import { processResourceActionSet } from '~/views-components/context-menu/action-sets/process-resource-action-set';
import { progressIndicatorActions } from '~/store/progress-indicator/progress-indicator-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';
};
};
-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