Merge pull request #1586 from silx-kit/hdf5-errors-2

Propagate and improve handling of HDF5 errors

packages/app/src/App.module.css

@@ -154,6 +154,20 @@
   margin-left: 0.5rem;
 }
 
+.detailedError {
+  composes: error from global;
+  overflow: auto;
+  scrollbar-width: thin;
+}
+
+.detailedError > summary {
+  cursor: pointer;
+}
+
+.detailedError > pre {
+  font-size: 0.875em;
+}
+
 .retryBtn {
   composes: btnClean btnLink from global;
 }

packages/app/src/ErrorFallback.tsx

@@ -6,6 +6,16 @@ import { CANCELLED_ERROR_MSG } from './providers/utils';
 function ErrorFallback(props: FallbackProps) {
   const { error, resetErrorBoundary } = props;
 
+  if (error.cause || error.cause instanceof Error) {
+    const { message } = error.cause;
+    return (
+      <details className={styles.detailedError}>
+        <summary>{error.message}</summary>
+        <pre>{message}</pre>
+      </details>
+    );
+  }
+
   return (
     <p className={styles.error}>
       {error.message}

packages/app/src/visualizer/Visualizer.module.css

@@ -21,7 +21,7 @@
   grid-template:
     'dimMapper bar' auto
     'dimMapper vis' 1fr
-    / auto 1fr;
+    / min-content 1fr;
 }
 
 .fallback {

packages/h5wasm/package.json

@@ -46,7 +46,7 @@
     }
   },
   "dependencies": {
-    "h5wasm": "0.7.1",
+    "h5wasm": "0.7.2",
     "nanoid": "5.0.5"
   },
   "devDependencies": {

packages/h5wasm/src/__snapshots__/h5wasm-api.test.ts.snap

@@ -1786,9 +1786,9 @@ exports[`test file matches snapshot 1`] = `
           0,
           0,
           0,
-          248,
-          215,
-          18,
+          240,
+          13,
+          19,
           0,
         ],
       ],
@@ -1802,9 +1802,9 @@ exports[`test file matches snapshot 1`] = `
           0,
           0,
           0,
-          104,
-          238,
-          18,
+          96,
+          36,
+          19,
           0,
         ],
       ],
@@ -1818,9 +1818,9 @@ exports[`test file matches snapshot 1`] = `
           0,
           0,
           0,
-          128,
-          238,
-          18,
+          120,
+          36,
+          19,
           0,
         ],
       ],
@@ -2095,9 +2095,9 @@ exports[`test file matches snapshot 1`] = `
       0,
       0,
       0,
-      96,
-      210,
-      18,
+      88,
+      8,
+      19,
       0,
     ],
   },
@@ -2126,25 +2126,25 @@ exports[`test file matches snapshot 1`] = `
       0,
       0,
       0,
-      176,
-      25,
+      168,
+      79,
       18,
       0,
       2,
       0,
       0,
       0,
-      96,
-      12,
+      88,
+      66,
       18,
       0,
       3,
       0,
       0,
       0,
-      240,
-      239,
-      18,
+      232,
+      37,
+      19,
       0,
     ],
   },

packages/h5wasm/src/h5wasm-api.ts

@@ -20,6 +20,7 @@ import { assertH5WasmDataset } from './guards';
 import type { H5WasmEntity } from './models';
 import type { Plugin } from './utils';
 import {
+  getEnhancedError,
   hasBigInts,
   parseEntity,
   PLUGINS_BY_FILTER_ID,
@@ -61,8 +62,12 @@ export class H5WasmApi extends DataProviderApi {
     // Ensure all filters are supported and loaded (if available)
     await this.processFilters(h5wDataset.filters);
 
-    const value = readSelectedValue(h5wDataset, selection);
-    return hasBigInts(dataset.type) ? sanitizeBigInts(value) : value;
+    try {
+      const value = readSelectedValue(h5wDataset, selection);
+      return hasBigInts(dataset.type) ? sanitizeBigInts(value) : value;
+    } catch (error) {
+      throw getEnhancedError(error);
+    }
   }
 
   public async getAttrValues(entity: Entity) {
@@ -118,6 +123,9 @@ export class H5WasmApi extends DataProviderApi {
   private async initH5Wasm(): Promise<typeof Module> {
     const module = await h5wasmReady;
 
+    // Throw HDF5 errors instead of just logging them
+    module.activate_throwing_error_handler();
+
     // Replace default plugins path
     module.remove_plugin_search_path(0);
     module.insert_plugin_search_path(PLUGINS_PATH, 0);
@@ -162,10 +170,12 @@ export class H5WasmApi extends DataProviderApi {
       }
 
       const plugin = PLUGINS_BY_FILTER_ID[filter.id];
-      if (!plugin || !this.getPlugin) {
-        throw new Error(
+      if (!plugin) {
+        // eslint-disable-next-line no-console
+        console.warn(
           `Compression filter ${filter.id} not supported (${filter.name})`,
         );
+        continue;
       }
 
       const pluginPath = `${PLUGINS_PATH}/libH5Z${plugin}.so`;
@@ -174,9 +184,11 @@ export class H5WasmApi extends DataProviderApi {
         continue; // plugin already loaded
       }
 
-      const buffer = await this.getPlugin(plugin);
+      const buffer = await this.getPlugin?.(plugin);
       if (!buffer) {
-        throw new Error(`Compression plugin ${plugin} not supported`);
+        // eslint-disable-next-line no-console
+        console.warn(`Compression plugin ${plugin} not available`);
+        continue;
       }
 
       h5Module.FS.writeFile(pluginPath, new Uint8Array(buffer));

packages/h5wasm/src/models.ts

@@ -3,3 +3,10 @@ import type { Group as H5WasmGroup } from 'h5wasm';
 export type H5WasmEntity = ReturnType<H5WasmGroup['get']>;
 
 export type H5WasmAttributes = H5WasmGroup['attrs'];
+
+export interface HDF5Diag {
+  major: string;
+  minor: string;
+  message: string;
+  origin: string;
+}

packages/h5wasm/src/utils.test.ts

@@ -0,0 +1,56 @@
+/* eslint-disable sonarjs/no-duplicate-string */
+import { describe, expect, it } from 'vitest';
+
+import { parseDiagnostics } from './utils';
+
+const HDF5_ERROR_MESSAGE = `HDF5-DIAG: Error detected in HDF5 (1.14.2) thread 0:
+  #000: /__w/libhdf5-wasm/libhdf5-wasm/build/1.14.2/_deps/hdf5-src/src/H5D.c line 1061 in H5Dread(): can't synchronously read data
+    major: Dataset
+    minor: Read failed
+  #001: /__w/libhdf5-wasm/libhdf5-wasm/build/1.14.2/_deps/hdf5-src/src/H5VLcallback.c line 2092 in H5VL_dataset_read_direct(): dataset read failed
+    major: Virtual Object Layer
+    minor: Read failed
+  #002: /__w/libhdf5-wasm/libhdf5-wasm/build/1.14.2/_deps/hdf5-src/src/H5Dchunk.c line 4468 in H5D__chunk_lock(): data pipeline read failed
+    major: Dataset
+    minor: Filter operation failed
+  #003: /__w/libhdf5-wasm/libhdf5-wasm/build/1.14.2/_deps/hdf5-src/src/H5Z.c line 1356 in H5Z_pipeline(): required filter 'SZ3 compressor/decompressor for floating-point data.' is not registered
+    major: Data filters
+    minor: Read failed
+`;
+
+describe('parseDiagnostics', () => {
+  it('should parse HDF5 error message and return diagnostics', () => {
+    const diagnostics = parseDiagnostics(HDF5_ERROR_MESSAGE);
+    expect(diagnostics).toEqual([
+      {
+        major: 'Dataset',
+        minor: 'Read failed',
+        message: "Can't synchronously read data",
+        origin:
+          '/__w/libhdf5-wasm/libhdf5-wasm/build/1.14.2/_deps/hdf5-src/src/H5D.c line 1061 in H5Dread()',
+      },
+      {
+        major: 'Virtual Object Layer',
+        minor: 'Read failed',
+        message: 'Dataset read failed',
+        origin:
+          '/__w/libhdf5-wasm/libhdf5-wasm/build/1.14.2/_deps/hdf5-src/src/H5VLcallback.c line 2092 in H5VL_dataset_read_direct()',
+      },
+      {
+        major: 'Dataset',
+        minor: 'Filter operation failed',
+        message: 'Data pipeline read failed',
+        origin:
+          '/__w/libhdf5-wasm/libhdf5-wasm/build/1.14.2/_deps/hdf5-src/src/H5Dchunk.c line 4468 in H5D__chunk_lock()',
+      },
+      {
+        major: 'Data filters',
+        minor: 'Read failed',
+        message:
+          "Required filter 'SZ3 compressor/decompressor for floating-point data.' is not registered",
+        origin:
+          '/__w/libhdf5-wasm/libhdf5-wasm/build/1.14.2/_deps/hdf5-src/src/H5Z.c line 1356 in H5Z_pipeline()',
+      },
+    ]);
+  });
+});

packages/h5wasm/src/utils.ts

@@ -37,7 +37,7 @@ import {
   Group as H5WasmGroup,
 } from 'h5wasm';
 
-import type { H5WasmAttributes, H5WasmEntity } from './models';
+import type { H5WasmAttributes, H5WasmEntity, HDF5Diag } from './models';
 
 // https://github.com/h5wasm/h5wasm-plugins#included-plugins
 export enum Plugin {
@@ -303,3 +303,66 @@ export function sanitizeBigInts(value: unknown): unknown {
 
   return value;
 }
+
+const DIAG_PREDICATES: ((diag: HDF5Diag) => boolean)[] = [
+  (diag: HDF5Diag) => {
+    return (
+      diag.major === 'Data filters' &&
+      /^required filter.*not registered$/iu.test(diag.message)
+    );
+  },
+];
+
+export function getEnhancedError(error: unknown): unknown {
+  if (!(error instanceof Error) || !error.message.startsWith('HDF5-DIAG')) {
+    return error;
+  }
+
+  const diagnostics = parseDiagnostics(error.message);
+  const opts = { cause: error };
+
+  for (const predicate of DIAG_PREDICATES) {
+    const diag = diagnostics.find(predicate);
+    if (diag) {
+      return new Error(diag.message, opts);
+    }
+  }
+
+  return new Error('Error detected in HDF5', opts);
+}
+
+const MESSAGE_LINE_REGEX = /#\d{3}: (\/.+ line \d+ in .+\(\)): (.+)$/u;
+const MAJOR_LINE_REGEX = /major: (.+)$/u;
+const MINOR_LINE_REGEX = /minor: (.+)$/u;
+
+/* Each HDF5 diagnostic entry is made up of three lines:
+ * 1. "#000: <origin>: <message>"
+ * 2. "major: <major>"
+ * 3. "major: <minor>"
+ */
+export function parseDiagnostics(msg: string): HDF5Diag[] {
+  // Ignore first line (generic error) and last line (empty)
+  const lines = msg.split(/\n/u).slice(1, -1);
+
+  if (lines.length % 3 !== 0) {
+    return [];
+  }
+
+  const diags: HDF5Diag[] = [];
+  for (let i = 0; i < lines.length; i += 3) {
+    const [, origin, message] = MESSAGE_LINE_REGEX.exec(lines[i]) || [];
+    const [, major] = MAJOR_LINE_REGEX.exec(lines[i + 1]) || [];
+    const [, minor] = MINOR_LINE_REGEX.exec(lines[i + 2]) || [];
+
+    if (origin && message && major && minor) {
+      diags.push({
+        major,
+        minor,
+        message: `${message.charAt(0).toUpperCase()}${message.slice(1)}`,
+        origin,
+      });
+    }
+  }
+
+  return diags;
+}