src/index.tsx

   1 // Copyright (C) The Arvados Authors. All rights reserved.
   2 //
   3 // SPDX-License-Identifier: AGPL-3.0
   4
   5 import * as React from 'react';
   6 import * as ReactDOM from 'react-dom';
   7 import { Provider } from "react-redux";
   8 import { MainPanel } from './views/main-panel/main-panel';
   9 import './index.css';
  10 import { Route } from 'react-router';
  11 import createBrowserHistory from "history/createBrowserHistory";
  12 import { History } from "history";
  13 import { configureStore, RootStore } from './store/store';
  14 import { ConnectedRouter } from "react-router-redux";
  15 import { ApiToken } from "./views-components/api-token/api-token";
  16 import { initAuth } from "./store/auth/auth-action";
  17 import { createServices } from "./services/services";
  18 import { MuiThemeProvider } from '@material-ui/core/styles';
  19 import { CustomTheme } from './common/custom-theme';
  20 import { fetchConfig } from './common/config';
  21 import { addMenuActionSet, ContextMenuKind } from './views-components/context-menu/context-menu';
  22 import { rootProjectActionSet } from "./views-components/context-menu/action-sets/root-project-action-set";
  23 import { projectActionSet } from "./views-components/context-menu/action-sets/project-action-set";
  24 import { resourceActionSet } from './views-components/context-menu/action-sets/resource-action-set';
  25 import { favoriteActionSet } from "./views-components/context-menu/action-sets/favorite-action-set";
  26 import { collectionFilesActionSet } from './views-components/context-menu/action-sets/collection-files-action-set';
  27 import { collectionFilesItemActionSet } from './views-components/context-menu/action-sets/collection-files-item-action-set';
  28 import { collectionActionSet } from './views-components/context-menu/action-sets/collection-action-set';
  29 import { collectionResourceActionSet } from './views-components/context-menu/action-sets/collection-resource-action-set';
  30 import { processActionSet } from './views-components/context-menu/action-sets/process-action-set';
  31 import { loadWorkbench } from './store/workbench/workbench-actions';
  32 import { Routes } from '~/routes/routes';
  33 import { trashActionSet } from "~/views-components/context-menu/action-sets/trash-action-set";
  34 import { ServiceRepository } from '~/services/services';
  35 import { initWebSocket } from '~/websocket/websocket';
  36 import { Config } from '~/common/config';
  37 import { addRouteChangeHandlers } from './routes/route-change-handlers';
  38 import { setCurrentTokenDialogApiHost } from '~/store/current-token-dialog/current-token-dialog-actions';
  39 import { processResourceActionSet } from '~/views-components/context-menu/action-sets/process-resource-action-set';
  40 import { progressIndicatorActions } from '~/store/progress-indicator/progress-indicator-actions';
  41 import { setUuidPrefix } from '~/store/workflow-panel/workflow-panel-actions';
  42 import { trashedCollectionActionSet } from '~/views-components/context-menu/action-sets/trashed-collection-action-set';
  43 import { ContainerRequestState } from '~/models/container-request';
  44 import { MountKind } from '~/models/mount-types';
  45 import { setBuildInfo } from '~/store/app-info/app-info-actions';
  46 import { getBuildInfo } from '~/common/app-info';
  47 import { DragDropContextProvider } from 'react-dnd';
  48 import HTML5Backend from 'react-dnd-html5-backend';
  49
  50 console.log(`Starting arvados [${getBuildInfo()}]`);
  51
  52 addMenuActionSet(ContextMenuKind.ROOT_PROJECT, rootProjectActionSet);
  53 addMenuActionSet(ContextMenuKind.PROJECT, projectActionSet);
  54 addMenuActionSet(ContextMenuKind.RESOURCE, resourceActionSet);
  55 addMenuActionSet(ContextMenuKind.FAVORITE, favoriteActionSet);
  56 addMenuActionSet(ContextMenuKind.COLLECTION_FILES, collectionFilesActionSet);
  57 addMenuActionSet(ContextMenuKind.COLLECTION_FILES_ITEM, collectionFilesItemActionSet);
  58 addMenuActionSet(ContextMenuKind.COLLECTION, collectionActionSet);
  59 addMenuActionSet(ContextMenuKind.COLLECTION_RESOURCE, collectionResourceActionSet);
  60 addMenuActionSet(ContextMenuKind.TRASHED_COLLECTION, trashedCollectionActionSet);
  61 addMenuActionSet(ContextMenuKind.PROCESS, processActionSet);
  62 addMenuActionSet(ContextMenuKind.PROCESS_RESOURCE, processResourceActionSet);
  63 addMenuActionSet(ContextMenuKind.TRASH, trashActionSet);
  64
  65 fetchConfig()
  66     .then(({ config, apiHost }) => {
  67         const history = createBrowserHistory();
  68         const services = createServices(config, {
  69             progressFn: (id, working) => {
  70                 store.dispatch(progressIndicatorActions.TOGGLE_WORKING({ id, working }));
  71             },
  72             errorFn: (id, error) => {
  73                 // console.error("Backend error:", error);
  74                 // store.dispatch(snackbarActions.OPEN_SNACKBAR({ message: "Backend error", kind: SnackbarKind.ERROR }));
  75             }
  76         });
  77         const store = configureStore(history, services);
  78
  79         store.subscribe(initListener(history, store, services, config));
  80         store.dispatch(initAuth());
  81         store.dispatch(setBuildInfo());
  82         store.dispatch(setCurrentTokenDialogApiHost(apiHost));
  83         store.dispatch(setUuidPrefix(config.uuidPrefix));
  84
  85         const TokenComponent = (props: any) => <ApiToken authService={services.authService} {...props} />;
  86         const MainPanelComponent = (props: any) => <MainPanel {...props} />;
  87
  88         const App = () =>
  89             <MuiThemeProvider theme={CustomTheme}>
  90                 <DragDropContextProvider backend={HTML5Backend}>
  91                     <Provider store={store}>
  92                         <ConnectedRouter history={history}>
  93                             <div>
  94                                 <Route path={Routes.TOKEN} component={TokenComponent} />
  95                                 <Route path={Routes.ROOT} component={MainPanelComponent} />
  96                             </div>
  97                         </ConnectedRouter>
  98                     </Provider>
  99                 </DragDropContextProvider>
 100             </MuiThemeProvider>;
 101
 102         ReactDOM.render(
 103             <App />,
 104             document.getElementById('root') as HTMLElement
 105         );
 106     });
 107
 108 const initListener = (history: History, store: RootStore, services: ServiceRepository, config: Config) => {
 109     let initialized = false;
 110     return async () => {
 111         const { router, auth } = store.getState();
 112         if (router.location && auth.user && !initialized) {
 113             initialized = true;
 114             initWebSocket(config, services.authService, store);
 115             await store.dispatch(loadWorkbench());
 116             addRouteChangeHandlers(history, store);
 117         }
 118     };
 119 };
 120
 121 const createDirectoriesArrayCollectorWorkflow = ({workflowService}: ServiceRepository) => {
 122     workflowService.create({
 123         name: 'Directories array collector',
 124         description: 'Workflow for collecting directories array',
 125         definition: "cwlVersion: v1.0\n$graph:\n- class: CommandLineTool\n\n  requirements:\n  - listing:\n    - entryname: input_collector.log\n      entry: |\n        \"multiple_collections\":\n          $(inputs.multiple_collections)\n\n    class: InitialWorkDirRequirement\n  inputs:\n  - type:\n      type: array\n      items: Directory\n    id: '#input_collector.cwl/multiple_collections'\n  outputs:\n  - type: File\n    outputBinding:\n      glob: '*'\n    id: '#input_collector.cwl/output'\n\n  baseCommand: [echo]\n  id: '#input_collector.cwl'\n- class: Workflow\n  doc: This is the description of the workflow\n  inputs:\n  - type:\n      type: array\n      items: Directory\n    label: Multiple Collections\n    doc: This should allow for selecting multiple collections.\n    id: '#main/multiple_collections'\n    default:\n    - class: Directory\n      location: keep:1e1682585d576f031b2d8b4944f989ee+57\n      basename: 1e1682585d576f031b2d8b4944f989ee+57\n    - class: Directory\n      location: keep:326f692370e9e121fcbd013796f7352a+57\n      basename: 326f692370e9e121fcbd013796f7352a+57\n  \n  outputs:\n  - type: File\n    outputSource: '#main/input_collector/output'\n\n    id: '#main/log_file'\n  steps:\n  - run: '#input_collector.cwl'\n    in:\n    - source: '#main/multiple_collections'\n      id: '#main/input_collector/multiple_collections'\n    out: ['#main/input_collector/output']\n    id: '#main/input_collector'\n  id: '#main'\n",
 126     });
 127 };
 128
 129 const createFilesArrayCollectorWorkflow = ({workflowService}: ServiceRepository) => {
 130     workflowService.create({
 131         name: 'Files array collector',
 132         description: 'Workflow for collecting files array',
 133         definition: "cwlVersion: v1.0\n$graph:\n- class: CommandLineTool\n\n  requirements:\n  - listing:\n    - entryname: input_collector.log\n      entry: |\n        \"multiple_files\":\n          $(inputs.multiple_files)\n\n    class: InitialWorkDirRequirement\n  inputs:\n  - type:\n      type: array\n      items: File\n    id: '#input_collector.cwl/multiple_files'\n  outputs:\n  - type: File\n    outputBinding:\n      glob: '*'\n    id: '#input_collector.cwl/output'\n\n  baseCommand: [cat]\n  id: '#input_collector.cwl'\n- class: Workflow\n  doc: This is the description of the workflow\n  inputs:\n  - type:\n      type: array\n      items: File\n    label: Multiple Files\n    doc: This should allow for selecting multiple files.\n    id: '#main/multiple_files'\n    default:\n      - class: File\n        location: keep:af831660d820bcbb98f473355e6e1b85+67/fileA\n        basename: fileA\n        nameroot: fileA\n        nameext: ''\n  outputs:\n  - type: File\n    outputSource: '#main/input_collector/output'\n\n    id: '#main/log_file'\n  steps:\n  - run: '#input_collector.cwl'\n    in:\n    - source: '#main/multiple_files'\n      id: '#main/input_collector/multiple_files'\n    out: ['#main/input_collector/output']\n    id: '#main/input_collector'\n  id: '#main'\n",
 134     });
 135 };
 136
 137 const createPrimitivesCollectorWorkflow = ({ workflowService }: ServiceRepository) => {
 138     workflowService.create({
 139         name: 'Primitive values collector',
 140         description: 'Workflow for collecting primitive values',
 141         definition: "cwlVersion: v1.0\n$graph:\n- class: CommandLineTool\n  requirements:\n  - listing:\n    - entryname: input_collector.log\n      entry: |\n        \"flag\":\n          $(inputs.example_flag)\n        \"string\":\n          $(inputs.example_string)\n        \"int\":\n          $(inputs.example_int)\n        \"long\":\n          $(inputs.example_long)\n        \"float\":\n          $(inputs.example_float)\n        \"double\":\n          $(inputs.example_double)\n    class: InitialWorkDirRequirement\n  inputs:\n  - type: double\n    id: '#input_collector.cwl/example_double'\n  - type: boolean\n    id: '#input_collector.cwl/example_flag'\n  - type: float\n    id: '#input_collector.cwl/example_float'\n  - type: int\n    id: '#input_collector.cwl/example_int'\n  - type: long\n    id: '#input_collector.cwl/example_long'\n  - type: string\n    id: '#input_collector.cwl/example_string'\n  outputs:\n  - type: File\n    outputBinding:\n      glob: '*'\n    id: '#input_collector.cwl/output'\n  baseCommand: [echo]\n  id: '#input_collector.cwl'\n- class: Workflow\n  doc: Workflw for collecting primitive values\n  inputs:\n  - type: double\n    label: Double value\n    doc: This should allow for entering a decimal number (64-bit).\n    id: '#main/example_double'\n    default: 0.3333333333333333\n  - type: boolean\n    label: Boolean Flag\n    doc: This should render as in checkbox.\n    id: '#main/example_flag'\n    default: true\n  - type: float\n    label: Float value\n    doc: This should allow for entering a decimal number (32-bit).\n    id: '#main/example_float'\n    default: 0.15625\n  - type: int\n    label: Integer Number\n    doc: This should allow for entering a number (32-bit signed).\n    id: '#main/example_int'\n    default: 2147483647\n  - type: long\n    label: Long Number\n    doc: This should allow for entering a number (64-bit signed).\n    id: '#main/example_long'\n    default: 9223372036854775807\n  - type: string\n    label: Freetext\n    doc: This should allow for entering an arbitrary char sequence.\n    id: '#main/example_string'\n    default: This is a string\n  outputs:\n  - type: File\n    outputSource: '#main/input_collector/output'\n    id: '#main/log_file'\n  steps:\n  - run: '#input_collector.cwl'\n    in:\n    - source: '#main/example_double'\n      id: '#main/input_collector/example_double'\n    - source: '#main/example_flag'\n      id: '#main/input_collector/example_flag'\n    - source: '#main/example_float'\n      id: '#main/input_collector/example_float'\n    - source: '#main/example_int'\n      id: '#main/input_collector/example_int'\n    - source: '#main/example_long'\n      id: '#main/input_collector/example_long'\n    - source: '#main/example_string'\n      id: '#main/input_collector/example_string'\n    out: ['#main/input_collector/output']\n    id: '#main/input_collector'\n  id: '#main'\n",
 142     });
 143 };
 144
 145 const createEnumCollectorWorkflow = ({ workflowService }: ServiceRepository) => {
 146     workflowService.create({
 147         name: 'Enum values collector',
 148         description: 'Workflow for collecting enum values',
 149         definition: "cwlVersion: v1.0\n$graph:\n- class: CommandLineTool\n  requirements:\n  - listing:\n    - entryname: input_collector.log\n      entry: |\n        \"enum_type\":\n          $(inputs.enum_type)\n\n    class: InitialWorkDirRequirement\n  inputs:\n  - type:\n      type: enum\n      symbols: ['#input_collector.cwl/enum_type/OTU table', '#input_collector.cwl/enum_type/Pathway\n          table', '#input_collector.cwl/enum_type/Function table', '#input_collector.cwl/enum_type/Ortholog\n          table']\n    id: '#input_collector.cwl/enum_type'\n  outputs:\n  - type: File\n    outputBinding:\n      glob: '*'\n    id: '#input_collector.cwl/output'\n  baseCommand: [echo]\n  id: '#input_collector.cwl'\n- class: Workflow\n  doc: This is the description of the workflow\n  inputs:\n  - type:\n      type: enum\n      symbols: ['#main/enum_type/OTU table', '#main/enum_type/Pathway table', '#main/enum_type/Function\n          table', '#main/enum_type/Ortholog table']\n      name: '#enum_typef4179c7f-45f9-482d-a5db-1abb86698384'\n    label: Enumeration Type\n    doc: This should render as a drop-down menu.\n    id: '#main/enum_type'\n    default: OTU table\n  outputs:\n  - type: File\n    outputSource: '#main/input_collector/output'\n    id: '#main/log_file'\n  steps:\n  - run: '#input_collector.cwl'\n    in:\n    - source: '#main/enum_type'\n      id: '#main/input_collector/enum_type'\n    out: ['#main/input_collector/output']\n    id: '#main/input_collector'\n  id: '#main'\n",
 150     });
 151 };
 152
 153 const createFilesCollectorWorkflow = ({ workflowService }: ServiceRepository) => {
 154     workflowService.create({
 155         name: 'File values collector',
 156         description: 'Workflow for collecting file values',
 157         definition: "cwlVersion: v1.0\n$graph:\n- class: CommandLineTool\n\n  requirements:\n  - listing:\n    - entryname: input_collector.log\n      entry: |\n        \"single_file\":\n          $(inputs.single_file.basename)\n        \"optional_file\":\n          $(inputs.optional_file.basename)\n\n    class: InitialWorkDirRequirement\n  inputs:\n  - type:\n    - 'null'\n    - File\n    id: '#input_collector.cwl/optional_file'\n  - type:\n    - 'null'\n    - File\n    id: '#input_collector.cwl/optional_file_missing_label'\n  - type: File\n    id: '#input_collector.cwl/single_file'\n  outputs:\n  - type: File\n    outputBinding:\n      glob: '*'\n    id: '#input_collector.cwl/output'\n\n  baseCommand: [echo]\n  id: '#input_collector.cwl'\n- class: Workflow\n  doc: This is the description of the workflow\n  inputs:\n  - type:\n    - 'null'\n    - File\n    label: Single File (Optional)\n    doc: This should allow for single File selection only. Input should be marked\n      as optional and not enforced by form validation.\n    id: '#main/optional_file'\n    default:\n      class: File\n      location: keep:af831660d820bcbb98f473355e6e1b85+67/fileA\n      basename: fileA\n      nameroot: fileA\n      nameext: ''\n  - type:\n    - 'null'\n    - File\n    doc: Label should be the input field name because of missing label.\n    id: '#main/optional_file_missing_label'\n  - type: File\n    label: Single File\n    doc: This should allow for single File selection only.\n    id: '#main/single_file'\n    default:\n      class: File\n      location: keep:af831660d820bcbb98f473355e6e1b85+67/fileA\n      basename: fileA\n      nameroot: fileA\n      nameext: ''\n  outputs:\n  - type: File\n    outputSource: '#main/input_collector/output'\n    id: '#main/log_file'\n  steps:\n  - run: '#input_collector.cwl'\n    in:\n    - source: '#main/optional_file'\n      id: '#main/input_collector/optional_file'\n    - source: '#main/single_file'\n      id: '#main/input_collector/single_file'\n    out: ['#main/input_collector/output']\n    id: '#main/input_collector'\n  id: '#main'\n",
 158     });
 159 };
 160
 161 const createCollectionCollectorWorkflow = ({ workflowService }: ServiceRepository) => {
 162     workflowService.create({
 163         name: 'Collection value collector',
 164         description: 'Workflow for collecting a collecion',
 165         definition: "cwlVersion: v1.0\n$graph:\n- class: CommandLineTool\n\n  requirements:\n  - listing:\n    - entryname: input_collector.log\n      entry: |\n        \"collection\":\n          $(inputs.collection.location)\n\n    class: InitialWorkDirRequirement\n  inputs:\n  - type: Directory\n    id: '#input_collector.cwl/collection'\n\n  outputs:\n  - type: File\n    outputBinding:\n      glob: '*'\n    id: '#input_collector.cwl/output'\n\n  baseCommand: [echo]\n  id: '#input_collector.cwl'\n- class: Workflow\n  doc: This is the description of the workflow\n  inputs:\n  - type: Directory\n    label: Single Collection\n    doc: This should allow for single Collection selection only.\n    id: '#main/collection'\n    default:\n      class: Directory\n      location: keep:af831660d820bcbb98f473355e6e1b85+67\n      basename: af831660d820bcbb98f473355e6e1b85+67\n  outputs:\n  - type: File\n    outputSource: '#main/input_collector/output'\n\n    id: '#main/log_file'\n  steps:\n  - run: '#input_collector.cwl'\n    in:\n    - source: '#main/collection'\n      id: '#main/input_collector/collection'\n    out: ['#main/input_collector/output']\n    id: '#main/input_collector'\n  id: '#main'\n",
 166     });
 167 };
 168
 169 const createSampleProcess = ({ containerRequestService }: ServiceRepository) => {
 170     containerRequestService.create({
 171         ownerUuid: 'c97qk-j7d0g-s3ngc1z0748hsmf',
 172         name: 'Simple process 7',
 173         state: ContainerRequestState.COMMITTED,
 174         mounts: {
 175             '/var/spool/cwl': {
 176                 kind: MountKind.COLLECTION,
 177                 writable: true,
 178             },
 179             'stdout': {
 180                 kind: MountKind.MOUNTED_FILE,
 181                 path: '/var/spool/cwl/cwl.output.json'
 182             },
 183             '/var/lib/cwl/workflow.json': {
 184                 kind: MountKind.JSON,
 185                 content: {
 186                     "cwlVersion": "v1.0",
 187                     "$graph": [
 188                         {
 189                             "class": "CommandLineTool",
 190                             "requirements": [
 191                                 {
 192                                     "listing": [
 193                                         {
 194                                             "entryname": "input_collector.log",
 195                                             "entry": "$(inputs.single_file.basename)\n"
 196                                         }
 197                                     ],
 198                                     "class": "InitialWorkDirRequirement"
 199                                 }
 200                             ],
 201                             "inputs": [
 202                                 {
 203                                     "type": "File",
 204                                     "id": "#input_collector.cwl/single_file"
 205                                 }
 206                             ],
 207                             "outputs": [
 208                                 {
 209                                     "type": "File",
 210                                     "outputBinding": {
 211                                         "glob": "*"
 212                                     },
 213                                     "id": "#input_collector.cwl/output"
 214                                 }
 215                             ],
 216                             "baseCommand": [
 217                                 "echo"
 218                             ],
 219                             "id": "#input_collector.cwl"
 220                         },
 221                         {
 222                             "class": "Workflow",
 223                             "doc": "This is the description of the workflow",
 224                             "inputs": [
 225                                 {
 226                                     "type": "File",
 227                                     "label": "Single File",
 228                                     "doc": "This should allow for single File selection only.",
 229                                     "id": "#main/single_file"
 230                                 }
 231                             ],
 232                             "outputs": [
 233                                 {
 234                                     "type": "File",
 235                                     "outputSource": "#main/input_collector/output",
 236                                     "id": "#main/log_file"
 237                                 }
 238                             ],
 239                             "steps": [
 240                                 {
 241                                     "run": "#input_collector.cwl",
 242                                     "in": [
 243                                         {
 244                                             "source": "#main/single_file",
 245                                             "id": "#main/input_collector/single_file"
 246                                         }
 247                                     ],
 248                                     "out": [
 249                                         "#main/input_collector/output"
 250                                     ],
 251                                     "id": "#main/input_collector"
 252                                 }
 253                             ],
 254                             "id": "#main"
 255                         }
 256                     ]
 257                 },
 258             },
 259             '/var/lib/cwl/cwl.input.json': {
 260                 kind: MountKind.JSON,
 261                 content: {
 262                     "single_file": {
 263                         "class": "File",
 264                         "location": "keep:233454526794c0a2d56a305baeff3d30+145/1.txt",
 265                         "basename": "fileA"
 266                     }
 267                 },
 268             }
 269         },
 270         runtimeConstraints: {
 271             API: true,
 272             vcpus: 1,
 273             ram: 1073741824,
 274         },
 275         containerImage: 'arvados/jobs:1.1.4.20180618144723',
 276         cwd: '/var/spool/cwl',
 277         command: [
 278             'arvados-cwl-runner',
 279             '--local',
 280             '--api=containers',
 281             "--project-uuid=c97qk-j7d0g-s3ngc1z0748hsmf",
 282             '/var/lib/cwl/workflow.json#main',
 283             '/var/lib/cwl/cwl.input.json'
 284         ],
 285         outputPath: '/var/spool/cwl',
 286         priority: 1,
 287     });
 288 };
 289