---
swagger: "2.0"
info:
  title: vcellapi
  version: 1.0.0
  description: vcellapi as of VCell 6.2 build 23
schemes:
  - https
host: vcellapi.cam.uchc.edu:443
basePath: /.
paths:
  /publication:
    get:
      produces:
        - application/json
      responses:
        200:
          description: list of publications
          schema:
            type: array
            items:
              $ref: '#/definitions/Publication'
      parameters:
        - name: pubId
          in: query
          required: false
          type: string
          description: refines list of one publication matching the id or empty list
        - name: orderBy
          in: query
          required: false
          type: string
          enum:
            - year_asc
            - year_desc
          description: sort by year (...doesnt work ...)
      description: list of modeling publications featuring VCell models
  /publication/{publicationid}:
    get:
      produces:
        - application/json
      responses:
        200:
          description: publication matching id
          schema:
            $ref: '#/definitions/Publication'
        404:
          description: publication not found
      parameters:
        - name: publicationid
          in: path
          required: true
          type: string
          description: publication id
  /biomodel:
    get:
      produces:
        - application/json
      responses:
        200:
          description: Success
          schema:
            type: array
            items:
              $ref: '#/definitions/Biomodel'
      parameters:
        - name: bmName
          in: query
          required: false
          type: string
          description: biomodel name
        - name: bmId
          in: query
          required: false
          type: string
          description: biomodel key
        - name: category
          in: query
          required: false
          type: string
          enum:
            - all
            - public
            - shared
            - mine
            - tutorials
            - educational
          default: all
          description: category of models to include in search
        - name: owner
          in: query
          required: false
          type: string
          description: vcell userid of owner (Owner also excepts all public, shared, education and tutorial ... for now)
        - name: savedLow
          in: query
          required: false
          type: integer
          description: minimum save date (unix timestamp)
        - name: savedHigh
          in: query
          required: false
          type: integer
          description: maximum save date (unix timestamp)
        - name: startRow
          in: query
          required: false
          type: integer
          default: 1
          description: result set  page starting row
        - name: maxRows
          in: query
          required: false
          type: integer
          default: 10
          description: result set page size
        - name: orderBy
          in: query
          required: false
          type: string
          enum:
            - date_desc
            - date_asc
            - name_asc
            - name_desc
          default: date_desc
          description: sort order by date or name
      description: biomodel metadata
  /biomodel/{biomodelid}:
    get:
      produces:
        - application/json
      responses:
        200:
          description: Success
          schema:
            $ref: '#/definitions/Biomodel'
        404:
          description: biomodel not found
      parameters:
        - name: biomodelid
          in: path
          required: true
          type: string
      description: metadata for a particular biomodel
  /biomodel/{biomodelid}/diagram:
    get:
      produces:
        - image/png
      responses:
        200:
          description: normal
        404:
          description: biomodel not found
      parameters:
        - name: biomodelid
          in: path
          required: true
          type: string
  /biomodel/{biomodelid}/biomodel.vcml:
    get:
      produces:
        - application/xml
      responses:
        200:
          description: normal
          schema:
            type: string
        404:
          description: biomodel not found
      parameters:
        - name: biomodelid
          in: path
          required: true
          type: string
  /biomodel/{biomodelid}/simulation/{simulationid}:
    get:
      responses:
        200:
          description: Success
          schema:
            $ref: '#/definitions/Simulation'
        404:
          description: simulation not found
      parameters:
        - name: biomodelid
          in: path
          required: true
          type: string
        - name: simulationid
          in: path
          required: true
          type: string
  /simtask:
    get:
      responses:
        200:
          description: Success
          schema:
            type: array
            items:
              $ref: '#/definitions/Simtask'
  /simstatus:
    get:
      responses:
        200:
          description: Success
  /simdata/{simulationid}:
    get:
      responses:
        200:
          description: Success
      parameters:
        - name: simulationid
          in: path
          required: true
          type: string
  /simdata/{simulationid}/jobindex/{jobindexid}:
    get:
      responses:
        200:
          description: Success
      parameters:
        - name: simulationid
          in: path
          required: true
          type: string
        - name: jobindexid
          in: path
          required: true
          type: string
  /logout:
    get:
      responses:
        200:
          description: Success
  /loginform:
    get:
      responses:
        200:
          description: Success
  /login:
    post:
      responses:
        200:
          description: Success
      parameters:
        - name: Payload
          description: Request Body
          required: false
          in: body
          schema:
            type: object
            properties:
              payload:
                type: string
  /biomodel/{biomodelid}/simulation/{simulationid}/startSimulation:
    post:
      responses:
        200:
          description: Success
      parameters:
        - name: biomodelid
          in: path
          required: true
          type: string
        - name: simulationid
          in: path
          required: true
          type: string
        - name: Payload
          description: Request Body
          required: false
          in: body
          schema:
            type: object
            properties:
              payload:
                type: string
  /biomodel/{biomodelid}/simulation/{simulationid}/save:
    post:
      responses:
        200:
          description: Success
        302:
          description: Redirect to new biomodelid,simulationid /biomodel/newbiomodelid/simulation/newsimulationid
      parameters:
        - name: biomodelid
          in: path
          required: true
          type: string
          description: biomodel id
        - name: simulationid
          in: path
          required: true
          type: string
          description: simulation id
        - name: overrides
          description: send new parameter overrides for cloned simulation
          required: true
          in: body
          schema:
            type: array
            items:
              $ref: '#/definitions/ParameterOverride'
      description: redirect is RESTful, but not sure if must standard for an API. 
  /biomodel/{biomodelid}/simulation/{simulationid}/stopSimulation:
    post:
      responses:
        200:
          description: Success
      parameters:
        - name: biomodelid
          in: path
          required: true
          type: string
        - name: simulationid
          in: path
          required: true
          type: string
        - name: Payload
          description: Request Body
          required: false
          in: body
          schema:
            type: object
            properties:
              payload:
                type: string
definitions:
  Biomodel:
    type: object
    required:
      - bmKey
    properties:
      bmKey:
        type: string
        description: biomodel key
      name:
        type: string
        description: biomodel name
      ownerName:
        type: string
        description: vcell userid of owner
      ownerKey:
        type: string
        description: vcell key of owner
      privacy:
        type: integer
        description: 0 is public, 1 is private, n > 1 is group id
      groupUsers:
        type: array
        items:
          type: string
          description: vcell userid
      savedDate:
        type: integer
        description: unix timestamp when saved
      annot:
        type: string
        description: free text annotation
      branchID:
        type: integer
        description: branch id shared by all versions of same biomodel
      modelKey:
        type: string
        description: model (physiology) key for biomodel
      simulations:
        type: array
        items:
          $ref: '#/definitions/Simulation'
      applications:
        type: array
        items:
          $ref: '#/definitions/Application'
  Application:
    type: object
    properties:
      key:
        type: string
        description: application key
      branchId:
        type: integer
        description: branch id shared by all versions of this application
      name:
        type: string
        description: name of application
      ownerName:
        type: string
        description: vcell userid of application owner (same as biomodel/simulations)
      ownerKey:
        type: string
        description: vcell user key of application owner
      mathKey:
        type: string
        description: key of math description (same as mathKey for matching simulations)
  Simulation:
    type: object
    properties:
      key:
        type: string
        description: simulation key
      branchId:
        type: integer
        description: branch id shared by all versions of this simulation
      name:
        type: string
        description: name of simulation
      ownerName:
        type: string
        description: vcell userid of simulation owner
      ownerKey:
        type: string
        description: vcell user key of simulation owner
      mathKey:
        type: string
        description: key of math description (same as simulation owner; either application or math model)
      solverName:
        type: string
        description: solver name
      scanCount:
        type: integer
        description: number of individual runs in parameter scan (see overrides)
      bioModelLink:
        $ref: '#/definitions/SimBioModelLink'
      overrides:
        type: array
        items:
          $ref: '#/definitions/ParameterOverride'
      parameters:
        type: array
        items:
          $ref: '#/definitions/Parameter'
  SimBioModelLink:
    type: object
    properties:
      bioModelKey:
        type: string
        description: biomodel key
      bioModelBranchId:
        type: integer
        description: branch id shared by all version of this biomodel
      bioModelName:
        type: string
        description: biomodel name
      simContextKey:
        type: string
        description: application key
      simContextBranchId:
        type: integer
        description: branch id shared by all versions of this applicaiton
      simContextName:
        type: string
        description: application name
  ParameterOverride:
    type: object
    required:
      - name
      - otype
      - values
      - cardinality
    properties:
      name:
        type: string
        description: parameter name
      otype:
        enum:
          - none
          - single
          - list
          - linearInterval
          - logInterval
          - variable
        description: type of override
      values:
        type: array
        items:
          type: number
        description: list of new values (for type single or list) or min,max iinterval limits (for type linearInterval or logInterval)
      cardinality:
        type: integer
        default: 1
        description: number of parameter samples
      expression:
        type: string
        description: infix expression for parameter value (in terms of other parameter names)
  Parameter:
    type: object
    properties:
      name:
        type: string
        description: parameter name (in math namescope)
      defaultValue:
        type: number
        description: nominal parameter value (if not overridden)
      modelSymbolContext:
        type: string
        description: path to context within biomodel where biological symbol is defined
      modelSymbolType:
        type: string
        description: type of biological symbol
      modelSymbolName:
        type: string
        description: local name of biological symbol (unique within namescope)
      modelSymbolDesc:
        type: string
        description: description of biological symbol
      modelSymbolUnit:
        type: string
        description: SI unit symbol for biological symbol
  Publication:
    type: object
    required:
      - pubKey
      - title
      - authors
      - year
      - citation
    properties:
      pubKey:
        type: string
        description: publication key
      title:
        type: string
        description: publication title
      authors:
        type: array
        items:
          type: string
        description: publication author list in order of citation
      year:
        type: integer
      citation:
        type: string
      pubmedid:
        type: integer
      doi:
        type: string
      endnoteid:
        type: string
      url:
        type: string
      wittid:
        type: string
      biomodelReferences:
        type: array
        items:
          $ref: '#/definitions/BiomodelReference'
      mathmodelReferences:
        type: array
        items:
          $ref: '#/definitions/MathomodelReference'
  BiomodelReference:
    type: object
    properties:
      bmKey:
        type: string
      name:
        type: string
      ownerName:
        type: string
      ownerKey:
        type: string
  MathomodelReference:
    type: object
    properties:
      mmKey:
        type: string
      name:
        type: string
      ownerName:
        type: string
      ownerKey:
        type: string
  Simtask:
    type: object
    properties:
      simKey:
        type: string
        description: simulation key
      simName:
        type: string
        description: name of simulation
      userName:
        type: string
        description: vcell userid of simulation owner
      userKey:
        type: string
        description: vcell user key of simulation owner
      status:
        type: string
        enum:
          - waiting
          - queued
          - dispatched
          - running
          - completed
          - failed
          - stopped
        description: simulation job status
      submitdate:
        type: integer
        description: unix timestamp of submission time
      startdate:
        type: integer
        description: unix timestamp of start time
      enddate:
        type: integer
        description: unix timestamp of end time
      jobIndex:
        type: integer
        description: job index into simulation scan count (0 to scanCount-1)
      taskId:
        type: integer
        description: ordinal to specify a transaction number (currently counts by 16 to allow for automatic restarts stored in last 3 bits)
      message:
        type: string
        description: user consumable status message
      site:
        type: string
        description: vcell site job was executed on (REL,BETA,ALPHA if a production job)
      computeHost:
        type: string
        description: host where simulation was executed
      schedulerStatus:
        type: string
        enum:
          - waiting
          - queued
          - dispatched
          - running
          - completed
          - stopped
          - failed
        description: status of internal queue
      hasData:
        type: boolean
        description: stored data is available for this simulation
      scanCount:
        type: integer
        description: scan count of the simulation (see jobIndex)
      progress:
        type: number
        description: progress (from 0.0 to 1.0)
      myQueueOrdinal:
        type: integer
        description: this jobs position in the user's queue
      globalQueueOrdinal:
        type: integer
        description: this jobs position in the global queue
      bioModelLink:
        $ref: '#/definitions/SimBioModelLink'