Collaborative Drug Discovery Protocols API
Protocols and their readout data
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OpenAPI Specification
openapi: 3.2.0
info:
contact:
url: https://support.collaborativedrug.com/hc/en-us/requests/new
description: 'Collaborative Drug Discovery provides an API (Application Programming
Interface) that can be used for secure programmatic access to your vault
data.'
license:
name: Proprietary
url: https://support.collaborativedrug.com/hc/en-us/requests/new
title: CDD Protocols API
version: 1.0.0
servers:
- url: https://app.collaborativedrug.com/api/v1
security:
- ApiKeyAuth: []
tags:
- description: Protocols and their readout data
name: Protocols
paths:
/vaults/{vault_id}/protocols:
get:
description: List protocols in the vault. Supports pagination (`page_size`, `offset`), asynchronous retrieval (`async=true`), `only_ids`, `no_runs` (omit run data), and filtering by name, project, molecule, plate, and dates.
operationId: getProtocols
parameters:
- in: path
name: vault_id
required: true
schema:
$ref: '#/components/schemas/vault_id'
- description: Maximum number of records to return (default 50, maximum 1000).
in: query
name: page_size
schema:
type: integer
- description: Number of records to skip (for pagination).
in: query
name: offset
schema:
type: integer
- description: If true, run the listing as an asynchronous export.
in: query
name: async
schema:
type: boolean
- description: If true, return only the ids of matching protocols.
in: query
name: only_ids
schema:
type: boolean
- description: If true, omit run data from each protocol.
in: query
name: no_runs
schema:
type: boolean
- description: Comma-separated protocol names to filter by.
in: query
name: names
schema:
type: string
- description: Comma-separated protocol ids to filter by.
in: query
name: protocols
schema:
type: string
- description: Comma-separated project ids to filter by.
in: query
name: projects
schema:
type: string
responses:
'200':
content:
application/json:
schema:
properties:
count:
type: integer
objects:
items:
$ref: '#/components/schemas/protocol_object'
type: array
offset:
type: integer
page_size:
type: integer
required:
- count
- objects
type: object
description: A page of protocols
'401':
content:
application/json:
schema:
$ref: '#/components/schemas/error_apikey'
description: Missing or invalid API key
summary: Get protocols
tags:
- Protocols
/vaults/{vault_id}/protocols/{id}:
get:
description: Retrieve a single protocol. Pass `no_runs=true` to omit run data.
operationId: getProtocol
parameters:
- in: path
name: vault_id
required: true
schema:
$ref: '#/components/schemas/vault_id'
- description: Numeric identifier of the protocol
in: path
name: id
required: true
schema:
type: integer
- description: If true, omit run data from the response.
in: query
name: no_runs
schema:
type: boolean
responses:
'200':
content:
application/json:
schema:
$ref: '#/components/schemas/protocol_object'
description: The protocol
'401':
content:
application/json:
schema:
$ref: '#/components/schemas/error_apikey'
description: Missing or invalid API key
'404':
content:
application/json:
schema:
$ref: '#/components/schemas/error'
description: Protocol not found, or vault is unauthorized
summary: Get a protocol
tags:
- Protocols
put:
description: Update a protocol's definition (name, projects, and protocol field values). This does not modify readout definitions. Requires write permission.
operationId: updateProtocol
parameters:
- in: path
name: vault_id
required: true
schema:
$ref: '#/components/schemas/vault_id'
- description: Numeric identifier of the protocol
in: path
name: id
required: true
schema:
type: integer
requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/protocol_update'
required: true
responses:
'200':
content:
application/json:
schema:
$ref: '#/components/schemas/protocol_object'
description: The updated protocol
'401':
content:
application/json:
schema:
$ref: '#/components/schemas/error_apikey'
description: Missing or invalid API key
'404':
content:
application/json:
schema:
$ref: '#/components/schemas/error'
description: Protocol not found, or vault is unauthorized
'422':
content:
application/json:
schema:
$ref: '#/components/schemas/error'
description: Validation error
summary: Update a protocol
tags:
- Protocols
/vaults/{vault_id}/protocols/{protocol_id}/data:
get:
description: Retrieve the readout data (detail rows, with any matching aggregate-row readouts merged in) for a protocol. Supports pagination and filtering by molecule, plate, run, and project. Pass `format=csv` to produce a CSV export instead of JSON.
operationId: getProtocolData
parameters:
- in: path
name: vault_id
required: true
schema:
$ref: '#/components/schemas/vault_id'
- description: Numeric identifier of the protocol
in: path
name: protocol_id
required: true
schema:
type: integer
- description: Maximum number of records to return (default 50, maximum 1000).
in: query
name: page_size
schema:
type: integer
- description: Number of records to skip (for pagination).
in: query
name: offset
schema:
type: integer
- description: If true, run the query as an asynchronous export.
in: query
name: async
schema:
type: boolean
- description: If "csv", produce a CSV export instead of a JSON page.
in: query
name: format
schema:
type: string
- description: Comma-separated molecule ids to filter by.
in: query
name: molecules
schema:
type: string
- description: Comma-separated run ids to filter by.
in: query
name: runs
schema:
type: string
- description: Comma-separated plate ids to filter by.
in: query
name: plates
schema:
type: string
- description: Comma-separated project ids to filter by.
in: query
name: projects
schema:
type: string
responses:
'200':
content:
application/json:
schema:
properties:
count:
type: integer
objects:
items:
properties:
batch:
type: integer
id:
type: integer
molecule:
type: integer
readouts:
additionalProperties: true
description: Readout values keyed by readout definition id.
type: object
run:
type: integer
well:
additionalProperties: true
type: object
type: object
type: array
offset:
type: integer
page_size:
type: integer
required:
- count
- objects
type: object
description: A page of protocol readout data
'401':
content:
application/json:
schema:
$ref: '#/components/schemas/error_apikey'
description: Missing or invalid API key
summary: Get protocol data
tags:
- Protocols
/vaults/{vault_id}/batches/{batch_id}/protocols/{id}/plot:
get:
description: Generate dose-response plot image(s) for a batch within a protocol. Returns a ZIP archive containing one PNG per dose-response calculation when the protocol has more than one, or a single PNG when there is only one.
operationId: getDoseResponsePlot
parameters:
- in: path
name: vault_id
required: true
schema:
$ref: '#/components/schemas/vault_id'
- description: Numeric identifier of the batch
in: path
name: batch_id
required: true
schema:
type: integer
- description: Numeric identifier of the protocol
in: path
name: id
required: true
schema:
type: integer
- description: Image size multiplier.
in: query
name: size
schema:
enum:
- small
- medium
- large
type: string
- description: Comma-separated run ids to restrict the plotted data to.
in: query
name: runs
schema:
type: string
responses:
'200':
content:
application/octet-stream:
schema:
format: binary
type: string
application/zip:
schema:
format: binary
type: string
description: A ZIP archive of PNGs (when the protocol has several dose-response calculations) or a single PNG served as `application/octet-stream` (when it has only one).
'401':
content:
application/json:
schema:
$ref: '#/components/schemas/error_apikey'
description: Missing or invalid API key
'404':
content:
application/json:
schema:
$ref: '#/components/schemas/error'
description: No data found for this batch/protocol, or vault is unauthorized
summary: Get dose-response plot
tags:
- Protocols
components:
schemas:
error:
description: A general error response containing an error message and HTTP status code
properties:
code:
description: HTTP status code
type: integer
example: 404
error:
description: Human-readable error message
type: string
example: Resource not found
type: object
protocol_update:
description: Attributes for updating a protocol's definition (not its readout definitions). Only the supplied fields are changed.
example:
name: My Inhibition Screen
projects:
- 12
protocol_fields:
Category: Biochemical
properties:
name:
type: string
projects:
description: Project ids the protocol belongs to (replaces the existing set).
items:
type: integer
type: array
protocol_fields:
additionalProperties: true
description: Custom protocol field values, keyed by field name.
type: object
type: object
error_apikey:
description: Whenever the given API key doesn't allow access to the given vault or the vault doesn't exist
properties:
code:
default: 401
type: integer
error:
default: key not authorized for access to this vault
type: string
type: object
protocol_object:
description: A protocol (assay definition) and its readout definitions, calculations, and runs.
properties:
calculations:
description: Calculation definitions on the protocol.
items:
additionalProperties: true
type: object
type: array
category:
description: Value of the Category protocol field, echoed at top level when present.
type: string
class:
example: protocol
type: string
created_at:
format: date-time
type: string
data_set:
description: Id of the data set the protocol belongs to.
type: integer
description:
description: Value of the Description protocol field, echoed at top level when present.
type: string
hit_definitions:
items:
additionalProperties: true
type: object
type: array
id:
type: integer
modified_at:
format: date-time
type: string
name:
type: string
ontology_annotations:
items:
additionalProperties: true
type: object
type: array
owner:
description: Full name of the protocol owner.
type: string
projects:
description: Project ids the protocol belongs to.
items:
type: integer
type: array
protocol_fields:
additionalProperties: true
description: Custom protocol field values, keyed by field name.
type: object
protocol_statistics:
items:
additionalProperties: true
type: object
type: array
readout_definitions:
description: The readout definitions of the protocol.
items:
additionalProperties: true
type: object
type: array
runs:
description: Runs of the protocol. Omitted when the request passes `no_runs=true`.
items:
additionalProperties: true
type: object
type: array
required:
- id
- class
- name
type: object
vault_id:
description: Numeric identifier of the vault
type: integer
securitySchemes:
ApiKeyAuth:
in: header
name: X-CDD-Token
type: apiKey