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'), ''))
Body
application/json
Response
200 - application/json
OK
⌘I