From 9d5f51f513b8f0d5559d881d4cd797c16029b8aa Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Sun, 6 Mar 2022 17:32:32 -0800
Subject: [PATCH] improve handling of compressed files
- fix loading of some compressed files within sessions
- ignore some hidden MACOSX files
---
CHANGELOG.md | 1 +
src/mol-plugin-state/manager/snapshots.ts | 6 +++---
src/mol-util/data-source.ts | 4 +++-
src/mol-util/zip/zip.ts | 6 +++++-
4 files changed, 12 insertions(+), 5 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index db302d901..da5f9bd68 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ Note that since we don't clearly distinguish between a public and private interf
- Fix handling of mmcif with empty ``label_*`` fields
- Add LoadTrajectory action
- Add Zenodo import extension (load structures, trajectories, and volumes)
+- Fix loading of some compressed files within sessions
## [v3.3.1] - 2022-02-27
diff --git a/src/mol-plugin-state/manager/snapshots.ts b/src/mol-plugin-state/manager/snapshots.ts
index 698764e46..1b9f6cc33 100644
--- a/src/mol-plugin-state/manager/snapshots.ts
+++ b/src/mol-plugin-state/manager/snapshots.ts
@@ -238,12 +238,12 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<{
}
} else {
const data = await this.plugin.runTask(readFromFile(file, 'zip'));
- const assets = Object.create(null);
+ const assetData = Object.create(null);
objectForEach(data, (v, k) => {
if (k === 'state.json' || k === 'assets.json') return;
const name = k.substring(k.indexOf('/') + 1);
- assets[name] = new File([v], name);
+ assetData[name] = v;
});
const stateFile = new File([data['state.json']], 'state.json');
const stateData = await this.plugin.runTask(readFromFile(stateFile, 'string'));
@@ -253,7 +253,7 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<{
const json = JSON.parse(await this.plugin.runTask(readFromFile(file, 'string')));
for (const [id, asset] of json) {
- this.plugin.managers.asset.set(asset, assets[id]);
+ this.plugin.managers.asset.set(asset, new File([assetData[id]], asset.name));
}
}
diff --git a/src/mol-util/data-source.ts b/src/mol-util/data-source.ts
index 794c2e4d4..265bfaa80 100644
--- a/src/mol-util/data-source.ts
+++ b/src/mol-util/data-source.ts
@@ -130,13 +130,15 @@ function getCompression(name: string) {
DataCompressionMethod.None;
}
+const reFilterPath = /^(__MACOSX|.DS_Store)/;
+
async function decompress(ctx: RuntimeContext, data: Uint8Array, compression: DataCompressionMethod): Promise<Uint8Array> {
switch (compression) {
case DataCompressionMethod.None: return data;
case DataCompressionMethod.Gzip: return ungzip(ctx, data);
case DataCompressionMethod.Zip:
const parsed = await unzip(ctx, data.buffer);
- const names = Object.keys(parsed);
+ const names = Object.keys(parsed).filter(n => !reFilterPath.test(n));
if (names.length !== 1) throw new Error('can only decompress zip files with a single entry');
return parsed[names[0]] as Uint8Array;
}
diff --git a/src/mol-util/zip/zip.ts b/src/mol-util/zip/zip.ts
index b81bccf49..ea838f5c3 100644
--- a/src/mol-util/zip/zip.ts
+++ b/src/mol-util/zip/zip.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*
@@ -15,6 +15,10 @@ import { _inflate } from './inflate';
import { _deflateRaw } from './deflate';
import { RuntimeContext, Task } from '../../mol-task';
+export function Unzip(buf: ArrayBuffer, onlyNames = false) {
+ return Task.create('Unzip', ctx => unzip(ctx, buf, onlyNames));
+}
+
export async function unzip(runtime: RuntimeContext, buf: ArrayBuffer, onlyNames = false) {
const out: { [k: string]: Uint8Array | { size: number, csize: number } } = Object.create(null);
const data = new Uint8Array(buf);
--
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