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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'
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