molstar
Version:
A comprehensive macromolecular library.
231 lines (230 loc) • 14.3 kB
JavaScript
"use strict";
/**
* Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.DownloadFile = exports.OpenFiles = void 0;
var tslib_1 = require("tslib");
var mol_state_1 = require("../../mol-state");
var mol_task_1 = require("../../mol-task");
var assets_1 = require("../../mol-util/assets");
var file_info_1 = require("../../mol-util/file-info");
var param_definition_1 = require("../../mol-util/param-definition");
var zip_1 = require("../../mol-util/zip/zip");
var objects_1 = require("../objects");
function processFile(file, plugin, format, visuals) {
var _a, _b;
return tslib_1.__awaiter(this, void 0, void 0, function () {
var info, isBinary, data, provider, parsed;
return tslib_1.__generator(this, function (_c) {
switch (_c.label) {
case 0:
info = (0, file_info_1.getFileInfo)(file.file);
isBinary = plugin.dataFormats.binaryExtensions.has(info.ext);
return [4 /*yield*/, plugin.builders.data.readFile({ file: file, isBinary: isBinary })];
case 1:
data = (_c.sent()).data;
provider = format === 'auto'
? plugin.dataFormats.auto(info, (_a = data.cell) === null || _a === void 0 ? void 0 : _a.obj)
: plugin.dataFormats.get(format);
if (!!provider) return [3 /*break*/, 3];
plugin.log.warn("OpenFiles: could not find data provider for '".concat(info.ext, "'"));
return [4 /*yield*/, plugin.state.data.build().delete(data).commit()];
case 2:
_c.sent();
return [2 /*return*/];
case 3: return [4 /*yield*/, provider.parse(plugin, data)];
case 4:
parsed = _c.sent();
if (!visuals) return [3 /*break*/, 6];
return [4 /*yield*/, ((_b = provider.visuals) === null || _b === void 0 ? void 0 : _b.call(provider, plugin, parsed))];
case 5:
_c.sent();
_c.label = 6;
case 6: return [2 /*return*/];
}
});
});
}
;
exports.OpenFiles = mol_state_1.StateAction.build({
display: { name: 'Open Files', description: 'Load one or more files and optionally create default visuals' },
from: objects_1.PluginStateObject.Root,
params: function (a, ctx) {
var _a = ctx.dataFormats, extensions = _a.extensions, options = _a.options;
return {
files: param_definition_1.ParamDefinition.FileList({ accept: Array.from(extensions.values()).map(function (e) { return ".".concat(e); }).join(',') + ',.gz,.zip', multiple: true }),
format: param_definition_1.ParamDefinition.MappedStatic('auto', {
auto: param_definition_1.ParamDefinition.EmptyGroup(),
specific: param_definition_1.ParamDefinition.Select(options[0][0], options)
}),
visuals: param_definition_1.ParamDefinition.Boolean(true, { description: 'Add default visuals' }),
};
}
})(function (_a, plugin) {
var params = _a.params, state = _a.state;
return mol_task_1.Task.create('Open Files', function (taskCtx) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
return tslib_1.__generator(this, function (_a) {
switch (_a.label) {
case 0:
plugin.behaviors.layout.leftPanelTabName.next('data');
return [4 /*yield*/, state.transaction(function () { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
var _i, _a, file, zippedFiles, _b, _c, _d, _e, _f, fn, filedata, asset, format, e_1;
return tslib_1.__generator(this, function (_g) {
switch (_g.label) {
case 0:
if (params.files === null) {
plugin.log.error('No file(s) selected');
return [2 /*return*/];
}
_i = 0, _a = params.files;
_g.label = 1;
case 1:
if (!(_i < _a.length)) return [3 /*break*/, 14];
file = _a[_i];
_g.label = 2;
case 2:
_g.trys.push([2, 12, , 13]);
if (!(file.file && file.name.toLowerCase().endsWith('.zip'))) return [3 /*break*/, 9];
_b = zip_1.unzip;
_c = [taskCtx];
return [4 /*yield*/, file.file.arrayBuffer()];
case 3: return [4 /*yield*/, _b.apply(void 0, _c.concat([_g.sent()]))];
case 4:
zippedFiles = _g.sent();
_d = 0, _e = Object.entries(zippedFiles);
_g.label = 5;
case 5:
if (!(_d < _e.length)) return [3 /*break*/, 8];
_f = _e[_d], fn = _f[0], filedata = _f[1];
if (!(filedata instanceof Uint8Array) || filedata.length === 0)
return [3 /*break*/, 7];
asset = assets_1.Asset.File(new File([filedata], fn));
return [4 /*yield*/, processFile(asset, plugin, 'auto', params.visuals)];
case 6:
_g.sent();
_g.label = 7;
case 7:
_d++;
return [3 /*break*/, 5];
case 8: return [3 /*break*/, 11];
case 9:
format = params.format.name === 'auto' ? 'auto' : params.format.params;
return [4 /*yield*/, processFile(file, plugin, format, params.visuals)];
case 10:
_g.sent();
_g.label = 11;
case 11: return [3 /*break*/, 13];
case 12:
e_1 = _g.sent();
console.error(e_1);
plugin.log.error("Error opening file '".concat(file.name, "'"));
return [3 /*break*/, 13];
case 13:
_i++;
return [3 /*break*/, 1];
case 14: return [2 /*return*/];
}
});
}); }).runInContext(taskCtx)];
case 1:
_a.sent();
return [2 /*return*/];
}
});
}); });
});
exports.DownloadFile = mol_state_1.StateAction.build({
display: { name: 'Download File', description: 'Load one or more file from an URL' },
from: objects_1.PluginStateObject.Root,
params: function (a, ctx) {
var options = tslib_1.__spreadArray(tslib_1.__spreadArray([], ctx.dataFormats.options, true), [['zip', 'Zip'], ['gzip', 'Gzip']], false);
return {
url: param_definition_1.ParamDefinition.Url(''),
format: param_definition_1.ParamDefinition.Select(options[0][0], options),
isBinary: param_definition_1.ParamDefinition.Boolean(false),
visuals: param_definition_1.ParamDefinition.Boolean(true, { description: 'Add default visuals' }),
};
}
})(function (_a, plugin) {
var params = _a.params, state = _a.state;
return mol_task_1.Task.create('Open Files', function (taskCtx) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
return tslib_1.__generator(this, function (_a) {
switch (_a.label) {
case 0:
plugin.behaviors.layout.leftPanelTabName.next('data');
return [4 /*yield*/, state.transaction(function () { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
var data, zippedFiles, _i, _a, _b, fn, filedata, asset, url, info, provider, data, parsed, e_2;
var _c, _d, _e;
return tslib_1.__generator(this, function (_f) {
switch (_f.label) {
case 0:
_f.trys.push([0, 15, , 16]);
if (!(params.format === 'zip' || params.format === 'gzip')) return [3 /*break*/, 10];
return [4 /*yield*/, plugin.builders.data.download({ url: params.url, isBinary: true })];
case 1:
data = _f.sent();
if (!(params.format === 'zip')) return [3 /*break*/, 7];
return [4 /*yield*/, (0, zip_1.unzip)(taskCtx, ((_c = data.obj) === null || _c === void 0 ? void 0 : _c.data).buffer)];
case 2:
zippedFiles = _f.sent();
_i = 0, _a = Object.entries(zippedFiles);
_f.label = 3;
case 3:
if (!(_i < _a.length)) return [3 /*break*/, 6];
_b = _a[_i], fn = _b[0], filedata = _b[1];
if (!(filedata instanceof Uint8Array) || filedata.length === 0)
return [3 /*break*/, 5];
asset = assets_1.Asset.File(new File([filedata], fn));
return [4 /*yield*/, processFile(asset, plugin, 'auto', params.visuals)];
case 4:
_f.sent();
_f.label = 5;
case 5:
_i++;
return [3 /*break*/, 3];
case 6: return [3 /*break*/, 9];
case 7:
url = assets_1.Asset.getUrl(params.url);
info = (0, file_info_1.getFileInfo)(url);
return [4 /*yield*/, processFile(assets_1.Asset.File(new File([(_d = data.obj) === null || _d === void 0 ? void 0 : _d.data], info.name)), plugin, 'auto', params.visuals)];
case 8:
_f.sent();
_f.label = 9;
case 9: return [3 /*break*/, 14];
case 10:
provider = plugin.dataFormats.get(params.format);
if (!provider) {
plugin.log.warn("DownloadFile: could not find data provider for '".concat(params.format, "'"));
return [2 /*return*/];
}
return [4 /*yield*/, plugin.builders.data.download({ url: params.url, isBinary: params.isBinary })];
case 11:
data = _f.sent();
return [4 /*yield*/, provider.parse(plugin, data)];
case 12:
parsed = _f.sent();
if (!params.visuals) return [3 /*break*/, 14];
return [4 /*yield*/, ((_e = provider.visuals) === null || _e === void 0 ? void 0 : _e.call(provider, plugin, parsed))];
case 13:
_f.sent();
_f.label = 14;
case 14: return [3 /*break*/, 16];
case 15:
e_2 = _f.sent();
console.error(e_2);
plugin.log.error("Error downloading '".concat(typeof params.url === 'string' ? params.url : params.url.url, "'"));
return [3 /*break*/, 16];
case 16: return [2 /*return*/];
}
});
}); }).runInContext(taskCtx)];
case 1:
_a.sent();
return [2 /*return*/];
}
});
}); });
});