?: number;
+    columns?: Array<{
+        key: string;
+        label: string;
+    }>;
+    rows?: Record<string, unknown>[];
+    displayColumns?: string[];
+    displayRows?: Record<string, unknown>[];
+    table?: {
+        columns: Array<{
+            key: string;
+            label: string;
+        }>;
+        rows: Record<string, unknown>[];
+    };
+}
+export declare function createRetrieveExpression(options: CreateRetrieveExpressionOptions): Promise<MetaRetrieveStepResult>;
+export declare function saveRetrieveExpression(options: SaveRetrieveExpressionOptions): Promise<MetaRetrieveSaveResult>;
+export declare function checkRetrieveExpression(options: CheckRetrieveExpressionOptions): Promise<MetaRetrieveSaveResult>;
+/**
+ * 读取当前已生成的检索式（不重新执行），用于历史切换后展示。
+ *
+ * @param options 工作流与可选节点 ID。
+ * @returns 归一化后的检索式结果（含 expressionMarkdown）。
+ */
+export declare function getRetrieveExpression(options: GetRetrieveExpressionOptions): Promise<MetaRetrieveStepResult>;
+export declare function rerunRetrieveExpression(options: RerunRetrieveExpressionOptions): Promise<MetaRetrieveStepResult>;
+/**
+ * 执行文献检索；若当前已在检索结果节点，会先内部清理旧节点再带检索式重建（对齐网站 retrieve 页）。
+ *
+ * @param options 工作流与可选编辑后的检索式。
+ * @returns 检索步骤结果（含 tableMarkdown）。
+ */
+export declare function createRetrieveLiterature(options: CreateRetrieveLiteratureOptions): Promise<MetaRetrieveStepResult>;
+export declare function listRetrieveLiterature(options: ListRetrieveLiteratureOptions): Promise<MetaRetrieveSaveResult>;
+export declare function addRetrieveLiterature(options: AddRetrieveLiteratureOptions): Promise<MetaRetrieveSaveResult>;
+export declare function runCreateRetrieveExpression(options: CreateRetrieveExpressionOptions): Promise<void>;
+export declare function runSaveRetrieveExpression(options: SaveRetrieveExpressionOptions): Promise<void>;
+export declare function runCheckRetrieveExpression(options: CheckRetrieveExpressionOptions): Promise<void>;
+export declare function runGetRetrieveExpression(options: GetRetrieveExpressionOptions): Promise<void>;
+export declare function runRerunRetrieveExpression(options: RerunRetrieveExpressionOptions): Promise<void>;
+export declare function runCreateRetrieveLiterature(options: CreateRetrieveLiteratureOptions): Promise<void>;
+export declare function runListRetrieveLiterature(options: ListRetrieveLiteratureOptions): Promise<void>;
+export declare function runAddRetrieveLiterature(options: AddRetrieveLiteratureOptions): Promise<void>;
+//# sourceMappingURL=retrieve.d.ts.map

package/cli/dist/modules/meta/retrieve.d.ts.map

@@ -0,0 +1 @@
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