@fnndsc/cumin 3.8.0 → 3.9.0

package/dist/groups/chrisGroups.d.ts

@@ -1,11 +1,77 @@
 /**
- * @file ChRIS Group resources.
+ * @file ChRIS group resources and membership operations.
  * @module
  */
 import { ChRISResourceGroup } from '../resources/chrisResourceGroup.js';
+import { type Result } from '../utils/result.js';
+/** Represents a ChRIS group resource. */
+export interface ChrisGroup {
+    id: number;
+    name: string;
+}
+/** Represents a user's membership in a ChRIS group. */
+export interface ChrisGroupMember {
+    id: number;
+    username: string;
+}
 /**
  * Group handler for ChRIS user groups.
  */
 export declare class ChRISGroupGroup extends ChRISResourceGroup {
     constructor();
+    /**
+     * Resolves one group resource through this resource group.
+     *
+     * @param groupID - Numeric CUBE group identifier.
+     * @returns The group resource, or null after recording a useful error.
+     */
+    private group_get;
+    /**
+     * Fetches all groups, following the API's pagination links.
+     *
+     * @returns Every visible CUBE group, or Err on failure.
+     */
+    groups_getAll(): Promise<Result<ChrisGroup[]>>;
+    /**
+     * Fetches every user belonging to one group.
+     *
+     * @param groupID - Numeric CUBE group identifier.
+     * @returns Every group membership, or Err on failure.
+     */
+    members_getAll(groupID: number): Promise<Result<ChrisGroupMember[]>>;
+    /**
+     * Adds an existing CUBE user to one group.
+     *
+     * @param groupID - Numeric CUBE group identifier.
+     * @param username - Existing CUBE username to add.
+     * @returns The created membership, or Err when CUBE refuses the operation.
+     */
+    user_add(groupID: number, username: string): Promise<Result<ChrisGroupMember>>;
+    /**
+     * Removes a CUBE user from one group.
+     *
+     * @param groupID - Numeric CUBE group identifier.
+     * @param username - Existing CUBE username to remove.
+     * @returns True after deletion, or Err when the membership does not exist or deletion fails.
+     */
+    user_remove(groupID: number, username: string): Promise<Result<boolean>>;
 }
+/** @returns Every visible CUBE group, or Err on failure. */
+export declare function groups_getAll(): Promise<Result<ChrisGroup[]>>;
+/**
+ * @param groupID - Numeric CUBE group identifier.
+ * @returns Every membership in the group, or Err on failure.
+ */
+export declare function groupMembers_getAll(groupID: number): Promise<Result<ChrisGroupMember[]>>;
+/**
+ * @param groupID - Numeric CUBE group identifier.
+ * @param username - Existing CUBE username to add.
+ * @returns The created membership, or Err on failure.
+ */
+export declare function groupUser_add(groupID: number, username: string): Promise<Result<ChrisGroupMember>>;
+/**
+ * @param groupID - Numeric CUBE group identifier.
+ * @param username - Existing CUBE username to remove.
+ * @returns True after deletion, or Err on failure.
+ */
+export declare function groupUser_remove(groupID: number, username: string): Promise<Result<boolean>>;

package/dist/groups/chrisGroups.js

@@ -1,11 +1,18 @@
 "use strict";
 /**
- * @file ChRIS Group resources.
+ * @file ChRIS group resources and membership operations.
  * @module
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.ChRISGroupGroup = void 0;
+exports.groups_getAll = groups_getAll;
+exports.groupMembers_getAll = groupMembers_getAll;
+exports.groupUser_add = groupUser_add;
+exports.groupUser_remove = groupUser_remove;
+const adapter_js_1 = require("../chrisapi/adapter.js");
+const errorStack_js_1 = require("../error/errorStack.js");
 const chrisResourceGroup_js_1 = require("../resources/chrisResourceGroup.js");
+const result_js_1 = require("../utils/result.js");
 /**
  * Group handler for ChRIS user groups.
  */
@@ -13,6 +20,169 @@ class ChRISGroupGroup extends chrisResourceGroup_js_1.ChRISResourceGroup {
     constructor() {
         super('Groups', 'getGroups');
     }
+    /**
+     * Resolves one group resource through this resource group.
+     *
+     * @param groupID - Numeric CUBE group identifier.
+     * @returns The group resource, or null after recording a useful error.
+     */
+    async group_get(groupID) {
+        const client = await this.client_get();
+        if (!client) {
+            errorStack_js_1.errorStack.stack_push('error', 'Not connected to ChRIS. Please log in.');
+            return null;
+        }
+        const group = await client.getGroup(groupID);
+        if (!group)
+            errorStack_js_1.errorStack.stack_push('error', `Group ${groupID} was not found.`);
+        return group;
+    }
+    /**
+     * Fetches all groups, following the API's pagination links.
+     *
+     * @returns Every visible CUBE group, or Err on failure.
+     */
+    async groups_getAll() {
+        try {
+            const client = await this.client_get();
+            if (!client) {
+                errorStack_js_1.errorStack.stack_push('error', 'Not connected to ChRIS. Please log in.');
+                return (0, result_js_1.Err)();
+            }
+            const groups = [];
+            let offset = 0;
+            while (true) {
+                const page = await client.getGroups({ offset });
+                const pageGroups = (0, adapter_js_1.listData_get)(page);
+                groups.push(...pageGroups);
+                if (!page.hasNextPage || pageGroups.length === 0)
+                    break;
+                offset += pageGroups.length;
+            }
+            return (0, result_js_1.Ok)(groups);
+        }
+        catch (error) {
+            const message = error instanceof Error ? error.message : String(error);
+            errorStack_js_1.errorStack.stack_push('error', `Failed to fetch groups: ${message}`);
+            return (0, result_js_1.Err)();
+        }
+    }
+    /**
+     * Fetches every user belonging to one group.
+     *
+     * @param groupID - Numeric CUBE group identifier.
+     * @returns Every group membership, or Err on failure.
+     */
+    async members_getAll(groupID) {
+        try {
+            const group = await this.group_get(groupID);
+            if (!group)
+                return (0, result_js_1.Err)();
+            const members = [];
+            let offset = 0;
+            while (true) {
+                const page = await group.getUsers({ offset });
+                const membershipResources = (0, adapter_js_1.items_get)(page);
+                const pageMembers = await Promise.all(membershipResources.map(async (membershipResource) => {
+                    const userResource = await membershipResource.getUser();
+                    const member = (0, adapter_js_1.itemData_get)(userResource);
+                    if (!member)
+                        throw new Error('group membership carried no linked user data');
+                    return member;
+                }));
+                members.push(...pageMembers);
+                if (!page.hasNextPage || membershipResources.length === 0)
+                    break;
+                offset += membershipResources.length;
+            }
+            return (0, result_js_1.Ok)(members);
+        }
+        catch (error) {
+            const message = error instanceof Error ? error.message : String(error);
+            errorStack_js_1.errorStack.stack_push('error', `Failed to fetch users for group ${groupID}: ${message}`);
+            return (0, result_js_1.Err)();
+        }
+    }
+    /**
+     * Adds an existing CUBE user to one group.
+     *
+     * @param groupID - Numeric CUBE group identifier.
+     * @param username - Existing CUBE username to add.
+     * @returns The created membership, or Err when CUBE refuses the operation.
+     */
+    async user_add(groupID, username) {
+        try {
+            const group = await this.group_get(groupID);
+            if (!group)
+                return (0, result_js_1.Err)();
+            const membershipResource = await group.adminAddUser(username);
+            const userResource = await membershipResource.getUser();
+            const membership = (0, adapter_js_1.itemData_get)(userResource);
+            if (!membership) {
+                errorStack_js_1.errorStack.stack_push('error', `CUBE returned no membership for ${username}.`);
+                return (0, result_js_1.Err)();
+            }
+            return (0, result_js_1.Ok)(membership);
+        }
+        catch (error) {
+            const message = error instanceof Error ? error.message : String(error);
+            errorStack_js_1.errorStack.stack_push('error', `Failed to add ${username} to group ${groupID}: ${message}`);
+            return (0, result_js_1.Err)();
+        }
+    }
+    /**
+     * Removes a CUBE user from one group.
+     *
+     * @param groupID - Numeric CUBE group identifier.
+     * @param username - Existing CUBE username to remove.
+     * @returns True after deletion, or Err when the membership does not exist or deletion fails.
+     */
+    async user_remove(groupID, username) {
+        try {
+            const group = await this.group_get(groupID);
+            if (!group)
+                return (0, result_js_1.Err)();
+            const membership = await group.getUser(username);
+            if (!membership) {
+                errorStack_js_1.errorStack.stack_push('error', `${username} is not a member of group ${groupID}.`);
+                return (0, result_js_1.Err)();
+            }
+            await membership.delete();
+            return (0, result_js_1.Ok)(true);
+        }
+        catch (error) {
+            const message = error instanceof Error ? error.message : String(error);
+            errorStack_js_1.errorStack.stack_push('error', `Failed to remove ${username} from group ${groupID}: ${message}`);
+            return (0, result_js_1.Err)();
+        }
+    }
 }
 exports.ChRISGroupGroup = ChRISGroupGroup;
+/** @returns Every visible CUBE group, or Err on failure. */
+async function groups_getAll() {
+    return new ChRISGroupGroup().groups_getAll();
+}
+/**
+ * @param groupID - Numeric CUBE group identifier.
+ * @returns Every membership in the group, or Err on failure.
+ */
+async function groupMembers_getAll(groupID) {
+    return new ChRISGroupGroup().members_getAll(groupID);
+}
+/**
+ * @param groupID - Numeric CUBE group identifier.
+ * @param username - Existing CUBE username to add.
+ * @returns The created membership, or Err on failure.
+ */
+async function groupUser_add(groupID, username) {
+    return new ChRISGroupGroup().user_add(groupID, username);
+}
+/**
+ * @param groupID - Numeric CUBE group identifier.
+ * @param username - Existing CUBE username to remove.
+ * @returns True after deletion, or Err on failure.
+ */
+async function groupUser_remove(groupID, username) {
+    return new ChRISGroupGroup().user_remove(groupID, username);
+}
 //# sourceMappingURL=chrisGroups.js.map

package/dist/groups/chrisGroups.js.map

@@ -1 +1 @@
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package/dist/index.d.ts

@@ -32,6 +32,7 @@ export * from "./io/node_io";
 export * from "./utils/keypair";
 export * from "./utils/searchable";
 export * from "./utils/result";
+export * from "./utils/retry";
 export * from "./utils/envelope";
 export * from "./cache";
 export * from "./path/chrisPath";
@@ -41,6 +42,7 @@ export * from "./tags/chrisTags";
 export * from "./groups/chrisGroups";
 export * from "./pluginmetas/chrisPluginMetas";
 export * from "./workflows/chrisWorkflows";
+export * from "./output/runtimeOutput";
 export { listData_get, itemData_get, items_get } from "./chrisapi/adapter";
 export type { ListResource, Resource, ItemResource, PluginInstance, Feed, FileBrowserFolder, UserFile, PACSFile, } from "./chrisapi/adapter";
 /**

package/dist/index.js

@@ -50,6 +50,7 @@ __exportStar(require("./io/node_io"), exports);
 __exportStar(require("./utils/keypair"), exports);
 __exportStar(require("./utils/searchable"), exports);
 __exportStar(require("./utils/result"), exports);
+__exportStar(require("./utils/retry"), exports);
 __exportStar(require("./utils/envelope"), exports);
 __exportStar(require("./cache"), exports);
 __exportStar(require("./path/chrisPath"), exports);
@@ -59,6 +60,7 @@ __exportStar(require("./tags/chrisTags"), exports);
 __exportStar(require("./groups/chrisGroups"), exports);
 __exportStar(require("./pluginmetas/chrisPluginMetas"), exports);
 __exportStar(require("./workflows/chrisWorkflows"), exports);
+__exportStar(require("./output/runtimeOutput"), exports);
 // Re-export chrisapi types so downstream packages don't import chrisapi directly
 var adapter_1 = require("./chrisapi/adapter");
 Object.defineProperty(exports, "listData_get", { enumerable: true, get: function () { return adapter_1.listData_get; } });

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;AAEA;;;;;;;;GAQG;;;;;;;;;;;;;;;;;AA8EH,4CAKC;AAjFD,qCAAmB;AACnB,qDAAmC;AACnC,kDAAgC;AAChC,oDAAkC;AAClC,4DAA0C;AAC1C,yDAAuC;AACvC,yDAAuC;AACvC,mEAAiD;AACjD,6DAA2C;AAC3C,mDAAiC;AACjC,6DAA2C;AAC3C,iEAA+C;AAC/C,8DAA4C;AAC5C,yEAAuD;AACvD,iEAA+C;AAC/C,2DAAyC;AACzC,0DAAwC;AACxC,8DAA4C;AAC5C,+CAA6B;AAC7B,0CAAwB;AACxB,+CAA6B;AAC7B,kDAAgC;AAChC,qDAAmC;AACnC,iDAA+B;AAC/B,gDAA8B;AAC9B,mDAAiC;AACjC,0CAAwB;AACxB,mDAAiC;AACjC,4DAA0C;AAC1C,qDAAmC;AACnC,mDAAiC;AACjC,uDAAqC;AACrC,iEAA+C;AAC/C,6DAA2C;AAC3C,yDAAuC;AAEvC,iFAAiF;AACjF,8CAA2E;AAAlE,uGAAA,YAAY,OAAA;AAAE,uGAAA,YAAY,OAAA;AAAE,oGAAA,SAAS,OAAA;AAiC9C;;;;;GAKG;AACI,KAAK,UAAU,gBAAgB,CAAC,GAAW;IAChD,MAAM,OAAO,GAAW,OAAO,CAAC;IAChC,wCAAwC;IACxC,6CAA6C;IAC7C,OAAO,OAAO,CAAC;AACjB,CAAC;AAED;;GAEG;AACH,KAAK,UAAU,IAAI;IACjB,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,CAAC;AAC5B,CAAC;AAED,gEAAgE;AAChE,qCAAqC;AACrC,IAAI,OAAO,CAAC,IAAI,KAAK,MAAM,EAAE,CAAC;IAC5B,IAAI,EAAE,CAAC,KAAK,CAAC,CAAC,KAAK,EAAE,EAAE;QACrB,OAAO,CAAC,KAAK,CAAC,oBAAoB,EAAE,KAAK,CAAC,CAAC;QAC3C,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC,CAAC,CAAC;AACL,CAAC"}

package/dist/io/chrisIO.d.ts

@@ -42,6 +42,20 @@ export declare class ChrisIO {
      * @param fileId - The ID of the file to download.
      * @returns A Result containing the stream/blob and optional size metadata.
      */
+    /**
+     * Fetches a downloadable file resource by id, trying the userfiles
+     * collection first and falling back to PACS files.
+     *
+     * Filebrowser folder listings mix file kinds (a /SERVICES path holds PACS
+     * files, a /home path holds userfiles) but yield only numeric ids, so the
+     * downloader must probe both collections; a PACS id is invisible at the
+     * userfiles endpoint and previously read as "not found".
+     *
+     * @param client - The connected ChRIS client.
+     * @param fileId - The file id from a folder listing.
+     * @returns The file resource, or null when neither collection knows the id.
+     */
+    private downloadableFile_get;
     file_downloadStream(fileId: number): Promise<Result<{
         stream: unknown;
         size?: number;

package/dist/io/chrisIO.js

@@ -76,6 +76,36 @@ class ChrisIO {
      * @param fileId - The ID of the file to download.
      * @returns A Result containing the stream/blob and optional size metadata.
      */
+    /**
+     * Fetches a downloadable file resource by id, trying the userfiles
+     * collection first and falling back to PACS files.
+     *
+     * Filebrowser folder listings mix file kinds (a /SERVICES path holds PACS
+     * files, a /home path holds userfiles) but yield only numeric ids, so the
+     * downloader must probe both collections; a PACS id is invisible at the
+     * userfiles endpoint and previously read as "not found".
+     *
+     * @param client - The connected ChRIS client.
+     * @param fileId - The file id from a folder listing.
+     * @returns The file resource, or null when neither collection knows the id.
+     */
+    async downloadableFile_get(client, fileId) {
+        try {
+            const userFile = await client.getUserFile(fileId);
+            if (userFile)
+                return userFile;
+        }
+        catch {
+            // Fall through to the PACS collection.
+        }
+        try {
+            const pacsClient = client;
+            return await pacsClient.getPACSFile(fileId);
+        }
+        catch {
+            return null;
+        }
+    }
     async file_downloadStream(fileId) {
         const client = await this.client_get();
         if (!client) {
@@ -83,7 +113,7 @@ class ChrisIO {
             return (0, result_js_1.Err)();
         }
         try {
-            const userFile = await client.getUserFile(fileId);
+            const userFile = await this.downloadableFile_get(client, fileId);
             if (!userFile) {
                 errorStack_js_1.errorStack.stack_push("error", `File ID ${fileId} not found (404) or access denied (403).`);
                 return (0, result_js_1.Err)();
@@ -120,7 +150,7 @@ class ChrisIO {
             return null;
         }
         try {
-            const userFile = await client.getUserFile(fileId);
+            const userFile = await this.downloadableFile_get(client, fileId);
             if (!userFile) {
                 // This is a common case: the file ID was scraped from a listing, but
                 // the file itself is not retrievable (e.g. 404, or permissions)

package/dist/io/chrisIO.js.map

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package/dist/jobs/chrisJob.js

@@ -122,6 +122,10 @@ class ChRISJob {
                 await new Promise(resolve => setTimeout(resolve, 2000));
             }
             catch (e) {
+                // A poll failure ends the stream early; tell the consumer why
+                // instead of presenting the break as normal completion.
+                const msg = e instanceof Error ? e.message : String(e);
+                errorStack_js_1.errorStack.stack_push("warning", `Log stream ended early: status poll failed: ${msg}`);
                 break;
             }
         }

package/dist/jobs/chrisJob.js.map

@@ -1 +1 @@
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package/dist/output/runtimeOutput.d.ts

@@ -0,0 +1,49 @@
+/**
+ * @file Runtime output port.
+ *
+ * Provides a narrow host-installed output port for lower-layer operational
+ * messages. Cumin and Salsa must not depend upward on a terminal or Brasa,
+ * but their command-time notices still need a destination selected by the
+ * host. The default preserves standalone CLI behavior; a host may replace it
+ * with a surface-aware writer.
+ *
+ * @module
+ */
+/** A destination for unstructured command-time output. */
+export interface RuntimeOutput {
+    /**
+     * Writes ordinary output.
+     *
+     * @param chunk - Text or bytes to deliver.
+     * @returns Nothing.
+     */
+    data_write(chunk: string | Buffer): void;
+    /**
+     * Writes diagnostic output.
+     *
+     * @param chunk - Text or bytes to deliver.
+     * @returns Nothing.
+     */
+    err_write(chunk: string | Buffer): void;
+}
+/**
+ * Installs the runtime output destination.
+ *
+ * @param output - The host-owned output destination.
+ * @returns The previously active destination.
+ */
+export declare function runtimeOutput_set(output: RuntimeOutput): RuntimeOutput;
+/**
+ * Writes ordinary runtime output through the active host destination.
+ *
+ * @param chunk - Text or bytes to deliver.
+ * @returns Nothing.
+ */
+export declare function runtimeOutput_data(chunk: string | Buffer): void;
+/**
+ * Writes diagnostic runtime output through the active host destination.
+ *
+ * @param chunk - Text or bytes to deliver.
+ * @returns Nothing.
+ */
+export declare function runtimeOutput_err(chunk: string | Buffer): void;

package/dist/output/runtimeOutput.js

@@ -0,0 +1,51 @@
+"use strict";
+/**
+ * @file Runtime output port.
+ *
+ * Provides a narrow host-installed output port for lower-layer operational
+ * messages. Cumin and Salsa must not depend upward on a terminal or Brasa,
+ * but their command-time notices still need a destination selected by the
+ * host. The default preserves standalone CLI behavior; a host may replace it
+ * with a surface-aware writer.
+ *
+ * @module
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.runtimeOutput_set = runtimeOutput_set;
+exports.runtimeOutput_data = runtimeOutput_data;
+exports.runtimeOutput_err = runtimeOutput_err;
+const consoleOutput = {
+    data_write: (chunk) => { process.stdout.write(chunk); },
+    err_write: (chunk) => { process.stderr.write(chunk); },
+};
+let activeOutput = consoleOutput;
+/**
+ * Installs the runtime output destination.
+ *
+ * @param output - The host-owned output destination.
+ * @returns The previously active destination.
+ */
+function runtimeOutput_set(output) {
+    const previous = activeOutput;
+    activeOutput = output;
+    return previous;
+}
+/**
+ * Writes ordinary runtime output through the active host destination.
+ *
+ * @param chunk - Text or bytes to deliver.
+ * @returns Nothing.
+ */
+function runtimeOutput_data(chunk) {
+    activeOutput.data_write(chunk);
+}
+/**
+ * Writes diagnostic runtime output through the active host destination.
+ *
+ * @param chunk - Text or bytes to deliver.
+ * @returns Nothing.
+ */
+function runtimeOutput_err(chunk) {
+    activeOutput.err_write(chunk);
+}
+//# sourceMappingURL=runtimeOutput.js.map

package/dist/output/runtimeOutput.js.map

@@ -0,0 +1 @@
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package/dist/pacs/chrisPACS.d.ts

@@ -172,6 +172,8 @@ export interface SeriesRetrieveStatus {
     expectedFiles: number;
     actualFiles: number;
     status: "pending" | "pulling" | "pulled" | "error";
+    /** CUBE storage folder the series landed in, or null when nothing arrived. */
+    folderPath: string | null;
 }
 /**
  * Study with series status information.
@@ -191,6 +193,32 @@ export interface PACSQueryStatusReport {
     retrieveId?: number;
     studies: StudyRetrieveStatus[];
 }
+/** A series' presence in CUBE storage: registered file count and folder. */
+export interface SeriesStorageState {
+    /** Number of PACSFiles registered for the series. */
+    fileCount: number;
+    /** Display folder path (leading slash), or null when nothing arrived. */
+    folderPath: string | null;
+}
+/**
+ * Resolves a series' CUBE storage state: its registered file count and the
+ * folder it landed in.
+ *
+ * With `retry` options, re-probes across the registration lag between a PACS
+ * push completing and the PACSSeries record becoming queryable, returning the
+ * first state that carries a folder. This is the one series-storage resolver;
+ * the per-package copies it replaces are gone.
+ *
+ * @param seriesInstanceUID - The series instance UID to inspect.
+ * @param retry - Optional bounded re-probing: total attempts and the delay
+ *   between them.
+ * @returns Result containing the storage state; failures resolve to an empty
+ *   state (count 0, no folder) rather than failing the whole report.
+ */
+export declare function seriesStorage_resolve(seriesInstanceUID: string, retry?: {
+    attempts: number;
+    delayMs: number;
+}): Promise<Result<SeriesStorageState>>;
 /**
  * Reports the retrieve status for a PACS query.
  *