Basespace API

Base URL: /v2, Version: 2.0.0

Basespace REST API

For descriptions of the V1 API, see V1 API Reference.

Default request content-types: application/json
Default response content-types: application/json
Schemes: https

Summary

Applications

Operation Description
GET /applications

Get a list of available applications

GET /applications/{id}

Get information about an app

GET /applications/{id}/qcthresholds

Get a list of QC thresholds applied to an analysis workflow

PUT /applications/{id}/qcthresholds

Add or update the QC thresholds applied to an analysis workflow

GET /applications/{id}/settings

Get the settings of an application or workflow

GET /applications/{id}/workflowdependencies

Get a list of workflow dependencies on an analysis workflow

PUT /applications/{id}/workflowdependencies

Add or update the workflow dependencies of an analysis workflow

POST /applications/{id}/workflows

Create or update an analysis workflow

Analyses

Operation Description
GET /appsessions

Get a list of analyses

DELETE /appsessions/{id}

Delete a specific analysis

GET /appsessions/{id}

Get information about an analysis

POST /appsessions/{id}

Update an analysis

GET /appsessions/{id}/comments

Get a list of comments made about an analysis

GET /appsessions/{id}/logfiles

Get a list of logs of an analysis

GET /appsessions/{id}/properties

Get a list of properties of an analysis

POST /appsessions/{id}/properties

Add or update properties of an analysis

DELETE /appsessions/{id}/properties/{name}

Delete a property of an analysis

GET /appsessions/{id}/properties/{name}

Get information about a property of an analysis

GET /appsessions/{id}/properties/{name}/items

Get a list of items from a property of an analysis

POST /appsessions/{id}/stop

Stop an analysis from running

Trash

Operation Description
DELETE /trash

Delete all items in the trash

GET /trash

Get a list of items in the trash

GET /trash/{id}

Get information about an item in the trash

POST /trash/{id}/restorefromtrash

Restore an item from the trash back to its active state

Users

Operation Description
GET /users/{id}

Get information about a user

GET /users/{id}/settings

Get a list of the user's settings

POST /users/{id}/settings

Update the user's settings

GET /users/current

Get information about the current user's account

GET /users/current/subscription

Get information about the user’s subscriptions

GET /users/current/usage

Get usage statistics for the user

GET /users/current/workgroups

Get a list of workgroups the user belongs to

GET /workgroups/{id}

Get information about a workgroup

Biosamples

Operation Description
GET /biosamples

Get a list of biosamples

GET /biosamples/{biosampleid}/labrequeues

Get a list of a biosample’s lab requeues

GET /biosamples/{id}

Get information about a biosample

POST /biosamples/{id}

Update a Biosample

GET /biosamples/{id}/libraries

Get a list of a biosample’s libraries

GET /biosamples/{id}/runlanesummaries

Get information about biosample’s lane mapping

POST /biosamples/bulkupdate

Update the default project of many biosamples

Datasets

Operation Description
GET /datasets

Get a list of datasets

GET /datasets/{id}

Get information about a dataset

POST /datasets/{id}

Update an existing dataset

GET /datasets/{id}/comments

Get a list of comments made about a dataset

GET /datasets/{id}/files

Get a list of files of a dataset

GET /datasettypes/{id}

Get information about a dataset type

GET /projects/{id}/datasets

Get a list of datasets in a project

Runs

Operation Description
GET /instrumentstatistics

Get instrument statistics

GET /runs/{id}/files

Get a list of files of a run

Lab Requeues

Operation Description
GET /labrequeues

Get a list of lab requeues

GET /labrequeues/{id}

Get information about a specific labrequeue

POST /libraries/{libraryid}/labrequeues

Add a lab requeue request for more yield from a library

POST /librarypools/{poolid}/labrequeues

Add a lab requeue request for more yield from a pool

POST /preprequests/{preprequestid}/labrequeues

Add a lab requeue request for more yield from a biosample

Lanes

Operation Description
GET /laneqcthresholds

Get a list of QC thresholds applied to lanes

PUT /laneqcthresholds

Add or update the QC thresholds applied to lanes

GET /lanes/{id}

Get information about a lane

POST /lanes/{id}

Update a lane

GET /lanes/{id}/comments

Get a list of comments on a lane

Libraries

Operation Description
GET /libraries

Get a list of libraries

Pools

Operation Description
POST /librarypools/{id}

Update a pool

GET /librarypools/{id}/libraries

Get a list of libraries of a pool

Projects

Operation Description
GET /projects/{id}

Get information about a project

Security

api_key

Type: apiKey
Name:

x-access-token

In:

header

basespace_auth

Type: oauth2
Flow:

application

TokenUrl:

http://login.illumina.com

Scopes:
admin: placeholder

Description:

OAuth V2 authentication

Paths

Get a list of available applications

GET /applications

Tags: Applications
category

Return all apps that belong to a specific category that a user has access to (examples include: Native, Workflow, Other). Only a single category can be specified in a given call

query string
references

Returns all analysis workflows that a user has access to that were created from a particular app, denoted by its unique slug ID

query string
sortby

The field(s) used to sort the result set

query string , x ∈ { DateCreated , DatePublished , Id , Name , VersionNumber }
offset

The starting offset to read

query integer
limit

The maximum number of items to return

query integer
sortdir

The sort direction for the result set

query string
id

The Id of the resource

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get information about an app

GET /applications/{id}

Tags: Applications
id path string
propertieslimit

Returns only the specified number of properties for the application.

query integer
propertyitemslimit

Returns only the specified number of property items per property for the application

query integer

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get a list of QC thresholds applied to an analysis workflow

GET /applications/{id}/qcthresholds

Tags: Applications
id

The Id of the resource

path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Add or update the QC thresholds applied to an analysis workflow

PUT /applications/{id}/qcthresholds

Tags: Applications

List the QC thresholds to be updated. You must include the name of the metric to be thresholded, the type of logical operator, the dataset type unique ID to apply the threshold to, and the threshold values.

qcthresholds query object[] , comma separated (qcthresholds=aaa,bbb)
id

The Id of the resource

path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get the settings of an application or workflow

GET /applications/{id}/settings

Tags: Applications
id

The Id of the resource

path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get a list of workflow dependencies on an analysis workflow

GET /applications/{id}/workflowdependencies

Tags: Applications
id

The Id of the resource

path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Add or update the workflow dependencies of an analysis workflow

PUT /applications/{id}/workflowdependencies

Tags: Applications

Add the required triggers for the analysis workflow to launch. Workflows can depend on a certain amount of biosample actual yield to show up or they can depend on another app completing.

version query string
dependencies query object[] , comma separated (dependencies=aaa,bbb)
id

The Id of the resource

path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Create or update an analysis workflow

POST /applications/{id}/workflows

Tags: Applications

Create an analysis workflow using the settings, app, and version of an existing appsession.

Uses default content-types: application/json

id

Applicaiton Id

path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get a list of analyses

GET /appsessions

Tags: Analyses
appid

Filter by ID of application used

query integer
applicationfamilyslugs

Filter by application family

query string[] , comma separated (applicationfamilyslugs=aaa,bbb)
datemodified query string
executionstatus

Filter by execution status

query string
qcstatus

Filter by QC status

query string
deliverystatus

Filter by delivery status

query string
name query string
output.projects

Filter by ID of output project

query integer[] , comma separated (output.projects=aaa,bbb)
input.runs

Filter by ID of run input

query integer[] , comma separated (input.runs=aaa,bbb)
input.biosamples

Filter by ID of biosample input

query integer[] , comma separated (input.biosamples=aaa,bbb)
include

Additional resources to include

query string , x ∈ { Children , Logs }
propertyfilters

Filter by appsessions include the specified property names

query string[] , comma separated (propertyfilters=aaa,bbb)
usercreatedby

ID of user who created appsession

query integer
sortby

The field(s) used to sort the result set

query string , x ∈ { Name , Id , AppId , ExecutionStatus , ModifiedOn , DateCreated , AppName , TotalSize , QcStatus , DeliveryStatus }
offset

The starting offset to read

query integer
limit

The maximum number of items to return

query integer
sortdir

The sort direction for the result set

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Delete a specific analysis

DELETE /appsessions/{id}

Tags: Analyses
id

Appsession ID

path string
preserve

Preserve "Metadata", to keep records, but not files, of an appsession

query string
bypasstrash

Select true to go straight to deletion

query boolean

Uses default content-types: application/json

200 OK

OK

205 Reset Content

Reset Content

default #/responses/default

An Error Occured

Get information about an analysis

GET /appsessions/{id}

Tags: Analyses
id

Appsession ID

path string
include

Additional resources to include

query string , x ∈ { Children , Logs }
showhiddenitems

ShowHiddenItems

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Update an analysis

POST /appsessions/{id}

Tags: Analyses

The Execution Status cannot be changed since it is an automated status tracking the progress of running the app. The Qc Status may be updated only when the Execution Status is set to “Complete” or “Aborted”. Delivery Status may be updated at any time. Comments can be added when updating statuses.

Uses default content-types: application/json

id

Appsession ID

path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get a list of comments made about an analysis

GET /appsessions/{id}/comments

Tags: Analyses
id

Appsession ID

path string
sortby

The field(s) used to sort the result set

query string , x ∈ { Timestamp }
offset

The starting offset to read

query integer
limit

The maximum number of items to return

query integer
sortdir

The sort direction for the result set

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get a list of logs of an analysis

GET /appsessions/{id}/logfiles

Tags: Analyses
id

Appsession ID

path string
filesetid query string
extensions

Filter by file extension

query string
directory

Filter by directory path (root is /)

query string
includesubdirectories

Whether to return subdirectories

query boolean
excludevcfindexfolder

Whether to exclude VCF index folders

query boolean
excludebamcoveragefolder

Whether to exclude BAM coverage folders

query boolean
excludesystemfolder

Whether to exclude system folders

query boolean
excludeemptyfiles

Whether to exclude empty files

query boolean
filehrefcontentresolution

Resolves the HrefContent to the direct file URI to avoid a hop to GET: files/{id}/content

query boolean
statuses

Optionally filter by status (default complete)

query string[] , comma separated (statuses=aaa,bbb)
turbomode query boolean
pathprefix

To be pre-fixed in the path of the file

query string
sortby

The field(s) used to sort the result set

query string , x ∈ { Id , DateCreated , Path , Name }
offset

The starting offset to read

query integer
limit

The maximum number of items to return

query integer
sortdir

The sort direction for the result set

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get a list of properties of an analysis

GET /appsessions/{id}/properties

Tags: Analyses
id

Appsession ID

path string
propertieslimit

Limit the # of properties returned

query integer
propertyitemslimit

Limit the # of property items returned per property

query integer
propertyfilters

Filter by property name

query string[] , comma separated (propertyfilters=aaa,bbb)
showhiddenitems

Show Hidden projects and Datasets

query string
sortby

The field(s) used to sort the result set

query string , x ∈ { Name }
offset

The starting offset to read

query integer
limit

The maximum number of items to return

query integer
sortdir

The sort direction for the result set

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Add or update properties of an analysis

POST /appsessions/{id}/properties

Tags: Analyses

Uses default content-types: application/json

id

Appsession ID

path string

Uses default content-types: application/json

200 OK

OK

201 Created

Created

default #/responses/default

An Error Occured

Delete a property of an analysis

DELETE /appsessions/{id}/properties/{name}

Tags: Analyses
id

Appsession ID

path string
name

Property name

path string

Uses default content-types: application/json

204 No Content

No Content

default #/responses/default

An Error Occured

Get information about a property of an analysis

GET /appsessions/{id}/properties/{name}

Tags: Analyses
id

Appsession ID

path string
name

Property name

path string
showhiddenitems

Hidden filter

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get a list of items from a property of an analysis

GET /appsessions/{id}/properties/{name}/items

Tags: Analyses
id

Appsession ID

path string
name

Property name

path string
showhiddenitems

Hidden filter

query string
sortby

The field(s) used to sort the result set

query string , x ∈ { DateCreated }
offset

The starting offset to read

query integer
limit

The maximum number of items to return

query integer
sortdir

The sort direction for the result set

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Stop an analysis from running

POST /appsessions/{id}/stop

Tags: Analyses

The analysis must have a status of “Running” or “Pending”. Stopping a running analysis will update the status to “Aborted”. Stopping a pending analysis will update the status to “Canceled”.

Uses default content-types: application/json

id

Appsession ID

path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get a list of biosamples

GET /biosamples

Tags: Biosamples
biosamplename

Only return biosamples with the given BioSampleName(s)

query string[] , comma separated (biosamplename=aaa,bbb)
include

Sub elements to include in the response

query string[] , comma separated (include=aaa,bbb)
propertynamestartswith query string[] , comma separated (propertynamestartswith=aaa,bbb)
status

Only return biosamples with the given Status(es)

query string[] , comma separated (status=aaa,bbb)
labstatus

Only return biosamples with the given LabStatus(es)

query string[] , comma separated (labstatus=aaa,bbb)
projectid

Only return biosamples with the specified default projects or datasets in those projects

query string[] , comma separated (projectid=aaa,bbb)
sortby

The field(s) used to sort the result set

query string , x ∈ { Id , BioSampleName , Nickname , DateModified , UserOwnedBy , Project , Subject , LabStatus , Status }
offset

The starting offset to read

query integer
limit

The maximum number of items to return

query integer
sortdir

The sort direction for the result set

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Update the default project of many biosamples

POST /biosamples/bulkupdate

Tags: Biosamples

Setting a new default project of a biosample will redirect newly created datasets to the new project.

Uses default content-types: application/json

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get a list of a biosample’s lab requeues

GET /biosamples/{biosampleid}/labrequeues

Tags: Biosamples

All lab requeues, from each of the types, are listed here. A pool lab requeue will show up on the list of lab requeues for all biosamples that make up the pool.

biosampleid

Biosample ID

path string
type

Specify which type of lab requeue to be listed e.g. NewBioSampleLibrary, AdditionalYieldOfLibraryPool, or AdditionalYieldOfFinishedLibrary.

query string
sortby

The field(s) used to sort the result set

query string , x ∈ { Id , DateModified , Type , RequestedAdditionalYield , DateCreated }
offset

The starting offset to read

query integer
limit

The maximum number of items to return

query integer
sortdir

The sort direction for the result set

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get information about a biosample

GET /biosamples/{id}

Tags: Biosamples
id

Biosample ID

path string
include

Sub elements to include in the response

query string[] , comma separated (include=aaa,bbb)

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Update a Biosample

POST /biosamples/{id}

Tags: Biosamples

Setting a new default project of a biosample will redirect newly created datasets to the new project. The biosample status may transition between any of the possible statuses. Setting a biosample to canceled will automatically cancel all analyses in progress for that biosample.

Uses default content-types: application/json

id

Biosample ID

path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get a list of a biosample’s libraries

GET /biosamples/{id}/libraries

Tags: Biosamples
id

Biosample ID

path string
include

Sub elements to include in the response: LibraryIndex, YieldInformation

query string[] , comma separated (include=aaa,bbb)
sortby

The field(s) used to sort the result set

query string , x ∈ { Id , Name , DateCreated , DateModified , ProjectName , Biomolecule , Status , UserOwnedBy }
offset

The starting offset to read

query integer
limit

The maximum number of items to return

query integer
sortdir

The sort direction for the result set

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get information about biosample’s lane mapping

GET /biosamples/{id}/runlanesummaries

Tags: Biosamples
id

Biosample ID

path string
sortby

The field(s) used to sort the result set

query string , x ∈ { CreatedOn , ModifiedOn }
offset

The starting offset to read

query integer
limit

The maximum number of items to return

query integer
sortdir

The sort direction for the result set

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get a list of datasets

GET /datasets

Tags: Datasets
include

Can specify to return Properties, which returns an additional properties section for each dataset. Or return AppSessionRoot, which returns information about the root analysis of a workflow in the AppSession section for each dataset it applies to.

query string[] , comma separated (include=aaa,bbb)
propertyfilters

Specify which properties to include in the properties section, e.g. Input.BioSamples, Input.Libraries, or Input.Runs.

query string[] , comma separated (propertyfilters=aaa,bbb)
datasettypes

Return datasets of this type or excluding this type. Supports comma-separated lists.

query string[] , comma separated (datasettypes=aaa,bbb)
qcstatus

Return datasets of this QC status.

query string[] , comma separated (qcstatus=aaa,bbb)
uploadstatus

Return datasets of this file upload status.

query string[] , comma separated (uploadstatus=aaa,bbb)
inputbiosamples

Return datasets related to this biosample ID.

query integer[] , comma separated (inputbiosamples=aaa,bbb)
inputruns

Return datasets related to this run ID.

query integer[] , comma separated (inputruns=aaa,bbb)
sortby

The field(s) used to sort the result set

query string , x ∈ { Name , DateCreated , DateModified , AppSessionName , ApplicationName , ProjectName }
offset

The starting offset to read

query integer
limit

The maximum number of items to return

query integer
sortdir

The sort direction for the result set

query string

Uses default content-types: application/json

200 OK

A list of datasets

default #/responses/default

An Error Occured

Get information about a dataset

GET /datasets/{id}

Tags: Datasets
id

Dataset ID

path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Update an existing dataset

POST /datasets/{id}

Tags: Datasets

The QcStatus of a dataset may only be updated when the UploadStatus is set to “Complete”. The QcStatus may then be updated to one of the following values: QcFailed or QcPassed. A comment may be entered into the Comment field when updating the dataset QcStatus.

Uses default content-types: application/json

id

Dataset ID

path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get a list of comments made about a dataset

GET /datasets/{id}/comments

Tags: Datasets
id

Dataset ID

path string
sortby

The field(s) used to sort the result set

query string , x ∈ { Timestamp }
offset

The starting offset to read

query integer
limit

The maximum number of items to return

query integer
sortdir

The sort direction for the result set

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get a list of files of a dataset

GET /datasets/{id}/files

Tags: Datasets
filesetid query string
extensions

Filter by file extension

query string
directory

Filter by directory path (root is /)

query string
includesubdirectories

Whether to return subdirectories

query boolean
excludevcfindexfolder

Whether to exclude VCF index folders

query boolean
excludebamcoveragefolder

Whether to exclude BAM coverage folders

query boolean
excludesystemfolder

Whether to exclude system folders

query boolean
excludeemptyfiles

Whether to exclude empty files

query boolean
filehrefcontentresolution

Resolves the HrefContent to the direct file URI to avoid a hop to GET: files/{id}/content

query boolean
statuses

Optionally filter by status (default complete)

query string[] , comma separated (statuses=aaa,bbb)
turbomode query boolean
pathprefix

To be pre-fixed in the path of the file

query string
sortby

The field(s) used to sort the result set

query string , x ∈ { Id , DateCreated , Path , Name }
offset

The starting offset to read

query integer
limit

The maximum number of items to return

query integer
sortdir

The sort direction for the result set

query string
id

The Id of the resource

path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get information about a dataset type

GET /datasettypes/{id}

Tags: Datasets
id

Dataset type ID

path string
include query string[] , comma separated (include=aaa,bbb)

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get instrument statistics

GET /instrumentstatistics

Tags: Runs

Get instrument statistics for given serial numbers and time range. Returned data can be grouped by month or week.

serialnumbers

Comma-separated list of serial numbers.

path string
fromdate

From date in user ISO 8601 format.

path none
todate

To date in ISO 8601 format. Defaults to current date if not specified.

query none
binby

BinBy can be 'week' or 'month'.

query string
timezone

User timezone for binning.

path string
sortby

The field(s) used to sort the result set

query string , x ∈ { Id , Name }
offset

The starting offset to read

query integer
limit

The maximum number of items to return

query integer
sortdir

The sort direction for the result set

query string
id

The Id of the resource

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get a list of lab requeues

GET /labrequeues

Tags: Lab Requeues
status

Only return labrequeues with the given Status(es)

query string[] , comma separated (status=aaa,bbb)
type

Only return labrequeues with the given LabRequeueTypes(s)

query string[] , comma separated (type=aaa,bbb)
sortby

The field(s) used to sort the result set

query string , x ∈ { Id , DateModified , Type , RequestedAdditionalYield , DateCreated }
offset

The starting offset to read

query integer
limit

The maximum number of items to return

query integer
sortdir

The sort direction for the result set

query string
id

The Id of the resource

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get information about a specific labrequeue

GET /labrequeues/{id}

Tags: Lab Requeues
id

Labrequeue ID

path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get a list of QC thresholds applied to lanes

GET /laneqcthresholds

Tags: Lanes

The QC thresholds are applied to a user's account. Any runs uploaded in that user's context will automatically have all lanes of the flowcell undergo automatic QC based on the QC thresholds. Thresholds are saved either to a lane, or to a lane and read number.

id

The Id of the resource

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Add or update the QC thresholds applied to lanes

PUT /laneqcthresholds

Tags: Lanes

List the QC thresholds to be updated.

qcthresholds query object[] , comma separated (qcthresholds=aaa,bbb)
id

The Id of the resource

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get information about a lane

GET /lanes/{id}

Tags: Lanes
id

The Id of the resource

path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Update a lane

POST /lanes/{id}

Tags: Lanes

The status of a lane may be updated to the following values: QcFailed, QcPassed.

Uses default content-types: application/json

id path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get a list of comments on a lane

GET /lanes/{id}/comments

Tags: Lanes
id

Lane ID

path string
sortby

The field(s) used to sort the result set

query string , x ∈ { Timestamp }
offset

The starting offset to read

query integer
limit

The maximum number of items to return

query integer
sortdir

The sort direction for the result set

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get a list of libraries

GET /libraries

Tags: Libraries
status query string[] , comma separated (status=aaa,bbb)
sortby

The field(s) used to sort the result set

query string , x ∈ { Id , Name , DateCreated , DateModified , ProjectName , Biomolecule , Status , UserOwnedBy }
offset

The starting offset to read

query integer
limit

The maximum number of items to return

query integer
sortdir

The sort direction for the result set

query string
id

The Id of the resource

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Add a lab requeue request for more yield from a library

POST /libraries/{libraryid}/labrequeues

Tags: Lab Requeues

The requested additional yield is the total yield to be requested for the whole pool. To estimate how much yield will be added from each library, divide the requested additional yield by the number of libraries in the pool.

Uses default content-types: application/json

libraryid path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Update a pool

POST /librarypools/{id}

Tags: Pools

The status of a pool may be updated to the following values: Active, Failed, Consumed or QCFailed. Setting a pool to Failed or QCFailed will exclude all FASTQ datasets created from the pool from app launch when one of its biosamples are selected as an input. This is also reflected on the Actual Yield of each biosample in the pool.

Uses default content-types: application/json

id

The Id of the resource

path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get a list of libraries of a pool

GET /librarypools/{id}/libraries

Tags: Pools
include

Sub elements to include in the response: LibraryIndex, YieldInformation

query string[] , comma separated (include=aaa,bbb)
sortby

The field(s) used to sort the result set

query string , x ∈ { Id , Name , DateCreated , DateModified , ProjectName , Biomolecule , Status , UserOwnedBy }
offset

The starting offset to read

query integer
limit

The maximum number of items to return

query integer
sortdir

The sort direction for the result set

query string
id

The Id of the resource

path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Add a lab requeue request for more yield from a pool

POST /librarypools/{poolid}/labrequeues

Tags: Lab Requeues

Uses default content-types: application/json

poolid path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Add a lab requeue request for more yield from a biosample

POST /preprequests/{preprequestid}/labrequeues

Tags: Lab Requeues

Request a requeue for a new library, given an existing preprequest.

Uses default content-types: application/json

preprequestid path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get information about a project

GET /projects/{id}

Tags: Projects
propertieslimit query integer
propertyitemslimit query integer
include query string[] , comma separated (include=aaa,bbb)
id

The Id of the resource

path string

Uses default content-types: application/json

200 OK

Get information about a project

default

An error occurred.

Get a list of datasets in a project

GET /projects/{id}/datasets

Tags: Datasets
id

Project ID

path string
sortby

The field(s) used to sort the result set

query string , x ∈ { Name , DateCreated , DateModified , AppSessionName , ApplicationName , ProjectName }
offset

The starting offset to read

query integer
limit

The maximum number of items to return

query integer
sortdir

The sort direction for the result set

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get a list of files of a run

GET /runs/{id}/files

Tags: Runs
extensions

The file extensions to filter by (comma-separated)

query string
directory

The directory path to filter by (root is /)

query string
filehrefcontentresolution

Resolves the HrefContent to the direct file URI to avoid a hop to GET: files/{id}/content

query boolean
recursive

If a 'directory' is provided, files in subfolders of the given directory are also included

query boolean
statuses

Optionally filter by status (default complete)

query string[] , comma separated (statuses=aaa,bbb)
include

Possible values: 'Subdirectories', 'TotalCount'

query string[] , comma separated (include=aaa,bbb)
pathprefix

To be pre-fixed in the path of the file

query string
sortby

The field(s) used to sort the result set

query string , x ∈ { Id , DateCreated , Path , Name }
offset

The starting offset to read

query integer
limit

The maximum number of items to return

query integer
sortdir

The sort direction for the result set

query string
id

The Id of the resource

path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Delete all items in the trash

DELETE /trash

Tags: Trash

Deleting all items from the trash is a non-reversible action. All items and their files will be removed from Sequence Hub permanently.

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get a list of items in the trash

GET /trash

Tags: Trash
sortby

The field(s) used to sort the result set

query string , x ∈ { DateDeleted , TotalSize }
offset

The starting offset to read

query integer
limit

The maximum number of items to return

query integer
sortdir

The sort direction for the result set

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get information about an item in the trash

GET /trash/{id}

Tags: Trash
id

The Id of the resource

path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Restore an item from the trash back to its active state

POST /trash/{id}/restorefromtrash

Tags: Trash

The ID used in this endpoint is the ID given to the item when it is put in the trash, not the original ID from the resource, i.e. its project ID. Please use the GET /v2/trash endpoint to find the item’s trash ID.

Uses default content-types: application/json

id

The Id of the resource

path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get information about the current user's account

GET /users/current

Tags: Users
options query string
include query string[] , comma separated (include=aaa,bbb)
id

The Id of the resource

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get information about the user’s subscriptions

GET /users/current/subscription

Tags: Users
id

The Id of the resource

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get usage statistics for the user

GET /users/current/usage

Tags: Users

Information about storage and compute usage will be returned for the user’s personal account, as well as any workgroups they own.

includeloggedinuser query boolean
periods query integer
refreshcache query boolean
sortby

The field(s) used to sort the result set

query string , x ∈ { Start , End }
offset

The starting offset to read

query integer
limit

The maximum number of items to return

query integer
sortdir

The sort direction for the result set

query string
id

The Id of the resource

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get a list of workgroups the user belongs to

GET /users/current/workgroups

Tags: Users
includeloggedinuser

Includes current user

query boolean
activeonly

Excludes inactive workgroups

query boolean
refreshcache

This will force a refresh on the workgroup subscriptions

query boolean
sortby

The field(s) used to sort the result set

query string , x ∈ { Id , Name }
offset

The starting offset to read

query integer
limit

The maximum number of items to return

query integer
sortdir

The sort direction for the result set

query string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get information about a user

GET /users/{id}

Tags: Users
options query string
include query string[] , comma separated (include=aaa,bbb)
id

The Id of the resource

path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get a list of the user's settings

GET /users/{id}/settings

Tags: Users
sortby

The field(s) used to sort the result set

query string , x ∈ { Id , DateModified , Name }
offset

The starting offset to read

query integer
limit

The maximum number of items to return

query integer
sortdir

The sort direction for the result set

query string
id

The Id of the resource

path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Update the user's settings

POST /users/{id}/settings

Tags: Users

A user may have settings such as how they receive notifications and expiration time on lab requeues. This currently only works with a session cookie.

Uses default content-types: application/json

id

The Id of the resource

path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Get information about a workgroup

GET /workgroups/{id}

Tags: Users
id

Workgroup ID

path string

Uses default content-types: application/json

200 OK

OK

default

An error occurred.

Response definitions

default

An Error Occured

Schema definitions

AnalysisSettings: object

ReverseComplementI5Index: boolean

ApiAgreementCompact: object

Href: string
Id: string
Title: string
Url: string
Category: string
AgreementStatus: string
DateSigned: string (date-time)

AppResultCompact: object

Id: string
Href: string
UserOwnedBy: V1pre3UserCompact
Name: string
Status: string
StatusSummary: string
DateCreated: string (date-time)
TotalSize: integer (int64)
AppSession: AppSessionCompact
Projects: object[]
IsDeleted: boolean

AppSessionCompact: object

Id: string
Name: string
Href: string
Application: V1pre3ApplicationCompact
UserCreatedBy: V1pre3UserCompact
Status: string
QcStatus: string
StatusSummary: string
Purpose: string
DateCreated: string (date-time)
ModifiedOn: string (date-time)
DateCompleted: string (date-time)
TotalSize: integer (int64)
Properties: V2PropertyContainer
IsDeleted: boolean

ComputeStatistics: object

Unit: string
Amount: number

DateTimeOffset: object

Now: DateTimeOffset
UtcNow: DateTimeOffset
DateTime: string (date-time)
UtcDateTime: string (date-time)
LocalDateTime: string (date-time)
Date: string (date-time)
Day: integer (int32)
DayOfWeek: string , x ∈ { Sunday , Monday , Tuesday , Wednesday , Thursday , Friday , Saturday }
DayOfYear: integer (int32)
Hour: integer (int32)
Millisecond: integer (int32)
Minute: integer (int32)
Month: integer (int32)
Offset: TimeSpan
Second: integer (int32)
Ticks: integer (int64)
UtcTicks: integer (int64)
TimeOfDay: TimeSpan
Year: integer (int32)

GenomeCompact: object

Id: string
DisplayName: string
SpeciesName: string
Source: string
Build: string
Href: string
HrefFileSets: string
HrefAnnotations: string

IApplicationCompact: object

IBiologicalSampleCompact: object

IBiologicalSampleCompactList: object

IProjectCompact: object

IPropertyContainer: object

DisplayedCount: integer (int32)
TotalCount: integer (int32)
Href: string

IUserCompact: object

Lane: object

Id: string
Href: string
Density: number (float)
ErrorRate: number (float)
ErrorRate100: number (float)
ErrorRate35: number (float)
ErrorRate50: number (float)
ErrorRate75: number (float)
IntensityCycle1: number (float)
LaneNumber: integer (int32)
MaxCycleCalled: integer (int32)
MaxProjectedYieldInGbp: number (float)
PercentAligned: number (float)
PercentGtQ30: number (float)
PercentPf: number (float)
Phasing: number (float)
PrePhasing: number (float)
ProjectedYieldInGbp: number (float)
Reads: integer (int64)
ReadsPf: integer (int64)
Status: string
Yield: number (float)
HrefComments: string
ContainsComments: boolean
HrefLaneSequencingStats: string

LibraryContainerCompact: object

Id: string
Href: string
ContainerType: string
UserContainerId: string
LibraryPrep: string
LibraryPrepKit: LibraryPrepKitCompact
UserOwnedBy: V1pre3UserCompact
LibraryCount: integer (int32)
DateModified: string (date-time)
NumberOfSamples: integer (int32)
PoolPlexity: integer (int32)
PrepRun: V1pre3RunCompact

LibraryIndexCompact: object

Id: string
Name: string
Sequence: string
ReagentGuidePosition: string
Incompatibility: string

LibraryPrepKitCompact: object

Id: string
Href: string
Name: string
UserOwnedBy: V1pre3UserCompact
ValidIndexingStrategies: string
ValidReadTypes: string
NumIndexCycles: integer (int32)
AdapterSequenceRead1: string
AdapterSequenceRead2: string
DateModified: string (date-time)
State: string
DefaultRead1Cycles: integer
DefaultRead2Cycles: integer
ProtocolVersion: string
LibraryType: string
PrepKitFamilySlug: string

LoggedInUser: object

Id: string
Name: string
Email: string

MapContent: object

NameAndId: object

Id: string
Name: string

Permissions: object

UserOperations: string[]
string
AccessTokenOperations: string[]
string

PrepModule: object

Name: string
Parameters: object[]

PrepModuleParameter: object

Name: string
Value: string

PrepSettings: object

LibraryPrepName: string
ProtocolVersion: string
HrefDefaultProject: string
Modules: object[]

RegisteredInstrumentCompact: object

InstrumentId: integer (int64)
Name: string
SerialNumber: string

SampleCompact: object

Id: string
Href: string
IsMerged: boolean
UserOwnedBy: V1pre3UserCompact
Name: string
ExperimentName: string
SampleId: string
Status: string
StatusSummary: string
DateCreated: string (date-time)
TotalSize: integer (int64)
AppSession: AppSessionCompact
Projects: object[]
Library: SampleLibrary
Genome: GenomeCompact
Read1: integer
Read2: integer
NumReadsPF: integer (int64)
NumReadsRaw: integer (int64)
TotalReadsRaw: integer (int64)
TotalReadsPF: integer (int64)
TotalClustersRaw: integer (int64)
TotalClustersPF: integer (int64)
IsPairedEnd: boolean
IsDeleted: boolean

SampleLibrary: object

Properties: V2PropertyContainer
OwnerUser: V1pre3UserCompact
Id: string
Href: string
BiologicalSample: V1pre3BiologicalSampleCompact
ContainerPosition: string
Index1: LibraryIndexCompact
Index2: LibraryIndexCompact
DateModified: string (date-time)
LibraryPrep: LibraryPrepKitCompact
Project: V1pre3ProjectCompact
Container: LibraryContainerCompact
ContainerEndPosition: string
LibraryName: string
InsertSize: string
State: string

SequencingStatsCompact: object

Chemistry: string
ErrorRate: number (float)
ErrorRateR1: number (float)
ErrorRateR2: number (float)
Href: string
IntensityCycle1: number (float)
IsIndexed: boolean
MaxCycleCalled: integer (int32)
MaxCycleExtracted: integer (int32)
MaxCycleScored: integer (int32)
NonIndexedErrorRate: number (float)
NonIndexedIntensityCycle1: number (float)
NonIndexedPercentAligned: number (float)
NonIndexedPercentGtQ30: number (float)
NonIndexedProjectedTotalYield: number (float)
NonIndexedYieldTotal: number (float)
NumCyclesIndex1: integer (int32)
NumCyclesIndex2: integer (int32)
NumCyclesRead1: integer (int32)
NumCyclesRead2: integer (int32)
NumLanes: integer (int32)
NumReads: integer (int32)
NumSurfaces: integer (int32)
NumSwathsPerLane: integer (int32)
NumTilesPerSwath: integer (int32)
PercentAligned: number (float)
PercentGtQ30: number (float)
PercentGtQ30R1: number (float)
PercentGtQ30R2: number (float)
PercentPf: number (float)
PercentResynthesis: number (float)
PhasingR1: number (float)
PhasingR2: number (float)
PrePhasingR1: number (float)
PrePhasingR2: number (float)
ProjectedTotalYield: number (float)
ReadsPfTotal: integer (int64)
ReadsTotal: integer (int64)
YieldTotal: number (float)

Species: object

Id: string
Name: string

StorageStatistics: object

Unit: string
Quota: integer (int64)

The total amount of Data the user is permitted to use.

TotalSize: integer (int64)
TotalSharedSize: integer (int64)
TotalOwnedSize: integer (int64)
TotalRunsSize: integer (int64)
TotalProjectsSize: integer (int64)
ProjectsOwnedSize: integer (int64)
ProjectsSharedSize: integer (int64)
RunsOwnedSize: integer (int64)
RunsSharedSize: integer (int64)
TotalTrashSize: integer (int64)

StringICollection: object

Count: integer (int32)
IsReadOnly: boolean

StringIEqualityComparer: object

StringV2DatasetAttributeDefinition[]KeyCollection: object

Count: integer (int32)

StringV2DatasetAttributeDefinition[]ValueCollection: object

Count: integer (int32)

SubscriptionStorage: object

UnitOfMeasure: string
Quota: number (double)

SystemObject: object

TimeSpan: object

Ticks: integer (int64)
Days: integer (int32)
Hours: integer (int32)
Milliseconds: integer (int32)
Minutes: integer (int32)
Seconds: integer (int32)
TotalDays: number (double)
TotalHours: number (double)
TotalMilliseconds: number (double)
TotalMinutes: number (double)
TotalSeconds: number (double)

V1pre3Application: object

LongDescription: string
UserOwnedBy: IUserCompact
HrefSettings: string
HrefAgreements: string
Files: object[]
Agreements: object[]
HrefStoreVersion: string
HrefUserVersion: string
ClientId: string
Properties: IPropertyContainer
ReleaseNotes: string
WhatsNew: string
BypassForm: boolean
IsFree: boolean
ComputeCostPerMinute: number
DatasetTypesOutput: object[]
DatasetTypesInput: object[]
Id: string
Href: string
Name: string
CompanyName: string
VersionNumber: string
HrefLogo: string
HomepageUri: string
ShortDescription: string
DateCreated: string (date-time)
DatePublished: string (date-time)
PublishStatus: string
IsBillingActivated: boolean
Category: string
Classifications: string[]
string
AppFamilySlug: string
AppVersionSlug: string
Features: string[]
string
LockStatus: string
WorkflowSourceApplication: V1pre3ApplicationCompact

V1pre3ApplicationCompact: object

Id: string
Href: string
Name: string
CompanyName: string
VersionNumber: string
HrefLogo: string
HomepageUri: string
ShortDescription: string
DateCreated: string (date-time)
DatePublished: string (date-time)
PublishStatus: string
IsBillingActivated: boolean
Category: string
Classifications: string[]
string
AppFamilySlug: string
AppVersionSlug: string
Features: string[]
string
LockStatus: string
WorkflowSourceApplication: V1pre3ApplicationCompact

V1pre3ApplicationCompactList: object

V1pre3ApplicationSettings: object

Id: string
Href: string
RedirectUri: string
ClientId: string
ClientSecret: string
LaunchSources: string[]
string
LaunchPermissions: string[]
string
InvitedUsers: object[]
HrefLogo: string
HrefScreenshot: string
CompanyName: string
Category: string
HomepageUri: string
Classifications: string[]
string
FeatureFlags: string[]
string
IsAnyVersionPublished: boolean

V1pre3ApplicationsSortFieldsV2Paging: object

DisplayedCount: integer (int32)
TotalCount: integer (int32)
Offset: integer (int32)
Limit: integer (int32)
SortDir: string , x ∈ { Asc , Desc }
SortBy: string , x ∈ { DateCreated , DatePublished , Id , Name , VersionNumber }

V1pre3BiologicalSampleCompact: object

Id: string
Href: string
UserSampleId: string
Name: string
NucleicAcid: string
Species: Species
Project: V1pre3ProjectCompact
UserOwnedBy: V1pre3UserCompact
LibraryCount: integer (int32)
DateModified: string (date-time)

V1pre3DirectoryCompact: object

Href: string
Name: string

V1pre3FileCompact: object

Id: string
Href: string
HrefContent: string
Name: string
ContentType: string
Size: integer (int64)
Path: string
DateCreated: string (date-time)
ParentSample: SampleCompact
ParentAppResult: AppResultCompact
ParentRun: V1pre3RunCompact
ParentGenome: GenomeCompact
ParentAppSession: AppSessionCompact
ParentProjects: object[]
Category: string
ETag: string
ParentDataset: V2DatasetCompact
ParentProject: IProjectCompact

V1pre3FilesSortFieldsV2Paging: object

DisplayedCount: integer (int32)
TotalCount: integer (int32)
Offset: integer (int32)
Limit: integer (int32)
SortDir: string , x ∈ { Asc , Desc }
SortBy: string , x ∈ { Id , DateCreated , Path , Name }

V1pre3LibraryPoolCompact: object

Id: string
Href: string
UserPoolId: string
UserOwnedBy: V1pre3UserCompact
LibraryCount: integer (int32)
DateModified: string (date-time)
DateCreated: string (date-time)
Status: string
LibraryPrep: StringICollection

V1pre3PostTrashItemRestoreFromTrashRequest: object

V1pre3Project: object

HrefSamples: string
HrefAppResults: string
HrefDatasets: string
HrefBaseSpaceUI: string
Properties: V2PropertyContainer
Id: string
UserOwnedBy: V1pre3UserCompact
Href: string
Name: string
Description: string
DateCreated: string (date-time)
DateModified: string (date-time)
HasCollaborators: boolean
IsTransferPending: boolean
IsDeleted: boolean
TotalSize: integer (int64)
Permissions: Permissions

V1pre3ProjectCompact: object

Id: string
UserOwnedBy: V1pre3UserCompact
Href: string
Name: string
Description: string
DateCreated: string (date-time)
DateModified: string (date-time)
HasCollaborators: boolean
IsTransferPending: boolean
IsDeleted: boolean
TotalSize: integer (int64)
Permissions: Permissions

V1pre3PropertyItemSortFieldsV2Paging: object

DisplayedCount: integer (int32)
TotalCount: integer (int32)
Offset: integer (int32)
Limit: integer (int32)
SortDir: string , x ∈ { Asc , Desc }
SortBy: string , x ∈ { DateCreated }

V1pre3PropertyOptionsRequest: object

AllowDuplicates: boolean
Ordered: boolean
AllowArrayItemNulls: boolean

V1pre3PropertySortFieldsV2Paging: object

DisplayedCount: integer (int32)
TotalCount: integer (int32)
Offset: integer (int32)
Limit: integer (int32)
SortDir: string , x ∈ { Asc , Desc }
SortBy: string , x ∈ { Name }

V1pre3RunCompact: object

Id: string
Href: string
Name: string
Number: integer (int32)
ExperimentName: string
Status: string
ReagentBarcode: string
FlowcellBarcode: string
BufferBarcode: string
DateCreated: string (date-time)
DateModified: string (date-time)
AggregateRunState: string
UserOwnedBy: V1pre3UserCompact
UserLockedBy: V1pre3UserCompact
InstrumentLockedBy: RegisteredInstrumentCompact
TotalSize: integer (int64)
PlatformName: string
Workflow: string
Instrument: RegisteredInstrumentCompact
InstrumentName: string
InstrumentType: string
NumCyclesRead1: integer (int32)
NumCyclesRead2: integer (int32)
NumCyclesIndex1: integer (int32)
NumCyclesIndex2: integer (int32)
HrefBaseSpaceUI: string
HasCollaborators: boolean
IsTransferPending: boolean
IsDeleted: boolean
IsFileDataDeleted: boolean
SequencingStats: SequencingStatsCompact
PrepSettings: PrepSettings
ExpectedInstrumentCompletionDate: string (date-time)
PrepErrorCode: string
AnalysisSettings: AnalysisSettings
LaneAndQcStatus: string
LimsStatus: string
Side: string
DateInstrumentStarted: string (date-time)
DateInstrumentCompleted: string (date-time)

V1pre3TrashItem: object

IncludedSamples: object[]
IncludedAppResults: object[]
IncludedAppSessions: object[]
UserDeletedBy: V1pre3UserCompact
Id: string
Name: string
Href: string
DateDeleted: string (date-time)
TotalSize: integer (int64)
DeletedRun: V1pre3RunCompact
DeletedAppSession: AppSessionCompact
DeletedProject: V1pre3ProjectCompact
DeletedSample: SampleCompact
DeletedAppResult: AppResultCompact
DeletedDataset: V2DatasetCompact
IsVisibleInTrash: boolean
ChildCount: integer (int32)
HrefPostRestoreFromTrash: string
Includes: string[]
string

V1pre3TrashItemCompact: object

Id: string
Name: string
Href: string
DateDeleted: string (date-time)
TotalSize: integer (int64)
DeletedRun: V1pre3RunCompact
DeletedAppSession: AppSessionCompact
DeletedProject: V1pre3ProjectCompact
DeletedSample: SampleCompact
DeletedAppResult: AppResultCompact
DeletedDataset: V2DatasetCompact
IsVisibleInTrash: boolean
ChildCount: integer (int32)
HrefPostRestoreFromTrash: string
Includes: string[]
string

V1pre3TrashItemCompactList: object

V1pre3TrashItemsSortFieldsV2Paging: object

DisplayedCount: integer (int32)
TotalCount: integer (int32)
Offset: integer (int32)
Limit: integer (int32)
SortDir: string , x ∈ { Asc , Desc }
SortBy: string , x ∈ { DateDeleted , TotalSize }

V1pre3User: object

Email: string
DateLastActive: string (date-time)
DateCreated: string (date-time)
HrefRuns: string
HrefProjects: string
Roles: string[]
string
StorageStatistics: StorageStatistics
Features: string[]
string
LoggedInUser: LoggedInUser
HrefHistory: string
HrefDomain: string
IsWorkgroup: boolean
Id: string
Href: string
Name: string
GravatarUrl: string
HrefProperties: string
DomainName: string
ExternalDomainId: string

V1pre3UserCompact: object

Id: string
Href: string
Name: string
DateCreated: string (date-time)
GravatarUrl: string
HrefProperties: string
DomainName: string
ExternalDomainId: string

V2AggregateUsage: object

Name: string
AggregateUsageType: string
ProductUsages: object[]

V2AnalysisWorkflowDependenciesResponse: object

Version: string
Dependencies: object[]

V2AnalysisWorkflowDependency: object

Type: string

The type of dependency to add, valid operators include: “BioSampleYield”, “AppCompletion”

Attributes: object[]

Sections containing a list of attributes and their values defining the app launch dependency, specific to the dependency type given

object
key: string
value: SystemObject
Dependencies: object[]

Optional nested dependencies, not needed for BioSampleYield or AppCompletion dependency types

V2AppSession: object

OriginatingUri: string
HrefLogs: string
Children: object[]
RunningDuration: integer (int32)
ComputeStatistics: ComputeStatistics
Id: string
Name: string
Href: string
Application: V1pre3ApplicationCompact
UserCreatedBy: V1pre3UserCompact
ExecutionStatus: string
QcStatus: string
StatusSummary: string
Purpose: string
DateCreated: string (date-time)
DateModified: string (date-time)
DateCompleted: string (date-time)
TotalSize: integer (int64)
Properties: V2PropertyContainer
IsDeleted: boolean
DeliveryStatus: string
ContainsComments: boolean
AppSessionParent: V2AppSessionCompact
AppSessionRoot: V2AppSessionCompact
HrefComments: string

V2AppSessionCompact: object

Id: string
Name: string
Href: string
Application: V1pre3ApplicationCompact
UserCreatedBy: V1pre3UserCompact
ExecutionStatus: string
QcStatus: string
StatusSummary: string
Purpose: string
DateCreated: string (date-time)
DateModified: string (date-time)
DateCompleted: string (date-time)
TotalSize: integer (int64)
Properties: V2PropertyContainer
IsDeleted: boolean
DeliveryStatus: string
ContainsComments: boolean
AppSessionParent: V2AppSessionCompact
AppSessionRoot: V2AppSessionCompact
HrefComments: string

V2AppSessionCompactList: object

V2AppSessionsSortFieldsV2Paging: object

DisplayedCount: integer (int32)
TotalCount: integer (int32)
Offset: integer (int32)
Limit: integer (int32)
SortDir: string , x ∈ { Asc , Desc }
SortBy: string , x ∈ { Name , Id , AppId , ExecutionStatus , ModifiedOn , DateCreated , AppName , TotalSize , QcStatus , DeliveryStatus }

V2BiologicalSample: object

YieldCalculationLogs: string
Id: string
Href: string
UserOwnedBy: V1pre3UserCompact
BioSampleName: string
Nickname: string
DefaultProject: V1pre3ProjectCompact
DateModified: string (date-time)
DateCreated: string (date-time)
Subject: V2SubjectCompact
ContainerName: string
ContainerPosition: string
Status: string
LabStatus: string
PrepRequests: object[]
LibraryPreps: object[]
Yields: object[]
Properties: V2PropertyContainer
HasQcPassedFastqDatasets: boolean

V2BiologicalSampleCompact: object

Id: string
Href: string
UserOwnedBy: V1pre3UserCompact
BioSampleName: string
Nickname: string
DefaultProject: V1pre3ProjectCompact
DateModified: string (date-time)
DateCreated: string (date-time)
Subject: V2SubjectCompact
ContainerName: string
ContainerPosition: string
Status: string
LabStatus: string
PrepRequests: object[]
LibraryPreps: object[]
Yields: object[]
Properties: V2PropertyContainer
HasQcPassedFastqDatasets: boolean

V2BiologicalSampleCompactList: object

V2BiologicalSampleLibraryYield: object

LibraryPrep: LibraryPrepKitCompact
TotalExpectedYield: integer (int64)
TotalActualYield: integer (int64)
TotalFastqDatasets: integer (int64)
TotalLanes: integer (int64)

V2BiologicalSamplesSortFieldsV2Paging: object

DisplayedCount: integer (int32)
TotalCount: integer (int32)
Offset: integer (int32)
Limit: integer (int32)
SortDir: string , x ∈ { Asc , Desc }
SortBy: string , x ∈ { Id , BioSampleName , Nickname , DateModified , UserOwnedBy , Project , Subject , LabStatus , Status }

V2Comment: object

Id: string
Href: string
User: V1pre3UserCompact
Body: string
Action: string
HrefApplication: string
PriorValue: string
NewValue: string
DateCreated: string (date-time)
DateModified: string (date-time)

V2CommentList: object

Items: object[]
Paging: V2CommentSortFieldsV2Paging

V2CommentSortFieldsV2Paging: object

DisplayedCount: integer (int32)
TotalCount: integer (int32)
Offset: integer (int32)
Limit: integer (int32)
SortDir: string , x ∈ { Asc , Desc }
SortBy: string , x ∈ { Timestamp }

V2CreateExistingLibraryLabRequeueRequest: object

RequestedAdditionalYield: integer (int64)
LIMSId: string

V2CreateExistingPoolLabRequeueRequest: object

RequestedAdditionalYield: integer (int64)
LIMSId: string

V2CreateNewLibraryLabRequeueRequest: object

RequestedAdditionalYield: integer (int64)
LIMSId: string

V2Dataset: object

ValidationsPerformed: string[]
string
Id: string
Href: string
HrefFiles: string
HrefBaseSpaceUI: string
Name: string
DateCreated: string (date-time)
DateModified: string (date-time)
AppSession: V2AppSessionCompact
Project: V1pre3ProjectCompact
TotalSize: integer (int64)
IsDeleted: boolean
IsFileDataDeleted: boolean
UserOwnedBy: V1pre3UserCompact
DatasetType: V2DatasetTypeCompact
Properties: V2PropertyContainer
QcStatus: string
QcStatusSummary: string
UploadStatus: string
UploadStatusSummary: string
ValidationStatus: string
V1pre3Id: string
HrefComments: string
ContainsComments: boolean
OriginDataset: V2DatasetCompact

V2DatasetAttributeDefinition: object

Name: string
Title: string
Description: string
IsRequired: boolean
Default: SystemObject
Type: string
Pattern: string
MinLength: integer (int32)
MaxLength: integer (int32)
Minimum: number (double)
Maximum: number (double)

V2DatasetCompact: object

Id: string
Href: string
HrefFiles: string
HrefBaseSpaceUI: string
Name: string
DateCreated: string (date-time)
DateModified: string (date-time)
AppSession: V2AppSessionCompact
Project: V1pre3ProjectCompact
TotalSize: integer (int64)
IsDeleted: boolean
IsFileDataDeleted: boolean
UserOwnedBy: V1pre3UserCompact
DatasetType: V2DatasetTypeCompact
Properties: V2PropertyContainer
QcStatus: string
QcStatusSummary: string
UploadStatus: string
UploadStatusSummary: string
ValidationStatus: string
V1pre3Id: string
HrefComments: string
ContainsComments: boolean
OriginDataset: V2DatasetCompact

V2DatasetCompactList: object

V2DatasetsSortFieldsV2Paging: object

DisplayedCount: integer (int32)
TotalCount: integer (int32)
Offset: integer (int32)
Limit: integer (int32)
SortDir: string , x ∈ { Asc , Desc }
SortBy: string , x ∈ { Name , DateCreated , DateModified , AppSessionName , ApplicationName , ProjectName }

V2DatasetType: object

Namespace: string
HrefDocs: string
DescriptionMarkdown: string
UserCreatedBy: V1pre3UserCompact
AttributeSchema: V2DatasetTypeAttributeSchema
ConformsTo: object[]
Id: string
Href: string
Name: string
ConformsToIds: string[]
string

V2DatasetTypeAttributeSchema: object

V2DatasetTypeCompact: object

Id: string
Href: string
Name: string
ConformsToIds: string[]
string

V2Error: object

ErrorCode: string
ErrorMessage: string
RequestId: string

V2FilesList: object

SubDirectories: object[]
Items: object[]
Paging: V1pre3FilesSortFieldsV2Paging

V2InstrumentStat: object

InstrumentId: integer (int64)
Name: string
SerialNumber: string
InstrumentType: string
TotalRunTime: number (double)
FromDate: DateTimeOffset
ToDate: DateTimeOffset
Bins: object[]

V2InstrumentStatisticsSortFieldsV2Paging: object

DisplayedCount: integer (int32)
TotalCount: integer (int32)
Offset: integer (int32)
Limit: integer (int32)
SortDir: string , x ∈ { Asc , Desc }
SortBy: string , x ∈ { Id , Name }

V2InstrumentStatList: object

V2InstrumentStatsBin: object

FromDate: DateTimeOffset
ToDate: DateTimeOffset
TotalRunTime: number (double)

V2LabRequeue: object

Properties: V2PropertyContainer
Id: string
Href: string
Status: string
Type: string
BioSample: V2BiologicalSampleCompact
UserOwnedBy: V1pre3UserCompact
DateCreated: string (date-time)
DateModified: string (date-time)
RequestedAdditionalYield: integer (int64)
MatchedYield: integer (int64)
MissingYield: integer (int64)
LIMSId: string
PrepType: string
HrefSampleLibrary: string
HrefLibraryPool: string
HrefPrepRequest: string

V2LabRequeueCompact: object

Id: string
Href: string
Status: string
Type: string
BioSample: V2BiologicalSampleCompact
UserOwnedBy: V1pre3UserCompact
DateCreated: string (date-time)
DateModified: string (date-time)
RequestedAdditionalYield: integer (int64)
MatchedYield: integer (int64)
MissingYield: integer (int64)
LIMSId: string
PrepType: string
HrefSampleLibrary: string
HrefLibraryPool: string
HrefPrepRequest: string

V2LabRequeueCompactList: object

V2LabRequeueList: object

V2LabRequeueSortFieldsV2Paging: object

DisplayedCount: integer (int32)
TotalCount: integer (int32)
Offset: integer (int32)
Limit: integer (int32)
SortDir: string , x ∈ { Asc , Desc }
SortBy: string , x ∈ { Id , DateModified , Type , RequestedAdditionalYield , DateCreated }

V2LibraryCompact: object

Id: string
Href: string
Name: string
DateCreated: string (date-time)
DateModified: string (date-time)
Status: string
BioSample: V2BiologicalSampleCompact
LibraryPrep: LibraryPrepKitCompact
Project: V1pre3ProjectCompact
Container: LibraryContainerCompact
Pools: object[]
PoolComponentActualYieldInBps: integer (int64)
InsertSize: string
Biomolecule: string
Index1: LibraryIndexCompact
Index1Sequence: string
Index2: LibraryIndexCompact
Index2Sequence: string
UserOwnedBy: V1pre3UserCompact

V2LibraryCompactExtended: object

BioSampleName: string
ProjectName: string
Id: string
Href: string
Name: string
DateCreated: string (date-time)
DateModified: string (date-time)
Status: string
BioSample: V2BiologicalSampleCompact
LibraryPrep: LibraryPrepKitCompact
Project: V1pre3ProjectCompact
Container: LibraryContainerCompact
Pools: object[]
PoolComponentActualYieldInBps: integer (int64)
InsertSize: string
Biomolecule: string
Index1: LibraryIndexCompact
Index1Sequence: string
Index2: LibraryIndexCompact
Index2Sequence: string
UserOwnedBy: V1pre3UserCompact

V2LibraryCompactExtendedV2LibrarySortFieldsResourceList: object

Items: object[]
DisplayedCount: integer (int32)
TotalCount: integer (int32)
Offset: integer (int32)
Limit: integer (int32)
SortDir: string , x ∈ { Asc , Desc }
SortBy: string , x ∈ { Id , Name , DateCreated , DateModified , ProjectName , Biomolecule , Status , UserOwnedBy }

V2LibraryCompactList: object

V2LibrarySortFieldsV2Paging: object

DisplayedCount: integer (int32)
TotalCount: integer (int32)
Offset: integer (int32)
Limit: integer (int32)
SortDir: string , x ∈ { Asc , Desc }
SortBy: string , x ∈ { Id , Name , DateCreated , DateModified , ProjectName , Biomolecule , Status , UserOwnedBy }

V2PeriodAggregateUsage: object

Name: string
Start: string (date-time)
End: string (date-time)
AggregateUsages: object[]

V2PeriodAggregateUsageList: object

V2PeriodAggregateUsageSortFieldsV2Paging: object

DisplayedCount: integer (int32)
TotalCount: integer (int32)
Offset: integer (int32)
Limit: integer (int32)
SortDir: string , x ∈ { Asc , Desc }
SortBy: string , x ∈ { Start , End }

V2PostApplicationIdWorkflowsRequest: object

Name: string

The name of the analysis workflow

ShortDescription: string

Description of the analysis workflow

AppSessionId: string

The ID of the appsession to gather settings from when creating the workflow

V2PostAppSessionsIdRequest: object

Name: string

The name of the appsession

ExecutionStatus: string

Immutable

StatusSummary: string

A summary of why or how the status changed, seen in the tooltip when clicking an analysis’ status

QcStatus: string

Possible values are: QcPassed, QcFailed, Discarded

DeliveryStatus: string

Possible values are: Undefined, DoNotDeliver, OnHold, ReadyForDelivery, DeliveryFailed, DeliveryInProgress, Delivered

Comment: string

Limited to 1024 characters

V2PostAppSessionsIdStopRequest: object

V2PostAppSessionsPropertiesRequest: object

Properties: object[]

V2PostBioSamplesBulkUpdateRequest: object

Ids: string[]

List the IDs of the biosamples to be updated

string
DefaultProjectId: string

Define the ID of the project to set as the default project

V2PostDatasetsIdRequest: object

DatasetTypeId: string
Attributes: object[]
object
key: string
value: object[]
object
key: string
value: SystemObject
QcStatus: string
QcStatusSummary: string
UploadStatus: string
UploadStatusSummary: string
Comment: string

V2PostLanesIdRequest: object

Status: string
Comment: string

V2PostLibraryPoolIdRequest: object

UserPoolId: string
Notes: string
Status: string

Possible values are: Active, Failed, Consumed, QCFailed

V2PostUserSettingsRequest: object

UserSettings: object[]

V2PrepRequest: object

Id: string
Href: string
Status: string
BioSample: V2BiologicalSampleCompact
LibraryPrep: LibraryPrepKitCompact
DateCreated: string (date-time)
DateModified: string (date-time)
RequiredYield: integer (int64)
RequiredYieldGb: number (double)
LIMSId: string
CreatedFromFileName: string

V2ProductUsage: object

ProductType: string
ProductName: string
Amount: number (double)

V2Property: object

UserModifiedBy: V1pre3UserCompact
ApplicationModifiedBy: V1pre3ApplicationCompact
DateModified: string (date-time)
Type: string
Href: string
Name: string
Description: string
Content: string
ContentMap: MapContent
Application: V1pre3ApplicationCompact
AppSession: V2AppSessionCompact
BioSample: V2BiologicalSampleCompact
Dataset: V2DatasetCompact
File: V1pre3FileCompact
SampleLibrary: V2LibraryCompact
LibraryPool: V1pre3LibraryPoolCompact
Project: V1pre3ProjectCompact
Run: V1pre3RunCompact
Subject: V2SubjectCompact
User: V1pre3UserCompact
ContentMapItems: object[]
ContentItems: string[]
string
ApplicationItems: object[]
AppSessionItems: object[]
BioSampleItems: object[]
DatasetItems: object[]
FileItems: object[]
SampleLibraryItems: object[]
LibraryPoolItems: object[]
ProjectItems: object[]
RunItems: object[]
SubjectItems: object[]
UserItems: object[]
HrefItems: string
ItemsDisplayedCount: integer (int32)
ItemsTotalCount: integer (int32)
AllowDuplicates: boolean

V2PropertyCompact: object

Type: string
Href: string
Name: string
Description: string
Content: string
ContentMap: MapContent
Application: V1pre3ApplicationCompact
AppSession: V2AppSessionCompact
BioSample: V2BiologicalSampleCompact
Dataset: V2DatasetCompact
File: V1pre3FileCompact
SampleLibrary: V2LibraryCompact
LibraryPool: V1pre3LibraryPoolCompact
Project: V1pre3ProjectCompact
Run: V1pre3RunCompact
Subject: V2SubjectCompact
User: V1pre3UserCompact
ContentMapItems: object[]
ContentItems: string[]
string
ApplicationItems: object[]
AppSessionItems: object[]
BioSampleItems: object[]
DatasetItems: object[]
FileItems: object[]
SampleLibraryItems: object[]
LibraryPoolItems: object[]
ProjectItems: object[]
RunItems: object[]
SubjectItems: object[]
UserItems: object[]
HrefItems: string
ItemsDisplayedCount: integer (int32)
ItemsTotalCount: integer (int32)
AllowDuplicates: boolean

V2PropertyCompactList: object

V2PropertyContainer: object

Items: object[]
DisplayedCount: integer (int32)
TotalCount: integer (int32)
Href: string

V2PropertyForPosts: object

Id: string
Type: string
Name: string
Description: string
Items: string[]
string
ContentMap: MapContent
ItemsMap: object[]
Content: string
Options: V1pre3PropertyOptionsRequest

V2PropertyItem: object

Id: string
Content: string
Application: V1pre3ApplicationCompact
AppSession: V2AppSessionCompact
BioSample: V2BiologicalSampleCompact
Dataset: V2DatasetCompact
File: V1pre3FileCompact
SampleLibrary: V2LibraryCompact
LibraryPool: V1pre3LibraryPoolCompact
Project: V1pre3ProjectCompact
Run: V1pre3RunCompact
Subject: V2SubjectCompact
User: V1pre3UserCompact
ContentMap: MapContent

V2PropertyItemList: object

V2QcThreshold: object

Name: string

Name of the metric

Operator: string

Valid operators: “Equal”, “LessThan”, “GreaterThan”, “LessThanOrEqual”, “GreaterThanOrEqual”, “NotEqual”, “Between”, “Outside”

DatasetTypeId: string

The dataset type slug, e.g. illumina.issac.v4

ThresholdValues: object[]

Integer values of the thresholds. A comma separated list can be given for the “Between” and “Outside” operators

Group: string

V2QcThresholdResponse: object

QcThresholds: object[]

V2RunLaneSummary: object

RunId: string
HrefBaseSpaceUI: string
ExperimentName: string
FlowcellBarcode: string
Workflow: string
DateModified: string (date-time)
RunStatus: string
UserOwnedBy: V1pre3UserCompact
LaneId: string
LaneNumber: integer (int32)
LaneStatus: string
LibraryName: string
FastQStatus: string

V2RunLaneSummaryList: object

V2RunLaneSummarySortFieldsV2Paging: object

DisplayedCount: integer (int32)
TotalCount: integer (int32)
Offset: integer (int32)
Limit: integer (int32)
SortDir: string , x ∈ { Asc , Desc }
SortBy: string , x ∈ { CreatedOn , ModifiedOn }

V2SubjectCompact: object

Id: string
Href: string
UserOwnedBy: V1pre3UserCompact
UserSubjectId: string
Description: string
Species: Species
Gender: string

V2UpdateBiologicalSampleRequest: object

BioSampleName: string

The name of the biosample, which must be unique and only contain alphanumeric, dash, or underscore letters

DefaultProjectId: string

Define the ID of the project to set as the default project

SubjectId: string
ContainerName: string

The name of the plate or tube containing the biosample, typically its barcode

ContainerPosition: string

The location of the biosample within a plate or other container, typically the well it is in

Status: string

Possible values are: New, Active, Done, QcFailed, Canceled

V2UserSetting: object

Id: string

Optional

Href: string

Reference link

Name: string

Name of the setting, must use alphanumeric, dash or underscore characters

Value: SystemObject
Type: string

Data type, possible values include: bool, string

V2UserSettingList: object

V2UserSettingsResponse: object

UserSettings: object[]

V2UserSettingsSortFieldsV2Paging: object

DisplayedCount: integer (int32)
TotalCount: integer (int32)
Offset: integer (int32)
Limit: integer (int32)
SortDir: string , x ∈ { Asc , Desc }
SortBy: string , x ∈ { Id , DateModified , Name }

V2UserSubscription: object

Name: string
Plan: string
ExpirationDate: string (date-time)
StartDate: string (date-time)
IsActive: boolean
Storage: SubscriptionStorage
Wallet: Wallet

V2Workgroup: object

Id: string
ExternalProviderId: string
Name: string
DomainName: string
IsCollaborative: boolean
Subscription: V2UserSubscription
DisplayName: string

V2WorkgroupList: object

Items: object[]
Paging: V2WorkgroupSortFieldsV2Paging

V2WorkgroupSortFieldsV2Paging: object

DisplayedCount: integer (int32)
TotalCount: integer (int32)
Offset: integer (int32)
Limit: integer (int32)
SortDir: string , x ∈ { Asc , Desc }
SortBy: string , x ∈ { Id , Name }

Wallet: object

ICreditBalance: integer (int64)
ICreditUsage: integer (int64)