About SynBioHub

What is SynBioHub?

SynBioHub includes two projects:

An open source software project providing a web interface for the storing and publishing of synthetic biology designs.
A public instance of the aforementioned software project at synbiohub.org, allowing users to upload and share designs.

What can SynBioHub be used for?

SynBioHub can be used to publish a library of synthetic parts and designs as a service, to share designs with collaborators, and to store designs of biological systems locally. Data in SynBioHub can be accessed via the HTTP API, Java API, or Python API where it can then be integrated into CAD tools for building genetic designs. SynBioHub contains an interface for users to upload new biological data to the database, to visualize DNA parts, to perform queries to access desired parts, and to download SBOL, GenBank, FASTA, etc.

Publications

McLaughlin, James Alastair, et al. "SynBioHub: a standards-enabled design repository for synthetic biology." ACS synthetic biology 7.2 (2018): 682-688.
Mante, Jeanet, Zach Zundel, and Chris J. Myers. "Extending SynBioHub's Functionality with Plugins." ACS Synthetic Biology (2020).
Zhang, Michael, Zach Zundel, and Chris J. Myers. "SBOLExplorer: Data Infrastructure and Data Mining for Genetic Design Repositories." ACS synthetic biology 8.10 (2019): 2287-2294.

Contributors

Dr. James Alastair McLaughlin (Newcastle University)
Prof. Chris J. Myers (University of Utah)
Dr. Goksel Misirli (Newcastle University)
Prof. Anil Wipat (Newcastle University)
Zach Zundel (University of Utah)
James Scholz (University of Utah)

An earlier version of SynBioHub known as SBOL Stack was developed by the following people:

Dr. Curtis Madsen (Boston University)
Dr. James Alastair McLaughlin (Newcastle University)
Dr. Goksel Misirli (Newcastle University)
Dr. Matthew Pocock (Turing Ate My Hamster Ltd.)
Dr. Keith Flanagan (Newcastle University)
Dr. Jennifer Hallinan (Macquarie University)
Prof. Anil Wipat (Newcastle University)

Web Design

Antarctic Design

Installation

From Prebuilt Image

Install Docker

First, install Docker and Docker Compose.

Ensure that the Docker daemon is running on your system before continuing. On Mac and Windows, a small whale icon in the system tray indicates Docker is running.

On Ubuntu, start docker using:

systemctl start docker

Starting a SynBioHub Instance

First, pull the docker-compose configuration::

git clone https://github.com/synbiohub/synbiohub-docker

Then, start SynBioHub with:

docker-compose --file ./synbiohub-docker/docker-compose.yml up

If you would like to start SynBioHub with SBOLExplorer use the following commands instead:

sysctl -w vm.max_map_count=262144

docker-compose --file ./synbiohub-docker/docker-compose.yml --file ./synbiohub-docker/docker-compose.explorer.yml up

Configuring

In a web browser, visit

http://localhost:7777/

On the first startup, you will be taken to the SynBioHub Setup Page, which enables basic setup of the site. After the first setup, the Admin Portal will allow admin users to update their site configuration.

SendGrid email setup

In order to enable SynBioHub to send account-related emails, you need a SendGrid account and API key. Once you have created your account, you should click "Settings" in the left bar, then "API Keys". On the resulting page, click the "Create API Key" button in the upper-right corner, and give your new API key a name. You should see the key on the next page. Copy the key and paste it into the "SendGrid API Key" in the Mail page on the SynBioHub admin dashboard. Save the API key in SynBioHub and you are ready to begin sending email.

Updating

To update a container, pull the new version and start it.

cd synbiohub-docker

git pull

cd ..

## if you are not running SBOL Explorer

docker-compose --file synbiohub-docker/docker-compose.yml pull synbiohub

docker-compose --file synbiohub-docker/docker-compose.yml up

## If you are running SBOL Explorer:

docker-compose --file synbiohub-docker/docker-compose.yml --file synbiohub-docker/docker-compose.explorer.yml pull synbiohub

docker-compose --file synbiohub-docker/docker-compose.yml --file synbiohub-docker/docker-compose.explorer.yml up

PERSISTENT LOGS UPDATE

If you are updating from a version earlier than 1.5.2, then you must execute the following command to setup persistent log files:

docker exec -it synbiohub-docker_synbiohub_1 mkdir /mnt/data/logs

If you are updating from a version of SynBioHub earlier than 1.3.0 to 1.3.0 or later, you must execute the following steps to persist your data between instances!

docker exec synbiohub cp /opt/synbiohub/synbiohub.sqlite /mnt/data/synbiohub.sqlite

docker exec synbiohub cp -R /opt/synbiohub/uploads /mnt/data/uploads

docker exec synbiohub chown synbiohub /mnt/data/synbiohub.sqlite

docker exec synbiohub chgrp synbiohub /mnt/data/synbiohub.sqlite

docker exec synbiohub chown -R synbiohub /mnt/data/uploads

docker exec synbiohub chgrp -R synbiohub /mnt/data/uploads

To update to the latest version of SynBioHub, first stop and remove the container:

docker stop synbiohub

docker rm synbiohub

Then pull the latest version:

docker pull synbiohub/synbiohub:1.3.0

Finally, run a new container with the latest image:

docker run -v synbiohub:/mnt -p 7777:7777 --name synbiohub -d synbiohub/synbiohub:1.3.0

From Source

Follow the instructions on the GitHub README to install SynBioHub locally on your system. If you would like SynBioHub to run as a service, you can enable Virtuoso using systemd or open a virtual terminal using tmux or GNU screen and run

sudo /usr/local/bin/virtuoso-t +configfile $YOUR_CONFIG_FILE

You should also run SynBioHub as a system service or using a virtual terminal and the command

npm start

If you are doing development work, you can start SynBioHub with the command

npm run-script dev

which will restart the application with any change to the JavaScript source.

NGINX configuration

Instructions for managing nginx server blocks can be found here.

The server block for a SynBioHub installation listening on port 7777 is to the right

client_max_body_size 800m;
proxy_connect_timeout 6000;
proxy_send_timeout 6000;
proxy_read_timeout 6000;
send_timeout 6000;
server {
        listen 80;
        server_name _;

        location / {
                proxy_set_header X-Real-IP  $remote_addr;
                proxy_set_header X-Forwarded-Server $host;
                proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
                proxy_set_header Host $host;
                proxy_pass http://127.0.0.1:7777$request_uri;
        }
}

This is most useful when you would like to host SynBioHub on a subdomain alongside other content (using nginx as an HTTP proxy) or using HTTPS.

User Endpoints

Endpoints that control user related functions

POST <SynBioHub URL>/login

This POST request requires email (or username)/password and returns a user token that should be passed in the X-authorization header to view private objects and submit new objects, etc.

curl -X POST -H "Accept: text/plain" -d "email=<email>&password=<password>" <SynBioHub URL>/login

import requests

response = requests.post(
    '<SynBioHub URL>/login',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'email': '<email>',
        'password' : '<password>',
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
var url ='<SynBioHub URL>/login';
var headers = {
    "Accept": "text/plain",
}

const params = new URLSearchParams();
params.append('email', '<email>');
params.append('password', '<password>');

fetch(url, { method: 'POST', headers: headers, body: params})
    .then(res => res.text())
    .then(body => console.log(body));

Parameter	Description
email	The e-mail address (or username) of the user to login with.
password	The password of the user.

Logout

POST <SynBioHub URL>/logout

This post request logs out the user specified in the X-authorization header.

curl -X POST -H "Accept: text/plain" -H "X-authorization: <token>" <SynBioHub URL>/logout

import requests

response = requests.post(
    '<SynBioHub URL>/logout',
    headers={
    'X-authorization': '<token>',
    'Accept': 'text/plain'
    }
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/logout'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Register

POST <SynBioHub URL>/register

curl -X POST -H "Accept: text/plain" -d "username=<username>&name=<name>&affiliation=<affiliation>&email=<email>&password1=<password1>&password2=<password2>" <SynBioHub URL>/register

import requests
response = requests.post(
    '<SynBioHub URL>/register',
    headers={
        'Accept': 'text/plain'
    },
    data={
        'username': '<username>',
        'name' : '<name>',
        'affiliation' : '<affiliation>',
        'email' : '<email>',
        'password1' : '<password1>',
        'password2' : '<password2>'
        },
)
print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/register'
var headers={
    "Accept" : "text/plain; charset=UTF-8"
};

const params = new URLSearchParams();
params.append('username', '<username>');
params.append('name', '<name>');
params.append('affiliation', '<affiliation>');
params.append('email', '<email>');
params.append('password1', '<password1>');
params.append('password2', '<password2>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
username	Username of the user
name	Name of the user
affiliation	Affiliation of the user
email	Email address of the user
password1	Password of the user
password2	Password confirmation

Request Reset Password Token

POST <SynBioHub URL>/resetPassword

Request a reset password token.

curl -X POST -H "Accept: text/plain" -d "email=<email>" <SynBioHub URL>/resetPassword

import requests
response = requests.post(
    '<SynBioHub URL>/resetpassword',
    headers={
        'Accept': 'text/plain'
    },
    data={
        'email': '<email>'
        },
)
print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/resetPassword'
var headers={
    "Accept" : "text/plain; charset=UTF-8"
};

const params = new URLSearchParams();
params.append('email', '<email>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
email	Email address of the user to send password reset link

Set New Password

POST <SynBioHub URL>/setNewPassword

Resets the user's password with the provided token and two copies of the new password.

curl -X POST -H "Accept: text/plain" -d "token=<token>&password1=<password1>&password2=<password2>" <SynBioHub URL>/setNewPassword

import requests
response = requests.post(
    '<SynBioHub URL>/setNewPassword',
    headers={
        'Accept': 'text/plain'
    },
    data={
        'token': '<token>',
        'password1': '<password1>',
        'password2': '<password2>'
        },
)
print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/setNewPassword'
var headers={
    "Accept" : "text/plain; charset=UTF-8"
};

const params = new URLSearchParams();
params.append('token', '<token>');
params.append('password1', '<password1>');
params.append('password2', '<password2>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
token	Token received by email to reset a password
password1	New password
password2	Confirm new password

View Profile

GET <SynBioHub URL>/profile

View the user's profile.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <SynBioHub URL>/profile

This endpoint returns JSON metadata of the form 

{
    "id":1,
    "name":"Test User",
    "username":"testuser",
    "email":"test@user.synbiohub",
    "affiliation":"jimmy",
    "password":"",
    "graphUri":"http://localhost:7777/usertestuser",\
    "isAdmin":true,\
    "resetPasswordLink":"",\
    "isCurator":true,\
    "isMember":true,
    "createdAt":"2020-05-19T14:44:44.204Z",
    "updatedAt":"2020-05-20T21:11:21.934Z","user_external_profiles":[]
}

import requests

response = requests.get(
    '<SynBioHub URL>/profile',
    headers={
    'X-authorization': '<token>',
    'Accept': 'text/plain'
    }
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const url = '<SynBioHub URL>/profile'   
const headers={
        "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};
fetch(url, { method: 'GET', headers: headers})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Note that the X-authorization header is required for this endpoint.

Update Profile

POST <SynBioHub URL>/profile

Update the user's profile.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "name=<name>&affiliation=<affiliation>&email=<email>&password1=<password1>&password2=<password2>" <SynBioHub URL>/profile

import requests
response = requests.post(
    '<SynBioHub URL>/profile',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'name': '<name>',
        'affiliation' : '<affiliation>',
        'email' : '<email>',
        'password1' : '<password1>',
        'password2' : '<password2>',

        },
)
print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/profile'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('name', '<name>');
params.append('affiliation', '<affiliation>');
params.append('email', '<email>');
params.append('password1', '<password1>');
params.append('password2', '<password2>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
name	Name of the user
affiliation	Affiliation of the user
email	Email address of the user
password1	Password of the user
password2	Password confirmation

Note that the X-authorization header is required for this endpoint.

Search Endpoints

The following endpoints are used to search within SynBioHub.

Search Metadata

GET <SynBioHub URL>/search/<key>=<value>&...&<search string>/?offset=#&limit=#

const fetch = require("node-fetch");
const Url = '<SynBioHub URL>/search/<key>=<value>&...&<search string>/?offset=#&limit=#'
const otherPram={
    headers:{
        "content-type" : "text/plain; charset=UTF-8"
    },
    method:"GET"
};
fetch(Url,otherPram)
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

import requests

response = requests.get(
    '<SynBioHub URL>/search/<key>=<value>&...&<search string>/?offset=#&limit=#',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" '<SynBioHub URL>/search/<key>=<value>&...&<search string>/?offset=#&limit=#

This endpoint returns JSON metadata of the form 
[
    {
        "uri":"<SynBioHub URL>/public/igem/BBa_K1404008/1",
        "name":"BBa_K1404008",
        "description":"p70-CsgA-His*2, double His-tagged curli generator",
        "displayId":"BBa_K1404008",
        "version":"1"
    },

    ...
]

Returns the metadata for the object from the specified search query. The search query is composed of a series of key value pairs as described below:

Key/value pair	Description
objectType=value	The type of object to search for ( objectType=ComponentDefinition)
sbolTag=value	A tag in the SBOL namespace to search for ( role=<http://identifiers.org/so/SO:0000316>)
collection=value	Matches objects that are members of the specified collection (collection=<http://synbiohub.org/public/igem/igem_collection>)
dcterms:tag=value	A tag in the dcterms namespace to search for ( dcterms:title='pLac'&) - note this requires an exact match
namespace/tag=value	A full namespace with tag separated by appropriate delimiter ( <http://sbols.org/v2#role>=<http://identifiers.org/so/SO:0000316>)

After the key/value pairs, an optional search string can be provided that will be used to search for partial matches in the displayId, name, or description fields.

Finally, the URL can end with an offset (where you want to start) and limit parameter (how many results you want to get).

Count Search Results

GET <SynBioHub URL>/searchCount/<key>=<value>&...&<search string>/

Returns the number of items matching the search result.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" '<SynBioHub URL>/searchCount/<key>=<value>&...&<search string>/'

import requests

response = requests.get(
    '<SynBioHub URL>/searchCount/<key>=<value>&...&<search string>/',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const Url = '<SynBioHub URL>/searchCount/<key>=<value>&...&<search string>/'
const otherPram={
    headers:{
        "content-type" : "text/plain; charset=UTF-8"
    },
    method:"GET"
};
fetch(Url,otherPram)
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Key/value pair	Description
objectType=value	The type of object to search for ( objectType=ComponentDefinition)
sbolTag=value	A tag in the SBOL namespace to search for ( role=http://identifiers.org/so/SO:0000316)
collection=value	Matches objects that are members of the specified collection (collection=http://synbiohub.org/public/igem/igem_collection)
dcterms:tag=value	A tag in the dcterms namespace to search for ( dcterms:title='pLac'&) - note this requires an exact match
namespace/tag=value	A full namespace with tag separated by appropriate delimiter ( http://sbols.org/v2#role=http://identifiers.org/so/SO:0000316)

After the key/value pairs, an optional search string can be provided that will be used to search for partial matches in the displayId, name, or description fields.

Search Root Collections

GET <SynBioHub URL>/rootCollections

Returns all root collections.


curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <SynBioHub URL>/rootCollections

This endpoint returns JSON metadata of the form:

[
    ...,
    {
    "uri":"<SynBioHub URL>/public/igem/igem_collection/1",
    "name":"iGEM Parts Registry",
    "description":"The iGEM Registry is a growing collection of genetic parts that can be mixed and matched to build synthetic biology devices and systems.  As part of the synthetic biology community's efforts to make biology easier to engineer, it provides a source of genetic parts to iGEM teams and academic labs.",
    "displayId":"igem_collection",
    "version":"1"
    },
    ...
]

import requests

response = requests.get(
    '<SynBioHub URL>/rootCollections',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const Url = '<SynBioHub URL>/rootCollections'
const otherPram={
    headers:{
        "content-type" : "text/plain; charset=UTF-8"
    },
    method:"GET"
};
fetch(Url,otherPram)
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Search Submissions

GET <SynBioHub URL>/manage

Returns the meta data on all submissions for the user specified by the X-authorization token.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <SynBioHub URL>/manage

This endpoint returns JSON metadata of the form:

[...
    {
    "displayId":"bruh_collection",
    "version":"1",
    "name":"bruh",
    "description":"testbruh",
    "type":"http://sbols.org/v2#Collection",
    "uri":"http://localhost:7777/user/testuser/bruh/bruh_collection/1",
    "typeName":"Collection",
    "url":"/user/testuser/bruh/bruh_collection/1",
    "triplestore":"private",
    "prefix":""
    }
...]

import requests

response = requests.get(
    '<SynBioHub URL>/manage',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const url = '<SynBioHub URL>/manage'
const headers={
        "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};
fetch(url, { method: 'GET', headers: headers})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Search Shared Objects

GET <SynBioHub URL>/shared

Returns the meta data on objects that other users have shared with the user specified by the X-authorization token.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <SynBioHub URL>/shared

This endpoint returns JSON metadata of the form:

[...
    {
    "displayId":"bruh_collection",
    "version":"1",
    "name":"bruh",
    "description":"testbruh",
    "type":"http://sbols.org/v2#Collection",
    "uri":"http://localhost:7777/user/testuser/bruh/bruh_collection/1",
    "typeName":"Collection",
    "url":"/user/testuser/bruh/bruh_collection/1",
    "triplestore":"private",
    "prefix":""
    }
...]

import requests

response = requests.get(
    '<SynBioHub URL>/shared',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const url = '<SynBioHub URL>/shared'
const headers={
        "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};
fetch(url, { method: 'GET', headers: headers})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Search Sub-Collections

GET <URI>/subCollections

Returns the collections that are members of another collection.

import requests

response = requests.get(
    '<URI>/subcollections',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <URI>/subcollections

This endpoint returns JSON metadata of the form:
[
    {
        "uri":"<SynBioHub URL>/public/bsu/SpaRK_collection/1",
        "name":"SpaRK","description":"SpaRK",
        "displayId":"SpaRK_collection",
        "version":"1"
    }

]

const fetch = require("node-fetch");
const Url = '<URI>/subcollections'
const otherPram={
    headers:{
        "content-type" : "text/plain; charset=UTF-8"
    },
    method:"GET"
};
fetch(Url,otherPram)
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Search Twins

GET <URI>/twins

Returns other components that have the same sequence.

import requests

response = requests.get(
    '<URI>/twins',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <URI>/twins

const fetch = require("node-fetch");
const Url = '<URI>/twins'
const otherPram={
    headers:{
        "content-type" : "text/plain; charset=UTF-8"
    },
    method:"GET"
};
fetch(Url,otherPram)
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Search Similar

GET <URI>/similar

Returns other components that have similar sequences.

Note that this endpoint only works if SBOLExplorer is activated.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <URI>/similar

import requests

response = requests.get(
    '<URI>/similar',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const Url = '<URI>/similar'
const otherPram={
    headers:{
        "content-type" : "text/plain; charset=UTF-8"
    },
    method:"GET"
};
fetch(Url,otherPram)
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Search Uses

GET <URI>/uses

Returns any other object that refers to this object, for example, if this is a component, it will return all other components that use this as a sub-component.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <URI>/uses

This endpoint returns JSON metadata of the form:

[
    {
        "type":"http://sbols.org/v2#Collection",
        "uri":"<SynBioHub URL>/public/bsu/bsu_collection/1",
        "name":"Bacillus subtilis Collection",
        "description":"This collection includes information about promoters, operators, CDSs and proteins from Bacillus subtilis. Functional interactions such as transcriptional activation and repression, protein production and various protein-protein interactions are also included.",
        "displayId":"bsu_collection",
        "version":"1"
    }
]

import requests

response = requests.get(
    '<URI>/uses',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const Url = '<SynBioHub URL>/public/bsu/BO_5629/1/uses'
const otherPram={
    headers:{
        "content-type" : "text/plain; charset=UTF-8"
    },
    method:"GET"
};
fetch(Url,otherPram)
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Count Objects by Type

GET <SynBioHub URL>/<ObjectType>/count

Returns the number of objects with a specified object type.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <SynBioHub URL>/<ObjectType>/Count

import requests

response = requests.get(
    '<SynBioHub URL>/<ObjectType>/Count',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const Url = '<SynBioHub URL>/<ObjectType>/Count'
const otherPram={
    headers:{
        "content-type" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
    },
    method:"GET"
};
fetch(Url,otherPram)
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Note that you can replace <ObjectType> with any SBOL object type, such as ComponentDefinition, SequenceAnnotation, etc. See here for more object types

SPARQL Query

GET <SynBioHub URL>/sparql?query=<SPARQL query>

Returns the results of the SPARQL query in JSON format.

curl -X GET -H "Accept: application/json" <SynBioHub URL>/sparql?query=<SPARQL query>

This endpoint returns JSON metadata of the form:

[...
    { 
        "s": { "type": "uri", "value": "<SynBioHub URL>/public/igem/BBa_K1732001/annotation2443059/range2443059/1" }    , 
        "p": { "type": "uri", "value": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" }  , 
        "o": { "type": "uri", "value": "http://sbols.org/v2#Range" }
    }
...]

import requests

response = requests.get(
    '<SynBioHub URL>/sparql?query=<SPARQL query>',
    headers={
        'Accept': 'application/json',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const Url = '<SynBioHub URL>/sparql?query=<SPARQL query>'
const otherPram={
    headers:{
        "content-type" : "application/json; charset=UTF-8"
    },
    method:"GET"
};
fetch(Url,otherPram)
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Sequence Search

GET <SynBioHub URL>/search/<key>=<value>&...

Returns the result of a sequence search in JSON format. The first key/value pair must be the sequence. Various options that can be adjusted are described below:

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" '<SynBioHub URL>/search/<key>=<value>&...'

import requests

response = requests.get(
    '<SynBioHub URL>/search/<key>=<value>&',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const Url = '<SynBioHub URL>/search/<key>=<value>&...'
const otherPram={
    headers:{
        "content-type" : "text/plain; charset=UTF-8"
    },
    method:"GET"
};
fetch(Url,otherPram)
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Key/value pair	Description
globalsequence=value	Sequence to globally search. Must be the first key/value pair. Corresponds to the --usearch_global option in VSEARCH. (globalsequence=cctagatcgctag)
sequence=value	Search only for exact matches of the sequence. Must be the first key/value pair.Corresponds to the --search_exact option in VSEARCH. (sequence=cctagatcgctag)
file_search=value	Specify a file path for sequence searching. Must be URL encoded, and must be the first key/value pair. Default search method is global. (file_search=%2Fpath%2Fto%2Ffile)
maxaccepts=value	Maximum number of hits to accept before stopping the search. Note that the higher the value, the longer the runtime. Corresponds to the --maxaccepts flag in VSEARCH. (maxaccepts=100)
maxrejects=value	Maximum number of non-matching target sequences to consider before stopping the search. Corresponds to the --maxrejects flag in VSEARCH. (maxrejects=100)
id=value	Reject the sequence match if the pairwise identity is lower than the number specified. Value between 0 and 1. Corresponds to the --id flag in VSEARCH (id=0.8)
iddef=value	Changes the pairwise identity definition used by the id option. Values accepted are: 0. CD-HIT definition: (matching columns) / (shortest sequence length). 1. edit distance: (matching columns) / (alignment length). 2. edit distance excluding terminal gaps (default definition for --id). 3. Marine Biological Lab definition counting each gap opening (internal or terminal) as a single mismatch, whether or not the gap was extended: 1.0 - [(mismatches + gap openings)/(longest sequence length)] 4. BLAST definition, equivalent to --iddef 1 for global pairwise alignments. Corresponds to the --iddef option in VSEARCH. (iddef=2)

Returns the sequence search data in a JSON-readable format with the specified key/value pairs:

Key/value pair	Description
"type": "[value]"	Component Definition Type
"uri": "[value]"	URI of part on SynBioHub
"name": "[value]"	Name of part on SynBioHub
"Description": "[value]"	Description of part on SynBioHub
"displayID: "[value]"	Display ID of part
"version": "[value]"	Version of part
"percentMatch": "[value]"	Percentage match to query part
"strandAlignment": "[value]"	Target strand orientation
"CIGAR": "[value]"	Short for "Compact Idiosyncratic Gapped Alignment Report". Learn more here.

Download Endpoints

The following endpoints are for downloading content from SynBioHub in various formats.

Download SBOL

GET <URI>/sbol OR GET <URI>

Returns the object from the specified URI in SBOL format.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <URI>/sbol

import requests

response = requests.get(
    '<URI>/sbol',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const Url = '<URI>/sbol'
const otherPram={
    headers:{
    "content-type" : "text/plain; charset=UTF-8"
    },
    method:"GET"
};
fetch(Url,otherPram)
.then(res => res.buffer()).then(buf => console.log(buf.toString()))
.catch (error=>console.log(error))

Download Non-Recursive SBOL

GET <URI>/sbolnr

Returns the object from the specified URI in SBOL format non-recursively ( i.e. fetches the object without its children.)

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <URI>/sbolnr

import requests

response = requests.get(
    '<URI>/sbolnr',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const Url = '<URI>/sbolnr'
const otherPram={
    headers:{
    "content-type" : "text/plain; charset=UTF-8"
    },
    method:"GET"
};
fetch(Url,otherPram)
.then(res => res.buffer()).then(buf => console.log(buf.toString()))
.catch (error=>console.log(error))

Download Metadata

GET <URI>/metadata

Returns the metadata for the object from the specified URI.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <URI>/metadata

import requests

response = requests.get(
    '<URI>/metadata',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const Url = '<URI>/metadata'
const otherPram={
    headers:{
        "content-type" : "text/plain; charset=UTF-8"
    },
    method:"GET"
};
fetch(Url,otherPram)
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Download GenBank

GET <URI>/gb

Returns the object from the specified URI in GenBank format.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <URI>/gb

import requests

response = requests.get(
    '<URI>/gb',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const Url = '<URI>/gb'
const otherPram={
    headers:{
        "content-type" : "text/plain; charset=UTF-8"
    },
    method:"GET"
};
fetch(Url,otherPram)
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Download FASTA

GET <URI>/fasta

Returns the object from the specified URI in FASTA format.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <URI>/fasta

import requests

response = requests.get(
    '<URI>/fasta',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const Url = '<URI>/fasta'
const otherPram={
    headers:{
        "content-type" : "text/plain; charset=UTF-8"
    },
    method:"GET"
};
fetch(Url,otherPram)
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Download GFF3

GET <URI>/gff

Returns the object from the specified URI in GFF3 format.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <URI>/gff

import requests

response = requests.get(
    '<URI>/gff',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const Url = '<URI>/gff'
const otherPram={
    headers:{
        "content-type" : "text/plain; charset=UTF-8"
    },
    method:"GET"
};
fetch(Url,otherPram)
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Download Attachment

GET <URI>/download

Returns the source for an attachment to the specified URI.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <URI>/download -O --compressed

const fetch = require("node-fetch");
const Url = '<URI>/download'
const otherPram={
    headers:{
        "content-type" : "text/plain; charset=UTF-8"
    },
    method:"GET"
};
fetch(Url,otherPram)
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

import requests

response = requests.get(
    '<URI>/sbolnr',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

Submission Endpoints

The following endpoints are for managing submissions on SynBioHub.

Submit

POST <SynBioHub URL>/submit

Create a new collection including the elements within a file or add to a preexisting collection using the elements within a file.

curl -X POST -H "Accept: text/plain" -H "X-authorization: <token>" -F id=<id> -F version=<version> -F name=<name> -F description=<description> -F citations=<citations> -F overwrite_merge=<overwrite_merge> -F file=@<filename> <SynBioHub URL>/submit

import requests

response = requests.post(
    '<SynBioHub URL>/submit',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    files={
    'files': open('<file.txt>','rb'),
    },
    data={
        'id': '<id>',
        'version' : '<version>',
        'name' : '<name>',
        'description' : '<description>',
        'citations' : '<citations>',
        'overwrite_merge' : '<tabState>'
    },

)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const FormData = require('form-data');
const { createReadStream } = require('fs');
const url = '<SynBioHub URL>/submit'
const stream = createReadStream('input.txt');
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const form = new FormData();
form.append('id', '<id>');
form.append('version', '<version>');
form.append('name', '<name>');
form.append('description', '<description>');
form.append('citations', '<citations>');
form.append('overwrite_merge', '<overwrite_merge>');
form.append('file', stream);

fetch(url, { method: 'POST', headers: headers, body:form})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
id	a user-defined string identifier for the submission; alphanumeric and underscores only, (ex.`BBa_R0010`)
version	the version string to associate with the submission, (ex. `1`)
name	the name string to assign to the submission
description	the description string to assign to the submission
citations	a list of comma separated pubmed IDs of citations to store with the submission
overwrite_merge	'0' prevent if submission exists, '1' overwrite if submission exists, '2' to merge and prevent if submission exists, '3' to merge and overwrite matching URIs
file	contents of an SBOL2, SBOL1, GenBank, FASTA, GFF3, ZIP, or COMBINE Archive file
rootCollections	the URI of the collection to be submitted into

If creating a collection, provide the id, version, name, description, citations, and optionally a file. In this case, overwrite_merge should be 0 or 1. If submitting the contents into an existing collection, otherwise, only provide a URI for the rootCollections that you are submitting into and the file that you are submitting.

Make Public Collection

POST <URI>/makePublic

Makes the collection specified by the URI public.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "id=<id>&version=<version>&name=<name>&description=<description>&citations=<citations>&tabState=<tabState>" <URI>/makePublic

import requests

response = requests.post(
    '<URI>/makePublic',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'id': '<id>',
        'version' : '<version>',
        'name' : '<name>',
        'description' : '<description>',
        'citations' : '<citations>',
        'tabState' : '<tabState>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<URI>/makePublic'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('id', '<id>');
params.append('version', '<version>');
params.append('name', '<name>');
params.append('description', '<description>');
params.append('citations', '<citations>');
params.append('tabState', '<tabState>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
id	The id for the new collection.
version	The version for the new collection.
name	The name for the new collection (optional: default is existing name).
description	The description for the new collection (optional: default is existing description).
citations	The comma-separated listed of PubMed ids (optional: default is existing citations).
tabState	Use "new" for moving to a new public collection, and "existing" if moving into an existing public collection.
collections	If moving into an existing collection, collections is the URI of the collection

Remove Collection

GET <URI>/removeCollection

Removes the collection specified by the URI.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <URI>/removeCollection

import requests

response = requests.get(
    '<URI>/removeCollection',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const Url = '<URI>/removeCollection'
const otherPram={
    headers:{
    "content-type" : "text/plain; charset=UTF-8"
    },
    method:"GET"
};
fetch(Url,otherPram)
.then(res => res.buffer()).then(buf => console.log(buf.toString()))
.catch (error=>console.log(error))

Remove Object

GET <URI>/remove

Remove the object specified by the URI, and the references to that object.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <URI>/remove

import requests

response = requests.get(
    '<URI>/remove',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const Url = '<URI>/remove'
const otherPram={
    headers:{
    "content-type" : "text/plain; charset=UTF-8"
    },
    method:"GET"
};
fetch(Url,otherPram)
.then(res => res.buffer()).then(buf => console.log(buf.toString()))
.catch (error=>console.log(error))

Replace Object

GET <URI>/replace

Remove the object specified from URI, but leave references to the object.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <URI>/remove

import requests

response = requests.get(
    '<URI>/replace',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const Url = '<URI>/replace'
const otherPram={
    headers:{
    "content-type" : "text/plain; charset=UTF-8"
    },
    method:"GET"
};
fetch(Url,otherPram)
.then(res => res.buffer()).then(buf => console.log(buf.toString()))
.catch (error=>console.log(error))

Update Collection Icon

POST <URI>/icon

Updates the collection's icon.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -F "collectionIcon=@<icon>" <URI>/icon

import requests

response = requests.post(
    '<URI>/icon',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    files={
        'collectionIcon': open('<icon.png>', 'rb'),
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { createReadStream } = require('fs');
const FormData = require('form-data');
const url = '<SynBioHub URL>/icon'
const stream = createReadStream('<icon path>');
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new FormData();
params.append('collectionIcon', stream);

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
collectionIcon	The desired collection icon.

Permission Endpoints

The following endpoints are for managing permissions on SynBioHub.

Add Owner

POST <URI>/addOwner

Adds an owner to an object specfied by the URI.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "user=<user>&uri=<uri>" <URI>/addOwner

import requests

response = requests.post(
    '<URI>/addOwner',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'user': '<user>',
        'uri' : '<uri>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<URI>/addOwner'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('user', '<user>');
params.append('uri', '<uri>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
user	The user id of owner being added.
uri	The identity of the object to add owner to.

Remove Owner

POST <URI>/removeOwner/<username>

Removes an owner from an object specified by the URI.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "userUri=<userUri>" <URI>/removeOwner/<username>

import requests

response = requests.post(
    '<URI>/removeOwner/<username>',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'userUri': '<userUri>',
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<URI>/removeOwner/<username>'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('userUri', '<userUri>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
userUri	The user URI of the user being removed.

Edit Endpoints

These endpoints allow you to edit various fields within each object.

Edit Mutable Descriptions

POST <SynBioHub URL>/updateMutableDescription

Edit the mutable description of an object specified by the URI.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "uri=<uri>&value=<value>" <SynBioHub URL>/updateMutableDescription

import requests

response = requests.post(
    '<SynBioHub URL>/updateMutableDescription',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'uri': '<uri>',
        'value' : '<value>'
        },
)

print(response.status_code)
print(response.content)


const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/updateMutableDescription'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('uri', '<uri>');
params.append('value', '<value>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
uri	The identity of the object to update.
value	The new value for the mutable description

Edit Mutable Notes

POST <SynBioHub URL>/updateMutableNotes

Edit the mutable notes of an object specified by the URI.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "uri=<uri>&value=<value>" <SynBioHub URL>/updateMutableNotes

import requests

response = requests.post(
    '<SynBioHub URL>/updateMutableNotes',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'uri': '<uri>',
        'value' : '<value>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/updateMutableNotes'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};


const params = new URLSearchParams();
params.append('uri', '<uri>');
params.append('value', '<value>');


fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
uri	The identity of the object to update.
value	The new value for the mutable notes.

Edit Mutable Source

POST <SynBioHub URL>/updateMutableSource

Edit the mutable source of an object specified by the URI.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "uri=<uri>&value=<value>" <SynBioHub URL>/updateMutableSource

import requests

response = requests.post(
    '<SynBioHub URL>/updateMutableSource',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'uri': '<uri>',
        'value' : '<value>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/updateMutableSource'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('uri', '<uri>');
params.append('value', '<value>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
uri	The identity of the object to update.
value	The new value for the mutable source.

Edit Citations

POST <SynBioHub URL>/updateCitations

Edit the citations of an object specified by the URI.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "uri=<uri>&value=<value>" <SynBioHub URL>/updateCitations

import requests

response = requests.post(
    '<SynBioHub URL>/updateCitations',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'uri': '<uri>',
        'value' : '<value>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/updateCitations'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('uri', '<uri>');
params.append('value', '<value>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
uri	The identity of the object to update.
value	The new value for the citation.

Edit Field

POST <URI>/edit/<field>

Edit field of an object.

curl -X POST -H "Accept: text/plain" -H "X-authorization: <token>" -d "previous=<previous>&object=<test>&pred=<pred>"  <URI>/edit/<field>

import requests

response = requests.post(
    '<URI>/edit/<field>',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'previous': '<previous>',
        'object' : '<object>',
        'pred' : '<pred>',
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<URI>/edit/<field>'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('previous', '<previous>');
params.append('object', '<object>');
params.append('pred', '<pred>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
previous	The previous value of the field.
object	The new value of the field.
pred	A predicate for an annotation.

Possible fields to edit: title description role wasDerivedFrom type annotation

Add Field

POST <URI>/add/<field>

Add field to an object.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "object=<object>&pred=<pred>"  <URI>/add/<field>

import requests

response = requests.post(
    '<URI>/add/<field>',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'object' : '<object>',
        'pred' : '<pred>',
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/add/<field>'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('object', '<object>');
params.append('pred', '<pred>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
object	The new value of the field.
pred	A predicate for an annotation.

Possible fields to add: role type wasDerivedFrom annotation

Remove Field

POST <URI>/remove/<field>

Remove field from an object.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "object=<object>&pred=<pred>"  <URI>/remove/<field>

import requests

response = requests.post(
    '<URI>/remove/<field>',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'object' : '<object>',
        'pred' : '<pred>',
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<URI>/remove/<field>'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('object', '<object>');
params.append('pred', '<pred>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
object	The value of the field to remove.
pred	A predicate for an annotation.

Possible fields to remove: role type title description wasDerivedFrom annotation

Add to Collection

POST <URI>/addToCollection

Add member specified by the URI to a collection specified by the collections parameter.

curl -X POST -H "Accept: text/plain" -H "X-authorization: <token>" -d "collections=<collections>" <URI>/addToCollection

import requests

response = requests.post(
    '<URI>/addToCollection',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'collections': '<collections>',
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<URI>/addToCollection'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('collections', '<collections');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
collections	The URI of collection to add a member to.

Remove Membership

POST <URI>/removeMembership

Remove a member specified by the member parameter of a collection specified by the URI.

curl -X POST -H "Accept: text/plain" -H "X-authorization: <token>" -d "member=<member>" <URI>/removeMembership

import requests

response = requests.post(
    '<URI>/removeMembership',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'member': '<member>',
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<URI>/removeMembership'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('member', '<member>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
member	The URI of the object to remove as a member.

Attachment Endpoints

The following endpoints are for creating attachments on SynBioHub.

Attach File

POST <URI>/attach

Attach a specified file to a given URI.

curl -X POST -H "Accept: text/plain" -H "X-authorization: <token>" -F 'file=@<filename>' <URI>/attach

import requests

response = requests.post(
    '<URI>/attach',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    files={
    'file': open('<file>','rb'),
    },

)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const FormData = require('form-data');
const { createReadStream } = require('fs');
const url = '<URI>/attach'
const stream = createReadStream('<file>');
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const form = new FormData();
form.append('file', stream);

fetch(url, { method: 'POST', headers: headers, body:form})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
file	The name of the file to attach.

Attach URL

POST <URI>/attachURL

Attach a specified URL to a given URI.

curl -X POST -H "Accept: text/plain" -H "X-authorization: <token>" -d "url=<url>&name=<name>&type=<type>" <URI>/attachURL

import requests

response = requests.post(
    '<URI>/attachURL',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'url': '<url>',
        'name' : '<name>',
        'type' : '<type>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<URI>/attachURL'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('url', '<url>');
params.append('name', '<name>');
params.append('type', '<type>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
url	The URL to attach.
name	The name of the attachment.
type	The format type of the object at the URL.

Download Attachment

GET <URI>/download

Returns the source for an attachment to the specified URI.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <URI>/download -O --compressed

const fetch = require("node-fetch");
const Url = '<URI>/download'
const otherPram={
    headers:{
        "content-type" : "text/plain; charset=UTF-8"
    },
    method:"GET"
};
fetch(Url,otherPram)
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

import requests

response = requests.get(
    '<URI>/download',
    params={'X-authorization': 'token'},
    headers={'Accept': 'text/plain'},
)

print(response.status_code)
print(response.content)

Administration Endpoints

The following endpoints are for users with administration privileges.

SPARQL Admin Query

GET <SynBioHub URL>/admin/sparql?query=<SPARQL query>

Returns the results of the SPARQL admin query in JSON format.

curl -X GET -H "Accept: application/json" '<SynBioHub URL>/admin/sparql?query=<SPARQL query>

import requests

response = requests.get(
    '<SynBioHub URL>/admin/sparql?query=<SPARQL query>',
    headers={
        'Accept': 'application/json',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const Url = '<SynBioHub URL>/admin/sparql?query=<SPARQL query>'
const otherPram={
    headers:{
        "content-type" : "application/json; charset=UTF-8",
    "X-authorization" : "<token>"
    },
    method:"GET"
};
fetch(Url,otherPram)
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Get Status

GET <SynBioHub URL>/admin

Returns configuration options for SynBioHub.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <SynBioHub URL>/admin

import requests

response = requests.get(
    '<SynBioHub URL>/admin',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const url = '<SynBioHub URL>/admin'
const headers={
        "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};
fetch(url, { method: 'GET', headers: headers})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Get Virtuoso Status

GET <SynBioHub URL>/admin/virtuoso

Returns 200 when Virtuoso is alive and 500 when it is not.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <SynBioHub URL>/admin/virtuoso

import requests

response = requests.get(
    '<SynBioHub URL>/admin/virtuoso',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const url = '<SynBioHub URL>/admin/virtuoso'
const headers={
        "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};
fetch(url, { method: 'GET', headers: headers})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

View Graphs

GET <SynBioHub URL>/admin/graphs

Returns existing graphs and its number of triples.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <SynBioHub URL>/admin/graphs

import requests

response = requests.get(
    '<SynBioHub URL>/admin/graphs',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const url = '<SynBioHub URL>/admin/graphs'
const headers={
        "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};
fetch(url, { method: 'GET', headers: headers})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

View Log

GET <SynBioHub URL>/admin/log

Returns the SynBioHub log file.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <SynBioHub URL>/admin/log

import requests

response = requests.get(
    '<SynBioHub URL>/admin/log',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const url = '<SynBioHub URL>/admin/log'
const headers={
        "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};
fetch(url, { method: 'GET', headers: headers})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

View Current Mail Settings

GET <SynBioHub URL>/admin/mail

Returns the current mail configuration.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <SynBioHub URL>/admin/mail

import requests

response = requests.get(
    '<SynBioHub URL>/admin/mail',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const url = '<SynBioHub URL>/admin/mail'
const headers={
        "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};
fetch(url, { method: 'GET', headers: headers})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Update Mail Settings

POST <SynBioHub URL>/admin/mail

Update the mail configuration.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "key=<key>&fromEmail=<fromEmail>" <SynBioHub URL>/admin/mail

import requests

response = requests.post(
    '<SynBioHub URL>/admin/mail',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'key': '<key>',
        'fromEmail' : '<fromEmail>',
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/admin/mail'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('key', '<key>');
params.append('fromEmail', '<fromEmail>');


fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
key	SendGrid API Key
fromEmail	SendGrid from Email

View Plugins

GET <SynBioHub URL>/admin/plugins

View current plugins.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <SynBioHub URL>/admin/plugins

import requests

response = requests.get(
    '<SynBioHub URL>/admin/plugins',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const url = '<SynBioHub URL>/admin/plugins'
const headers={
        "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};
fetch(url, { method: 'GET', headers: headers})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Save Plugin

POST <SynBioHub URL>/admin/savePlugin

Save a new plugin.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "id=<id>&category=<category>&name=<name>&url=<url>" <SynBioHub URL>/admin/savePlugin

import requests

response = requests.post(
    '<SynBioHub URL>/admin/savePlugin',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'id': '<id>',
        'category' : '<category>',
        'name' : '<name>',
        'url' : '<url>',
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/admin/savePlugin'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('id', '<id>');
params.append('category', '<category>');
params.append('name', '<name>');
params.append('url', '<url>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
id	Id of plugin, if adding a plugin, id should be New.
category	Type of plugin (rendering, submit, download).
name	Name of the plugin.
url	URL for the plugin.

Delete Plugin

POST <SynBioHub URL>/admin/deletePlugin

Delete a plugin.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "id=<id>&category=<category>" <SynBioHub URL>/admin/deletePlugin

import requests

response = requests.post(
    '<SynBioHub URL>/admin/deletePlugin',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'id': '<id>',
        'category' : '<category>',
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/admin/deletePlugin'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('id', '<id>');
params.append('category', '<category>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
id	The id of the plugin.
category	The type of plugin (rendering, submit, download).

View Registries

GET <SynBioHub URL>/admin/registries

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <SynBioHub URL>/admin/registries

import requests

response = requests.get(
    '<SynBioHub URL>/admin/registries',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const url = '<SynBioHub URL>/admin/registries'
const headers={
        "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};
fetch(url, { method: 'GET', headers: headers})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

View current registries.

Save Registry

POST <SynBioHub URL>/admin/saveRegistry

Save a new registry.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "uri=<uri>&url=<url>" <SynBioHub URL>/admin/saveRegistry

import requests

response = requests.post(
    '<SynBioHub URL>/admin/saveRegistry',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'uri': '<uri>',
        'url' : '<url>',

        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/admin/saveRegistry'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('uri', '<uri>');
params.append('url', '<url>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
uri	URI prefix for the registry.
url	URL for the registry.

Delete Registry

POST <SynBioHub URL>/admin/deleteRegistry

Delete a registry.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "uri=<uri> <SynBioHub URL>/admin/deleteRegistry

import requests

response = requests.post(
    '<SynBioHub URL>/admin/deleteRegistry',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'uri': '<uri>',

        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/admin/deleteRegistry'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('uri', '<uri>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
uri	URI prefix of the registry to delete.

Set Administrator Email

POST <SynBioHub URL>/admin/setAdministratorEmail

Update Web Of Registries administrator email.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "administratorEmail=<administratorEmail>" <SynBioHub URL>/admin/setAdministratorEmail

import requests

response = requests.post(
    '<SynBioHub URL>/admin/setAdministratorEmail',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'administratorEmail': '<administratorEmail>',

        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/admin/setAdministratorEmail'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('administratorEmail', '<administratorEmail>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
administratorEmail	Administrator email address.

Retrieve From Web Of Registries

POST <SynBioHub URL>/admin/retrieveFromWebOfRegistries

Update registries from Web-of-Registries.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" <SynBioHub URL>/admin/retrieveFromWebOfRegistries

import requests

response = requests.post(
    '<SynBioHub URL>/admin/retrieveFromWebOfRegistries',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/admin/retrieveFromWebOfRegistries'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Federate

POST <SynBioHub URL>/admin/federate

Send request to join Web-of-Registries for a SynBioHub.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "administratorEmail=<administratorEmail>&webOfRegistries=<webOfRegistries>" <SynBioHub URL>/admin/federate

import requests

response = requests.post(
    '<SynBioHub URL>/admin/federate',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'administratorEmail': '<administratorEmail>',
        'webOfRegistries' : '<webOfRegistries>',
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/admin/federate'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('administratorEmail', '<administratorEmail>');
params.append('webOfRegistries','<webOfRegistries>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
administratorEmail	Administrator email address
webOfRegistries	URL for the Web-of-Registries

View Remotes

GET <SynBioHub URL>/admin/remotes

View current remotes.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <SynBioHub URL>/admin/remotes

import requests

response = requests.get(
    '<SynBioHub URL>/admin/remotes',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const url = '<SynBioHub URL>/admin/remotes'
const headers={
        "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};
fetch(url, { method: 'GET', headers: headers})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Save Benchling Remote

POST <SynBioHub URL>/admin/saveRemote

Save a new Benchling remote.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "
type=benchling&id=<id>&benchlingApiToken=<BenchlingApitoken>&rejectUnauthorized=<rejectUnauthorizaed>&folderPrefix=<folderPrefix>&defaultFolderId=<defaultFolderId>&isPublic=<isPublic>&rootCollectionsDisplayId=<rootCollectionsDisplayId>&rootCollectionName=<rootCollectionName>&rootCollectionDesciption=root<CollectionDescription>" <SynBioHub URL>/admin/saveRemote

import requests

response = requests.post(
    '<SynBioHub URL>/admin/saveRemote',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
    'type': 'benchling',
    'id': '<id>',
    'benchlingApiToken': 'benchlingApiToken',
    'rejectUnauthorized': '<rejectUnauthorized>',
    'folderprefix': '<folderprefix>',
    'defaultFolderId': '<defaultFolderId',
    'isPublic': '<isPublic>',
    'rootCollectionsDisplayId': '<rootColelctionsDisplayId>',
    'rootCollectionName': '<rootCollectionName>',
    'rootCollectionDescription': '<rootCollectionDescription>'
       },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/admin/saveRemote'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('type', 'benchling');
params.append('id', '<id>');
params.append('benchlingApiToken', '<benchlingApiToken>');
params.append('rejectUnauthorized', '<rejectUnauthorized>');
params.append('folderprefix', '<folderprefix>');
params.append('defaultFolderId', '<defaultFolderId');
params.append('isPublic', '<isPublic>');
params.append('rootCollectionsDisplayId', '<rootColelctionsDisplayId>');
params.append('rootCollectionName', '<rootCollectionName>');
params.append('rootCollectionDescription', '<rootCollectionDescription>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))

    .catch (error=>console.log(error))

Parameter	Description
id	Id of the Benchling remote.
url	URL for the Benchling remote.
benchlingApiToken	API token for the Benchling remote.
rejectUnauthorized	Check SSL certificate?
folderPrefix	Prefix to use for folders on Benchling.
sequenceSuffix	Suffix to use for sequences found on Benchling.
defaultFolderId	Default folder on Benchling to access.
isPublic	Should the remote be visible publicly?
rootCollectionDisplayId	Display id for the root collection on the remote.
rootCollectionName	Name for the root collection on the remote.
rootCollectionDescription	Description for the root collection on the remote.

*Note that rejectUnauthorized and isPublic are set to true by defeault. If the new remote isn't one of these, please remove the parameter completely from the request.

Save ICE Remote

POST <SynBioHub URL>/admin/saveRemote

Save a new ICE remote.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "type=ice&id=<id>&url='<url>'&iceApiTokenClient=<iceApiTokenClient>&iceApiToken=<iceApiToken>&iceApiTokenOwner=<iceApiTokenOwner>&iceCollection&<iceCollection>&rejectUnauthorized=<rejectUnauthorized>&folderPrefix=<folderPrefix>&sequenceSuffix=<sequenceSuffix>&defaultFolderId=<defaultFolderId>&groupId=<groupId>&pi=<pi>&piEmail=<piEmail>&isPublic=<isPublic>&partNumberPrefix=<partNumberPrefix>&rootCollectionDisplayId=<rootCollectionDisplayId>&rootCollectionName=<rootCollectionName>&rootCollectionDescription=<rootCollectionDescription>" <SynBioHub URL>/admin/saveRemote

import requests

response = requests.post(
    '<SynBioHub URL>/admin/saveRemote',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'type': 'ice',
        'id' : '<id>',
        'url' : '<url>',
        'iceApiTokenClient' : '<iceApiTokenClient>',
        'iceApiToken' : '<iceApiToken>',
        'iceApiTokenOwner' : '<iceApiTokenOwner>',
        'iceCollection' : '<iceCollection>',
        'rejectUnauthorized' : '<rejectUnauthorized>',
        'folderPrefix' : '<folderPrefix>',
        'sequenceSuffix' : '<sequenceSuffix>',
        'defaultFolderId' : '<defaultFolderId>',
        'groupId' : '<groupId>',
        'pi' : '<pi>',
        'piEmail' : '<piEmail>',
        'isPublic' : '<isPublic>',
        'partNumberPrefix' : '<partNumberPrefix>',
        'rootCollectionDisplayId' : '<rootCollectionDisplayId>',
        'rootCollectionName' : '<rootCollectionName>',
        'rootCollectionDescription' : '<rootCollectionDescription>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/admin/saveRemote'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('type', 'ice');
params.append('id', '<id>');
params.append('url', '<url>');
params.append('iceApiTokenClient', '<iceApiTokenClient>');
params.append('iceApiToken', '<iceApiToken>');
params.append('iceApiTokenOwner', '<iceApiTokenOwner>');
params.append('iceCollection', '<iceCollection>');
params.append('rejectUnauthorized', '<rejectUnauthorized>');
params.append('folderPrefix', '<folderPrefix>');
params.append('sequenceSuffix', '<sequenceSuffix>');
params.append('defaultFolderId', '<defaultFolderId>');
params.append('groupId', '<groupId>');
params.append('pi', '<pi>');
params.append('piEmail', '<piEmail>');
params.append('isPublic', '<isPublic>');
params.append('partNumberPrefix', '<partNumberPrefix>');
params.append('rootCollectionDisplayId', '<rootCollectionDisplayId>');
params.append('rootCollectionName', '<rootCollectionName>');
params.append('rootCollectionDescription', '<rootCollectionDescription>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
id	Id of the ICE remote
url	URL for the ICE remote
iceApiTokenClient	ICE API token client
iceApiToken	ICE API token
iceApiTokenOwner	ICE API token owner
iceCollection	ICE collection
rejectUnauthorized	Check SSL certificate?
folderPrefix	Prefix to use for folders on ICE
sequenceSuffix	Suffix to use for sequences found on Benchling
defaultFolderId	Default folder on Benchling to access
groupId	Group id on ICE
pi	Principal Investigator name
piEmail	Principal Investigator email
isPublic	Should the remote be visible publicly?
partNumberPrefix	Prefix to use for parts
rootCollectionDisplayId	Display id for the root collection on the remote
rootCollectionName	Name for the root collection on the remote
rootCollectionDescription	Description for the root collection on the remote

*Note that rejectUnauthorized and isPublic are set to true by defeault. If the new remote isn't one of these, please remove the parameter completely from the request.

Delete Remote

POST <SynBioHub URL>/admin/deleteRemote

Delete a remote.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "id=<id>" <SynBioHub>/admin/deleteRemote

import requests

response = requests.post(
    '<SynBioHub URL>/admin/deleteRemote',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'id': '<id>',
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub>/admin/deleteRemote'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('id', '<id>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
id	Id of the remote configuration to remove.

View SBOLExplorer Log

GET <SynBioHub URL>/admin/explorerlog

View the SBOLExplorer log.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <SynBioHub URL>/admin/explorerlog

import requests

response = requests.get(
    '<SynBioHub URL>/admin/explorerlog',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const url = '<SynBioHub URL>/admin/explorerlog'
const headers={
        "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};
fetch(url, { method: 'GET', headers: headers})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

View SBOLExplorer Indexing Log

GET <SynBioHub URL>/admin/explorerIndexingLog

View the SBOLExplorer index log.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <SynBioHub URL>/admin/explorerIndexingLog

import requests

response = requests.get(
    '<SynBioHub URL>/admin/explorerIndexingLog',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const url = '<SynBioHub URL>/admin/explorerIndexingLog'
const headers={
        "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};
fetch(url, { method: 'GET', headers: headers})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

View SBOLExplorer Config

GET <SynBioHub URL>/admin/explorer

View the current SBOLExplorer config.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <SynBioHub URL>/admin/explorer

import requests

response = requests.get(
    '<SynBioHub URL>/admin/explorer',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const url = '<SynBioHub URL>/admin/explorer'
const headers={
        "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};
fetch(url, { method: 'GET', headers: headers})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Update SBOLExplorer Config

POST <SynBioHub URL>/admin/explorer

Update the SBOLExplorer config.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "id=<id>&useSBOLExplorer=<useSBOLExplorer>&SBOLExplorerEndpoint=<SBOLExplorerEndpoint>&useDistributedSearch=<useDistributedSearch>&pagerankTolerance=<pagerangeTolerance>&uclustIdentity=<uclustIdentity>&synbiohubPublicGraph=<synbiohubPublicGraph>&elasticsearchEndpont=<elasticsearchEndpoint>&elasticsearchIndexName=<elasticSearchIndexName>&spraqlEndpoint=<sparqlEndpoint> <SynBioHub URL>/admin/explorer

import requests

response = requests.post(
    '<SynBioHub URL>/admin/explorer',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'id': '<id>',
    'useSBOLExplorer': '<useSBOLExplorer>',
    'SBOLExplorerEndpoint': '<SBOLExplorerEndpoint>',
    'useDistributedSearch': '<useDistributedSearch>'
    'pagerankTolerance': '<pagerangeTolerance>',
    'uclustIdentity': '<uclustIdentity>',
    'elasticsearchEndpont':'<elasticsearchEndpoint>',
    'elasticsearchIndexName':'<elasticSearchIndexName>',
    'spraqlEndpoint':'<sparqlEndpoint>',
    'useCron': '<autoUpdateIndex>',
    'cronDay': '<days>',
    'whichSearch': '<USchecked>' ? 'usearch' : 'vsearch'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/admin/explorer'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = {
    'useSBOLExplorer': '<useSBOLExplorer>'
    'SBOLExplorerEndpoint': '<SBOLExplorerEndpoint>', 
    'useDistributedSearch': '<useDistributedSearch>',
    'pagerankTolerance': '<pagerangeTolerance>',
    'uclustIdentity': '<uclustIdentity>',
    'elasticsearchEndpont': '<elasticsearchEndpoint>',
    'elasticsearchIndexName': '<elasticSearchIndexName>',
    'spraqlEndpoint': '<sparqlEndpoint>',
    'useCron': '<autoUpdateIndex>',
    'cronDay': '<days>',
    'whichSearch': '<USchecked>' ? 'usearch' : 'vsearch'
}

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
useSBOLExplorer	Boolean indicating whether SBOLExplorer is to be used or not
SBOLExplorerEndpoint	The endpoint where SBOLExplorer can be found
useDistributedSearch	Boolean indicating whether distributed search should be used
pagerankTolerance	The Pagerank tolerance factor
uclustIdentity	The UClust clustering identity
elasticsearchEndpoint	The endpoint where Elasticsearch can be found
elasticsearchIndexName	The Elasticsearch index name
sparqlEndpoint	The Virtuoso SPARQL endpoint
useCron	Update the index automatically
cronDay	How often the index is automatically updated
whichSearch	Which algorithms to use, 'usearch' or 'vsearch'

Update SBOLExplorer Index

POST <SynBioHub URL>/admin/explorerUpdateIndex

Updates SBOLExplorer index.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" <SynBioHub URL>/admin/explorerUpdateIndex

import requests

response = requests.post(
    '<SynBioHub URL>/admin/explorerUpdateIndex',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/admin/explorerUpdateIndex'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

View Theme

GET <SynBioHub URL>/admin/theme

View the current theme.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <SynBioHub URL>/admin/theme

import requests

response = requests.get(
    '<SynBioHub URL>/admin/theme',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const url = '<SynBioHub URL>/admin/theme'
const headers={
        "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};
fetch(url, { method: 'GET', headers: headers})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Update Theme

POST <SynBioHub URL>/admin/theme

Update the theme.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -F instanceName=<instanceName> -F frontPageText=<frontPageText> -F baseColor=<baseColor> -F showModuleInteractions=<showModuleInteractions> -F logo=@<path> <SynBioHub URL>/admin/theme

import requests
import os

image_filename = os.path.basename('<path>');

response = requests.post(
    '<SynBioHub URL>/admin/theme',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'instanceName': '<instanceName>',
        'frontPageText' : '<frontPageText>',
        'baseColor' : '<basecolor>',
        'showModuleInteractions' : 'ok',
   },
    files={
        'logo' : (image_filename, open('<path>', 'rb')),
}
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { createReadStream } = require('fs');
const FormData = require('form-data');
const url = '<SynBioHub URL>/admin/theme'
const stream = createReadStream('<logo>');
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new FormData();
params.append('instanceName', '<instanceName>');
params.append('frontPageText', '<frontPageText>');
params.append('baseColor', '<baseColor>');
params.append('showModuleInteractions', 'yes');
params.append('logo', stream);

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
instanceName	Name of the SynBioHub instance
frontPageText	Text to show on front page of the SynBioHub intance
baseColor	Base color to use fo this SynBioHub instance
showModuleInteractions	Should module interactions be shown using VisBol?

*Note that showModuleInteractions are set to true by defeault. If the SynBioHub instance shouldn't have this, please remove the parameter completely from the request.

View Users Config

GET <SynBioHub URL>/admin/users

View the current users.

curl -X GET -H "Accept: text/plain" -H "X-authorization: <token>" <SynBioHub URL>/admin/users

import requests

response = requests.get(
    '<SynBioHub URL>/admin/users',
    headers={
        'Accept': 'text/plain',
        'X-authorization': '<token>'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const url = '<SynBioHub URL>/admin/users'
const headers={
        "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};
fetch(url, { method: 'GET', headers: headers})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Update Users Config

POST <SynBioHub URL>/admin/users

Update the user config.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "allowPublicSignup=true" <SynBioHub URL>/admin/users

import requests

response = requests.post(
    '<SynBioHub URL>/admin/users',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'allowPublicSignup': 'true',
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/admin/users'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('allowPublicSignup', 'true');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
allowPublicSignup	Flag indicating if public signup is allowed.

*Note that allowPublicSignup is set to true by defeault. If the new user isn't one of these, please remove the parameter completely from the request.

Create New User

POST <SynBioHub URL>/admin/newUser

Create a new user.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "username=<token>&name=<name>&email=<email>&affiliation=<affiliation>&isMember=1&isCurator=1&isAdmin=1" <SynBioHub URL>/admin/newUser

import requests

response = requests.post(
    '<SynBioHub URL>/admin/newUser',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'username': '<username>',
        'name' : '<name>',
        'email' : '<email>',
        'affiliation' : '<affiliation>',
        'isMember' : '1',
        'isCurator' : '1',
    'isAdmin' : '1',
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/admin/newUser'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('username', '<username>');
params.append('name', '<name>');
params.append('email', '<email>');
params.append('affiliation', '<affiliation>');
params.append('isMember', '1');
params.append('isCurator', '1');
params.append('isAdmin', '1');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
username	The username of new user.
name	The name of the new user.
email	The email of the new user.
affiliation	The affiliation of the new user.
isMember	Is the new user a member of the team?
isCurator	Is the new user a curator?
isAdmin	Is the new user an admin?

*Note that isMember, isCurator, and isAdmin are set to true by defeault. If the new user isn't one of these, please remove the parameter completely from the request.

*Note that this endpoint also requires SendGrid to be setup.

Update User

POST <SynBioHub URL>/admin/updateUser

Update a user's settings.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "id=<id>&name=<name>&email=<email>&affiliation=<affiliation>&isMember=1&isCurator=1&isAdmin=1" <SynBioHub URL>/admin/updateUser

import requests

response = requests.post(
    '<SynBioHub URL>/admin/updateUser',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'id': '<id>',
        'name' : '<name>',
        'email' : '<email>',
        'affiliation' : '<affilition>',
        'isMember' : '1',
    'isCurator' : '1',
    'isAdmin' : '1'
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/admin/updateUser'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('id', '<id>');
params.append('name', '<name>');
params.append('email', '<email>');
params.append('affiliation', '<affiliation>');
params.append('isMember', '1');
params.append('isCurator', '1');
params.append('isAdmin', '1');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
id	The ID of the user to update.
name	The name of the user to update to.
email	The email of the user to update to.
affiliation	The affiliation of the user to update to.
isMember	Is this user a member?
isCurator	Is this user a curator?
isAdmin	Is this user an admin?

Note that isMember, isCurator, and isAdmin are set to true by defeault. If the new user isn't one of these, please remove the parameter completely from the request.

Delete User

POST <SynBioHub URL>/admin/deleteUser

Delete a user.

curl -X POST -H "Accept: text/plain" -H "X-authorization:<token>" -d "id=<id>" <SynBioHub URL>/admin/deleteUser

import requests

response = requests.post(
    '<SynBioHub URL>/admin/deleteUser',
    headers={
        'X-authorization': '<token>',
        'Accept': 'text/plain'
    },
    data={
        'id': '<id>',
        },
)

print(response.status_code)
print(response.content)

const fetch = require("node-fetch");
const { URLSearchParams } = require('url');
const url = '<SynBioHub URL>/admin/deleteUser'
var headers={
    "Accept" : "text/plain; charset=UTF-8",
    "X-authorization" : "<token>"
};

const params = new URLSearchParams();
params.append('id', '<id>');

fetch(url, { method: 'POST', headers: headers, body:params})
    .then(res => res.buffer()).then(buf => console.log(buf.toString()))
    .catch (error=>console.log(error))

Parameter	Description
id	The Id of user to delete.

Plugins

Plugin Specification

Plugins must provide three endpoints, /status, /evaluate, and /run.

Status endpoint The status endpoint should listen for HTTP GET requests and return an HTTP 200 OK and (optionally) a short message if the plugin service is ready to handle requests. Otherwise, an HTTP error code and short error message should be returned.

Evaluate endpoint The evaluate endpoint should listen for HTTP POST requests, and return an HTTP 200 OK if the request can be handled by the run endpoint. The body of evaluate requests sent to each plugin type is described below.

Run endpoint The run endpoint should listen for HTTP POST requests, and return an HTTP 200 OK with the result of the plugin operation. The body of run requests sent to each plugin type is described below.

Implementation

Plugins and SynBioHub will communicate using HTTP. The end user’s browser will not communicate with the plugin server.

Submission

For both the evaluate and run endpoints, SynBioHub will send a JSON object structured as follows: { manifest: { files: [ ... ] } }

Each file in files will have the following parameters:

1. filename: The name of the file

2. type: the Content-Type of the file

3. url: A URL where the file can be accessed

Evaluate endpoint

SynBioHub will send an HTTP POST request containing the manifest to the submit plugin's evaluate endpoint. The plugin should respond with HTTP 200 OK if the plugin can handle the submission.

Run endpoint

SynBioHub will send an HTTP POST request containing the manifest to the submit plugin's run endpoint. It will also send the instanceUrl parameter. The plugin should respond with an HTTP response and file attachment, which represents the submission.

Download

Evaluate endpoint

SynBioHub will send an HTTP POST request to the download plugin's evaluate endpoint. The body of the request will contain a JSON containing:

1. type: The RDF type of the top-level object

The plugin should respond with an HTTP 200 OK if the request can be handled.

Run endpoint

SynBioHub will send an HTTP POST request to the dwonload plugin’s run endpoint. The body of the request will contain a JSON object containing:

1. complete_sbol: the single-use URL for the complete object to operate on

2. shallow_sbol: the single-use URL for a summarized or truncated view of the object

3. top_level: the top-level URL of the SBOL object

4. instanceUrl: the top-level URL of the SBOL object

5. size: a number representing an estimate of the size of the object, probably triple count

The plugin should respond with an HTTP request and file attachment which represents the object.

Visualization

The response of visualization plugins should be HTML which will be displayed on the top-level page. Rendering responses may be cached to improve performance.

Evaluate endpoint

SynBioHub will send an HTTP POST request to the visualization plugin's evaluate endpoint. The body of the request will contain a JSON containing:

1. type: The RDF type of the top-level object

Run endpoint

SynBioHub will send an HTTP POST request to the visualization plugin’s run endpoint. The body of the request will contain a JSON object containing:

1. complete_sbol: the single-use URL for the complete object to operate on

2. shallow_sbol: the single-use URL for a summarized or truncated view of the object

3. top_level: the top-level URL of the SBOL object

4. instanceUrl: the top-level URL of the SBOL object

5. size: a number representing an estimate of the size of the object, probably triple count

The plugin should respond with an HTML page to be rendered in-frame on the corresponding SynBioHub page.

Errors

This error section is stored in a separate file in includes/_errors.md. Slate allows you to optionally separate out your docs into many files...just save them to the includes folder and add them to the top of your index.md's frontmatter. Files are included in the order listed.

The Kittn API uses the following error codes:

Error Code	Meaning
400	Bad Request -- Your request is invalid.
401	Unauthorized -- Your API key is wrong.
403	Forbidden -- The kitten requested is hidden for administrators only.
404	Not Found -- The specified kitten could not be found.
405	Method Not Allowed -- You tried to access a kitten with an invalid method.
406	Not Acceptable -- You requested a format that isn't json.
410	Gone -- The kitten requested has been removed from our servers.
418	I'm a teapot.
429	Too Many Requests -- You're requesting too many kittens! Slow down!
500	Internal Server Error -- We had a problem with our server. Try again later.
503	Service Unavailable -- We're temporarily offline for maintenance. Please try again later.

About SynBioHub

What is SynBioHub?

What can SynBioHub be used for?

Publications

Contributors

Installation

From Prebuilt Image

Install Docker

Starting a SynBioHub Instance

Configuring

SendGrid email setup

Updating

PERSISTENT LOGS UPDATE

If you are updating from a version of SynBioHub earlier than 1.3.0 to 1.3.0 or later, you must execute the following steps to persist your data between instances!

From Source

NGINX configuration

User Endpoints

Login

Logout

Register

Request Reset Password Token

Set New Password

View Profile

Update Profile

Search Endpoints

Search Metadata

Count Search Results

Search Root Collections

Search Submissions

Search Shared Objects

Search Sub-Collections

Search Twins

Search Similar

Search Uses

Count Objects by Type

SPARQL Query

Sequence Search

Download Endpoints

Download SBOL

Download Non-Recursive SBOL

Download Metadata

Download GenBank

Download FASTA

Download GFF3

Download Attachment

Submission Endpoints

Submit

Make Public Collection

Remove Collection

Remove Object

Replace Object

Update Collection Icon

Permission Endpoints

Add Owner

Remove Owner

Edit Endpoints

Edit Mutable Descriptions

Edit Mutable Notes

Edit Mutable Source

Edit Citations

Edit Field

Add Field

Remove Field

Add to Collection

Remove Membership

Attachment Endpoints

Attach File

Attach URL

Download Attachment

Administration Endpoints

SPARQL Admin Query

Get Status

Get Virtuoso Status

View Graphs

View Log

View Current Mail Settings

Update Mail Settings

View Plugins

Save Plugin

Delete Plugin