// Copyright (C) The Arvados Authors. All rights reserved. // // SPDX-License-Identifier: AGPL-3.0 import * as React from 'react'; import * as ReactDOM from 'react-dom'; import { Provider } from "react-redux"; import { MainPanel } from '~/views/main-panel/main-panel'; import '~/index.css'; import { Route, Switch } from 'react-router'; import createBrowserHistory from "history/createBrowserHistory"; import { History } from "history"; import { configureStore, RootStore } from '~/store/store'; import { ConnectedRouter } from "react-router-redux"; import { ApiToken } from "~/views-components/api-token/api-token"; import { initAuth } from "~/store/auth/auth-action"; import { createServices } from "~/services/services"; import { MuiThemeProvider } from '@material-ui/core/styles'; import { CustomTheme } from '~/common/custom-theme'; import { fetchConfig } from '~/common/config'; import { addMenuActionSet, ContextMenuKind } from '~/views-components/context-menu/context-menu'; import { rootProjectActionSet } from "~/views-components/context-menu/action-sets/root-project-action-set"; import { projectActionSet } from "~/views-components/context-menu/action-sets/project-action-set"; import { resourceActionSet } from '~/views-components/context-menu/action-sets/resource-action-set'; import { favoriteActionSet } from "~/views-components/context-menu/action-sets/favorite-action-set"; import { collectionFilesActionSet } from '~/views-components/context-menu/action-sets/collection-files-action-set'; import { collectionFilesItemActionSet } from '~/views-components/context-menu/action-sets/collection-files-item-action-set'; import { collectionFilesNotSelectedActionSet } from '~/views-components/context-menu/action-sets/collection-files-not-selected-action-set'; import { collectionActionSet } from '~/views-components/context-menu/action-sets/collection-action-set'; import { collectionResourceActionSet } from '~/views-components/context-menu/action-sets/collection-resource-action-set'; import { processActionSet } from '~/views-components/context-menu/action-sets/process-action-set'; import { loadWorkbench } from '~/store/workbench/workbench-actions'; import { Routes } from '~/routes/routes'; import { trashActionSet } from "~/views-components/context-menu/action-sets/trash-action-set"; import { ServiceRepository } from '~/services/services'; import { initWebSocket } from '~/websocket/websocket'; import { Config } from '~/common/config'; import { addRouteChangeHandlers } from './routes/route-change-handlers'; import { setCurrentTokenDialogApiHost } from '~/store/current-token-dialog/current-token-dialog-actions'; import { processResourceActionSet } from '~/views-components/context-menu/action-sets/process-resource-action-set'; import { progressIndicatorActions } from '~/store/progress-indicator/progress-indicator-actions'; import { setUuidPrefix } from '~/store/workflow-panel/workflow-panel-actions'; import { trashedCollectionActionSet } from '~/views-components/context-menu/action-sets/trashed-collection-action-set'; import { ContainerRequestState } from '~/models/container-request'; import { MountKind } from '~/models/mount-types'; import { setBuildInfo } from '~/store/app-info/app-info-actions'; import { getBuildInfo } from '~/common/app-info'; import { DragDropContextProvider } from 'react-dnd'; import HTML5Backend from 'react-dnd-html5-backend'; import { initAdvanceFormProjectsTree } from '~/store/search-bar/search-bar-actions'; import { repositoryActionSet } from '~/views-components/context-menu/action-sets/repository-action-set'; import { sshKeyActionSet } from '~/views-components/context-menu/action-sets/ssh-key-action-set'; import { keepServiceActionSet } from '~/views-components/context-menu/action-sets/keep-service-action-set'; import { loadVocabulary } from '~/store/vocabulary/vocabulary-actions'; import { virtualMachineActionSet } from '~/views-components/context-menu/action-sets/virtual-machine-action-set'; import { userActionSet } from '~/views-components/context-menu/action-sets/user-action-set'; import { computeNodeActionSet } from '~/views-components/context-menu/action-sets/compute-node-action-set'; import { apiClientAuthorizationActionSet } from '~/views-components/context-menu/action-sets/api-client-authorization-action-set'; console.log(`Starting arvados [${getBuildInfo()}]`); addMenuActionSet(ContextMenuKind.ROOT_PROJECT, rootProjectActionSet); addMenuActionSet(ContextMenuKind.PROJECT, projectActionSet); addMenuActionSet(ContextMenuKind.RESOURCE, resourceActionSet); addMenuActionSet(ContextMenuKind.FAVORITE, favoriteActionSet); addMenuActionSet(ContextMenuKind.COLLECTION_FILES, collectionFilesActionSet); addMenuActionSet(ContextMenuKind.COLLECTION_FILES_NOT_SELECTED, collectionFilesNotSelectedActionSet); addMenuActionSet(ContextMenuKind.COLLECTION_FILES_ITEM, collectionFilesItemActionSet); addMenuActionSet(ContextMenuKind.COLLECTION, collectionActionSet); addMenuActionSet(ContextMenuKind.COLLECTION_RESOURCE, collectionResourceActionSet); addMenuActionSet(ContextMenuKind.TRASHED_COLLECTION, trashedCollectionActionSet); addMenuActionSet(ContextMenuKind.PROCESS, processActionSet); addMenuActionSet(ContextMenuKind.PROCESS_RESOURCE, processResourceActionSet); addMenuActionSet(ContextMenuKind.TRASH, trashActionSet); addMenuActionSet(ContextMenuKind.REPOSITORY, repositoryActionSet); addMenuActionSet(ContextMenuKind.SSH_KEY, sshKeyActionSet); addMenuActionSet(ContextMenuKind.VIRTUAL_MACHINE, virtualMachineActionSet); addMenuActionSet(ContextMenuKind.KEEP_SERVICE, keepServiceActionSet); addMenuActionSet(ContextMenuKind.USER, userActionSet); addMenuActionSet(ContextMenuKind.NODE, computeNodeActionSet); addMenuActionSet(ContextMenuKind.API_CLIENT_AUTHORIZATION, apiClientAuthorizationActionSet); fetchConfig() .then(({ config, apiHost }) => { const history = createBrowserHistory(); const services = createServices(config, { progressFn: (id, working) => { store.dispatch(progressIndicatorActions.TOGGLE_WORKING({ id, working })); }, errorFn: (id, error) => { // console.error("Backend error:", error); // store.dispatch(snackbarActions.OPEN_SNACKBAR({ message: "Backend error", kind: SnackbarKind.ERROR })); } }); const store = configureStore(history, services); store.subscribe(initListener(history, store, services, config)); store.dispatch(initAuth()); store.dispatch(setBuildInfo()); store.dispatch(setCurrentTokenDialogApiHost(apiHost)); store.dispatch(setUuidPrefix(config.uuidPrefix)); store.dispatch(loadVocabulary); const TokenComponent = (props: any) => ; const MainPanelComponent = (props: any) => ; const App = () => ; ReactDOM.render( , document.getElementById('root') as HTMLElement ); }); const initListener = (history: History, store: RootStore, services: ServiceRepository, config: Config) => { let initialized = false; return async () => { const { router, auth } = store.getState(); if (router.location && auth.user && !initialized) { initialized = true; initWebSocket(config, services.authService, store); await store.dispatch(loadWorkbench()); addRouteChangeHandlers(history, store); // ToDo: move to searchBar component store.dispatch(initAdvanceFormProjectsTree()); } }; }; const createDirectoriesArrayCollectorWorkflow = ({ workflowService }: ServiceRepository) => { workflowService.create({ name: 'Directories array collector', description: 'Workflow for collecting directories array', 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 $(inputs.multiple_collections)\n\n class: InitialWorkDirRequirement\n inputs:\n - type:\n type: array\n items: Directory\n id: '#input_collector.cwl/multiple_collections'\n outputs:\n - type: File\n outputBinding:\n glob: '*'\n id: '#input_collector.cwl/output'\n\n baseCommand: [echo]\n id: '#input_collector.cwl'\n- class: Workflow\n doc: This is the description of the workflow\n inputs:\n - type:\n type: array\n items: Directory\n label: Multiple Collections\n doc: This should allow for selecting multiple collections.\n id: '#main/multiple_collections'\n default:\n - class: Directory\n location: keep:1e1682585d576f031b2d8b4944f989ee+57\n basename: 1e1682585d576f031b2d8b4944f989ee+57\n - class: Directory\n location: keep:326f692370e9e121fcbd013796f7352a+57\n basename: 326f692370e9e121fcbd013796f7352a+57\n \n outputs:\n - type: File\n outputSource: '#main/input_collector/output'\n\n id: '#main/log_file'\n steps:\n - run: '#input_collector.cwl'\n in:\n - source: '#main/multiple_collections'\n id: '#main/input_collector/multiple_collections'\n out: ['#main/input_collector/output']\n id: '#main/input_collector'\n id: '#main'\n", }); }; const createPrimitiveArraysCollectorWorkflow = ({ workflowService }: ServiceRepository) => { workflowService.create({ name: 'String, Int and Float arrays collector', description: 'Workflow for collecting primitive data arrays', definition: "cwlVersion: v1.0\n$graph:\n- class: CommandLineTool\n\n requirements:\n - listing:\n - entryname: input_collector.log\n entry: |\n \"string array\":\n $(inputs.example_string_array)\n \"int array\":\n $(inputs.example_int_array)\n \"float array\":\n $(inputs.example_float_array)\n\n class: InitialWorkDirRequirement\n inputs:\n - type:\n type: array\n items: string\n id: '#input_collector.cwl/example_string_array'\n - type:\n type: array\n items: int\n id: '#input_collector.cwl/example_int_array'\n - type:\n type: array\n items: float\n id: '#input_collector.cwl/example_float_array'\n \n outputs:\n - type: File\n outputBinding:\n glob: '*'\n id: '#input_collector.cwl/output'\n\n baseCommand: [echo]\n id: '#input_collector.cwl'\n- class: Workflow\n doc: This is the description of the workflow\n inputs:\n - type:\n type: array\n items: string\n label: Freetext Array\n doc: This should allow for entering multiple strings.\n id: '#main/example_string_array'\n default:\n - This is the first string\n - This is the second string\n - type:\n type: array\n items: int\n label: Integer Array\n doc: This should allow for entering multiple integers.\n id: '#main/example_int_array'\n default:\n - 3\n - 6\n - type:\n type: array\n items: float\n label: Float Array\n doc: This should allow for entering multiple floats.\n id: '#main/example_float_array'\n default:\n - 3.33\n - 66.6\n\n outputs:\n - type: File\n outputSource: '#main/input_collector/output'\n\n id: '#main/log_file'\n steps:\n - run: '#input_collector.cwl'\n in:\n - source: '#main/example_string_array'\n id: '#main/input_collector/example_string_array'\n - source: '#main/example_int_array'\n id: '#main/input_collector/example_int_array'\n - source: '#main/example_float_array'\n id: '#main/input_collector/example_float_array'\n out: ['#main/input_collector/output']\n id: '#main/input_collector'\n id: '#main'\n", }); }; const createFilesArrayCollectorWorkflow = ({ workflowService }: ServiceRepository) => { workflowService.create({ name: 'Files array collector', description: 'Workflow for collecting files array', definition: "cwlVersion: v1.0\n$graph:\n- class: CommandLineTool\n\n requirements:\n - listing:\n - entryname: input_collector.log\n entry: |\n \"multiple_files\":\n $(inputs.multiple_files)\n\n class: InitialWorkDirRequirement\n inputs:\n - type:\n type: array\n items: File\n id: '#input_collector.cwl/multiple_files'\n outputs:\n - type: File\n outputBinding:\n glob: '*'\n id: '#input_collector.cwl/output'\n\n baseCommand: [cat]\n id: '#input_collector.cwl'\n- class: Workflow\n doc: This is the description of the workflow\n inputs:\n - type:\n type: array\n items: File\n label: Multiple Files\n doc: This should allow for selecting multiple files.\n id: '#main/multiple_files'\n default:\n - class: File\n location: keep:af831660d820bcbb98f473355e6e1b85+67/fileA\n basename: fileA\n nameroot: fileA\n nameext: ''\n outputs:\n - type: File\n outputSource: '#main/input_collector/output'\n\n id: '#main/log_file'\n steps:\n - run: '#input_collector.cwl'\n in:\n - source: '#main/multiple_files'\n id: '#main/input_collector/multiple_files'\n out: ['#main/input_collector/output']\n id: '#main/input_collector'\n id: '#main'\n", }); }; const createPrimitivesCollectorWorkflow = ({ workflowService }: ServiceRepository) => { workflowService.create({ name: 'Primitive values collector', description: 'Workflow for collecting primitive values', definition: "cwlVersion: v1.0\n$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", }); }; const createEnumCollectorWorkflow = ({ workflowService }: ServiceRepository) => { workflowService.create({ name: 'Enum values collector', description: 'Workflow for collecting enum values', definition: "cwlVersion: v1.0\n$graph:\n- class: CommandLineTool\n requirements:\n - listing:\n - entryname: input_collector.log\n entry: |\n \"enum_type\":\n $(inputs.enum_type)\n\n class: InitialWorkDirRequirement\n inputs:\n - type:\n type: enum\n symbols: ['#input_collector.cwl/enum_type/OTU table', '#input_collector.cwl/enum_type/Pathway\n table', '#input_collector.cwl/enum_type/Function table', '#input_collector.cwl/enum_type/Ortholog\n table']\n id: '#input_collector.cwl/enum_type'\n outputs:\n - type: File\n outputBinding:\n glob: '*'\n id: '#input_collector.cwl/output'\n baseCommand: [echo]\n id: '#input_collector.cwl'\n- class: Workflow\n doc: This is the description of the workflow\n inputs:\n - type:\n type: enum\n symbols: ['#main/enum_type/OTU table', '#main/enum_type/Pathway table', '#main/enum_type/Function\n table', '#main/enum_type/Ortholog table']\n name: '#enum_typef4179c7f-45f9-482d-a5db-1abb86698384'\n label: Enumeration Type\n doc: This should render as a drop-down menu.\n id: '#main/enum_type'\n default: OTU table\n outputs:\n - type: File\n outputSource: '#main/input_collector/output'\n id: '#main/log_file'\n steps:\n - run: '#input_collector.cwl'\n in:\n - source: '#main/enum_type'\n id: '#main/input_collector/enum_type'\n out: ['#main/input_collector/output']\n id: '#main/input_collector'\n id: '#main'\n", }); }; const createFilesCollectorWorkflow = ({ workflowService }: ServiceRepository) => { workflowService.create({ name: 'File values collector', description: 'Workflow for collecting file values', definition: "cwlVersion: v1.0\n$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 $(inputs.optional_file.basename)\n\n class: InitialWorkDirRequirement\n inputs:\n - type:\n - 'null'\n - File\n id: '#input_collector.cwl/optional_file'\n - type:\n - 'null'\n - File\n id: '#input_collector.cwl/optional_file_missing_label'\n - type: File\n id: '#input_collector.cwl/single_file'\n outputs:\n - type: File\n outputBinding:\n glob: '*'\n id: '#input_collector.cwl/output'\n\n baseCommand: [echo]\n id: '#input_collector.cwl'\n- class: Workflow\n doc: This is the description of the workflow\n inputs:\n - type:\n - 'null'\n - File\n label: Single File (Optional)\n doc: This should allow for single File selection only. Input should be marked\n as optional and not enforced by form validation.\n id: '#main/optional_file'\n default:\n class: File\n location: keep:af831660d820bcbb98f473355e6e1b85+67/fileA\n basename: fileA\n nameroot: fileA\n nameext: ''\n - type:\n - 'null'\n - File\n doc: Label should be the input field name because of missing label.\n id: '#main/optional_file_missing_label'\n - type: File\n label: Single File\n doc: This should allow for single File selection only.\n id: '#main/single_file'\n default:\n class: File\n location: keep:af831660d820bcbb98f473355e6e1b85+67/fileA\n basename: fileA\n nameroot: fileA\n nameext: ''\n outputs:\n - type: File\n outputSource: '#main/input_collector/output'\n id: '#main/log_file'\n steps:\n - run: '#input_collector.cwl'\n in:\n - source: '#main/optional_file'\n id: '#main/input_collector/optional_file'\n - source: '#main/single_file'\n id: '#main/input_collector/single_file'\n out: ['#main/input_collector/output']\n id: '#main/input_collector'\n id: '#main'\n", }); }; const createCollectionCollectorWorkflow = ({ workflowService }: ServiceRepository) => { workflowService.create({ name: 'Collection value collector', description: 'Workflow for collecting a collecion', definition: "cwlVersion: v1.0\n$graph:\n- class: CommandLineTool\n\n requirements:\n - listing:\n - entryname: input_collector.log\n entry: |\n \"collection\":\n $(inputs.collection.location)\n\n class: InitialWorkDirRequirement\n inputs:\n - type: Directory\n id: '#input_collector.cwl/collection'\n\n outputs:\n - type: File\n outputBinding:\n glob: '*'\n id: '#input_collector.cwl/output'\n\n baseCommand: [echo]\n id: '#input_collector.cwl'\n- class: Workflow\n doc: This is the description of the workflow\n inputs:\n - type: Directory\n label: Single Collection\n doc: This should allow for single Collection selection only.\n id: '#main/collection'\n default:\n class: Directory\n location: keep:af831660d820bcbb98f473355e6e1b85+67\n basename: af831660d820bcbb98f473355e6e1b85+67\n outputs:\n - type: File\n outputSource: '#main/input_collector/output'\n\n id: '#main/log_file'\n steps:\n - run: '#input_collector.cwl'\n in:\n - source: '#main/collection'\n id: '#main/input_collector/collection'\n out: ['#main/input_collector/output']\n id: '#main/input_collector'\n id: '#main'\n", }); }; const createSampleProcess = ({ containerRequestService }: ServiceRepository) => { containerRequestService.create({ ownerUuid: 'c97qk-j7d0g-s3ngc1z0748hsmf', name: 'Simple process 7', state: ContainerRequestState.COMMITTED, mounts: { '/var/spool/cwl': { kind: MountKind.COLLECTION, writable: true, }, 'stdout': { kind: MountKind.MOUNTED_FILE, path: '/var/spool/cwl/cwl.output.json' }, '/var/lib/cwl/workflow.json': { kind: MountKind.JSON, content: { "cwlVersion": "v1.0", "$graph": [ { "class": "CommandLineTool", "requirements": [ { "listing": [ { "entryname": "input_collector.log", "entry": "$(inputs.single_file.basename)\n" } ], "class": "InitialWorkDirRequirement" } ], "inputs": [ { "type": "File", "id": "#input_collector.cwl/single_file" } ], "outputs": [ { "type": "File", "outputBinding": { "glob": "*" }, "id": "#input_collector.cwl/output" } ], "baseCommand": [ "echo" ], "id": "#input_collector.cwl" }, { "class": "Workflow", "doc": "This is the description of the workflow", "inputs": [ { "type": "File", "label": "Single File", "doc": "This should allow for single File selection only.", "id": "#main/single_file" } ], "outputs": [ { "type": "File", "outputSource": "#main/input_collector/output", "id": "#main/log_file" } ], "steps": [ { "run": "#input_collector.cwl", "in": [ { "source": "#main/single_file", "id": "#main/input_collector/single_file" } ], "out": [ "#main/input_collector/output" ], "id": "#main/input_collector" } ], "id": "#main" } ] }, }, '/var/lib/cwl/cwl.input.json': { kind: MountKind.JSON, content: { "single_file": { "class": "File", "location": "keep:233454526794c0a2d56a305baeff3d30+145/1.txt", "basename": "fileA" } }, } }, runtimeConstraints: { API: true, vcpus: 1, ram: 1073741824, }, containerImage: 'arvados/jobs:1.1.4.20180618144723', cwd: '/var/spool/cwl', command: [ 'arvados-cwl-runner', '--local', '--api=containers', "--project-uuid=c97qk-j7d0g-s3ngc1z0748hsmf", '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json' ], outputPath: '/var/spool/cwl', priority: 1, }); }; // force build comment #1