import * as React from 'react';
import * as ReactDOM from 'react-dom';
import { Provider } from "react-redux";
-import { Workbench } from './views/workbench/workbench';
+import { MainPanel } from './views/main-panel/main-panel';
import './index.css';
-import { Route } from 'react-router';
+import { Route, Switch } from 'react-router';
import createBrowserHistory from "history/createBrowserHistory";
import { History } from "history";
import { configureStore, RootStore } from './store/store';
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 { 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 { 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 { 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 { loadVocabulary } from '~/store/vocabulary/vocabulary-actions';
-const getBuildNumber = () => "BN-" + (process.env.REACT_APP_BUILD_NUMBER || "dev");
-const getGitCommit = () => "GIT-" + (process.env.REACT_APP_GIT_COMMIT || "latest").substr(0, 7);
-const getBuildInfo = () => getBuildNumber() + " / " + getGitCommit();
-
-const buildInfo = getBuildInfo();
-
-console.log(`Starting arvados [${buildInfo}]`);
+console.log(`Starting arvados [${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);
fetchConfig()
.then(({ config, apiHost }) => {
const history = createBrowserHistory();
- const services = createServices(config, (id, working) => {
- store.dispatch(progressIndicatorActions.TOGGLE({ id, working }));
+ 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) => <ApiToken authService={services.authService} {...props} />;
- const WorkbenchComponent = (props: any) => <Workbench authService={services.authService} buildInfo={buildInfo} {...props} />;
+ const MainPanelComponent = (props: any) => <MainPanel {...props} />;
const App = () =>
<MuiThemeProvider theme={CustomTheme}>
- <Provider store={store}>
- <ConnectedRouter history={history}>
- <div>
- <Route path={Routes.TOKEN} component={TokenComponent} />
- <Route path={Routes.ROOT} component={WorkbenchComponent} />
- </div>
- </ConnectedRouter>
- </Provider>
+ <DragDropContextProvider backend={HTML5Backend}>
+ <Provider store={store}>
+ <ConnectedRouter history={history}>
+ <Switch>
+ <Route path={Routes.TOKEN} component={TokenComponent} />
+ <Route path={Routes.ROOT} component={MainPanelComponent} />
+ </Switch>
+ </ConnectedRouter>
+ </Provider>
+ </DragDropContextProvider>
</MuiThemeProvider>;
ReactDOM.render(
<App />,
document.getElementById('root') as HTMLElement
);
-
-
});
const initListener = (history: History, store: RootStore, services: ServiceRepository, config: Config) => {
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
projects / arvados-workbench2.git / blobdiff