diff --git a/src/extensions/volumes-and-segmentations/index.ts b/src/extensions/volumes-and-segmentations/index.ts
index 8f66d7ed10805ae02c0cb8e8ceb32d97785e4a30..d62316598de4208898a15e1ca81aa73375079970 100644
--- a/src/extensions/volumes-and-segmentations/index.ts
+++ b/src/extensions/volumes-and-segmentations/index.ts
@@ -19,7 +19,7 @@ import { VolsegEntryFromRoot, VolsegGlobalStateFromRoot, VolsegStateFromEntry }
import { VolsegUI } from './ui';
-const DEBUGGING = window.location.hostname === 'localhost';
+const DEBUGGING = typeof window !== 'undefined' ? window?.location?.hostname === 'localhost' : false;
export const VolsegVolumeServerConfig = {
// DefaultServer: new PluginConfigItem('volseg-volume-server', DEFAULT_VOLUME_SERVER_V2),
diff --git a/src/mol-io/common/file-handle.ts b/src/mol-io/common/file-handle.ts
index e0b18b39c524a3ad4309400815b6f032aa68b498..724d18d8a382ad8d4f2019aa22f7a877168a009e 100644
--- a/src/mol-io/common/file-handle.ts
+++ b/src/mol-io/common/file-handle.ts
@@ -16,7 +16,7 @@ export interface FileHandle {
* @param position The offset from the beginning of the file from which data should be read.
* @param sizeOrBuffer The buffer the data will be read from.
* @param length The number of bytes to read.
- * @param byteOffset The offset in the buffer at which to start writing.
+ * @param byteOffset The offset in the buffer at which to start reading.
*/
readBuffer(position: number, sizeOrBuffer: SimpleBuffer | number, length?: number, byteOffset?: number): Promise<{ bytesRead: number, buffer: SimpleBuffer }>
diff --git a/src/mol-plugin-state/actions/file.ts b/src/mol-plugin-state/actions/file.ts
index ee81b0793d6aae3808e1a467f75ab1fc00393dfe..24e01503ad6b8433d4764d1eb028e3e595d3a4ed 100644
--- a/src/mol-plugin-state/actions/file.ts
+++ b/src/mol-plugin-state/actions/file.ts
@@ -8,13 +8,13 @@ import { PluginContext } from '../../mol-plugin/context';
import { StateAction } from '../../mol-state';
import { Task } from '../../mol-task';
import { Asset } from '../../mol-util/assets';
-import { getFileInfo } from '../../mol-util/file-info';
+import { getFileNameInfo } from '../../mol-util/file-info';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { unzip } from '../../mol-util/zip/zip';
import { PluginStateObject } from '../objects';
async function processFile(file: Asset.File, plugin: PluginContext, format: string, visuals: boolean) {
- const info = getFileInfo(file.file!);
+ const info = getFileNameInfo(file.file?.name ?? '');
const isBinary = plugin.dataFormats.binaryExtensions.has(info.ext);
const { data } = await plugin.builders.data.readFile({ file, isBinary });
const provider = format === 'auto'
@@ -111,8 +111,8 @@ export const DownloadFile = StateAction.build({
}
} else {
const url = Asset.getUrl(params.url);
- const info = getFileInfo(url);
- await processFile(Asset.File(new File([data.obj?.data as Uint8Array], info.name)), plugin, 'auto', params.visuals);
+ const fileName = getFileNameInfo(url).name;
+ await processFile(Asset.File(new File([data.obj?.data as Uint8Array], fileName)), plugin, 'auto', params.visuals);
}
} else {
const provider = plugin.dataFormats.get(params.format);
diff --git a/src/mol-plugin-state/actions/structure.ts b/src/mol-plugin-state/actions/structure.ts
index 61765b5a22b2ebc3d3b3592e98c5f0a48357fd20..b123cec15b73bb89c0b697a31ccbef4547cd4e90 100644
--- a/src/mol-plugin-state/actions/structure.ts
+++ b/src/mol-plugin-state/actions/structure.ts
@@ -18,7 +18,7 @@ import { Download } from '../transforms/data';
import { CustomModelProperties, CustomStructureProperties, ModelFromTrajectory, TrajectoryFromModelAndCoordinates } from '../transforms/model';
import { Asset } from '../../mol-util/assets';
import { PluginConfig } from '../../mol-plugin/config';
-import { getFileInfo } from '../../mol-util/file-info';
+import { getFileNameInfo } from '../../mol-util/file-info';
import { assertUnreachable } from '../../mol-util/type-helpers';
import { TopologyFormatCategory } from '../formats/topology';
import { CoordinatesFormatCategory } from '../formats/coordinates';
@@ -184,7 +184,7 @@ const DownloadStructure = StateAction.build({
for (const download of downloadParams) {
const data = await plugin.builders.data.download(download, { state: { isGhost: true } });
const provider = format === 'auto'
- ? plugin.dataFormats.auto(getFileInfo(Asset.getUrl(download.url)), data.cell?.obj!)
+ ? plugin.dataFormats.auto(getFileNameInfo(Asset.getUrl(download.url)), data.cell?.obj!)
: plugin.dataFormats.get(format);
if (!provider) throw new Error('unknown file format');
const trajectory = await plugin.builders.structure.parseTrajectory(data, provider);
@@ -385,7 +385,7 @@ export const LoadTrajectory = StateAction.build({
const processFile = async (file: Asset.File | null) => {
if (!file) throw new Error('No file selected');
- const info = getFileInfo(file.file!);
+ const info = getFileNameInfo(file.file?.name ?? '');
const isBinary = ctx.dataFormats.binaryExtensions.has(info.ext);
const { data } = await ctx.builders.data.readFile({ file, isBinary });
const provider = ctx.dataFormats.auto(info, data.cell?.obj!);
diff --git a/src/mol-plugin-state/actions/volume.ts b/src/mol-plugin-state/actions/volume.ts
index fad2beeca7da71321ecb2c52eadb3d0e711759f8..750509ba7a07ab1d280b7c3e943322ab14ea2ff8 100644
--- a/src/mol-plugin-state/actions/volume.ts
+++ b/src/mol-plugin-state/actions/volume.ts
@@ -8,7 +8,7 @@
import { PluginContext } from '../../mol-plugin/context';
import { StateAction, StateTransformer, StateSelection } from '../../mol-state';
import { Task } from '../../mol-task';
-import { getFileInfo } from '../../mol-util/file-info';
+import { getFileNameInfo } from '../../mol-util/file-info';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { PluginStateObject } from '../objects';
import { Download } from '../transforms/data';
@@ -119,7 +119,7 @@ const DownloadDensity = StateAction.build({
switch (src.name) {
case 'url':
downloadParams = src.params;
- provider = src.params.format === 'auto' ? plugin.dataFormats.auto(getFileInfo(Asset.getUrl(downloadParams.url)), data.cell?.obj!) : plugin.dataFormats.get(src.params.format);
+ provider = src.params.format === 'auto' ? plugin.dataFormats.auto(getFileNameInfo(Asset.getUrl(downloadParams.url)), data.cell?.obj!) : plugin.dataFormats.get(src.params.format);
break;
case 'pdb-xray':
entryId = src.params.provider.id;
diff --git a/src/mol-plugin-state/builder/data.ts b/src/mol-plugin-state/builder/data.ts
index 16dec53c0615b67b0905c22e99970edb865874f2..b57cb0fe960104457cb821e2366ff2ffbc8dfb2f 100644
--- a/src/mol-plugin-state/builder/data.ts
+++ b/src/mol-plugin-state/builder/data.ts
@@ -7,7 +7,7 @@
import { StateTransformer, StateTransform } from '../../mol-state';
import { PluginContext } from '../../mol-plugin/context';
import { Download, ReadFile, DownloadBlob, RawData } from '../transforms/data';
-import { getFileInfo } from '../../mol-util/file-info';
+import { getFileNameInfo } from '../../mol-util/file-info';
export class DataBuilder {
private get dataState() {
@@ -31,7 +31,7 @@ export class DataBuilder {
async readFile(params: StateTransformer.Params<ReadFile>, options?: Partial<StateTransform.Options>) {
const data = await this.dataState.build().toRoot().apply(ReadFile, params, options).commit({ revertOnError: true });
- const fileInfo = getFileInfo(params.file?.file || '');
+ const fileInfo = getFileNameInfo(params.file?.file?.name ?? '');
return { data: data, fileInfo };
}
diff --git a/src/mol-plugin-state/formats/provider.ts b/src/mol-plugin-state/formats/provider.ts
index 6fe0bed66998cbfb2f99ccefdcd4e9cf2be566f7..dc916cdf6f6f4f57fb7c982a98e07a1da77a010c 100644
--- a/src/mol-plugin-state/formats/provider.ts
+++ b/src/mol-plugin-state/formats/provider.ts
@@ -8,7 +8,7 @@
import { decodeMsgPack } from '../../mol-io/common/msgpack/decode';
import { PluginContext } from '../../mol-plugin/context';
import { StateObjectRef } from '../../mol-state';
-import { FileInfo } from '../../mol-util/file-info';
+import { FileNameInfo } from '../../mol-util/file-info';
import { PluginStateObject } from '../objects';
export interface DataFormatProvider<P = any, R = any, V = any> {
@@ -17,7 +17,7 @@ export interface DataFormatProvider<P = any, R = any, V = any> {
category?: string,
stringExtensions?: string[],
binaryExtensions?: string[],
- isApplicable?(info: FileInfo, data: string | Uint8Array): boolean,
+ isApplicable?(info: FileNameInfo, data: string | Uint8Array): boolean,
parse(plugin: PluginContext, data: StateObjectRef<PluginStateObject.Data.Binary | PluginStateObject.Data.String>, params?: P): Promise<R>,
visuals?(plugin: PluginContext, data: R): Promise<V> | undefined
}
@@ -25,7 +25,7 @@ export interface DataFormatProvider<P = any, R = any, V = any> {
export function DataFormatProvider<P extends DataFormatProvider>(provider: P): P { return provider; }
type cifVariants = 'dscif' | 'segcif' | 'coreCif' | -1
-export function guessCifVariant(info: FileInfo, data: Uint8Array | string): cifVariants {
+export function guessCifVariant(info: FileNameInfo, data: Uint8Array | string): cifVariants {
if (info.ext === 'bcif') {
try {
// TODO: find a way to run msgpackDecode only once
diff --git a/src/mol-plugin-state/formats/registry.ts b/src/mol-plugin-state/formats/registry.ts
index 090ce3f321635fc345a5542e6db394658fb1c49a..326f9093344a67685f41bd197955bb779739008b 100644
--- a/src/mol-plugin-state/formats/registry.ts
+++ b/src/mol-plugin-state/formats/registry.ts
@@ -5,7 +5,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { FileInfo } from '../../mol-util/file-info';
+import { FileNameInfo } from '../../mol-util/file-info';
import { PluginStateObject } from '../objects';
import { DataFormatProvider } from './provider';
import { BuiltInTrajectoryFormats } from './trajectory';
@@ -78,7 +78,7 @@ export class DataFormatRegistry {
this._map.delete(name);
}
- auto(info: FileInfo, dataStateObject: PluginStateObject.Data.Binary | PluginStateObject.Data.String) {
+ auto(info: FileNameInfo, dataStateObject: PluginStateObject.Data.Binary | PluginStateObject.Data.String) {
for (let i = 0, il = this.list.length; i < il; ++i) {
const p = this._list[i].provider;
diff --git a/src/mol-util/_spec/file-info.spec.ts b/src/mol-util/_spec/file-info.spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..aeb530fe37a4902a02b881c40a6ee56d89b62722
--- /dev/null
+++ b/src/mol-util/_spec/file-info.spec.ts
@@ -0,0 +1,29 @@
+/**
+ * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Russell Parker <russell@benchling.com>
+ */
+
+import { getFileNameInfo } from '../file-info';
+
+describe('getFileNameInfo', () => {
+ it('handles empty string', () => {
+ expect(getFileNameInfo('')).toEqual({ path: '', name: '', ext: '', base: '', dir: '', protocol: '', query: '' });
+ });
+
+ it('handles url', () => {
+ expect(getFileNameInfo('https://models.rcsb.org/4KTC.bcif')).toEqual({ path: 'models.rcsb.org/4KTC.bcif', name: '4KTC.bcif', ext: 'bcif', base: '4KTC', dir: 'models.rcsb.org/', protocol: 'https', query: '' })
+ });
+
+ it('handles compressed url', () => {
+ expect(getFileNameInfo('https://files.rcsb.org/download/7QPD.cif.gz?foo=bar')).toEqual({ path: 'files.rcsb.org/download/7QPD.cif.gz', name: '7QPD.cif.gz', ext: 'cif', base: '7QPD', dir: 'files.rcsb.org/download/', protocol: 'https', query: '?foo=bar' })
+ });
+
+ it('handles local path', () => {
+ expect(getFileNameInfo('/usr/local/data/structure.pdb')).toEqual({ path: '/usr/local/data/structure.pdb', name: 'structure.pdb', ext: 'pdb', base: 'structure', dir: '/usr/local/data/', protocol: '', query: '' })
+ });
+
+ it('handles local path with protocol', () => {
+ expect(getFileNameInfo('file:///usr/local/data/structure.pdb')).toEqual({ path: '/usr/local/data/structure.pdb', name: 'structure.pdb', ext: 'pdb', base: 'structure', dir: '/usr/local/data/', protocol: 'file', query: '' })
+ });
+});
diff --git a/src/mol-util/file-info.ts b/src/mol-util/file-info.ts
index 0477631a42e2e56ef40714e9831a2e889b827597..ed2fbfedeab823209b612214ada4204e3f6c954b 100644
--- a/src/mol-util/file-info.ts
+++ b/src/mol-util/file-info.ts
@@ -1,17 +1,15 @@
/**
- * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Russell Parker <russell@benchling.com>
*/
-/** A File or Blob object or a URL string */
-export type FileInput = File | Blob | string
-
// TODO only support compressed files for which uncompression support is available???
// TODO store globally with decompression plugins?
-const compressedExtList = ['gz', 'zip'];
+const COMPRESSED_EXT_LIST = ['gz', 'zip'];
-export interface FileInfo {
+export interface FileNameInfo {
path: string
name: string
ext: string
@@ -19,20 +17,12 @@ export interface FileInfo {
dir: string
protocol: string
query: string
- src: FileInput
}
-export function getFileInfo(file: FileInput): FileInfo {
- let path: string;
+export function getFileNameInfo(fileName: string): FileNameInfo {
+ let path: string = fileName;
let protocol = '';
- if (file instanceof File) {
- path = file.name;
- } else if (file instanceof Blob) {
- path = '';
- } else {
- path = file;
- }
const queryIndex = path.lastIndexOf('?');
const query = queryIndex !== -1 ? path.substring(queryIndex) : '';
path = path.substring(0, queryIndex === -1 ? path.length : queryIndex);
@@ -51,12 +41,14 @@ export function getFileInfo(file: FileInput): FileInfo {
const dir = path.substring(0, path.lastIndexOf('/') + 1);
- if (compressedExtList.includes(ext)) {
+ if (COMPRESSED_EXT_LIST.includes(ext)) {
const n = path.length - ext.length - 1;
+ // TODO: change logic to String.prototype.substring since substr is deprecated
ext = (path.substr(0, n).split('.').pop() || '').toLowerCase();
const m = base.length - ext.length - 1;
base = base.substr(0, m);
}
- return { path, name, ext, base, dir, protocol, query, src: file };
+ // Note: it appears that most of this data never gets used.
+ return { path, name, ext, base, dir, protocol, query };
}
\ No newline at end of file