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 { 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 { 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 { 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 { 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 { 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 { 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';
+import { groupActionSet } from '~/views-components/context-menu/action-sets/group-action-set';
+import { groupMemberActionSet } from '~/views-components/context-menu/action-sets/group-member-action-set';
+import { linkActionSet } from '~/views-components/context-menu/action-sets/link-action-set';
+import { loadFileViewersConfig } from '~/store/file-viewers/file-viewers-actions';
+import { collectionAdminActionSet } from '~/views-components/context-menu/action-sets/collection-admin-action-set';
+import { processResourceAdminActionSet } from '~/views-components/context-menu/action-sets/process-resource-admin-action-set';
+import { projectAdminActionSet } from '~/views-components/context-menu/action-sets/project-admin-action-set';
console.log(`Starting arvados [${getBuildInfo()}]`);
addMenuActionSet(ContextMenuKind.SSH_KEY, sshKeyActionSet);
addMenuActionSet(ContextMenuKind.VIRTUAL_MACHINE, virtualMachineActionSet);
addMenuActionSet(ContextMenuKind.KEEP_SERVICE, keepServiceActionSet);
+addMenuActionSet(ContextMenuKind.USER, userActionSet);
+addMenuActionSet(ContextMenuKind.LINK, linkActionSet);
+addMenuActionSet(ContextMenuKind.NODE, computeNodeActionSet);
+addMenuActionSet(ContextMenuKind.API_CLIENT_AUTHORIZATION, apiClientAuthorizationActionSet);
+addMenuActionSet(ContextMenuKind.GROUPS, groupActionSet);
+addMenuActionSet(ContextMenuKind.GROUP_MEMBER, groupMemberActionSet);
+addMenuActionSet(ContextMenuKind.COLLECTION_ADMIN, collectionAdminActionSet);
+addMenuActionSet(ContextMenuKind.PROCESS_ADMIN, processResourceAdminActionSet);
+addMenuActionSet(ContextMenuKind.PROJECT_ADMIN, projectAdminActionSet);
fetchConfig()
.then(({ config, apiHost }) => {
const store = configureStore(history, services);
store.subscribe(initListener(history, store, services, config));
- store.dispatch(initAuth());
+ store.dispatch(initAuth(config));
store.dispatch(setBuildInfo());
store.dispatch(setCurrentTokenDialogApiHost(apiHost));
- store.dispatch(setUuidPrefix(config.uuidPrefix));
store.dispatch(loadVocabulary);
+ store.dispatch(loadFileViewersConfig);
- const TokenComponent = (props: any) => <ApiToken authService={services.authService} {...props} />;
+ const TokenComponent = (props: any) => <ApiToken authService={services.authService} config={config} loadMainApp={true} {...props} />;
+ const FedTokenComponent = (props: any) => <ApiToken authService={services.authService} config={config} loadMainApp={false} {...props} />;
const MainPanelComponent = (props: any) => <MainPanel {...props} />;
const App = () =>
<ConnectedRouter history={history}>
<Switch>
<Route path={Routes.TOKEN} component={TokenComponent} />
+ <Route path={Routes.FED_LOGIN} component={FedTokenComponent} />
<Route path={Routes.ROOT} component={MainPanelComponent} />
</Switch>
</ConnectedRouter>
};
};
-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
projects / arvados-workbench2.git / blobdiff