adussaq-KINOME-1.0.0-swagger.yaml

swagger: '2.0'
info:
  version: 1.0.0
  title: kinomic database
  description: The API for the database for the kinomic toolbox (http://toolbox.kinomecore.com)
produces:
  - application/json
  - img/tiff
  - img/png
paths:
  /img/{img_file_name}:
    get:
      tags:
      - Database
      description: returns the tiff image that matches the given image file name (img_file_name).
      parameters:
      - in: path
        name: img_file_name
        required: true
        type: string
  /db/1.0.0/name/{doc_id}:
    get:
      tags:
      - Database
      description: returns all data for in the name collection that matches either {doc_id} or the query
      operationId: getDevices
      parameters:
      - in: path
        name: level
        required: true
        type: "string"
        default: "0.0"
        description: "Level 2.X.X data to be returned"
      - in: path
        name: doc_id
        required: false
        type: "string"
        description: "If one document is needed, and the id known, fill this in."
      - in: query
        name: find
        required: false
        type: json
        description: mongo query object https://docs.mongodb.com/manual/tutorial/query-documents/
      - in: query
        name: fields
        required: false
        type: json
        description: mongo fields object https://docs.mongodb.com/manual/tutorial/project-fields-from-query-results/
      - in: query
        name: sort
        required: false
        type: json
        description: mongo query object https://mongodb.github.io/node-mongodb-native/markdown-docs/queries.html#query-options
      - in: query
        name: limit
        required: false
        type: integer
        format: int32
        description: max number of records to return https://mongodb.github.io/node-mongodb-native/markdown-docs/queries.html#query-options
      - in: query
        name: skip
        required: false
        type: json
        description: mongo query object https://mongodb.github.io/node-mongodb-native/markdown-docs/queries.html#query-options
      - in: query
        name: maxTimeMS
        required: false
        type: integer
        format: int32
        description: max amount of time to wait for query return https://mongodb.github.io/node-mongodb-native/driver-articles/anintroductionto1_4_and_2_6.html#maxtimems
      responses:
        200:
          description: Some number of name data objects
          schema:
            type: array
            items:
              $ref: '#/definitions/names_json'

  /db/1.0.0/1.{level}/{doc_id}:
    get:
      tags:
      - Database
      description: returns all data for a given {level} that matches either {doc_id} or the query
      operationId: getDevices
      parameters:
      - in: path
        name: level
        required: true
        type: "string"
        default: "0.0"
        description: "Level 1.X.X data to be returned"
      - in: path
        name: doc_id
        required: false
        type: "string"
        description: "If one document is needed, and the id known, fill this in."
      - in: query
        name: find
        required: false
        type: json
        description: mongo query object https://docs.mongodb.com/manual/tutorial/query-documents/
      - in: query
        name: fields
        required: false
        type: json
        description: mongo fields object https://docs.mongodb.com/manual/tutorial/project-fields-from-query-results/
      - in: query
        name: sort
        required: false
        type: json
        description: mongo query object https://mongodb.github.io/node-mongodb-native/markdown-docs/queries.html#query-options
      - in: query
        name: limit
        required: false
        type: integer
        format: int32
        description: max number of records to return https://mongodb.github.io/node-mongodb-native/markdown-docs/queries.html#query-options
      - in: query
        name: skip
        required: false
        type: json
        description: mongo query object https://mongodb.github.io/node-mongodb-native/markdown-docs/queries.html#query-options
      - in: query
        name: maxTimeMS
        required: false
        type: integer
        format: int32
        description: max amount of time to wait for query return https://mongodb.github.io/node-mongodb-native/driver-articles/anintroductionto1_4_and_2_6.html#maxtimems
      responses:
        200:
          description: Some number of level 1 data objects
          schema:
            type: array
            items:
              $ref: '#/definitions/Level_1_json'
  /db/1.0.0/2.{level}/{doc_id}:
    get:
      tags:
      - Database
      description: returns all data for a given {level} that matches either {doc_id} or the query
      operationId: getDevices
      parameters:
      - in: path
        name: level
        required: true
        type: "string"
        default: "0.0"
        description: "Level 2.X.X data to be returned"
      - in: path
        name: doc_id
        required: false
        type: "string"
        description: "If one document is needed, and the id known, fill this in."
      - in: query
        name: find
        required: false
        type: json
        description: mongo query object https://docs.mongodb.com/manual/tutorial/query-documents/
      - in: query
        name: fields
        required: false
        type: json
        description: mongo fields object https://docs.mongodb.com/manual/tutorial/project-fields-from-query-results/
      - in: query
        name: sort
        required: false
        type: json
        description: mongo query object https://mongodb.github.io/node-mongodb-native/markdown-docs/queries.html#query-options
      - in: query
        name: limit
        required: false
        type: integer
        format: int32
        description: max number of records to return https://mongodb.github.io/node-mongodb-native/markdown-docs/queries.html#query-options
      - in: query
        name: skip
        required: false
        type: json
        description: mongo query object https://mongodb.github.io/node-mongodb-native/markdown-docs/queries.html#query-options
      - in: query
        name: maxTimeMS
        required: false
        type: integer
        format: int32
        description: max amount of time to wait for query return https://mongodb.github.io/node-mongodb-native/driver-articles/anintroductionto1_4_and_2_6.html#maxtimems
      responses:
        200:
          description: Some number of level 2 data objects
          schema:
            type: array
            items:
              $ref: '#/definitions/Level_2_json'
definitions:
  names_json:
    type: object
    properties:
      cyles:
        type: array
        description: cycle number of each image
        items:
          type: number
          format: int
      exposures:
        type: array
        description: exposure time of each image
        items:
          type: number
          format: int
      level:
        type: string
        value: "name"
      name:
        type: string
        description: "Barcode_arr combination"
      _id:
        type: string
        description: "uuid generated to be identical for each level"
      peptides:
        type: array
        description: "list of peptides on chip"
        items:
          type: array
          description: meta data array
          items:
            type: object
            description: meta data object
            properties:
              key: 
                type: string
              value:
                type: string
      run_data:
        type: array
        description: meta data array for run data, should be generate by every run
        items:
          type: object
          properties:
            key:
              type: string
            value:
              type: string | array
              description: "If entry is same for every image taken then it is a single string. Otherwise it is an array of strings."
            origin:
              type: string
              description: only occurs if signal file and background file generate different values for a given key.
      sample_data:
        type: array
        description: meta data array for samples
        items:
          type: object
          properties:
            key:
              type: string
            value:
              type: string
    description: "Name object"
  Level_1_json:
    type: object
    properties:
      background: 
        type: array
        description: "background values for each image/peptide"
        items: 
          type: array
          description: "For each image captured"
          items: 
            type: number
            format: double
            description: "For each spot/peptide on chip"
      background_valid: 
        type: array
        description: "background valid for each image/peptide ?"
        items: 
          type: array
          description: "For each image captured"
          items: 
            type: boolean
            description: "For each spot/peptide on chip"
      signal: 
        type: array
        description: "signal values for each image/peptide"
        items: 
          type: array
          description: "For each image captured"
          items: 
            type: number
            format: double
            description: "For each spot/peptide on chip"
      signal_valid: 
        type: array
        description: "signal valid for each image/peptide ?"
        items: 
          type: array
          description: "For each image captured"
          items: 
            type: boolean
            description: "For each spot/peptide on chip"
      cyles:
        type: array
        description: cycle number of each image
        items:
          type: number
          format: int
      exposures:
        type: array
        description: exposure time of each image
        items:
          type: number
          format: int
      level:
        type: string
        description: "data level, 1.0.0; 1.0.1 etc"
      name:
        type: string
        description: "Barcode_arr combination"
      _id:
        type: string
        description: "uuid generated to be identical for each level"
      peptides:
        type: array
        description: "list of peptides on chip"
        items:
          type: array
          description: meta data array
          items:
            type: object
            description: meta data object
            properties:
              key: 
                type: string
              value:
                type: string
      run_data:
        type: array
        description: meta data array for run data, should be generate by every run
        items:
          type: object
          properties:
            key:
              type: string
            value:
              type: string | array
              description: "If entry is same for every image taken then it is a single string. Otherwise it is an array of strings."
            origin:
              type: string
              description: only occurs if signal file and background file generate different values for a given key.
      sample_data:
        type: array
        description: meta data array for samples
        items:
          type: object
          properties:
            key:
              type: string
            value:
              type: string
    description: "Level 1 object"
  Level_2_json:
    type: object
    properties:
      kinetic:
        type: object
        properties:
          exposures: 
            type: array
            description: "All exposures that were utilited to create kinetic models, typically just 50ms."
            items:
              type: number
          equation_string: 
            type: string
            description: "'eval'-able string to resolve the equation object used to generate the parameterization."
          background: 
            type: array
            description: "background values for each image series"
            items: 
              type: array
              description: "For each peptide series captured"
              items: 
                type: object
                properties:
                  R2:
                    type: number
                    description: "R2 of the corresponding kinetic model"
                  WW:
                    type: number
                    description: "Wald-Wolfowitz p-value for the randomness of the residuals (higher = more random)"
                  paramters:
                    type: array
                    description: "Parameterization of curve fit"
                    items:
                      type: number
          signal:
            type: array
            description: "background values for each image series"
            items: 
              type: array
              description: "For each peptide series captured"
              items: 
                type: object
                properties:
                  R2:
                    type: number
                    description: "R2 of the corresponding kinetic model"
                  WW:
                    type: number
                    description: "Wald-Wolfowitz p-value for the randomness of the residuals (higher = more random)"
                  paramters:
                    type: array
                    description: "Parameterization of curve fit"
                    items:
                      type: number
      linear:
        type: object
        properties:
          cycles: 
            type: array
            description: "All cycle numbers that were utilited to create linear models, typically just post-wash."
            items:
              type: number
          background: 
            type: array
            description: "background values for each image series"
            items: 
              type: array
              description: "For each peptide series captured"
              items: 
                type: object
                properties:
                  R2:
                    type: number
                    description: "R2 of the corresponding kinetic model"
                  paramters:
                    type: array
                    description: "Parameterization of curve fit"
                    items:
                      type: number
          signal:
            type: array
            description: "background values for each image series"
            items: 
              type: array
              description: "For each peptide series captured"
              items: 
                type: object
                properties:
                  R2:
                    type: number
                    description: "R2 of the corresponding kinetic model"
                  paramters:
                    type: array
                    description: "Parameterization of curve fit"
                    items:
                      type: number
      level:
        type: string
        description: "data level, 1.0.0; 1.0.1 etc"
      name:
        type: string
        description: "Barcode_arr combination"
      _id:
        type: string
        description: "uuid generated to be identical for each level"
      peptides:
        type: array
        description: "list of peptides on chip"
        items:
          type: array
          description: meta data array
          items:
            type: object
            description: meta data object
            properties:
              key: 
                type: string
              value:
                type: string
      run_data:
        type: array
        description: meta data array for run data, should be generate by every run
        items:
          type: object
          properties:
            key:
              type: string
            value:
              type: string
              description: "If entry is same for every image taken then it is a single string and is kept. Otherwise it does not transfer to level 2."
            origin:
              type: string
              description: only occurs if signal file and background file generate different values for a given key.
      sample_data:
        type: array
        description: meta data array for samples
        items:
          type: object
          properties:
            key:
              type: string
            value:
              type: string
    description: "Level 2 object"
# Added by API Auto Mocking Plugin
host: db.kinomecore.com
basePath: /db/1.0.0
schemes:
  - http