Pre-Uploading Samples

POST

api

samples

preupload

{
  "sample_id": "<string>"
}

For situations where you’d like to create Samples on the One Codex Platform, but your NGS data is not yet available, we support a “pre-upload” workflow. Simply POST to the /preupload route to receive a unique sample ID. That sample ID may be then passed when uploading your data (see Starting an Upload) to upload data for the pre-uploaded sample instead of creating a new sample.

Samples created via the /preupload route will have a visibility property with a value awaiting data. These samples and their metadata will be private, though they may be shared with other accounts if associated with a project at creation time (see Sharing & Projects for more details on sharing data via projects).

Body

application/json

metadata

object

A metadata object.

metadata.custom

object

Arbitrary metadata is supported as part of a custom object. custom has two constraints: (1) it must have a depth of one (i.e., no nested records); and (2) only strings, numbers, boolean, and null values are supported as values. Example: {"lab_tech": "Linus Pauling", "amplicon_scheme": "V3-V4"}

metadata.date_collected

string | null

Timestamp for when the sample was collected.

metadata.date_sequenced

string | null

Timestamp for when the sample was sequenced.

metadata.description

string | null

metadata.external_sample_id

string | null

An arbitrary external sample ID, e.g., an ID in a LIMS. Up to 60 characters.

Maximum length: 60

metadata.library_type

enum<string> | null

An enum with the sample library type.

Available options:

WGS,

Targeted/16S,

Other

metadata.location_lat

number | null

The latitude (-90.0-90.0) of the sample location. By convention, we recommend using this for the location in which the physical specimen was collected.

Required range: -90 <= x <= 90

metadata.location_lon

number | null

The longitude (-180.0-180.0) of the sample location.

Required range: -180 <= x <= 180

metadata.location_string

string | null

Maximum length: 255

metadata.name

string | null

Maximum length: 255

metadata.platform

enum<string> | null

A enum with the name of the sequencing platform.

Available options:

454 sequencing,

454 GS FLX,

454 GS FLX Titanium,

Illumina,

Illumina Genome Analyzer II,

Illumina HiSeq,

Illumina HiSeq 1500,

Illumina HiSeq 2000,

Illumina HiSeq 2500,

Illumina HiSeq 3000,

Illumina HiSeq 4000,

Illumina HiSeq X,

Illumina iSeq 100,

Illumina MiniSeq,

Illumina MiSeq,

Illumina NextSeq,

Illumina NextSeq 500,

Illumina NextSeq 550,

Illumina NovaSeq,

Illumina NovaSeq 5000,

Illumina NovaSeq 6000,

BGISEQ,

BGISEQ 50,

Element,

Element AVITI,

Ion,

Ion S5,

Ion S5 XL,

Ion PGM,

Ion Proton,

Ion Torrent,

Oxford Nanopore,

Oxford Nanopore GridION X5,

Oxford Nanopore MinION,

Oxford Nanopore PromethION,

PacBio,

PacBio RS II,

PacBio Sequel,

PacBio Sequel II System,

PacBio Revio,

PacBio Onso,

SOLiD,

Solexa Genome Analyzer,

Sanger,

Other

metadata.sample_type

enum<string> | null

An enum with the sample type.

Available options:

Isolate,

Metagenomic,

Other

metadata.starred

boolean

default:false

Whether the sample has been starred by the user within the One Codex web application.

project

object

An optional project.

Response

200 - application/json

Successful operation

sample_id

string

Confirming an Upload Updating Samples

{
  "sample_id": "<string>"
}

API Basics

Samples

Metadata & Tags

Analyses

Jobs

Documents

Webhooks & Events

Sequencing

Body

Response