{"info":{"_postman_id":"7ee57590-3554-449d-ba78-d6df4ca14751","name":"Form Bio API Documentation","description":"

The Form Bio RESTful API provides operations for managing your organizations'/projects' data and scientific workflows.

Getting started guide

First off, you must have a Form Bio account, with access to an organization and project already configured. For details, see our website.

Secondly, you will need access to the Form Bio CLI.

Finally, once your Form Bio account is set up, you can get started with the API with these steps:

Install the Form Bio CLI: Please reach out to your Form Bio support team for instructions on getting started with the CLI.
Get access token: You will need to use the CLI to get an access token. Running formbio auth print-token will get you that.
- If you are not using Postman to make your API requests for you, you will need to use the value printed by this command as a bearer token Authorization header. To do this directly in a curl command, use -H \"Authorization: Bearer $(formbio auth print-token)\".
\n
Use the API! That's all there is to do!

Authentication

You must authenticate with a bearer token - the Form Bio CLI will help you there.

To get the authentication token, run formbio auth print-token.

To authenticate with this token, set a bearer Authorization header. For example, with curl -H \"Authorization: Bearer $(formbio auth print-token)\" or -H \"Authorization: Bearer {{token_value}}\".

If you are using Postman to do your API requests, you can set an accessToken variable.

Experimental API

Our entire API is currently \"experimental\" - that is, it is not GA, not even beta. It was built for internal use only. We allow experimental usage of these API operations until we have a public API in the future.

These API operations will likely change over time - at times significantly so.

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Operation(s) in this category allow you to access to the workflows available to a specific project.

List Project-Shared Workflow Versions

Lists all of the workflow versions available to a project. Each workflow can have multple versions, and all available versions are returned by this operation.

Request

GET https://prd-api.formbio.com/api/v1/orgs/{{organizationSlug}}/{{projectSlug}}/workflows

Body

none

Response

Status

200: success
401: not authenticated
403: user lacks sufficient permissions
404: organization not found
404: project not found
5xx: internal errors

Body

Format

Property workflowVersions contains an array of WorkflowVersion objects.

WorkflowVersion properties:

\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n

Property	Description
`repoName` string	combined with `org` and `workflowName`, makes up the unique address for a workflow. A single repo may contain multiple workflows. See `workflowName`.
`org` string	ID for the Form Bio organization that owns this workflow
`project` string	(will be deprecated) ID for the Form Bio project that owns this workflow
`workflowName` string	name of the workflow
`workflowVersion` string	name of the workflow version, often a semantic version like `1.0.0`
`workflowStatus` string	either `DRAFT` or `READY` - not yet of consequence, but will support an upcoming feature
`workflowVisibility` string	(will be deprecated a replaced without another feature) either `PUBLIC`, `ORGANIZATION`, or `PROJECT`. Public workflows can be used within any Form Bio project. Organization-visibility workflows can be used within any project within the owning Form Bio organization. Project-visibility workfiows can only be used within the owning Form Bio project. Visibility will evenutally be replaced by more granular and expressive workflow sharing.
`createdAt` string	when the workflow version was uploaded
`updatedAt` string	when the workflow version was updated. Only updates to metadata like `workflowStatus` and `worflowVisibility` are allowed. The schema or code of the workflow version cannot be changed.
`vizappExist` boolean	true if a Form Bio Viz App is available for successfully executed workflow runs
`createdBy` string	email address of the workflow version author
`workflowId` string	parent workflow ID
`workflowVersionId` string	unique ID of this workflow version
`workflowSchema` JSON	rich schema describing the workflow's metadata, inputs specification, and input UI specification. See https://formbio.notion.site/formbio/Workflow-Schema-Guide-2-0-867fe193e01044a6947b224a26f6f172

There may be other properties, but they are likely internal use only and can be ignored.

Example

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Workflow runs are launched for a specific project, and listing workflows available to a specific project is within the \"Project Workflow Access\" category.

Terminology

Workflow

A workflow represents a workflow that can be run on the Form Bio platform.

A workflow is uniquely identified by an Organization ID, a respository name, and a workflow name.

Workflow Version

Workflows are updated over time. When a workflow is updated a new version is published. The workflow schema and code for specific version are immutable.

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When you launch a workflow from within a project, the result is a Workflow Run.

Terminology

Workflow Run

A launch of a workflow from within a Form Bio project. A workflow run should consist of at least once execution. Typically the most recent execution is the one to care about.

Workflow Run Execution

A single workflow run may contain multiple executions. A single execution may be canceled or retried. These result in multiple executions.

Create Workflow Run

Launches a new workflow run within a project.

Request

POST https://prd-api.formbio.com/api/v1/orgs/{{organizationSlug}}/{{projectSlug}}/workflow-runs

Body

Format

JSON request body may contain the following properties. There are many options supported here, and the validation criteria are complex. We will describe the most common usage.

Some properties labeled below as required may technically be optional, or only required for some cases. It's best to always specify these.

\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n

Property	Description
`dryRun` boolean	(optional) creates a workflow run with no execution
`nextflowVersion` string	(optional) can specify nextflow version for nextflow workflows
`uploadedOrg` string	(required) the Form Bio organization that owns the workflow
`uploadedProj` string	(required, will be deprecated) the Form Bio project that owns the workflow
`params` JSON	(required) the workflow input parameters, see the workflow version's schema
`repository` string	(required) the workflow repository
`repositoryVersion` string	(required) the workflow version name (see workflow version's `workflowVersion` property.
`runName` string	(required) the name of the workflow run, recommended to make this unique, but not required
`executionEngine` string	(required) Should be `nextflow` for most workflows on the platform.

Example

{\n    \"executionEngine\": \"nextflow\",\n    \"params\": {\n        \"algo\": \"static\",\n        \"control_lane_number\": \"1\",\n        \"image\": \"formbio://my-organization/my-project/my-images/a.png\",\n        \"known_molecular_weights\": \"200,150,100,75,50,37.5,25,20,15,10,5\",\n        \"num_lanes\": \"5\",\n        \"num_proteins\": \"1\",\n        \"repoDir\": \"/seqprg\",\n        \"time_input\": \"0,1,2,5,30\",\n        \"version\": \"imageanalysis_1.0.0\"\n    },\n    \"repository\": \"formbio/nf-imageanalysis\",\n    \"runName\": \"test image analysis\",\n    \"uploadedOrg\": \"1ace39a1-f777-46d9-a21f-8823d9b8517f\",\n    \"uploadedProj\": \"32411019-a596-4a7e-91b0-c8843f05971a\",\n    \"repositoryVersion\": \"v1.0.0\",\n    \"workflowName\": \"imageanalysis\"\n}\n\n

Response

Status

201: success
401: not authenticated
403: user lacks permissions
400: quota exceeded
400: invalid request body
404: organization not found
404: project not found
5xx: internal errors

Body

Format

Contains a single string with the URL path for getting the new workflow run

Example

/api/v1/workflow-run/d5c2893e-3bb9-4a58-b126-2877aacf00e5\n\n

Get Workflow Run

Gets the details, including status, about a single workflow run.

Request

GET https://prd-api.formbio.com/api/v1/workflow-run/01234567-89ab-cdef-0123-456789abcdef

Body

none

Response

Status

201: success
401: not authenticated
403: user lacks permissions
400: quota exceeded
400: invalid request body
404: organization not found
404: project not found
5xx: internal errors

Body

Format

Workflow Run Properties

\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n

Property	Description
`createdAt` string	when the workflow run was created
`id` string	id of the workflow run
`name` string	name of the workflow run
`outputDirectory` string	where the files and directories the workflow run produces can be found
`nextflowVersion` string	what version of nextflow used for execution
`params` string	the workflow input parameters, see workflow schema
`repository` string	the workflow repository
`repositoryVersion` string	the workflow version `workflowVersion` property.
`canVisualizeWithRShiny` boolean	true of the workflow run produced a VizApp
`executions` array(WorkflowRunExecution)	a list of all the executions for this workflow run
`workflowPulledFrom` string	in most cases, should indicate that the workflow was successfully pulled from the Form Bio platform. Values other than `FORM` result from interal use cases. You should expect not to see different values from workflow runs you launch.
`workflowDisplayName` string	the display name of the executed workflow version
`workflowVersionID` string	the ID of the executed workflow version
`workflowRepo` string	repository from the executed workflow version
`uploadedOrg` string	the Form Bio organization that owns the workflow
`uploadedProj` string	(will be deprecated) the Form Bio project that owns the workflow
`executionEngine` string	the workflow execution engine, typically `nextflow`

Workflow Run Execution Properties

\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n

Property	Description
`id` string	the unique id of the execution
`userName` string	full name of the user who launched the execution
`userEmail` string	email address of the user who launched the execution
`status` string	status of the execution, can be `COMPLETED`, `FAILED`, `RUNNING`, `CANCELED`, `COMPLETED WITH WARNING`, or `PENDING`
`createdAt` string	when the execution was created
`updatedAt` string	when the execution was last updated
`completedAt` string	when the execution was completed

Example

{\n    \"createdAt\": \"2024-02-23T16:38:33.400151Z\",\n    \"id\": \"d5c2893e-3bb9-4a58-b126-2877aacf00e5\",\n    \"name\": \"test image analysis\",\n    \"outputDirectory\": \"formbio://my-organization/my-project/pipeline-outputs/imageanalysis/2024-02-23T16_38_33Z_d5c2893e-3bb9-4a58-b126-2877aacf00e5\",\n    \"nextflowVersion\": \"22.10.1\",\n    \"params\": {\n        \"algo\": \"static\",\n        \"control_lane_number\": \"1\",\n        \"image\": \"formbio://my-organization/my-project/my-images/a.png\",\n        \"known_molecular_weights\": \"200,150,100,75,50,37.5,25,20,15,10,5\",\n        \"num_lanes\": \"5\",\n        \"num_proteins\": \"1\",\n        \"repoDir\": \"/seqprg\",\n        \"time_input\": \"0,1,2,5,30\",\n        \"version\": \"imageanalysis_1.0.0\"\n    },\n    \"repository\": \"imageanalysis\",\n    \"repositoryVersion\": \"v1.0.0\",\n    \"canVisualizeWithRShiny\": false,\n    \"executions\": [\n        {\n            \"id\": \"ef9ba063-7396-44a5-a9ae-742fca4b9026\",\n            \"userName\": \"Nomen Nescio\",\n            \"userEmail\": \"nomen@acme.com\",\n            \"status\": \"COMPLETED\",\n            \"createdAt\": \"2024-02-23T16:38:33.400151Z\",\n            \"updatedAt\": \"2024-02-23T16:46:00.426042Z\",\n            \"completedAt\": \"2024-02-23T16:45:59.97021Z\",\n        }\n    ],\n    \"workflowPulledFrom\": \"FORM\",\n    \"workflowDisplayName\": \"SDS-Page Analysis\",\n    \"workflowVersionID\": \"15985e47-5bb6-4315-bb51-7a3d250295bc\",\n    \"workflowRepo\": \"nf-imageanalysis\",\n    \"uploadedOrg\": \"formbio\",\n    \"uploadedProj\": \"formbio-workflows\",\n    \"executionEngine\": \"nextflow\"\n}\n\n

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Terminology

Object

A file or directory

Get Object

Gets the data for a single object, optionally including a direct link for downloading.

This operation will eventually support operations like listing children or descendants. For now, it fully supports getting a single object and optional download URL.

Request

POST https://prd-api.formbio.com/api/v1/orgs/my-organization/my-project/storage/objects/my-object

Parameters

include: include additional details, supports value of downloadUrl

Body

none

Response

Status

200: success
401: not authenticated
403: user lacks permissions
404: organization not found
404: project not found
404: object not found
5xx: internal errors

Body

Format

Body will contain a results property with a list. This list should contain a single item with the following properties.

\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n

Property	Description
`createdAt` string	when the object was initially created
`updatedAt` string	when the object was last updated
`size` integer	size of the object in bytes, will be zero for directories
`name` string	full name of the object, relative to project, will ending in `/` if a directory
`crc32c` integer	CRC32C hash of the object data, will be zero for directories
`links` see below	API links for this object
`downloadUrl` see below	present if `include=downloadUrl` specified

`links` properties

\n\n\n\n\n\n\n\n\n\n\n\n\n

Property	Description
`self` string	link to `GET` this object

`downloadUrl` properties

\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n

Property	Description
`url` string	direct link to download this object directly from Google Storage API. See Google's docs for how to use these URLs: https://cloud.google.com/storage/docs/access-control/signed-urls
`proxiedUrl` string	alternative download URL, for proxying the download through the Form Bio platform's static IP. It's recommended to use the `url` URL if possible, as it offers the best performance. If a static IP is required, this `proxiedUrl` value can be used in an identical way.

Example

{\n    \"results\": [\n        {\n            \"createdAt\": \"2023-05-16T18:33:21.848Z\",\n            \"updatedAt\": \"2023-05-16T18:33:21.848Z\",\n            \"size\": 40,\n            \"name\": \"path/to/my/file\",\n            \"crc32c\": 1481199031,\n            \"links\": {\n                \"self\": \"/api/v1/orgs/my-organization/my-project/storage/objects/path/to/my/file\"\n            },\n            \"downloadUrl\": {\n                \"url\": \"https://storage.googleapis.com/formbio-prd-e9090877-d57b-4de7-88c9-566379aa2d4c/path/to/my/file?X-Goog-Algorithm=ETCETERA...\",\n                \"proxiedUrl\": \"https://sbx-datatransfer.formbio.com/storage.googleapis.com/formbio-prd-e9090877-d57b-4de7-88c9-566379aa2d4c/path/to/my/file?X-Goog-Algorithm=ETCETERA...\"\n            }\n        }\n    ]\n}\n\n

Create Directory

Creates an empty directory in a Form Bio project's storage.

Request

POST https://prd-api.formbio.com/api/v1/orgs/my-organization/my-project/vault/directory

Parameters

conflictStrategy string (optional): can be skip, merge, or replace, default behavior is to fail on conflict
createParents boolean (optional): will create intermediate missing directories, default is to fail when there are missing intermediate directories (similar to -p flag on mkdir)
directoryName string (required): full object name of the directory

Body

none

Response

Status

200: success
401: not authenticated
403: user lacks permissions
404: organization not found
404: project not found
409: conflict with fail conflict strategy
5xx: internal errors

Body

none

Create Resumable Upload

Initiates a resumanble upload for a single file, returning a signed URL to which the client can post multiple chunked requests. For usage, see https://cloud.google.com/storage/docs/resumable-uploads.

Request

POST https://prd-api.formbio.com/api/v1/orgs/my-organization/my-project/vault/resumable

Body

Format

\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n

Property	Description
`createParents` boolean	(optional) will create intermediate missing directories, default is to fail when there are missing intermediate directories (similar to `-p` flag on `mkdir`)
`conflictStrategy` string	can be `skip`, `merge`, or `replace`, default behavior is to `fail` on conflict
`objectName` string	full target object name of the file, as it should appear after being uploaded
`size` int	size in bytes of the file

Example

{\n    \"createParents\": true,\n    \"conflictStrategy\": \"merge\",\n    \"objectName\": \"path/to/my/file\",\n    \"size\": 40\n}\n\n

Response

Status

201: success
401: not authenticated
403: user lacks permissions
400: quota exceeded
400: invalid request body
404: organization not found
404: project not found
5xx: internal errors

Body

Format

\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n

Property	Description
`uri` string	URL to POST file data to
`proxiedURI` string	alternative URL to POST file data to, behind a FormBio static IP that can be
`size` string	same as `size` from request body
`objectName` string	same as `objectName` from request body
`createParents` string	same as `createParents` from request body
`conflictStrategy` string	same as `conflictStrategy` from request body

Example

{\n    \"uri\": \"https://storage.googleapis.com/upload/storage/v1/b/tundra-prd-ec101ba4-14da-40ec-8e15-d07b450a646f/o?uploadType=resumable\\u0026name=path/to/my/file\\u0026upload_id=3BktcPpNunNHR37kZmFfX51p3DZR3kaVnBZ39scLR7oVP3NkkBXFzayVxwLRZ3zpk33ViqryiLLbXVVkPv7vXz3ZZ3hDDkDV1uvD1xTpD335i-V3k\",\n    \"proxiedURI\": \"https://sbx-datatransfer.formbio.com/storage.googleapis.com/upload/storage/v1/b/tundra-prd-ec101ba4-14da-40ec-8e15-d07b450a646f/o?uploadType=resumable\\u0026name=path/to/my/file\\u0026upload_id=3BktcPpNunNHR37kZmFfX51p3DZR3kaVnBZ39scLR7oVP3NkkBXFzayVxwLRZ3zpk33ViqryiLLbXVVkPv7vXz3ZZ3hDDkDV1uvD1xTpD335i-V3k\",\n    \"size\": 40,\n    \"objectName\": \"path/to/my/file\",\n    \"createParents\": true,\n    \"conflictStrategy\": \"merge\"\n}\n\n

Delete Object

Deletes one or more objects from project storage, including descendants

Request

DELETE https://prd-api.formbio.com/api/v1/orgs/my-organization/my-project/vault

Body

Format

\n\n\n\n\n\n\n\n\n\n\n\n\n

Property	Description
`objects` array[string]	list of object names to delete

Example

{\n    \"objects\": [ \"path/to/my/file\" ]\n}\n\n

Response

Status

200: success
401: not authenticated
403: user lacks permissions
400: invalid request body
404: organization not found
404: project not found
5xx: internal errors

Body

none

\n","auth":{"type":"bearer","bearer":{"basicConfig":[{"key":"token","value":"run CLI command `formbio auth print-token` to get this value"}]},"isInherited":false},"event":[{"listen":"prerequest","script":{"id":"561fe177-4bbf-4a2f-9ccc-5d6bbdc6ce69","type":"text/javascript","exec":[""]}},{"listen":"test","script":{"id":"0988bcf4-6265-48eb-b263-c4912a3c3818","type":"text/javascript","exec":[""]}}],"_postman_id":"b61a4892-6cd6-4ea2-84ef-ab320157be6f"},{"name":"Vectorflow","item":[{"name":"Datacore","item":[],"id":"6567f258-cf91-40ce-8324-dfd5ab81b413","_postman_id":"6567f258-cf91-40ce-8324-dfd5ab81b413","description":"","auth":{"type":"noauth","isInherited":true,"source":{"_postman_id":"b4460d71-4359-44a2-9d3a-0a09b6603fab","id":"b4460d71-4359-44a2-9d3a-0a09b6603fab","name":"Internal","type":"folder"}}}],"id":"5701a4f5-6d37-4ec5-8c08-c7e905a73a31","_postman_id":"5701a4f5-6d37-4ec5-8c08-c7e905a73a31","description":"","auth":{"type":"noauth","isInherited":true,"source":{"_postman_id":"b4460d71-4359-44a2-9d3a-0a09b6603fab","id":"b4460d71-4359-44a2-9d3a-0a09b6603fab","name":"Internal","type":"folder"}}},{"name":"Organizations","item":[{"name":"Get Organizations","event":[{"listen":"test","script":{"id":"f1fc7b0b-d93e-4a11-b67f-208f9f08c0a8","exec":["pm.test(\"Status code is 200\", function () {"," pm.response.to.have.status(200);","});"],"type":"text/javascript"}}],"id":"a18b1936-c2c2-405b-8787-a085df4df5ff","protocolProfileBehavior":{"disableBodyPruning":true},"request":{"method":"GET","header":[],"url":"https://prd-api.formbio.com/api/v1/workflow-run/01234567-89ab-cdef-0123-456789abcdef","auth":{"type":"noauth","isInherited":true,"source":{"_postman_id":"b4460d71-4359-44a2-9d3a-0a09b6603fab","id":"b4460d71-4359-44a2-9d3a-0a09b6603fab","name":"Internal","type":"folder"}},"urlObject":{"path":["api","v1","workflow-run","01234567-89ab-cdef-0123-456789abcdef"],"host":["https://prd-api.formbio.com"],"query":[],"variable":[]}},"response":[],"_postman_id":"a18b1936-c2c2-405b-8787-a085df4df5ff"}],"id":"cc7b2589-e384-45c9-a22b-2eeff3c27907","_postman_id":"cc7b2589-e384-45c9-a22b-2eeff3c27907","description":"","auth":{"type":"noauth","isInherited":true,"source":{"_postman_id":"b4460d71-4359-44a2-9d3a-0a09b6603fab","id":"b4460d71-4359-44a2-9d3a-0a09b6603fab","name":"Internal","type":"folder"}}},{"name":"Projects","item":[],"id":"a4faff2a-79a7-436a-8a01-a00d8a08f92f","_postman_id":"a4faff2a-79a7-436a-8a01-a00d8a08f92f","description":"","auth":{"type":"noauth","isInherited":true,"source":{"_postman_id":"b4460d71-4359-44a2-9d3a-0a09b6603fab","id":"b4460d71-4359-44a2-9d3a-0a09b6603fab","name":"Internal","type":"folder"}}}],"id":"b4460d71-4359-44a2-9d3a-0a09b6603fab","description":"

This section describes the experimental features of the Form Bio RESTful API.

Use at your own discretion, as these operations will likely change over time.

\n","auth":{"type":"noauth","isInherited":false},"event":[{"listen":"prerequest","script":{"id":"2c6b342d-2166-4959-9a14-c39d5dff861d","type":"text/javascript","exec":[""]}},{"listen":"test","script":{"id":"d95adc34-2629-4660-8406-fb6688e5668c","type":"text/javascript","exec":[""]}}],"_postman_id":"b4460d71-4359-44a2-9d3a-0a09b6603fab"}],"event":[{"listen":"prerequest","script":{"id":"c2d7f8b3-299d-4851-8174-ba42d1c1def6","type":"text/javascript","requests":{},"exec":[""]}},{"listen":"test","script":{"id":"f9475c65-f329-494e-9bd6-d6bccaca9e74","type":"text/javascript","requests":{},"exec":[""]}}],"variable":[{"key":"baseUrl","value":"https://prd-api.formbio.com"},{"key":"accessToken","value":"run CLI command `formbio auth print-token` to get this value"},{"key":"organizationId","value":"my-organization"},{"key":"projectId","value":"my-project"},{"key":"workflowOrganizationId","value":"1ace39a1-f777-46d9-a21f-8823d9b8517f"},{"key":"workflowProjectId","value":"32411019-a596-4a7e-91b0-c8843f05971a"},{"key":"workflowRunId","value":"01234567-89ab-cdef-0123-456789abcdef"},{"key":"objectName","value":"my-object"},{"key":"objectSize","value":"40"}]}

Getting started guide

Authentication

Experimental API

List Project-Shared Workflow Versions

Request

Body

Response

Status

Body

Format

Example

Terminology

Workflow

Workflow Version

Terminology

Workflow Run

Workflow Run Execution

Create Workflow Run

Request

Body

Format

Example

Response

Status

Body

Format

Example

Get Workflow Run

Request

Body

Response

Status

Body

Format

Workflow Run Properties

Workflow Run Execution Properties

Example

Terminology

Object

Get Object

Request

Parameters

Body

Response

Status

Body

Format

links properties

downloadUrl properties

Example

Create Directory

Request

Parameters

Body

Response

Status

Body

Create Resumable Upload

Request

Body

Format

Example

Response

Status

Body

Format

Example

Delete Object

Request

Body

Format

Example

Response

Status

Body

`links` properties

`downloadUrl` properties