@fnndsc/salsa 4.5.4 → 4.5.6

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Files changed (9) hide show
  1. package/dist/files/fileLookup.d.ts +15 -1
  2. package/dist/files/fileLookup.js +95 -15
  3. package/dist/files/fileLookup.js.map +1 -1
  4. package/dist/index.d.ts +1 -0
  5. package/dist/index.js +3 -1
  6. package/dist/index.js.map +1 -1
  7. package/dist/vfs/providers/pacs.js +1 -0
  8. package/dist/vfs/providers/pacs.js.map +1 -1
  9. package/package.json +3 -3
package/dist/files/fileLookup.d.ts CHANGED
@@ -1,9 +1,23 @@
1
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  import { Result } from '@fnndsc/cumin';
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+ /**
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+ * Runs work in which each folder's file ids are listed once: a transfer of
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+ * many files. A scope inside a scope shares the outer one.
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+ *
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+ * @param operation - The work.
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+ * @returns What the work returns.
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+ *
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+ * @example
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+ * ```ts
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+ * const ids: number[] = await fileIds_memoRun(async () => resolveAll(paths));
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+ * ```
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+ */
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+ export declare function fileIds_memoRun<T>(operation: () => Promise<T>): Promise<T>;
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  /**
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  * Resolves an absolute ChRIS file path to its numeric file id.
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  *
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  * Lists the parent directory and matches on basename, tolerating the `? <name>`
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- * placeholder form the API sometimes returns.
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+ * placeholder form the API sometimes returns. Inside {@link fileIds_memoRun}
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+ * the listing is the transfer's, made once per folder.
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  *
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  * @param filePath - Absolute ChRIS file path.
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  * @returns Ok(fileId), or Err (with a message pushed to errorStack) on failure.
package/dist/files/fileLookup.js CHANGED
@@ -33,20 +33,106 @@ var __importStar = (this && this.__importStar) || (function () {
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  };
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  })();
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  Object.defineProperty(exports, "__esModule", { value: true });
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+ exports.fileIds_memoRun = fileIds_memoRun;
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  exports.pathFileId_resolve = pathFileId_resolve;
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  /**
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  * @file Resolve an absolute ChRIS file path to its numeric file id.
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  *
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+ * CUBE reads a file by id, and the id comes from listing the file's folder.
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+ * One file read lists its folder once; a transfer of a whole folder would
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+ * list that folder again for every file in it (223 files, 223 listings of
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+ * 223 rows). A transfer runs inside {@link fileIds_memoRun}, where each
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+ * folder is listed once and every file in it, in flight together or one
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+ * after another, takes its id from that listing. Outside a transfer nothing
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+ * is kept, so a read after an edit always lists afresh.
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+ *
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+ * Key components:
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+ * - pathFileId_resolve: a file path's id.
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+ * - fileIds_memoRun: runs work in which each folder's ids are listed once.
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+ *
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+ * Typical usage:
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+ * ```ts
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+ * await fileIds_memoRun(async () => {
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+ * for (const path of paths) await pathFileId_resolve(path);
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+ * });
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+ * ```
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+ *
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+ * Dependencies: cumin's file browser groups.
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+ *
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  * @module
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  */
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+ const node_async_hooks_1 = require("node:async_hooks");
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  const path = __importStar(require("path"));
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  const cumin_1 = require("@fnndsc/cumin");
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  const index_js_1 = require("./index.js");
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+ /** The memo of the transfer running on this async path, when one is. */
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+ const memoScope = new node_async_hooks_1.AsyncLocalStorage();
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+ /**
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+ * Runs work in which each folder's file ids are listed once: a transfer of
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+ * many files. A scope inside a scope shares the outer one.
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+ *
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+ * @param operation - The work.
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+ * @returns What the work returns.
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+ *
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+ * @example
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+ * ```ts
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+ * const ids: number[] = await fileIds_memoRun(async () => resolveAll(paths));
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+ * ```
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+ */
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+ async function fileIds_memoRun(operation) {
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+ if (memoScope.getStore() !== undefined)
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+ return operation();
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+ return memoScope.run(new Map(), operation);
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+ }
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+ /**
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+ * Lists one folder's files by basename.
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+ *
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+ * @param dir - The folder.
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+ * @returns The ids by basename (null for a row with no id), or why it could not be listed.
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+ */
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+ async function folderIds_list(dir) {
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+ const group = await (0, index_js_1.files_getGroup)('files', dir);
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+ if (!group)
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+ return { refused: '' };
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+ const results = await group.asset.resources_getAll();
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+ if (!results || !results.tableData)
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+ return { refused: `No files found in directory: ${dir}` };
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+ const ids = new Map();
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+ for (const row of results.tableData) {
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+ const basename = path.posix.basename(row.fname || '');
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+ const name = basename.startsWith('? ') ? basename.slice(2) : basename;
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+ if (!ids.has(name))
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+ ids.set(name, typeof row.id === 'number' ? row.id : null);
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+ }
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+ return { ids };
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+ }
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+ /**
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+ * One folder's ids: from the transfer's memo when one runs, else listed now.
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+ * A folder that could not be listed is not kept, so a retry lists again.
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+ *
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+ * @param dir - The folder.
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+ * @returns Its ids, or why it could not be listed.
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+ */
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+ async function folderIds_get(dir) {
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+ const memo = memoScope.getStore();
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+ if (memo === undefined)
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+ return folderIds_list(dir);
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+ const kept = memo.get(dir);
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+ if (kept !== undefined)
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+ return kept;
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+ const listing = folderIds_list(dir);
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+ memo.set(dir, listing);
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+ const answer = await listing;
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+ if ('refused' in answer)
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+ memo.delete(dir);
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+ return answer;
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+ }
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  /**
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  * Resolves an absolute ChRIS file path to its numeric file id.
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  *
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  * Lists the parent directory and matches on basename, tolerating the `? <name>`
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- * placeholder form the API sometimes returns.
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+ * placeholder form the API sometimes returns. Inside {@link fileIds_memoRun}
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+ * the listing is the transfer's, made once per folder.
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  *
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  * @param filePath - Absolute ChRIS file path.
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  * @returns Ok(fileId), or Err (with a message pushed to errorStack) on failure.
@@ -54,27 +140,21 @@ const index_js_1 = require("./index.js");
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  async function pathFileId_resolve(filePath) {
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  const dir = path.posix.dirname(filePath);
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  const name = path.posix.basename(filePath);
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- const group = await (0, index_js_1.files_getGroup)('files', dir);
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- if (!group) {
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- return (0, cumin_1.Err)();
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- }
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- const results = await group.asset.resources_getAll();
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- if (!results || !results.tableData) {
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- cumin_1.errorStack.stack_push('error', `No files found in directory: ${dir}`);
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+ const folder = await folderIds_get(dir);
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+ if ('refused' in folder) {
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+ if (folder.refused !== '')
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+ cumin_1.errorStack.stack_push('error', folder.refused);
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  return (0, cumin_1.Err)();
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  }
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- const file = results.tableData.find((f) => {
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- const basename = path.posix.basename(f.fname || '');
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- return basename === name || basename === `? ${name}`;
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- });
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- if (!file) {
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+ if (!folder.ids.has(name)) {
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  cumin_1.errorStack.stack_push('error', `File not found: ${name} in ${dir}`);
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  return (0, cumin_1.Err)();
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  }
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- if (typeof file.id !== 'number') {
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+ const id = folder.ids.get(name);
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+ if (typeof id !== 'number') {
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  cumin_1.errorStack.stack_push('error', `File has no valid ID: ${name}`);
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  return (0, cumin_1.Err)();
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  }
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- return (0, cumin_1.Ok)(file.id);
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+ return (0, cumin_1.Ok)(id);
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  }
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  //# sourceMappingURL=fileLookup.js.map
package/dist/files/fileLookup.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"fileLookup.js","sourceRoot":"","sources":["../../src/files/fileLookup.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAkEA,0CAGC;AAmDD,gDAsBC;AA9ID;;;;;;;;;;;;;;;;;;;;;;;;;GAyBG;AACH,uDAAqD;AACrD,2CAA6B;AAC7B,yCAQuB;AACvB,yCAA4C;AAc5C,wEAAwE;AACxE,MAAM,SAAS,GAAqC,IAAI,oCAAiB,EAAiB,CAAC;AAE3F;;;;;;;;;;;GAWG;AACI,KAAK,UAAU,eAAe,CAAI,SAA2B;IAClE,IAAI,SAAS,CAAC,QAAQ,EAAE,KAAK,SAAS;QAAE,OAAO,SAAS,EAAE,CAAC;IAC3D,OAAO,SAAS,CAAC,GAAG,CAAC,IAAI,GAAG,EAAE,EAAE,SAAS,CAAC,CAAC;AAC7C,CAAC;AAED;;;;;GAKG;AACH,KAAK,UAAU,cAAc,CAAC,GAAW;IACvC,MAAM,KAAK,GAAqD,MAAM,IAAA,yBAAc,EAAC,OAAO,EAAE,GAAG,CAAC,CAAC;IACnG,IAAI,CAAC,KAAK;QAAE,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,CAAC;IACnC,MAAM,OAAO,GAAgC,MAAM,KAAK,CAAC,KAAK,CAAC,gBAAgB,EAAE,CAAC;IAClF,IAAI,CAAC,OAAO,IAAI,CAAC,OAAO,CAAC,SAAS;QAAE,OAAO,EAAE,OAAO,EAAE,gCAAgC,GAAG,EAAE,EAAE,CAAC;IAC9F,MAAM,GAAG,GAA+B,IAAI,GAAG,EAAE,CAAC;IAClD,KAAK,MAAM,GAAG,IAAI,OAAO,CAAC,SAAsB,EAAE,CAAC;QACjD,MAAM,QAAQ,GAAW,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,IAAI,EAAE,CAAC,CAAC;QAC9D,MAAM,IAAI,GAAW,QAAQ,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC;QAC9E,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC;YAAE,GAAG,CAAC,GAAG,CAAC,IAAI,EAAE,OAAO,GAAG,CAAC,EAAE,KAAK,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;IAChF,CAAC;IACD,OAAO,EAAE,GAAG,EAAE,CAAC;AACjB,CAAC;AAED;;;;;;GAMG;AACH,KAAK,UAAU,aAAa,CAAC,GAAW;IACtC,MAAM,IAAI,GAA8B,SAAS,CAAC,QAAQ,EAAE,CAAC;IAC7D,IAAI,IAAI,KAAK,SAAS;QAAE,OAAO,cAAc,CAAC,GAAG,CAAC,CAAC;IACnD,MAAM,IAAI,GAAmC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;IAC3D,IAAI,IAAI,KAAK,SAAS;QAAE,OAAO,IAAI,CAAC;IACpC,MAAM,OAAO,GAAuB,cAAc,CAAC,GAAG,CAAC,CAAC;IACxD,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC;IACvB,MAAM,MAAM,GAAc,MAAM,OAAO,CAAC;IACxC,IAAI,SAAS,IAAI,MAAM;QAAE,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;IAC1C,OAAO,MAAM,CAAC;AAChB,CAAC;AAED;;;;;;;;;GASG;AACI,KAAK,UAAU,kBAAkB,CAAC,QAAgB;IACvD,MAAM,GAAG,GAAW,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC;IACjD,MAAM,IAAI,GAAW,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC;IAEnD,MAAM,MAAM,GAAc,MAAM,aAAa,CAAC,GAAG,CAAC,CAAC;IACnD,IAAI,SAAS,IAAI,MAAM,EAAE,CAAC;QACxB,IAAI,MAAM,CAAC,OAAO,KAAK,EAAE;YAAE,kBAAU,CAAC,UAAU,CAAC,OAAO,EAAE,MAAM,CAAC,OAAO,CAAC,CAAC;QAC1E,OAAO,IAAA,WAAG,GAAE,CAAC;IACf,CAAC;IAED,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC;QAC1B,kBAAU,CAAC,UAAU,CAAC,OAAO,EAAE,mBAAmB,IAAI,OAAO,GAAG,EAAE,CAAC,CAAC;QACpE,OAAO,IAAA,WAAG,GAAE,CAAC;IACf,CAAC;IAED,MAAM,EAAE,GAA8B,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;IAC3D,IAAI,OAAO,EAAE,KAAK,QAAQ,EAAE,CAAC;QAC3B,kBAAU,CAAC,UAAU,CAAC,OAAO,EAAE,yBAAyB,IAAI,EAAE,CAAC,CAAC;QAChE,OAAO,IAAA,WAAG,GAAE,CAAC;IACf,CAAC;IAED,OAAO,IAAA,UAAE,EAAC,EAAE,CAAC,CAAC;AAChB,CAAC"}
package/dist/index.d.ts CHANGED
@@ -5,6 +5,7 @@
5
5
  export * from './feeds/index.js';
6
6
  export * from './plugins/index.js';
7
7
  export * from './files/index.js';
8
+ export { fileIds_memoRun } from './files/fileLookup.js';
8
9
  export { PathMapper, pathMapper_get, logicalPath_resolve, linkCache_clear, type CacheStats } from './files/pathMapper.js';
9
10
  export * from './connect/index.js';
10
11
  export * from './context/index.js';
package/dist/index.js CHANGED
@@ -18,10 +18,12 @@ var __exportStar = (this && this.__exportStar) || function(m, exports) {
18
18
  for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
19
19
  };
20
20
  Object.defineProperty(exports, "__esModule", { value: true });
21
- exports.DATA_FACTS_READER = exports.dataFormat_deriveFromName = exports.dataFactsIO_build = exports.sourceFeed_parse = exports.procDataFacts_settled = exports.procDataFacts_feed = exports.procDataFacts_sweep = exports.feedDataFacts_read = exports.feedGraphData_ensure = exports.nodeJoins_resolve = exports.feedJoins_ensure = exports.signature_compute = exports.feedGraph_build = exports.PROC_TAGS_PREFIX = exports.FEED_VISIT_COALESCE_MS = exports.ROSTER_DELTA_PAGE = exports.ROSTER_FULL_WALK_MS = exports.FEED_RECHECK_MS = exports.procDataFacts_start = exports.procVisitState_reset = exports.procRoster_bootSync = exports.procRoster_syncStart = exports.procRoster_sync = exports.feedCached_isSettled = exports.feedVisit_sync = exports.feedStatus_refresh = exports.procTarget_parse = exports.procTarget_locate = exports.procFeed_probe = exports.feedMeta_ensure = exports.procFeed_refreshStart = exports.feedInstances_ensureStarted = exports.feedInstances_ensureLoaded = exports.procFeed_ensureLoaded = exports.procPipelineBackfill_status = exports.procTopologyCatchup_await = exports.procTopologyCatchup_status = exports.procTopologyCatchup_enqueue = exports.procTopology_await = exports.procTopology_status = exports.procTopology_retry = exports.procTopology_reconcileFeeds = exports.procTopology_warmup = exports.procCache_refresh = exports.linkCache_clear = exports.logicalPath_resolve = exports.pathMapper_get = exports.PathMapper = void 0;
21
+ exports.DATA_FACTS_READER = exports.dataFormat_deriveFromName = exports.dataFactsIO_build = exports.sourceFeed_parse = exports.procDataFacts_settled = exports.procDataFacts_feed = exports.procDataFacts_sweep = exports.feedDataFacts_read = exports.feedGraphData_ensure = exports.nodeJoins_resolve = exports.feedJoins_ensure = exports.signature_compute = exports.feedGraph_build = exports.PROC_TAGS_PREFIX = exports.FEED_VISIT_COALESCE_MS = exports.ROSTER_DELTA_PAGE = exports.ROSTER_FULL_WALK_MS = exports.FEED_RECHECK_MS = exports.procDataFacts_start = exports.procVisitState_reset = exports.procRoster_bootSync = exports.procRoster_syncStart = exports.procRoster_sync = exports.feedCached_isSettled = exports.feedVisit_sync = exports.feedStatus_refresh = exports.procTarget_parse = exports.procTarget_locate = exports.procFeed_probe = exports.feedMeta_ensure = exports.procFeed_refreshStart = exports.feedInstances_ensureStarted = exports.feedInstances_ensureLoaded = exports.procFeed_ensureLoaded = exports.procPipelineBackfill_status = exports.procTopologyCatchup_await = exports.procTopologyCatchup_status = exports.procTopologyCatchup_enqueue = exports.procTopology_await = exports.procTopology_status = exports.procTopology_retry = exports.procTopology_reconcileFeeds = exports.procTopology_warmup = exports.procCache_refresh = exports.linkCache_clear = exports.logicalPath_resolve = exports.pathMapper_get = exports.PathMapper = exports.fileIds_memoRun = void 0;
22
22
  __exportStar(require("./feeds/index.js"), exports);
23
23
  __exportStar(require("./plugins/index.js"), exports);
24
24
  __exportStar(require("./files/index.js"), exports);
25
+ var fileLookup_js_1 = require("./files/fileLookup.js");
26
+ Object.defineProperty(exports, "fileIds_memoRun", { enumerable: true, get: function () { return fileLookup_js_1.fileIds_memoRun; } });
25
27
  var pathMapper_js_1 = require("./files/pathMapper.js");
26
28
  Object.defineProperty(exports, "PathMapper", { enumerable: true, get: function () { return pathMapper_js_1.PathMapper; } });
27
29
  Object.defineProperty(exports, "pathMapper_get", { enumerable: true, get: function () { return pathMapper_js_1.pathMapper_get; } });
package/dist/index.js.map CHANGED
@@ -1 +1 @@
1
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+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AAAA;;;GAGG;;;;;;;;;;;;;;;;;AAEH,mDAAiC;AACjC,qDAAmC;AACnC,mDAAiC;AACjC,uDAAwD;AAA/C,gHAAA,eAAe,OAAA;AACxB,uDAA0H;AAAjH,2GAAA,UAAU,OAAA;AAAE,+GAAA,cAAc,OAAA;AAAE,oHAAA,mBAAmB,OAAA;AAAE,gHAAA,eAAe,OAAA;AACzE,qDAAmC;AACnC,qDAAmC;AACnC,mDAAiC;AACjC,uDAAqC;AACrC,kDAAgC;AAChC,mDAAiC;AACjC,sDAAoC;AACpC,iDAA+B;AAC/B,kDAAgC;AAChC,oDAAkC;AAClC,yDAAuC;AACvC,6DAA2C;AAC3C,uDAAqC;AACrC,qDAAmC;AACnC,kDAAgC;AAChC,mDAAiC;AACjC,mDAA0uB;AAAjuB,4GAAA,iBAAiB,OAAA;AAAE,8GAAA,mBAAmB,OAAA;AAAE,sHAAA,2BAA2B,OAAA;AAAE,6GAAA,kBAAkB,OAAA;AAAE,8GAAA,mBAAmB,OAAA;AAAE,6GAAA,kBAAkB,OAAA;AAAE,sHAAA,2BAA2B,OAAA;AAAE,qHAAA,0BAA0B,OAAA;AAAE,oHAAA,yBAAyB,OAAA;AAAE,sHAAA,2BAA2B,OAAA;AAAE,gHAAA,qBAAqB,OAAA;AAAE,qHAAA,0BAA0B,OAAA;AAAE,sHAAA,2BAA2B,OAAA;AAAE,gHAAA,qBAAqB,OAAA;AAA8B,0GAAA,eAAe,OAAA;AAAE,yGAAA,cAAc,OAAA;AAAE,4GAAA,iBAAiB,OAAA;AAAE,2GAAA,gBAAgB,OAAA;AAAqB,6GAAA,kBAAkB,OAAA;AAAE,yGAAA,cAAc,OAAA;AAAE,+GAAA,oBAAoB,OAAA;AAAE,0GAAA,eAAe,OAAA;AAAE,+GAAA,oBAAoB,OAAA;AAAE,8GAAA,mBAAmB,OAAA;AAAE,+GAAA,oBAAoB,OAAA;AAAE,8GAAA,mBAAmB,OAAA;AAAE,0GAAA,eAAe,OAAA;AAAE,8GAAA,mBAAmB,OAAA;AAAE,4GAAA,iBAAiB,OAAA;AAAE,iHAAA,sBAAsB,OAAA;AAExsB,2DAA+D;AAAtD,+GAAA,gBAAgB,OAAA;AACzB,mDAAwE;AAA/D,+GAAA,eAAe,OAAA;AAAE,iHAAA,iBAAiB,OAAA;AAE3C,mDAAyE;AAAhE,gHAAA,gBAAgB,OAAA;AAAE,iHAAA,iBAAiB,OAAA;AAC5C,iDAAyD;AAAhD,mHAAA,oBAAoB,OAAA;AAC7B,iDAA4N;AAAnN,iHAAA,kBAAkB,OAAA;AAAE,kHAAA,mBAAmB,OAAA;AAAE,iHAAA,kBAAkB,OAAA;AAAE,oHAAA,qBAAqB,OAAA;AAAE,+GAAA,gBAAgB,OAAA;AAAE,gHAAA,iBAAiB,OAAA;AAAE,wHAAA,yBAAyB,OAAA;AAAE,gHAAA,iBAAiB,OAAA"}
package/dist/vfs/providers/pacs.js CHANGED
@@ -194,6 +194,7 @@ async function series_retrieveAndCopy(seriesItem, studyUID, pacsserver, dest, id
194
194
  const cleanDesc = seriesItem.description.replace(/[\s/]/g, "_");
195
195
  const targetSeriesFolder = path_1.default.posix.join(dest, `Series_${seriesItem.uid}_${cleanDesc}`);
196
196
  (0, cumin_1.runtimeOutput_data)(`${chalk_1.default.gray(` -> Copying series files to '${targetSeriesFolder}'...`)}\n`);
197
+ // store-path: the folder CUBE registered for the series, into a destination `cp` resolved (storePath_resolve, both ends).
197
198
  const copySuccess = await (0, index_js_2.files_copyRecursively)(absoluteFolderPath, targetSeriesFolder);
198
199
  if (!copySuccess) {
199
200
  (0, cumin_1.runtimeOutput_err)(`${chalk_1.default.red(` ✗ Recursive copy failed from '${absoluteFolderPath}' to '${targetSeriesFolder}'`)}\n`);
package/dist/vfs/providers/pacs.js.map CHANGED
@@ -1 +1 @@
1
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1
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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@fnndsc/salsa",
3
- "version": "4.5.4",
3
+ "version": "4.5.6",
4
4
  "description": "Shared Application Logic and Service Assets for ChRIS",
5
5
  "repository": {
6
6
  "type": "git",
@@ -60,8 +60,8 @@
60
60
  "adm-zip": "npm:empty-npm-package@1.0.0"
61
61
  },
62
62
  "dependencies": {
63
- "@fnndsc/cumin": "^3.30.0",
64
- "@fnndsc/fond": "^0.6.1",
63
+ "@fnndsc/cumin": "^3.30.6",
64
+ "@fnndsc/fond": "^0.6.2",
65
65
  "ajv": "^8.17.1",
66
66
  "axios": "^1.6.8",
67
67
  "dcmjs": "^0.52.0",