@fnndsc/salsa 3.2.4

package/dist/vfs/providers/pacs.js.map

@@ -0,0 +1 @@
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package/dist/vfs/providers/pacsHelpers.d.ts

@@ -0,0 +1,27 @@
+/**
+ * @file Pure helpers for the PACS VFS provider.
+ *
+ * Tag extraction, path/query parsing, and study/series lookup — dependency-light
+ * (cumin only) so they load and unit-test without the provider's import cycle.
+ *
+ * @module
+ */
+import { Result } from "@fnndsc/cumin";
+/**
+ * Safely extracts a string value from a potentially object-wrapped DICOM tag.
+ *
+ * @param val - Potentially object-wrapped DICOM tag or raw string.
+ * @returns The string value of the DICOM tag.
+ */
+export declare function tag_extractValue(val: unknown): string;
+export declare function path_normalize(pathStr: string): string;
+export declare function queryId_extractFromFolder(folder: string): number;
+export declare function studies_extractFromDecoded(decodedJson: unknown): Record<string, unknown>[];
+export declare function series_extractFromStudy(studyObj: Record<string, unknown>): Record<string, unknown>[];
+export declare function study_findByUID(studies: Record<string, unknown>[], uid: string): Record<string, unknown> | undefined;
+export declare function series_findByUID(seriesArr: Record<string, unknown>[], uid: string): Record<string, unknown> | undefined;
+export declare function cpSrc_parse(src: string): Result<{
+    studyUID: string;
+    seriesUID?: string;
+    queryId: number;
+}>;

package/dist/vfs/providers/pacsHelpers.js

@@ -0,0 +1,108 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.tag_extractValue = tag_extractValue;
+exports.path_normalize = path_normalize;
+exports.queryId_extractFromFolder = queryId_extractFromFolder;
+exports.studies_extractFromDecoded = studies_extractFromDecoded;
+exports.series_extractFromStudy = series_extractFromStudy;
+exports.study_findByUID = study_findByUID;
+exports.series_findByUID = series_findByUID;
+exports.cpSrc_parse = cpSrc_parse;
+/**
+ * @file Pure helpers for the PACS VFS provider.
+ *
+ * Tag extraction, path/query parsing, and study/series lookup — dependency-light
+ * (cumin only) so they load and unit-test without the provider's import cycle.
+ *
+ * @module
+ */
+const cumin_1 = require("@fnndsc/cumin");
+/**
+ * Safely extracts a string value from a potentially object-wrapped DICOM tag.
+ *
+ * @param val - Potentially object-wrapped DICOM tag or raw string.
+ * @returns The string value of the DICOM tag.
+ */
+function tag_extractValue(val) {
+    if (val && typeof val === "object") {
+        const record = val;
+        if ("value" in record) {
+            return String(record.value ?? "");
+        }
+    }
+    return String(val ?? "");
+}
+function path_normalize(pathStr) {
+    let p = pathStr.startsWith("/") ? pathStr : "/" + pathStr;
+    if (p.length > 1 && p.endsWith("/"))
+        p = p.slice(0, -1);
+    return p;
+}
+function queryId_extractFromFolder(folder) {
+    const match = /_qid:(\d+)/.exec(folder);
+    return match ? Number(match[1]) : NaN;
+}
+function studies_extractFromDecoded(decodedJson) {
+    let studiesObj;
+    if (decodedJson && typeof decodedJson === "object") {
+        const record = decodedJson;
+        if ("studies" in record)
+            studiesObj = record.studies;
+        else if ("Studies" in record)
+            studiesObj = record.Studies;
+        else if ("results" in record)
+            studiesObj = record.results;
+        else
+            studiesObj = decodedJson;
+    }
+    else {
+        studiesObj = decodedJson;
+    }
+    const arr = Array.isArray(studiesObj) ? studiesObj : [studiesObj];
+    return arr;
+}
+function series_extractFromStudy(studyObj) {
+    const arr = Array.isArray(studyObj.series) ? studyObj.series :
+        Array.isArray(studyObj.Series) ? studyObj.Series :
+            Array.isArray(studyObj.results) ? studyObj.results :
+                Array.isArray(studyObj.data) ? studyObj.data :
+                    [];
+    return arr;
+}
+function study_findByUID(studies, uid) {
+    return studies.find((s) => {
+        const sUID = tag_extractValue(s.StudyInstanceUID || s.uid);
+        return sUID === uid;
+    });
+}
+function series_findByUID(seriesArr, uid) {
+    return seriesArr.find((s) => {
+        const sUID = tag_extractValue(s.SeriesInstanceUID || s.uid);
+        return sUID === uid;
+    });
+}
+function cpSrc_parse(src) {
+    const absolutePath = src.startsWith("/") ? src : "/" + src;
+    const parts = absolutePath.split("/").filter(Boolean);
+    if (parts.length < 4) {
+        cumin_1.errorStack.stack_push("error", `cp: Copying from '${src}' is not supported. Please specify a Study or Series directory.`);
+        return (0, cumin_1.Err)();
+    }
+    const studyFolder = parts[3];
+    if (!studyFolder.startsWith("Study_")) {
+        cumin_1.errorStack.stack_push("error", `cp: Invalid PACS Study folder format: '${studyFolder}'`);
+        return (0, cumin_1.Err)();
+    }
+    const studyUID = studyFolder.replace(/^Study_/, "").split("_")[0];
+    let seriesUID;
+    if (parts.length >= 5 && parts[4].startsWith("Series_")) {
+        seriesUID = parts[4].replace(/^Series_/, "").split("_")[0];
+    }
+    const queryId = queryId_extractFromFolder(parts[2]);
+    if (Number.isNaN(queryId)) {
+        cumin_1.errorStack.stack_push("error", `cp: Invalid query ID in path '${src}'`);
+        return (0, cumin_1.Err)();
+    }
+    return (0, cumin_1.Ok)({ studyUID, seriesUID, queryId });
+}
+//# sourceMappingURL=pacsHelpers.js.map

package/dist/vfs/providers/pacsHelpers.js.map

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package/dist/vfs/providers/pacs_content.d.ts

@@ -0,0 +1,27 @@
+/**
+ * @file PACS VFS Content Handler.
+ *
+ * Implements specialized virtual file reading and content generation
+ * for PACS queries metadata.json and image_slices.dcm.
+ *
+ * @module
+ */
+import { Result, PACSQueryDecodedResult } from "@fnndsc/cumin";
+/**
+ * Reads virtual file content under '/net/pacs'.
+ *
+ * Handles pretty-printed JSON series details for metadata.json and blocks image_slices.dcm.
+ *
+ * @param pathStr - The absolute virtual path of the file to read.
+ * @param queryResult_fetch - Callback to fetch decoded PACS query results (leveraging cache).
+ * @returns Promise resolving to a Result containing the file contents as a string.
+ */
+export declare function pacsVfs_read(pathStr: string, queryResult_fetch: (queryId: number) => Promise<PACSQueryDecodedResult | null>): Promise<Result<string>>;
+/**
+ * Reads virtual file binary content under '/net/pacs'.
+ *
+ * @param pathStr - The absolute virtual path of the file to read.
+ * @param queryResult_fetch - Callback to fetch decoded PACS query results (leveraging cache).
+ * @returns Promise resolving to a Result containing the file contents as a Buffer.
+ */
+export declare function pacsVfs_readBinary(pathStr: string, queryResult_fetch: (queryId: number) => Promise<PACSQueryDecodedResult | null>): Promise<Result<Buffer>>;

package/dist/vfs/providers/pacs_content.js

@@ -0,0 +1,137 @@
+"use strict";
+/**
+ * @file PACS VFS Content Handler.
+ *
+ * Implements specialized virtual file reading and content generation
+ * for PACS queries metadata.json and image_slices.dcm.
+ *
+ * @module
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.pacsVfs_read = pacsVfs_read;
+exports.pacsVfs_readBinary = pacsVfs_readBinary;
+const cumin_1 = require("@fnndsc/cumin");
+/**
+ * Safely extracts a string value from a potentially object-wrapped DICOM tag.
+ *
+ * @param val - Potentially object-wrapped DICOM tag or raw string.
+ * @returns The string value of the DICOM tag.
+ */
+function pacs_tagValueExtract(val) {
+    if (val && typeof val === "object") {
+        const record = val;
+        if ("value" in record) {
+            return String(record.value ?? "");
+        }
+    }
+    return String(val ?? "");
+}
+/**
+ * Reads virtual file content under '/net/pacs'.
+ *
+ * Handles pretty-printed JSON series details for metadata.json and blocks image_slices.dcm.
+ *
+ * @param pathStr - The absolute virtual path of the file to read.
+ * @param queryResult_fetch - Callback to fetch decoded PACS query results (leveraging cache).
+ * @returns Promise resolving to a Result containing the file contents as a string.
+ */
+async function pacsVfs_read(pathStr, queryResult_fetch) {
+    try {
+        let effectivePath = pathStr.startsWith("/") ? pathStr : "/" + pathStr;
+        if (effectivePath.length > 1 && effectivePath.endsWith("/")) {
+            effectivePath = effectivePath.slice(0, -1);
+        }
+        const parts = effectivePath.split("/").filter(Boolean);
+        if (parts.length !== 7 || parts[0] !== "net" || parts[1] !== "pacs" || parts[2] !== "queries") {
+            cumin_1.errorStack.stack_push("error", `File not found: ${pathStr}`);
+            return (0, cumin_1.Err)();
+        }
+        const queryFolder = parts[3];
+        const studyFolder = parts[4];
+        const seriesFolder = parts[5];
+        const filename = parts[6];
+        const queryId = Number(queryFolder.split("_")[0]);
+        if (Number.isNaN(queryId)) {
+            cumin_1.errorStack.stack_push("error", `Invalid query ID in path '${pathStr}'`);
+            return (0, cumin_1.Err)();
+        }
+        if (filename === "image_slices.dcm") {
+            cumin_1.errorStack.stack_push("error", "image_slices.dcm is a virtual placeholder. Use the 'cp' command on the containing Study or Series directory to download the DICOM files.");
+            return (0, cumin_1.Err)();
+        }
+        if (filename !== "metadata.json") {
+            cumin_1.errorStack.stack_push("error", `File not found: ${pathStr}`);
+            return (0, cumin_1.Err)();
+        }
+        const decoded = await queryResult_fetch(queryId);
+        if (!decoded || !decoded.json) {
+            cumin_1.errorStack.stack_push("error", `PACS query ${queryId} has no result payload.`);
+            return (0, cumin_1.Err)();
+        }
+        const studyUID = studyFolder.replace(/^Study_/, "").split("_")[0];
+        const seriesUID = seriesFolder.replace(/^Series_/, "").split("_")[0];
+        const decodedJson = decoded.json;
+        let studiesObj;
+        if (decodedJson && typeof decodedJson === "object") {
+            const record = decodedJson;
+            if ("studies" in record) {
+                studiesObj = record.studies;
+            }
+            else if ("Studies" in record) {
+                studiesObj = record.Studies;
+            }
+            else if ("results" in record) {
+                studiesObj = record.results;
+            }
+            else {
+                studiesObj = decodedJson;
+            }
+        }
+        else {
+            studiesObj = decodedJson;
+        }
+        const studies = Array.isArray(studiesObj) ? studiesObj : [studiesObj];
+        const studyObj = studies.find((s) => {
+            const sUID = pacs_tagValueExtract(s.StudyInstanceUID || s.uid);
+            return sUID === studyUID;
+        });
+        if (!studyObj) {
+            cumin_1.errorStack.stack_push("error", `Study with UID ${studyUID} not found in query results.`);
+            return (0, cumin_1.Err)();
+        }
+        const seriesArray = Array.isArray(studyObj.series) ? studyObj.series :
+            Array.isArray(studyObj.Series) ? studyObj.Series :
+                Array.isArray(studyObj.results) ? studyObj.results :
+                    Array.isArray(studyObj.data) ? studyObj.data :
+                        [];
+        const seriesObj = seriesArray.find((s) => {
+            const sUID = pacs_tagValueExtract(s.SeriesInstanceUID || s.uid);
+            return sUID === seriesUID;
+        });
+        if (!seriesObj) {
+            cumin_1.errorStack.stack_push("error", `Series with UID ${seriesUID} not found in study results.`);
+            return (0, cumin_1.Err)();
+        }
+        return (0, cumin_1.Ok)(JSON.stringify(seriesObj, null, 2));
+    }
+    catch (error) {
+        const msg = error instanceof Error ? error.message : String(error);
+        cumin_1.errorStack.stack_push("error", `PACS VFS read failed: ${msg}`);
+        return (0, cumin_1.Err)();
+    }
+}
+/**
+ * Reads virtual file binary content under '/net/pacs'.
+ *
+ * @param pathStr - The absolute virtual path of the file to read.
+ * @param queryResult_fetch - Callback to fetch decoded PACS query results (leveraging cache).
+ * @returns Promise resolving to a Result containing the file contents as a Buffer.
+ */
+async function pacsVfs_readBinary(pathStr, queryResult_fetch) {
+    const res = await pacsVfs_read(pathStr, queryResult_fetch);
+    if (res.ok) {
+        return (0, cumin_1.Ok)(Buffer.from(res.value, "utf-8"));
+    }
+    return (0, cumin_1.Err)();
+}
+//# sourceMappingURL=pacs_content.js.map

package/dist/vfs/providers/pacs_content.js.map

@@ -0,0 +1 @@
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package/dist/vfs/providers/proc.d.ts

@@ -0,0 +1,62 @@
+/**
+ * @file /proc VFS Provider
+ *
+ * Surfaces ChRIS plugin instances as a navigable DAG under /proc/jobs/.
+ * Backed by ProcCache (topology only — no status stored).
+ *
+ * Status is always fetched live:
+ * - cat .../status        → getPluginInstance(id)
+ * - ls -l /proc/jobs/N   → jobs_statusBatch(allNodeIDs) — parallel
+ * - ls /proc/jobs        → aggregate from ProcFeed job counters (no API)
+ *
+ * @module
+ */
+import { ProcFeed, Result } from '@fnndsc/cumin';
+import { VFSProvider, VFSItem, CpOptions } from '../provider.js';
+/** Derives aggregate feed status from stored job counters — no API call. */
+export declare function feedStatus_derive(feed: ProcFeed): string;
+export declare function procPath_parse(pathStr: string): {
+    feedID: number | null;
+    instanceID: number | null;
+    virtualFile: string | null;
+};
+/**
+ * VFS provider exposing running jobs and feeds under the /proc namespace.
+ */
+export declare class ProcVfsProvider implements VFSProvider {
+    readonly prefix: string;
+    list(pathStr: string, _options?: {
+        sort?: 'name' | 'size' | 'date' | 'owner';
+        reverse?: boolean;
+    }): Promise<Result<VFSItem[]>>;
+    read(pathStr: string): Promise<Result<string>>;
+    rm(pathStr: string, _options?: {
+        recursive?: boolean;
+        force?: boolean;
+    }): Promise<boolean>;
+    cp(_src: string, _dst: string, _options?: CpOptions): Promise<boolean>;
+    mv(_src: string, _dst: string): Promise<boolean>;
+    mkdir(_pathStr: string): Promise<boolean>;
+    touch(_pathStr: string): Promise<boolean>;
+    upload(_localPath: string, _remotePath: string): Promise<boolean>;
+    write(_pathStr: string, _content: string): Promise<boolean>;
+}
+/**
+ * Ensures instance topology is loaded for a feed without clearing existing data.
+ * Use this from proc find — it respects already-loaded feeds and the in-flight map.
+ * Use procCache_refresh(feedID) only when a forced reload is desired.
+ */
+export declare function procFeed_ensureLoaded(feedID: number): Promise<void>;
+/**
+ * Background topology warm-up — single paginated sweep of all plugin instances
+ * across all feeds. Replaces the per-feed fan-out that was O(feeds) round trips.
+ *
+ * Registers itself as the active sweep so that any concurrent
+ * feedInstances_ensureLoaded call waits for this sweep rather than launching
+ * its own per-feed API call.
+ */
+export declare function procTopology_warmup(): Promise<void>;
+/**
+ * Rebuilds the ProcCache, optionally scoped to one feed.
+ */
+export declare function procCache_refresh(feedID?: number): Promise<void>;