POST samples instances_init_upload
curl --request POST \
--url https://app.onecodex.com/api/v1/samples/init_upload \
--header 'Content-Type: application/json' \
--header 'X-API-Key: <api-key>' \
--data '
{
"filename": "<string>",
"external_sample_id": "<string>",
"interleaved": true,
"metadata": {
"custom": {},
"date_collected": "2023-11-07T05:31:56Z",
"date_sequenced": "2023-11-07T05:31:56Z",
"description": "<string>",
"external_sample_id": "LIMS-2024-00123",
"location_lat": 0,
"location_lon": 0,
"location_string": "<string>",
"name": "<string>",
"starred": false
},
"paired_end_filename": "<string>",
"project": {
"__DOLLAR_REF__": "/api/v1/projects/a1b2c3d4e5f67890"
},
"sample_id": "<string>",
"size": 1,
"tags": [],
"upload_type": "standard"
}
'import requests
url = "https://app.onecodex.com/api/v1/samples/init_upload"
payload = {
"filename": "<string>",
"external_sample_id": "<string>",
"interleaved": True,
"metadata": {
"custom": {},
"date_collected": "2023-11-07T05:31:56Z",
"date_sequenced": "2023-11-07T05:31:56Z",
"description": "<string>",
"external_sample_id": "LIMS-2024-00123",
"location_lat": 0,
"location_lon": 0,
"location_string": "<string>",
"name": "<string>",
"starred": False
},
"paired_end_filename": "<string>",
"project": { "__DOLLAR_REF__": "/api/v1/projects/a1b2c3d4e5f67890" },
"sample_id": "<string>",
"size": 1,
"tags": [],
"upload_type": "standard"
}
headers = {
"X-API-Key": "<api-key>",
"Content-Type": "application/json"
}
response = requests.post(url, json=payload, headers=headers)
print(response.text)const options = {
method: 'POST',
headers: {'X-API-Key': '<api-key>', 'Content-Type': 'application/json'},
body: JSON.stringify({
filename: '<string>',
external_sample_id: '<string>',
interleaved: true,
metadata: {
custom: {},
date_collected: '2023-11-07T05:31:56Z',
date_sequenced: '2023-11-07T05:31:56Z',
description: '<string>',
external_sample_id: 'LIMS-2024-00123',
location_lat: 0,
location_lon: 0,
location_string: '<string>',
name: '<string>',
starred: false
},
paired_end_filename: '<string>',
project: {__DOLLAR_REF__: '/api/v1/projects/a1b2c3d4e5f67890'},
sample_id: '<string>',
size: 1,
tags: [],
upload_type: 'standard'
})
};
fetch('https://app.onecodex.com/api/v1/samples/init_upload', options)
.then(res => res.json())
.then(res => console.log(res))
.catch(err => console.error(err));<?php
$curl = curl_init();
curl_setopt_array($curl, [
CURLOPT_URL => "https://app.onecodex.com/api/v1/samples/init_upload",
CURLOPT_RETURNTRANSFER => true,
CURLOPT_ENCODING => "",
CURLOPT_MAXREDIRS => 10,
CURLOPT_TIMEOUT => 30,
CURLOPT_HTTP_VERSION => CURL_HTTP_VERSION_1_1,
CURLOPT_CUSTOMREQUEST => "POST",
CURLOPT_POSTFIELDS => json_encode([
'filename' => '<string>',
'external_sample_id' => '<string>',
'interleaved' => true,
'metadata' => [
'custom' => [
],
'date_collected' => '2023-11-07T05:31:56Z',
'date_sequenced' => '2023-11-07T05:31:56Z',
'description' => '<string>',
'external_sample_id' => 'LIMS-2024-00123',
'location_lat' => 0,
'location_lon' => 0,
'location_string' => '<string>',
'name' => '<string>',
'starred' => false
],
'paired_end_filename' => '<string>',
'project' => [
'__DOLLAR_REF__' => '/api/v1/projects/a1b2c3d4e5f67890'
],
'sample_id' => '<string>',
'size' => 1,
'tags' => [
],
'upload_type' => 'standard'
]),
CURLOPT_HTTPHEADER => [
"Content-Type: application/json",
"X-API-Key: <api-key>"
],
]);
$response = curl_exec($curl);
$err = curl_error($curl);
curl_close($curl);
if ($err) {
echo "cURL Error #:" . $err;
} else {
echo $response;
}package main
import (
"fmt"
"strings"
"net/http"
"io"
)
func main() {
url := "https://app.onecodex.com/api/v1/samples/init_upload"
payload := strings.NewReader("{\n \"filename\": \"<string>\",\n \"external_sample_id\": \"<string>\",\n \"interleaved\": true,\n \"metadata\": {\n \"custom\": {},\n \"date_collected\": \"2023-11-07T05:31:56Z\",\n \"date_sequenced\": \"2023-11-07T05:31:56Z\",\n \"description\": \"<string>\",\n \"external_sample_id\": \"LIMS-2024-00123\",\n \"location_lat\": 0,\n \"location_lon\": 0,\n \"location_string\": \"<string>\",\n \"name\": \"<string>\",\n \"starred\": false\n },\n \"paired_end_filename\": \"<string>\",\n \"project\": {\n \"__DOLLAR_REF__\": \"/api/v1/projects/a1b2c3d4e5f67890\"\n },\n \"sample_id\": \"<string>\",\n \"size\": 1,\n \"tags\": [],\n \"upload_type\": \"standard\"\n}")
req, _ := http.NewRequest("POST", url, payload)
req.Header.Add("X-API-Key", "<api-key>")
req.Header.Add("Content-Type", "application/json")
res, _ := http.DefaultClient.Do(req)
defer res.Body.Close()
body, _ := io.ReadAll(res.Body)
fmt.Println(string(body))
}HttpResponse<String> response = Unirest.post("https://app.onecodex.com/api/v1/samples/init_upload")
.header("X-API-Key", "<api-key>")
.header("Content-Type", "application/json")
.body("{\n \"filename\": \"<string>\",\n \"external_sample_id\": \"<string>\",\n \"interleaved\": true,\n \"metadata\": {\n \"custom\": {},\n \"date_collected\": \"2023-11-07T05:31:56Z\",\n \"date_sequenced\": \"2023-11-07T05:31:56Z\",\n \"description\": \"<string>\",\n \"external_sample_id\": \"LIMS-2024-00123\",\n \"location_lat\": 0,\n \"location_lon\": 0,\n \"location_string\": \"<string>\",\n \"name\": \"<string>\",\n \"starred\": false\n },\n \"paired_end_filename\": \"<string>\",\n \"project\": {\n \"__DOLLAR_REF__\": \"/api/v1/projects/a1b2c3d4e5f67890\"\n },\n \"sample_id\": \"<string>\",\n \"size\": 1,\n \"tags\": [],\n \"upload_type\": \"standard\"\n}")
.asString();require 'uri'
require 'net/http'
url = URI("https://app.onecodex.com/api/v1/samples/init_upload")
http = Net::HTTP.new(url.host, url.port)
http.use_ssl = true
request = Net::HTTP::Post.new(url)
request["X-API-Key"] = '<api-key>'
request["Content-Type"] = 'application/json'
request.body = "{\n \"filename\": \"<string>\",\n \"external_sample_id\": \"<string>\",\n \"interleaved\": true,\n \"metadata\": {\n \"custom\": {},\n \"date_collected\": \"2023-11-07T05:31:56Z\",\n \"date_sequenced\": \"2023-11-07T05:31:56Z\",\n \"description\": \"<string>\",\n \"external_sample_id\": \"LIMS-2024-00123\",\n \"location_lat\": 0,\n \"location_lon\": 0,\n \"location_string\": \"<string>\",\n \"name\": \"<string>\",\n \"starred\": false\n },\n \"paired_end_filename\": \"<string>\",\n \"project\": {\n \"__DOLLAR_REF__\": \"/api/v1/projects/a1b2c3d4e5f67890\"\n },\n \"sample_id\": \"<string>\",\n \"size\": 1,\n \"tags\": [],\n \"upload_type\": \"standard\"\n}"
response = http.request(request)
puts response.read_body{
"sample_id": "<string>",
"upload_url": "<string>",
"additional_fields": {},
"fallback_options": {},
"paired_end_additional_fields": {},
"paired_end_upload_url": "<string>"
}Uploading Samples
Starting an Upload
POST
/
api
/
v1
/
samples
/
init_upload
POST samples instances_init_upload
curl --request POST \
--url https://app.onecodex.com/api/v1/samples/init_upload \
--header 'Content-Type: application/json' \
--header 'X-API-Key: <api-key>' \
--data '
{
"filename": "<string>",
"external_sample_id": "<string>",
"interleaved": true,
"metadata": {
"custom": {},
"date_collected": "2023-11-07T05:31:56Z",
"date_sequenced": "2023-11-07T05:31:56Z",
"description": "<string>",
"external_sample_id": "LIMS-2024-00123",
"location_lat": 0,
"location_lon": 0,
"location_string": "<string>",
"name": "<string>",
"starred": false
},
"paired_end_filename": "<string>",
"project": {
"__DOLLAR_REF__": "/api/v1/projects/a1b2c3d4e5f67890"
},
"sample_id": "<string>",
"size": 1,
"tags": [],
"upload_type": "standard"
}
'import requests
url = "https://app.onecodex.com/api/v1/samples/init_upload"
payload = {
"filename": "<string>",
"external_sample_id": "<string>",
"interleaved": True,
"metadata": {
"custom": {},
"date_collected": "2023-11-07T05:31:56Z",
"date_sequenced": "2023-11-07T05:31:56Z",
"description": "<string>",
"external_sample_id": "LIMS-2024-00123",
"location_lat": 0,
"location_lon": 0,
"location_string": "<string>",
"name": "<string>",
"starred": False
},
"paired_end_filename": "<string>",
"project": { "__DOLLAR_REF__": "/api/v1/projects/a1b2c3d4e5f67890" },
"sample_id": "<string>",
"size": 1,
"tags": [],
"upload_type": "standard"
}
headers = {
"X-API-Key": "<api-key>",
"Content-Type": "application/json"
}
response = requests.post(url, json=payload, headers=headers)
print(response.text)const options = {
method: 'POST',
headers: {'X-API-Key': '<api-key>', 'Content-Type': 'application/json'},
body: JSON.stringify({
filename: '<string>',
external_sample_id: '<string>',
interleaved: true,
metadata: {
custom: {},
date_collected: '2023-11-07T05:31:56Z',
date_sequenced: '2023-11-07T05:31:56Z',
description: '<string>',
external_sample_id: 'LIMS-2024-00123',
location_lat: 0,
location_lon: 0,
location_string: '<string>',
name: '<string>',
starred: false
},
paired_end_filename: '<string>',
project: {__DOLLAR_REF__: '/api/v1/projects/a1b2c3d4e5f67890'},
sample_id: '<string>',
size: 1,
tags: [],
upload_type: 'standard'
})
};
fetch('https://app.onecodex.com/api/v1/samples/init_upload', options)
.then(res => res.json())
.then(res => console.log(res))
.catch(err => console.error(err));<?php
$curl = curl_init();
curl_setopt_array($curl, [
CURLOPT_URL => "https://app.onecodex.com/api/v1/samples/init_upload",
CURLOPT_RETURNTRANSFER => true,
CURLOPT_ENCODING => "",
CURLOPT_MAXREDIRS => 10,
CURLOPT_TIMEOUT => 30,
CURLOPT_HTTP_VERSION => CURL_HTTP_VERSION_1_1,
CURLOPT_CUSTOMREQUEST => "POST",
CURLOPT_POSTFIELDS => json_encode([
'filename' => '<string>',
'external_sample_id' => '<string>',
'interleaved' => true,
'metadata' => [
'custom' => [
],
'date_collected' => '2023-11-07T05:31:56Z',
'date_sequenced' => '2023-11-07T05:31:56Z',
'description' => '<string>',
'external_sample_id' => 'LIMS-2024-00123',
'location_lat' => 0,
'location_lon' => 0,
'location_string' => '<string>',
'name' => '<string>',
'starred' => false
],
'paired_end_filename' => '<string>',
'project' => [
'__DOLLAR_REF__' => '/api/v1/projects/a1b2c3d4e5f67890'
],
'sample_id' => '<string>',
'size' => 1,
'tags' => [
],
'upload_type' => 'standard'
]),
CURLOPT_HTTPHEADER => [
"Content-Type: application/json",
"X-API-Key: <api-key>"
],
]);
$response = curl_exec($curl);
$err = curl_error($curl);
curl_close($curl);
if ($err) {
echo "cURL Error #:" . $err;
} else {
echo $response;
}package main
import (
"fmt"
"strings"
"net/http"
"io"
)
func main() {
url := "https://app.onecodex.com/api/v1/samples/init_upload"
payload := strings.NewReader("{\n \"filename\": \"<string>\",\n \"external_sample_id\": \"<string>\",\n \"interleaved\": true,\n \"metadata\": {\n \"custom\": {},\n \"date_collected\": \"2023-11-07T05:31:56Z\",\n \"date_sequenced\": \"2023-11-07T05:31:56Z\",\n \"description\": \"<string>\",\n \"external_sample_id\": \"LIMS-2024-00123\",\n \"location_lat\": 0,\n \"location_lon\": 0,\n \"location_string\": \"<string>\",\n \"name\": \"<string>\",\n \"starred\": false\n },\n \"paired_end_filename\": \"<string>\",\n \"project\": {\n \"__DOLLAR_REF__\": \"/api/v1/projects/a1b2c3d4e5f67890\"\n },\n \"sample_id\": \"<string>\",\n \"size\": 1,\n \"tags\": [],\n \"upload_type\": \"standard\"\n}")
req, _ := http.NewRequest("POST", url, payload)
req.Header.Add("X-API-Key", "<api-key>")
req.Header.Add("Content-Type", "application/json")
res, _ := http.DefaultClient.Do(req)
defer res.Body.Close()
body, _ := io.ReadAll(res.Body)
fmt.Println(string(body))
}HttpResponse<String> response = Unirest.post("https://app.onecodex.com/api/v1/samples/init_upload")
.header("X-API-Key", "<api-key>")
.header("Content-Type", "application/json")
.body("{\n \"filename\": \"<string>\",\n \"external_sample_id\": \"<string>\",\n \"interleaved\": true,\n \"metadata\": {\n \"custom\": {},\n \"date_collected\": \"2023-11-07T05:31:56Z\",\n \"date_sequenced\": \"2023-11-07T05:31:56Z\",\n \"description\": \"<string>\",\n \"external_sample_id\": \"LIMS-2024-00123\",\n \"location_lat\": 0,\n \"location_lon\": 0,\n \"location_string\": \"<string>\",\n \"name\": \"<string>\",\n \"starred\": false\n },\n \"paired_end_filename\": \"<string>\",\n \"project\": {\n \"__DOLLAR_REF__\": \"/api/v1/projects/a1b2c3d4e5f67890\"\n },\n \"sample_id\": \"<string>\",\n \"size\": 1,\n \"tags\": [],\n \"upload_type\": \"standard\"\n}")
.asString();require 'uri'
require 'net/http'
url = URI("https://app.onecodex.com/api/v1/samples/init_upload")
http = Net::HTTP.new(url.host, url.port)
http.use_ssl = true
request = Net::HTTP::Post.new(url)
request["X-API-Key"] = '<api-key>'
request["Content-Type"] = 'application/json'
request.body = "{\n \"filename\": \"<string>\",\n \"external_sample_id\": \"<string>\",\n \"interleaved\": true,\n \"metadata\": {\n \"custom\": {},\n \"date_collected\": \"2023-11-07T05:31:56Z\",\n \"date_sequenced\": \"2023-11-07T05:31:56Z\",\n \"description\": \"<string>\",\n \"external_sample_id\": \"LIMS-2024-00123\",\n \"location_lat\": 0,\n \"location_lon\": 0,\n \"location_string\": \"<string>\",\n \"name\": \"<string>\",\n \"starred\": false\n },\n \"paired_end_filename\": \"<string>\",\n \"project\": {\n \"__DOLLAR_REF__\": \"/api/v1/projects/a1b2c3d4e5f67890\"\n },\n \"sample_id\": \"<string>\",\n \"size\": 1,\n \"tags\": [],\n \"upload_type\": \"standard\"\n}"
response = http.request(request)
puts response.read_body{
"sample_id": "<string>",
"upload_url": "<string>",
"additional_fields": {},
"fallback_options": {},
"paired_end_additional_fields": {},
"paired_end_upload_url": "<string>"
}Start an upload by
POSTing the filename and size to /samples/init_upload. To actually perform the upload it is then necessary to transmit the file to the provided upload_url, with any additional_fields as needed. This second step varies depending on the upload_type. Currently only a standard upload type is available.
Performing the actual upload – “standard” upload type
The standard upload involves POSTing a sample up to 20GB in size to a provided HTTPS URL. TheContent-Type should be multipart/form-data and the additional_fields should be included in the POST body.
The workflow using httpie or Python requests is:
# Start the upload
http --auth $ONE_CODEX_API_KEY: POST \
https://app.onecodex.com/api/v1/samples/init_upload \
filename=HiSeq_accuracy.fa size:=1189333
# Returns a 200 response with the following JSON body:
# {
# "additional_fields": {
# "AWSAccessKeyId": "XXXXXXXXXXXXXXXXXXXX",
# "acl": "private",
# "key": "user_xxxxxxxxxxxxxxxx/file_yyyyyyyyyyyyyyyy/${filename}",
# "policy": "CiAgICAgICAgICAgAgICAgICB7ImJ1Y2tldCI6ICJyZWZnZW5vbWljcy11c2VyZGF0YS1kZXYtZW5jcnlwdGVkIiB9LAogICAS1lbmNyeXB0aW9uIjogIkFFUzI1NiJ9LAogICAgICAgICAgICAgICAgWyJzdGFydHMtd2l0aCIsICIka2V5IiwgInVzZXJfNGFkYTU2MTAzZDlhNDhiOC9maWxlXzI4NDU5NTA4NTkyYTQ4MWMvIl0sCiAgICAgICAgICAgICAgICB7InN1Y2Nlc3NfYWN0aW9uX3N0YXR1cyI6ICIyMDEifSwKICAgICAgICAgICAgICBdCiAgICAgICAgICAgIH0KICAgICAgICAgICAg",
# "signature": "ELADfQLgxXXXXXXXXx/5D99Q9AY=",
# "success_action_status": 201,
# "x-amz-server-side-encryption": "AES256"
# },
# "sample_id": "28459508592a481c",
# "upload_url": "https://refgenomics-userdata-dev-encrypted.s3.amazonaws.com"
# }
http -f POST \
https://sample-upload-bucket.s3.amazonaws.com \
AWSAccessKeyId="XXXXXXXXXXXXXXXXXXXX" acl="private" \
key="user_xxxxxxxxxxxxxxxx/file_yyyyyyyyyyyyyyyy/${filename}" \
policy="CiAgICAgICAgICAgAgICAgICB7ImJ1Y2tldCI6ICJyZWZnZW5vbWljcy11c2VyZGF0YS1kZXYtZW5jcnlwdGVkIiB9LAogICAS1lbmNyeXB0aW9uIjogIkFFUzI1NiJ9LAogICAgICAgICAgICAgICAgWyJzdGFydHMtd2l0aCIsICIka2V5IiwgInVzZXJfNGFkYTU2MTAzZDlhNDhiOC9maWxlXzI4NDU5NTA4NTkyYTQ4MWMvIl0sCiAgICAgICAgICAgICAgICB7InN1Y2Nlc3NfYWN0aW9uX3N0YXR1cyI6ICIyMDEifSwKICAgICAgICAgICAgICBdCiAgICAgICAgICAgIH0KICAgICAgICAgICAg" \
signature="ELADfQLgxXXXXXXXXx/5D99Q9AY=" success_action_status=201 \
x-amz-server-side-encryption="AES256" \
file@HiSeq_accuracy.fa
# Returns a 201 response
# Confirm the upload (see below)
http --auth $ONE_CODEX_API_KEY: POST \
https://app.onecodex.com/api/v1/samples/confirm_upload \
sample_id="28459508592a481c"
# Start the upload
resp = requests.post('https://app.onecodex.com/api/v1/init_upload',
json={'filename': 'HiSeq_accuracy.fa',
'size': os.path.getsize('HiSeq_accuracy.fa')},
auth=(os.getenv('ONE_CODEX_API_KEY'), '')
).json()
# Perform the upload (should return a 201)
requests.post(resp['upload_url'], data=resp['additional_fields'],
files={'file': open('HiSeq_accuracy.fa')})
# Finally, confirm the upload (should return a 200)
requests.post('https://app.onecodex.com/api/v1/samples/confirm_upload',
json={'sample_id': resp['sample_id']},
auth=(os.getenv('ONE_CODEX_API_KEY'), ''))
Authorizations
Body
application/json
The filename of the sample to be uploaded. FASTA and FASTQ records, optionally gzipped (and ending in .gz or .gzip) are supported. Filenames should only contain alphanumeric characters, dashes, underscores, and periods.
Pattern:
^[\w\.]+[\w\-\.\[\]\(\)\{\} ]*\.[\w\.]+$An optional external sample ID (see the Metadata resource) to match against pre-uploaded samples. Returns a 400 if no matching sample is found.
Whether the file is interleaved (true) or not (false).
An optional metadata object to be added to the sample.
Show child attributes
Show child attributes
Optional filename for paired end uploads.
Pattern:
^[\w\.]+[\w\-\.\[\]\(\)\{\} ]*\.[\w\.]+$An optional project into which to upload the sample.
Show child attributes
Show child attributes
An optional sample ID to match against pre-uploaded samples. Returns a 400 if no matching sample is found.
The size of the file in bytes.
Required range:
x >= 0An array of tags to be added to the sample.
Show child attributes
Show child attributes
The type of upload to initiate. Currently only standard uploads are supported via the init_upload route.
Allowed value:
"standard"Response
200 - application/json
OK
The sample ID. Use to confirm the upload.
Object storage location to POST the file to.
Additional fields to include in the object storage POST request.
Fallback options for the upload. Please contact support for help as needed.
Additional fields to include in the object storage POST request for the paired end file (optional).
Object storage location to POST the paired end file to (optional).
⌘I