@fnndsc/chili 3.2.5

package/dist/models/plugin.d.ts

@@ -0,0 +1,27 @@
+/**
+ * @file Models for Plugin operations.
+ *
+ * Defines the data structures for Plugins and Plugin Instances (execution results).
+ *
+ * @module
+ */
+import { ChrisPluginRaw } from './resource.js';
+/**
+ * Represents a ChRIS Plugin.
+ * Extends the raw resource definition with any view-specific needs.
+ */
+export interface Plugin extends ChrisPluginRaw {
+}
+/**
+ * Represents a running or completed Plugin Instance.
+ */
+export interface PluginInstance {
+    id: number;
+    title: string;
+    status: string;
+    plugin_name?: string;
+    start_date?: string;
+    end_date?: string;
+    feed_id?: number;
+    [key: string]: unknown;
+}

package/dist/models/plugin.js

@@ -0,0 +1 @@
+export {};

package/dist/models/resource.d.ts

@@ -0,0 +1,39 @@
+/**
+ * @file Models for raw ChRIS resources as returned by the API/Salsa.
+ *
+ * These interfaces describe the shape of the data objects found in the `tableData`
+ * arrays returned by Salsa's listing functions.
+ *
+ * @module
+ */
+/**
+ * Base interface for any ChRIS resource.
+ */
+export interface ChrisResourceRaw {
+    url?: string;
+    id?: number;
+    [key: string]: unknown;
+}
+/**
+ * Represents a File, Directory, or Link from the ChRIS filesystem.
+ * Note: Fields are optional because 'dirs', 'files', and 'links' endpoints
+ * return slightly different subsets of these fields.
+ */
+export interface ChrisFileOrDirRaw extends ChrisResourceRaw {
+    fname?: string;
+    path?: string;
+    fsize?: number;
+    owner_username?: string;
+    creation_date?: string;
+}
+/**
+ * Represents a ChRIS Plugin.
+ */
+export interface ChrisPluginRaw extends ChrisResourceRaw {
+    name: string;
+    version: string;
+    creation_date: string;
+    title?: string;
+    dock_image?: string;
+    public_repo?: string;
+}

package/dist/models/resource.js

@@ -0,0 +1,9 @@
+/**
+ * @file Models for raw ChRIS resources as returned by the API/Salsa.
+ *
+ * These interfaces describe the shape of the data objects found in the `tableData`
+ * arrays returned by Salsa's listing functions.
+ *
+ * @module
+ */
+export {};

package/dist/pacs/pacsQueryHandler.d.ts

@@ -0,0 +1,55 @@
+/**
+ * @file Handler for the PACS query command group.
+ *
+ * @module
+ */
+import { Command } from "commander";
+/**
+ * Handler for PACS queries commands.
+ */
+export declare class PACSQueryGroupHandler {
+    private baseGroupHandler;
+    private assetName;
+    constructor();
+    /**
+     * Render a decoded PACS query JSON payload into a readable string.
+     * Expected structure:
+     * [
+     *   { <study fields>, series: [ { <series fields> }, ... ] },
+     *   ...
+     * ]
+     * Falls back gracefully if structure varies.
+     */
+    private pacsResult_renderPretty;
+    private pacsserverContext_resolve;
+    private options_withPACSFilter;
+    pacsQueryCommand_setup(program: Command): void;
+    /**
+     * Registers the `list` subcommand (with PACS-server context filtering).
+     *
+     * @param parent - The parent `pacsqueries` command.
+     */
+    private listCommand_register;
+    /**
+     * Registers the `fieldslist` subcommand.
+     *
+     * @param parent - The parent `pacsqueries` command.
+     */
+    private fieldsListCommand_register;
+    /**
+     * Registers the `create <query>` subcommand.
+     *
+     * @param parent - The parent `pacsqueries` command.
+     */
+    private createCommand_register;
+    /**
+     * Registers the `decode <queryId>` subcommand.
+     *
+     * @param parent - The parent `pacsqueries` command.
+     */
+    private decodeCommand_register;
+    /**
+     * Build a PACS query payload from JSON or comma-separated key:value pairs.
+     */
+    private queryPayload_build;
+}

package/dist/pacs/pacsQueryHandler.js

@@ -0,0 +1,196 @@
+/**
+ * @file Handler for the PACS query command group.
+ *
+ * @module
+ */
+import { ChRISPACSQueryGroup, errorStack_getAllOfType, chrisContext, Context, } from "@fnndsc/cumin";
+import { pacsQueries_create, pacsQuery_resultDecode } from "@fnndsc/salsa";
+import { BaseGroupHandler } from "../handlers/baseGroupHandler.js";
+import { border_draw } from "../screen/screen.js";
+import { pacsQueryResult_renderPretty } from "./pacsResultRender.js";
+import { pacsQueryPayload_build } from "./pacsQueryPayload.js";
+/**
+ * Handler for PACS queries commands.
+ */
+export class PACSQueryGroupHandler {
+    constructor() {
+        this.assetName = "pacsqueries";
+        const chrisObject = new ChRISPACSQueryGroup();
+        this.baseGroupHandler = new BaseGroupHandler(this.assetName, chrisObject);
+    }
+    /**
+     * Render a decoded PACS query JSON payload into a readable string.
+     * Expected structure:
+     * [
+     *   { <study fields>, series: [ { <series fields> }, ... ] },
+     *   ...
+     * ]
+     * Falls back gracefully if structure varies.
+     */
+    pacsResult_renderPretty(payload) {
+        return pacsQueryResult_renderPretty(payload);
+    }
+    async pacsserverContext_resolve(overridePacsserver) {
+        if (overridePacsserver && overridePacsserver.length > 0) {
+            return overridePacsserver;
+        }
+        const current = await chrisContext.current_get(Context.PACSserver);
+        return current;
+    }
+    options_withPACSFilter(options, pacsserver) {
+        if (!pacsserver) {
+            return options;
+        }
+        const pacsFilter = /^\d+$/.test(pacsserver)
+            ? `pacs_id:${pacsserver}`
+            : `pacs_identifier:${pacsserver}`;
+        const searchParts = [];
+        if (options.search) {
+            searchParts.push(options.search);
+        }
+        searchParts.push(pacsFilter);
+        return { ...options, search: searchParts.join(",") };
+    }
+    pacsQueryCommand_setup(program) {
+        const pacsQueryCommand = program
+            .command(this.assetName)
+            .description("Interact with PACS queries");
+        this.listCommand_register(pacsQueryCommand);
+        this.fieldsListCommand_register(pacsQueryCommand);
+        this.createCommand_register(pacsQueryCommand);
+        this.decodeCommand_register(pacsQueryCommand);
+    }
+    /**
+     * Registers the `list` subcommand (with PACS-server context filtering).
+     *
+     * @param parent - The parent `pacsqueries` command.
+     */
+    listCommand_register(parent) {
+        const listCommand = this.baseGroupHandler.baseListCommand_create(async (options) => {
+            const pacsserver = await this.pacsserverContext_resolve(options.pacsserver);
+            if (!pacsserver) {
+                console.log(border_draw("No PACS server in context. Use --pacsserver or set via context."));
+                return;
+            }
+            const mergedOptions = this.options_withPACSFilter(options, pacsserver);
+            await this.baseGroupHandler.resources_list(mergedOptions);
+        });
+        listCommand.option("--pacsserver <pacsserver>", "PACS server ID or identifier to filter queries");
+        parent.addCommand(listCommand);
+    }
+    /**
+     * Registers the `fieldslist` subcommand.
+     *
+     * @param parent - The parent `pacsqueries` command.
+     */
+    fieldsListCommand_register(parent) {
+        parent
+            .command("fieldslist")
+            .description(`list the ${this.assetName} resource fields`)
+            .action(async () => {
+            await this.baseGroupHandler.resourceFields_list();
+        });
+    }
+    /**
+     * Registers the `create <query>` subcommand.
+     *
+     * @param parent - The parent `pacsqueries` command.
+     */
+    createCommand_register(parent) {
+        parent
+            .command("create <query>")
+            .description("Create a PACS query against the current or specified PACS server. <query> can be JSON or comma-separated key:value pairs.")
+            .option("--title <title>", "Title for the PACS query", `Query ${Date.now()}`)
+            .option("--description <description>", "Optional description for the PACS query")
+            .option("--pacsserver <pacsserver>", "PACS server ID or identifier (overrides context)")
+            .action(async (queryInput, options) => {
+            const pacsserver = await this.pacsserverContext_resolve(options.pacsserver);
+            if (!pacsserver) {
+                border_draw("No PACS server in context. Use --pacsserver or set via context.");
+                return;
+            }
+            const payload = pacsQueryPayload_build(queryInput, options.title, options.description);
+            if (!payload) {
+                console.log(border_draw("Invalid query format. Provide JSON or comma-separated key:value pairs."));
+                return;
+            }
+            const result = await pacsQueries_create(pacsserver, payload);
+            if (!result.ok) {
+                const errors = errorStack_getAllOfType("error");
+                if (errors.length) {
+                    errors.forEach((msg) => console.log(border_draw(msg)));
+                }
+                else {
+                    console.log(border_draw("Failed to create PACS query."));
+                }
+                return;
+            }
+            const created = result.value;
+            const msg = [
+                "Created PACS query",
+                `id=${created.id}`,
+                `status=${created.status || "unknown"}`,
+                `pacs=${pacsserver}`,
+                `title="${created.title ?? options.title ?? ""}"`,
+            ].join(" ");
+            console.log(border_draw(msg.trim()));
+        });
+    }
+    /**
+     * Registers the `decode <queryId>` subcommand.
+     *
+     * @param parent - The parent `pacsqueries` command.
+     */
+    decodeCommand_register(parent) {
+        parent
+            .command("decode <queryId>")
+            .description("Decode the result payload of a PACS query")
+            .option("--raw", "Print raw decoded JSON if available")
+            .action(async (queryId, options) => {
+            const idNum = Number(queryId);
+            if (Number.isNaN(idNum)) {
+                console.log(border_draw("queryId must be a number."));
+                return;
+            }
+            const result = await pacsQuery_resultDecode(idNum);
+            if (!result.ok) {
+                const errors = errorStack_getAllOfType("error");
+                if (errors.length) {
+                    errors.forEach((msg) => console.log(border_draw(msg)));
+                }
+                else {
+                    console.log(border_draw(`Failed to decode PACS query result for ${idNum}.`));
+                }
+                return;
+            }
+            const decoded = result.value;
+            // Prefer JSON, then text, else indicate base64 length
+            if (decoded.json !== undefined) {
+                if (options.raw) {
+                    console.log(border_draw(JSON.stringify(decoded.json, null, 2)));
+                    return;
+                }
+                const pretty = this.pacsResult_renderPretty(decoded.json);
+                if (pretty) {
+                    console.log(border_draw(pretty));
+                }
+                else {
+                    console.log(border_draw(JSON.stringify(decoded.json, null, 2)));
+                }
+            }
+            else if (decoded.text) {
+                console.log(border_draw(decoded.text));
+            }
+            else {
+                const len = decoded.raw.length;
+                console.log(border_draw(`Decoded payload available (base64 length ${len}), but not printable.`));
+            }
+        });
+    }
+    /**
+     * Build a PACS query payload from JSON or comma-separated key:value pairs.
+     */
+    queryPayload_build(queryInput, title, description) {
+        return pacsQueryPayload_build(queryInput, title, description);
+    }
+}

package/dist/pacs/pacsQueryPayload.d.ts

@@ -0,0 +1,19 @@
+/**
+ * @file Pure builder for PACS query creation payloads.
+ *
+ * Accepts a JSON string or comma-separated `key:value` pairs. Dependency-free
+ * (type-only import) for easy unit testing.
+ *
+ * @module
+ */
+import type { PACSQueryCreateData } from "@fnndsc/cumin";
+/**
+ * Builds a PACS query payload from either a JSON string or comma-separated
+ * `key:value` pairs.
+ *
+ * @param queryInput - JSON or comma-separated key:value query specification.
+ * @param title - Optional query title (defaults to a timestamped title).
+ * @param description - Optional query description.
+ * @returns The payload, or null if no usable query fields were parsed.
+ */
+export declare function pacsQueryPayload_build(queryInput: string, title?: string, description?: string): PACSQueryCreateData | null;

package/dist/pacs/pacsQueryPayload.js

@@ -0,0 +1,44 @@
+/**
+ * Builds a PACS query payload from either a JSON string or comma-separated
+ * `key:value` pairs.
+ *
+ * @param queryInput - JSON or comma-separated key:value query specification.
+ * @param title - Optional query title (defaults to a timestamped title).
+ * @param description - Optional query description.
+ * @returns The payload, or null if no usable query fields were parsed.
+ */
+export function pacsQueryPayload_build(queryInput, title, description) {
+    let queryObject = {};
+    try {
+        const parsed = JSON.parse(queryInput);
+        if (typeof parsed === "object" && parsed !== null) {
+            queryObject = parsed;
+        }
+    }
+    catch {
+        // Fallback to comma-separated key:value pairs
+        queryObject = queryInput.split(",").reduce((acc, part) => {
+            const [keyRaw, ...rest] = part.split(":");
+            if (!keyRaw || rest.length === 0) {
+                return acc;
+            }
+            const key = keyRaw.trim();
+            const value = rest.join(":").trim();
+            if (key && value) {
+                acc[key] = value;
+            }
+            return acc;
+        }, {});
+    }
+    if (Object.keys(queryObject).length === 0) {
+        return null;
+    }
+    const payload = {
+        title: title || `Query ${Date.now()}`,
+        query: JSON.stringify(queryObject),
+    };
+    if (description) {
+        payload.description = description;
+    }
+    return payload;
+}

package/dist/pacs/pacsResultRender.d.ts

@@ -0,0 +1,20 @@
+/**
+ * @file Pure rendering of PACS query result payloads into a human-readable,
+ * indented study/series listing.
+ *
+ * The CUBE PACS query result is a loosely-typed nested structure; these helpers
+ * extract DICOM tag values defensively and format them. Dependency-free for
+ * easy unit testing.
+ *
+ * @module
+ */
+/**
+ * Renders a PACS query result payload into a human-readable string.
+ *
+ * Accepts a single study object or an array of studies; each study may carry a
+ * nested series array under `series`/`Series`/`results`/`data`.
+ *
+ * @param payload - The PACS query result payload.
+ * @returns The formatted listing, or null if there is nothing to render.
+ */
+export declare function pacsQueryResult_renderPretty(payload: unknown): string | null;

package/dist/pacs/pacsResultRender.js

@@ -0,0 +1,141 @@
+/**
+ * @file Pure rendering of PACS query result payloads into a human-readable,
+ * indented study/series listing.
+ *
+ * The CUBE PACS query result is a loosely-typed nested structure; these helpers
+ * extract DICOM tag values defensively and format them. Dependency-free for
+ * easy unit testing.
+ *
+ * @module
+ */
+const STUDY_FIELD_ORDER = [
+    "AccessionNumber",
+    "PatientName",
+    "PatientID",
+    "PatientBirthDate",
+    "PatientSex",
+    "StudyDate",
+    "StudyDescription",
+    "StudyInstanceUID",
+    "ModalitiesInStudy",
+    "NumberOfStudyRelatedSeries",
+    "NumberOfStudyRelatedInstances",
+    "RetrieveAETitle",
+    "status",
+    "QueryRetrieveLevel",
+];
+const SERIES_FIELD_ORDER = [
+    "SeriesDescription",
+    "Modality",
+    "SeriesInstanceUID",
+    "NumberOfSeriesRelatedInstances",
+    "InstanceNumber",
+    "PerformedStationAETitle",
+    "RetrieveLevel",
+    "status",
+    "uid",
+];
+/**
+ * Extracts a `{ label, value }` DICOM tag from a value if it has the tag shape.
+ *
+ * @param val - A candidate tag value.
+ * @returns The resolved tag, or null if it is not tag-shaped.
+ */
+function tag_extract(val) {
+    if (val && typeof val === "object" && "value" in val) {
+        const tagObj = val;
+        const label = typeof tagObj.label === "string" && tagObj.label.length ? tagObj.label : "";
+        return { label, value: tagObj.value };
+    }
+    return null;
+}
+/**
+ * Extracts displayable fields from an object, preferring a given key order and
+ * optionally including all remaining scalar/tag keys. De-duplicates by label.
+ *
+ * @param obj - The source object.
+ * @param preferredOrder - Keys to emit first, in order.
+ * @param includeAll - Whether to also include remaining keys.
+ * @returns The collected fields.
+ */
+function fields_extract(obj, preferredOrder, includeAll) {
+    const collected = [];
+    const seen = new Set();
+    const field_push = (label, value) => {
+        if (label && !seen.has(label)) {
+            collected.push({ label, value });
+            seen.add(label);
+        }
+    };
+    const keys_scan = (keys) => {
+        for (const key of keys) {
+            const val = obj[key];
+            if (Array.isArray(val))
+                continue;
+            const tagVal = tag_extract(val);
+            if (tagVal) {
+                field_push(tagVal.label || key, tagVal.value);
+            }
+            else if (typeof val === "string" || typeof val === "number" || typeof val === "boolean") {
+                field_push(key, val);
+            }
+        }
+    };
+    keys_scan(preferredOrder);
+    if (includeAll) {
+        keys_scan(Object.keys(obj));
+    }
+    return collected;
+}
+/**
+ * Renders one study (and its nested series) into indented output lines.
+ *
+ * @param studyIdx - Zero-based study index.
+ * @param studyObj - The study object.
+ * @returns The rendered lines for this study.
+ */
+function study_renderLines(studyIdx, studyObj) {
+    const lines = [];
+    const seriesArr = Array.isArray(studyObj['series']) ? studyObj['series'] :
+        Array.isArray(studyObj['Series']) ? studyObj['Series'] :
+            Array.isArray(studyObj['results']) ? studyObj['results'] :
+                Array.isArray(studyObj['data']) ? studyObj['data'] :
+                    null;
+    const studyFields = fields_extract(studyObj, STUDY_FIELD_ORDER, true);
+    lines.push(`Study ${studyIdx + 1}`);
+    studyFields.forEach((f) => lines.push(`  ${f.label}: ${f.value}`));
+    if (seriesArr && seriesArr.length) {
+        seriesArr.forEach((series, idx) => {
+            if (!series || typeof series !== "object")
+                return;
+            const seriesFields = fields_extract(series, SERIES_FIELD_ORDER, false);
+            lines.push(`  Series ${idx + 1}`);
+            seriesFields.forEach((f) => lines.push(`    ${f.label}: ${f.value}`));
+        });
+    }
+    lines.push("");
+    return lines;
+}
+/**
+ * Renders a PACS query result payload into a human-readable string.
+ *
+ * Accepts a single study object or an array of studies; each study may carry a
+ * nested series array under `series`/`Series`/`results`/`data`.
+ *
+ * @param payload - The PACS query result payload.
+ * @returns The formatted listing, or null if there is nothing to render.
+ */
+export function pacsQueryResult_renderPretty(payload) {
+    if (!payload || typeof payload !== "object") {
+        return null;
+    }
+    const payloadArray = Array.isArray(payload) ? payload : [payload];
+    const lines = [];
+    payloadArray.forEach((item, idx) => {
+        if (item && typeof item === "object") {
+            lines.push(...study_renderLines(idx, item));
+        }
+    });
+    const output = lines.join("\n").trim();
+    return output.length ? output : null;
+}

package/dist/pacs/pacsRetrieveHandler.d.ts

@@ -0,0 +1,87 @@
+/**
+ * @file Handler for the PACS retrieve command group.
+ *
+ * @module
+ */
+import { Command } from "commander";
+/**
+ * Handler for PACS retrieve commands.
+ */
+export declare class PACSRetrieveGroupHandler {
+    private assetName;
+    /**
+     * Setup PACS retrieve commands on the parent command.
+     *
+     * @param program - Commander program instance.
+     */
+    pacsRetrieveCommand_setup(program: Command): void;
+    /**
+     * Handle the 'pull' command - create a new retrieve.
+     *
+     * @param queryIdStr - Query ID as string.
+     */
+    private retrieve_pull;
+    /**
+     * Handle the 'report' command - show detailed status.
+     *
+     * @param queryIdStr - Query ID as string.
+     */
+    private retrieve_report;
+    /**
+     * Handle the 'cancel' command - delete a retrieve.
+     *
+     * @param retrieveIdStr - Retrieve ID as string.
+     */
+    private retrieve_cancel;
+    /**
+     * Determine overall completion status from series statuses.
+     *
+     * @param report - The status report.
+     * @returns True if all series are pulled.
+     */
+    private allSeries_arePulled;
+    /**
+     * Render a status report into a human-readable string.
+     *
+     * @param report - The status report.
+     * @returns Formatted string.
+     */
+    private report_render;
+    /**
+     * Extract value from a DICOM tag object or return as-is.
+     *
+     * @param val - Potentially a tag object with {label, value} or a primitive.
+     * @returns The extracted value.
+     */
+    private tagValue_extract;
+    /**
+     * Render a single study to the lines array.
+     *
+     * @param study - Study status.
+     * @param studyNum - Study number (1-indexed).
+     * @param lines - Output lines array.
+     */
+    private study_renderTo;
+    /**
+     * Render a single series to the lines array.
+     *
+     * @param series - Series status.
+     * @param seriesNum - Series number (1-indexed).
+     * @param lines - Output lines array.
+     */
+    private series_renderTo;
+    /**
+     * Generate display string for series status.
+     *
+     * @param series - Series status.
+     * @returns Display string.
+     */
+    private series_statusDisplay;
+    /**
+     * Map retrieve status to display string.
+     *
+     * @param status - Raw status string.
+     * @returns Display-friendly status.
+     */
+    private status_mapToDisplay;
+}