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openapi: 3.0.3
info:
contact:
email: vcell_support@uchc.com
name: VCell API Support
url: https://vcell.org
description: VCell API
license:
name: MIT
url: http://opensource.org/licenses/MIT
termsOfService: Your terms of service here
title: VCell API
version: 1.0.1
servers:
- url: https://vcell.cam.uchc.edu
paths:
/api/v1/Simulation/{simID}/simulationStatus:
get:
operationId: getSimulationStatus
parameters:
- explode: false
in: path
name: simID
required: true
schema:
type: string
style: simple
- explode: true
in: query
name: bioModelID
required: false
schema:
type: string
style: form
- explode: true
in: query
name: mathModelID
required: false
schema:
type: string
style: form
responses:
"200":
content:
application/json:
schema:
$ref: '#/components/schemas/SimulationStatusPersistentRecord'
description: OK
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
summary: Get the status of simulation running
tags:
- Simulation Resource
x-accepts: application/json
/api/v1/Simulation/{simID}/startSimulation:
post:
operationId: startSimulation
parameters:
- explode: false
in: path
name: simID
required: true
schema:
type: string
style: simple
responses:
"200":
content:
application/json:
schema:
items:
$ref: '#/components/schemas/StatusMessage'
type: array
description: OK
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
summary: Start a simulation.
tags:
- Simulation Resource
x-accepts: application/json
/api/v1/Simulation/{simID}/stopSimulation:
post:
operationId: stopSimulation
parameters:
- explode: false
in: path
name: simID
required: true
schema:
type: string
style: simple
responses:
"200":
content:
application/json:
schema:
items:
$ref: '#/components/schemas/StatusMessage'
type: array
description: OK
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
summary: Stop a simulation.
tags:
- Simulation Resource
x-accepts: application/json
/api/v1/admin/usage:
get:
operationId: getUsage
responses:
"200":
content:
application/pdf:
schema:
format: binary
type: string
description: The PDF report
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
summary: Get usage summary
tags:
- Admin Resource
x-accepts: application/json
/api/v1/bioModel:
post:
operationId: saveBioModel
parameters:
- allowEmptyValue: true
description: Name to save new BioModel under. Leave blank if re-saving existing
BioModel.
explode: true
in: query
name: newName
required: false
schema:
type: string
style: form
- allowEmptyValue: true
description: The name of simulations that will be prepared for future execution.
explode: true
in: query
name: simsRequiringUpdates
required: false
schema:
items:
type: string
type: array
style: form
requestBody:
content:
application/xml:
schema:
type: string
description: BioModelVCML which will be saved.
required: true
responses:
"200":
content:
application/xml:
schema:
type: string
description: OK
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
description: Not Allowed
"422":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Unprocessable content submitted
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
summary: Save's the given BioModel. Optional parameters of name and simulations
to update due to math changes. Returns saved BioModel as VCML.
tags:
- Bio Model Resource
x-content-type: application/xml
x-accepts: application/json
/api/v1/bioModel/summaries:
get:
operationId: getBioModelSummaries
parameters:
- description: Includes BioModel summaries that are public or shared with requester.
Default is true.
explode: true
in: query
name: includePublicAndShared
required: false
schema:
type: boolean
style: form
responses:
"200":
content:
application/json:
schema:
items:
$ref: '#/components/schemas/BioModelSummary'
type: array
description: OK
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
summary: Return BioModel summaries.
tags:
- Bio Model Resource
x-accepts: application/json
/api/v1/bioModel/{bioModelID}:
delete:
operationId: deleteBioModel
parameters:
- explode: false
in: path
name: bioModelID
required: true
schema:
type: string
style: simple
responses:
"204":
description: No Content
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
summary: Delete the BioModel from VCell's database.
tags:
- Bio Model Resource
x-accepts: application/json
get:
operationId: getBioModel
parameters:
- explode: false
in: path
name: bioModelID
required: true
schema:
type: string
style: simple
responses:
"200":
content:
application/json:
schema:
$ref: '#/components/schemas/BioModel'
description: OK
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"404":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not found
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
summary: Get BioModel.
tags:
- Bio Model Resource
x-accepts: application/json
/api/v1/bioModel/{bioModelID}/summary:
get:
operationId: getBioModelSummary
parameters:
- explode: false
in: path
name: bioModelID
required: true
schema:
type: string
style: simple
responses:
"200":
content:
application/json:
schema:
$ref: '#/components/schemas/BioModelSummary'
description: OK
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
summary: "All of the text based information about a BioModel (summary, version,\
\ publication status, etc...), but not the actual BioModel itself."
tags:
- Bio Model Resource
x-accepts: application/json
/api/v1/bioModel/{bioModelID}/vcml_download:
get:
operationId: getBioModelVCML
parameters:
- explode: false
in: path
name: bioModelID
required: true
schema:
type: string
style: simple
responses:
"200":
content:
text/xml:
schema:
type: string
description: OK
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"404":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not found
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
summary: Get the BioModel in VCML format.
tags:
- Bio Model Resource
x-accepts: application/json
/api/v1/export/N5:
post:
description: "Create an N5 (ImageJ compatible) export. The request must contain\
\ the standard export information, exportable data type, dataset name, and\
\ sub-volume specifications."
operationId: exportN5
requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/N5ExportRequest'
responses:
"200":
content:
application/json:
schema:
format: int64
type: integer
description: OK
"400":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Bad Request.
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
description: Not Allowed
"422":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Unprocessable content submitted
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
tags:
- Export Resource
x-content-type: application/json
x-accepts: application/json
/api/v1/export/status:
get:
description: Get the status of your export jobs past the timestamp (Unix epoch
in seconds).
operationId: exportStatus
parameters:
- explode: true
in: query
name: timestamp
required: false
schema:
format: int64
type: integer
style: form
responses:
"200":
content:
application/json:
schema:
items:
$ref: '#/components/schemas/ExportEvent'
type: array
description: OK
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
description: Not Allowed
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
tags:
- Export Resource
x-accepts: application/json
/api/v1/fieldData/IDs:
get:
operationId: getAllIDs
responses:
"200":
content:
application/json:
schema:
items:
$ref: '#/components/schemas/FieldDataReference'
type: array
description: OK
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
summary: "Get all of the ids used to identify, and retrieve field data."
tags:
- Field Data Resource
x-accepts: application/json
/api/v1/fieldData/advancedCreate:
post:
operationId: advancedCreate
requestBody:
content:
multipart/form-data:
encoding:
extent:
contentType: application/json
style: form
annotation:
contentType: text/plain
style: form
fileName:
contentType: text/plain
style: form
times:
contentType: text/plain
style: form
file:
contentType: application/octet-stream
style: form
iSize:
contentType: application/json
style: form
channelNames:
contentType: text/plain
style: form
origin:
contentType: application/json
style: form
schema:
$ref: '#/components/schemas/advancedCreate_request'
responses:
"200":
content:
application/json:
schema:
$ref: '#/components/schemas/FieldDataSavedResults'
description: OK
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
description: Not Allowed
"422":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Unprocessable content submitted
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
summary: "Create Field Data with granular detail in one request.The following\
\ files are accepted: .tif and .zip."
tags:
- Field Data Resource
x-content-type: multipart/form-data
x-accepts: application/json
/api/v1/fieldData/analyzeFile:
post:
operationId: analyzeFile
requestBody:
content:
multipart/form-data:
schema:
$ref: '#/components/schemas/analyzeFile_request'
responses:
"200":
content:
application/json:
schema:
$ref: '#/components/schemas/FieldData'
description: OK
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
description: Not Allowed
"422":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Unprocessable content submitted
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
summary: "Analyze uploaded image file (Tiff, Zip, and Non-GPL BioFormats) and\
\ return field data. Color mapped images not supported (the colors in those\
\ images will be interpreted as separate channels). Filenames must be lowercase\
\ alphanumeric, and can contain underscores."
tags:
- Field Data Resource
x-content-type: multipart/form-data
x-accepts: application/json
/api/v1/fieldData/copyModelsFieldData:
post:
operationId: copyModelsFieldData
requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/SourceModel'
responses:
"200":
content:
application/json:
schema:
additionalProperties:
$ref: '#/components/schemas/ExternalDataIdentifier'
type: object
description: OK
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"422":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Unprocessable content submitted
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
summary: "Copy all existing field data from a BioModel/MathModel that you have\
\ access to, but don't own."
tags:
- Field Data Resource
x-content-type: application/json
x-accepts: application/json
/api/v1/fieldData/createFromFile:
post:
operationId: createFromFile
requestBody:
content:
multipart/form-data:
encoding:
file:
contentType: application/octet-stream
style: form
schema:
$ref: '#/components/schemas/createFromFile_request'
responses:
"200":
content:
application/json:
schema:
$ref: '#/components/schemas/FieldDataSavedResults'
description: OK
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
description: Not Allowed
"422":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Unprocessable content submitted
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
summary: "Submit a .zip or .tif file that converts into field data, with all\
\ defaults derived from the file submitted."
tags:
- Field Data Resource
x-content-type: multipart/form-data
x-accepts: application/json
/api/v1/fieldData/createFromSimulation:
post:
operationId: createFromSimulation
requestBody:
content:
application/x-www-form-urlencoded:
schema:
$ref: '#/components/schemas/createFromSimulation_request'
responses:
"201":
description: Created
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
summary: Create new field data from existing simulation results.
tags:
- Field Data Resource
x-content-type: application/x-www-form-urlencoded
x-accepts: application/json
/api/v1/fieldData/delete/{fieldDataID}:
delete:
operationId: delete
parameters:
- explode: false
in: path
name: fieldDataID
required: true
schema:
type: string
style: simple
responses:
"204":
description: No Content
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
summary: Delete the selected field data.
tags:
- Field Data Resource
x-accepts: application/json
/api/v1/fieldData/save:
post:
operationId: save
requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/FieldData'
responses:
"200":
content:
application/json:
schema:
$ref: '#/components/schemas/FieldDataSavedResults'
description: OK
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
description: Not Allowed
"422":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Unprocessable content submitted
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
summary: "Take the generated field data, and save it to the server. User may\
\ adjust the analyzed file before uploading to edit defaults."
tags:
- Field Data Resource
x-content-type: application/json
x-accepts: application/json
/api/v1/fieldData/shape/{fieldDataID}:
get:
operationId: getShapeFromID
parameters:
- explode: false
in: path
name: fieldDataID
required: true
schema:
type: string
style: simple
responses:
"200":
content:
application/json:
schema:
$ref: '#/components/schemas/FieldDataShape'
description: OK
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"404":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not found
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
summary: "Get the shape of the field data. That is it's size, origin, extent,\
\ times, and data identifiers."
tags:
- Field Data Resource
x-accepts: application/json
/api/v1/geometry:
post:
description: Save's VCML with <Geometry> as the root element.
operationId: saveGeometry
parameters:
- description: Name to save new Geometry under. Leave blank if re-saving existing
Geometry.
explode: true
in: query
name: newName
required: false
schema:
type: string
style: form
requestBody:
content:
application/xml:
schema:
type: string
required: true
responses:
"200":
content:
application/xml:
schema:
type: string
description: OK
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
description: Not Allowed
"422":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Unprocessable content submitted
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
tags:
- Geometry Resource
x-content-type: application/xml
x-accepts: application/json
/api/v1/geometry/summaries:
get:
description: Return Geometry summaries.
operationId: getGeometrySummaries
parameters:
- description: Include Geometry summaries that are public and shared with the
requester. Default is true.
explode: true
in: query
name: includePublicAndShared
required: false
schema:
type: boolean
style: form
responses:
"200":
content:
application/json:
schema:
items:
$ref: '#/components/schemas/GeometrySummary'
type: array
description: OK
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
tags:
- Geometry Resource
x-accepts: application/json
/api/v1/geometry/summary/{id}:
get:
description: "All of the text based information about a Geometry (dimensions,\
\ extent, origin, etc...), but not the actual Geometry itself."
operationId: getGeometrySummary
parameters:
- explode: false
in: path
name: id
required: true
schema:
type: string
style: simple
responses:
"200":
content:
application/json:
schema:
$ref: '#/components/schemas/GeometrySummary'
description: OK
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"404":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not found
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
tags:
- Geometry Resource
x-accepts: application/json
/api/v1/geometry/{id}:
delete:
description: Remove specific Geometry.
operationId: deleteGeometry
parameters:
- explode: false
in: path
name: id
required: true
schema:
type: string
style: simple
responses:
"204":
description: No Content
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"404":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not found
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
tags:
- Geometry Resource
x-accepts: application/json
get:
description: Returns <Geometry> as root element in VCML format.
operationId: getGeometryVCML
parameters:
- explode: false
in: path
name: id
required: true
schema:
type: string
style: simple
responses:
"200":
content:
application/xml:
schema:
type: string
description: OK
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"404":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not found
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
tags:
- Geometry Resource
x-accepts: application/json
/api/v1/helloworld:
get:
operationId: getHelloWorld
responses:
"200":
content:
application/json:
schema:
$ref: '#/components/schemas/HelloWorldMessage'
description: OK
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
summary: Get hello world message.
tags:
- Hello World
x-accepts: application/json
/api/v1/image:
post:
description: Save the VCML representation of an image.
operationId: saveImageVCML
parameters:
- description: Name to save new ImageVCML under. Leave blank if re-saving existing
ImageVCML.
explode: true
in: query
name: name
required: false
schema:
type: string
style: form
requestBody:
content:
application/json:
schema:
type: string
required: true
responses:
"200":
content:
text/plain:
schema:
type: string
description: OK
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"422":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Unprocessable content submitted
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
tags:
- VC Image Resource
x-content-type: application/json
x-accepts: application/json
/api/v1/image/summaries:
get:
description: Return Image summaries.
operationId: getImageSummaries
parameters:
- description: Include Image summaries that are public and shared with the requester.
Default is true.
explode: true
in: query
name: includePublicAndShared
required: false
schema:
type: boolean
style: form
responses:
"200":
content:
application/json:
schema:
items:
$ref: '#/components/schemas/VCImageSummary'
type: array
description: OK
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
tags:
- VC Image Resource
x-accepts: application/json
/api/v1/image/summary/{id}:
get:
description: "All of the miscellaneous information about an Image (Extent, ISize,\
\ preview, etc...), but not the actual Image itself."
operationId: getImageSummary
parameters:
- explode: false
in: path
name: id
required: true
schema:
type: string
style: simple
responses:
"200":
content:
application/json:
schema:
$ref: '#/components/schemas/VCImageSummary'
description: OK
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"404":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not found
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
tags:
- VC Image Resource
x-accepts: application/json
/api/v1/image/{id}:
delete:
description: Remove specific image VCML.
operationId: deleteImageVCML
parameters:
- explode: false
in: path
name: id
required: true
schema:
type: string
style: simple
responses:
"204":
description: No Content
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"404":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not found
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
tags:
- VC Image Resource
x-accepts: application/json
get:
description: Get specific image VCML.
operationId: getImageVCML
parameters:
- explode: false
in: path
name: id
required: true
schema:
type: string
style: simple
responses:
"200":
content:
text/plain:
schema:
type: string
description: OK
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"404":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not found
"422":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Unprocessable content submitted
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
tags:
- VC Image Resource
x-accepts: application/json
/api/v1/mathModel:
post:
operationId: saveMathModel
parameters:
- description: Name to save new MathModel under. Leave blank if re-saving existing
MathModel.
explode: true
in: query
name: newName
required: false
schema:
type: string
style: form
- description: The name of simulations that will be prepared for future execution.
explode: true
in: query
name: simNames
required: false
schema:
items:
type: string
type: array
style: form
requestBody:
content:
application/xml:
schema:
type: string
required: true
responses:
"200":
content:
application/xml:
schema:
type: string
description: OK
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
description: Not Allowed
"422":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Unprocessable content submitted
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
tags:
- Math Model Resource
x-content-type: application/xml
x-accepts: application/json
/api/v1/mathModel/summaries:
get:
description: Return MathModel summaries.
operationId: getSummaries
parameters:
- description: Include MathModel summaries that are public and shared with the
requester. Default is true.
explode: true
in: query
name: includePublicAndShared
required: false
schema:
type: boolean
style: form
responses:
"200":
content:
application/json:
schema:
items:
$ref: '#/components/schemas/MathModelSummary'
type: array
description: OK
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
tags:
- Math Model Resource
x-accepts: application/json
/api/v1/mathModel/summary/{id}:
get:
description: "All of the text based information about a MathModel (summary,\
\ version, publication status, etc...), but not the actual MathModel itself."
operationId: getSummary
parameters:
- explode: false
in: path
name: id
required: true
schema:
type: string
style: simple
responses:
"200":
content:
application/json:
schema:
$ref: '#/components/schemas/MathModelSummary'
description: OK
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"404":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not found
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
tags:
- Math Model Resource
x-accepts: application/json
/api/v1/mathModel/{id}:
delete:
description: Remove specific Math Model.
operationId: deleteMathModel
parameters:
- explode: false
in: path
name: id
required: true
schema:
type: string
style: simple
responses:
"204":
description: No Content
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"404":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not found
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
tags:
- Math Model Resource
x-accepts: application/json
get:
description: Returns MathModel in VCML format.
operationId: getVCML
parameters:
- explode: false
in: path
name: id
required: true
schema:
type: string
style: simple
responses:
"200":
content:
application/xml:
schema:
type: string
description: OK
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"404":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not found
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
tags:
- Math Model Resource
x-accepts: application/json
/api/v1/publications:
get:
operationId: getPublications
responses:
"200":
content:
application/json:
schema:
items:
$ref: '#/components/schemas/Publication'
type: array
description: OK
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
summary: Get all publications
tags:
- Publication Resource
x-accepts: application/json
post:
operationId: createPublication
requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/Publication'
responses:
"200":
content:
application/json:
schema:
format: int64
type: integer
description: OK
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
summary: Create publication
tags:
- Publication Resource
x-content-type: application/json
x-accepts: application/json
put:
operationId: updatePublication
requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/Publication'
responses:
"200":
content:
application/json:
schema:
$ref: '#/components/schemas/Publication'
description: OK
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
summary: Update publication
tags:
- Publication Resource
x-content-type: application/json
x-accepts: application/json
/api/v1/publications/{id}:
delete:
operationId: deletePublication
parameters:
- explode: false
in: path
name: id
required: true
schema:
format: int64
type: integer
style: simple
responses:
"204":
description: No Content
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"404":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not found
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
summary: Delete publication
tags:
- Publication Resource
x-accepts: application/json
get:
operationId: getPublicationById
parameters:
- explode: false
in: path
name: id
required: true
schema:
format: int64
type: integer
style: simple
responses:
"200":
content:
application/json:
schema:
$ref: '#/components/schemas/Publication'
description: OK
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
summary: Get publication by ID
tags:
- Publication Resource
x-accepts: application/json
/api/v1/solver/getFVSolverInput:
post:
operationId: getFVSolverInputFromSBML
requestBody:
content:
multipart/form-data:
schema:
$ref: '#/components/schemas/getFVSolverInputFromSBML_request'
responses:
"200":
content:
application/octet-stream:
schema:
format: binary
type: string
description: OK
"422":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Unprocessable content submitted
summary: Retrieve finite volume input from SBML spatial model.
tags:
- Solver Resource
x-content-type: multipart/form-data
x-accepts: application/json
/api/v1/solver/getFVSolverInputFromVCML:
post:
operationId: getFVSolverInputFromVCML
requestBody:
content:
multipart/form-data:
schema:
$ref: '#/components/schemas/getFVSolverInputFromVCML_request'
responses:
"200":
content:
application/octet-stream:
schema:
format: binary
type: string
description: OK
"422":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Unprocessable content submitted
summary: Retrieve finite volume input from SBML spatial model.
tags:
- Solver Resource
x-content-type: multipart/form-data
x-accepts: application/json
/api/v1/users/bearerToken:
post:
operationId: getLegacyApiToken
responses:
"200":
content:
application/json:
schema:
$ref: '#/components/schemas/AccesTokenRepresentationRecord'
description: OK
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
description: Not Allowed
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
summary: Get token for legacy API
tags:
- Users Resource
x-accepts: application/json
/api/v1/users/forgotLegacyPassword:
post:
operationId: forgotLegacyPassword
parameters:
- explode: true
in: query
name: userID
required: false
schema:
type: string
style: form
responses:
"200":
description: Legacy password sent in email
"401":
description: Need to login to Auth0
"403":
description: Not Allowed
"500":
description: Internal Error
security:
- openId:
- user
summary: "The end user has forgotten the legacy password they used for VCell,\
\ so they will be emailed it."
tags:
- Users Resource
x-accepts: application/json
/api/v1/users/guestBearerToken:
post:
operationId: getGuestLegacyApiToken
responses:
"200":
content:
application/json:
schema:
$ref: '#/components/schemas/AccesTokenRepresentationRecord'
description: OK
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
summary: Method to get legacy tokens for guest users
tags:
- Users Resource
x-accepts: application/json
/api/v1/users/mapUser:
post:
operationId: mapUser
requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/UserLoginInfoForMapping'
responses:
"200":
content:
application/json:
schema:
type: boolean
description: OK
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
summary: map vcell user
tags:
- Users Resource
x-content-type: application/json
x-accepts: application/json
/api/v1/users/mappedUser:
get:
operationId: getMappedUser
responses:
"200":
content:
application/json:
schema:
$ref: '#/components/schemas/UserIdentityJSONSafe'
description: "Successful, returning the identity"
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
description: Not Allowed
"409":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Conflict with server state.
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
summary: Get mapped VCell identity
tags:
- Users Resource
x-accepts: application/json
/api/v1/users/me:
get:
operationId: getMe
responses:
"200":
content:
application/json:
schema:
$ref: '#/components/schemas/Identity'
description: OK
summary: Get current user
tags:
- Users Resource
x-accepts: application/json
/api/v1/users/newUser:
post:
operationId: mapNewUser
requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/UserRegistrationInfo'
responses:
"200":
description: "Successful, returning the identity"
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
description: Not Allowed
"409":
description: "VCell Identity not mapped, userid already exists"
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
summary: create vcell user
tags:
- Users Resource
x-content-type: application/json
x-accepts: application/json
/api/v1/users/processMagicLink:
get:
operationId: processMagicLink
parameters:
- explode: true
in: query
name: magic
required: false
schema:
type: string
style: form
responses:
"200":
description: User mapped successfully
"400":
description: Invalid or expired magic link
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
summary: Process the magic link and map the user
tags:
- Users Resource
x-accepts: application/json
/api/v1/users/requestRecoveryEmail:
post:
operationId: requestRecoveryEmail
parameters:
- explode: true
in: query
name: email
required: false
schema:
type: string
style: form
- explode: true
in: query
name: userID
required: false
schema:
type: string
style: form
responses:
"200":
description: magic link sent in email if appropriate
"400":
description: unable to process request
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
description: Not Allowed
"404":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not found
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
summary: request a recovery email to link a VCell account.
tags:
- Users Resource
x-accepts: application/json
/api/v1/users/unmapUser/{userName}:
put:
operationId: unmapUser
parameters:
- explode: false
in: path
name: userName
required: true
schema:
type: string
style: simple
responses:
"200":
content:
application/json:
schema:
type: boolean
description: OK
"401":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Authenticated
"403":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Not Allowed
"500":
content:
application/json:
schema:
$ref: '#/components/schemas/VCellHTTPError'
description: Data Access Exception
security:
- openId:
- user
summary: remove vcell identity mapping
tags:
- Users Resource
x-accepts: application/json
components:
schemas:
AccesTokenRepresentationRecord:
example:
creationDateSeconds: 0
userId: userId
expireDateSeconds: 6
userKey: userKey
token: token
properties:
token:
type: string
creationDateSeconds:
format: int64
type: integer
expireDateSeconds:
format: int64
type: integer
userId:
type: string
userKey:
type: string
type: object
AnalyticCurve:
allOf:
- $ref: '#/components/schemas/Curve'
properties:
type:
default: AnalyticCurve
type: string
expX:
type: string
expY:
type: string
expZ:
type: string
offset:
$ref: '#/components/schemas/Coordinate'
analyticOffset:
$ref: '#/components/schemas/Coordinate'
defaultNumSamples:
format: int32
type: integer
segmentCount:
format: int32
type: integer
valid:
type: boolean
required:
- type
type: object
AnnotatedFunctionDTO:
example:
functionName: functionName
domain:
name: name
functionType:
defaultUnits: defaultUnits
name: name
typeName: typeName
defaultLabel: defaultLabel
units: units
label: label
type: 0
variableDomain: null
legacyWarn: true
error: error
category: null
functionExpression: functionExpression
properties:
functionName:
type: string
functionExpression:
type: string
error:
type: string
domain:
$ref: '#/components/schemas/Domain'
functionType:
$ref: '#/components/schemas/VariableType'
category:
$ref: '#/components/schemas/FunctionCategory'
type: object
Application:
type: object
ApplicationInfo:
example:
geometryName: geometryName
name: name
type: null
dimensions: 7
properties:
name:
type: string
type:
$ref: '#/components/schemas/MathType'
dimensions:
format: int32
type: integer
geometryName:
type: string
type: object
BatchSystemType:
enum:
- PBS
- SGE
- SLURM
type: string
BioModel:
example:
branchID: branchID
physModelKey: physModelKey
bmKey: bmKey
ownerName: ownerName
name: name
privacy: 0
groupUsers:
- groupUsers
- groupUsers
annot: annot
simulationKeyList:
- null
- null
ownerKey: ownerKey
savedDate: 6
applications:
- null
- null
properties:
bmKey:
type: string
name:
type: string
privacy:
format: int32
type: integer
groupUsers:
items:
type: string
type: array
savedDate:
format: int64
type: integer
annot:
type: string
branchID:
type: string
physModelKey:
type: string
ownerName:
type: string
ownerKey:
type: string
simulationKeyList:
items:
$ref: '#/components/schemas/KeyValue'
type: array
applications:
items:
$ref: '#/components/schemas/Application'
type: array
type: object
BioModelChildSummary:
example:
simulationContextAnnotations:
- simulationContextAnnotations
- simulationContextAnnotations
scAnnots:
- scAnnots
- scAnnots
simulationContextNames:
- simulationContextNames
- simulationContextNames
geoNames:
- geoNames
- geoNames
geometryDimensions:
- 2
- 2
geometryNames:
- geometryNames
- geometryNames
simAnnots:
- - simAnnots
- simAnnots
- - simAnnots
- simAnnots
geoDims:
- 5
- 5
appTypes:
- null
- null
scNames:
- scNames
- scNames
applicationInfo:
- geometryName: geometryName
name: name
type: null
dimensions: 7
- geometryName: geometryName
name: name
type: null
dimensions: 7
simNames:
- - simNames
- simNames
- - simNames
- simNames
properties:
scNames:
items:
type: string
type: array
scAnnots:
items:
type: string
type: array
geoNames:
items:
type: string
type: array
geoDims:
items:
format: int32
type: integer
type: array
appTypes:
items:
$ref: '#/components/schemas/MathType'
type: array
simNames:
items:
items:
type: string
type: array
type: array
simAnnots:
items:
items:
type: string
type: array
type: array
geometryDimensions:
items:
format: int32
type: integer
type: array
geometryNames:
items:
type: string
type: array
simulationContextAnnotations:
items:
type: string
type: array
simulationContextNames:
items:
type: string
type: array
applicationInfo:
items:
$ref: '#/components/schemas/ApplicationInfo'
type: array
type: object
BioModelSummary:
example:
summary:
simulationContextAnnotations:
- simulationContextAnnotations
- simulationContextAnnotations
scAnnots:
- scAnnots
- scAnnots
simulationContextNames:
- simulationContextNames
- simulationContextNames
geoNames:
- geoNames
- geoNames
geometryDimensions:
- 2
- 2
geometryNames:
- geometryNames
- geometryNames
simAnnots:
- - simAnnots
- simAnnots
- - simAnnots
- simAnnots
geoDims:
- 5
- 5
appTypes:
- null
- null
scNames:
- scNames
- scNames
applicationInfo:
- geometryName: geometryName
name: name
type: null
dimensions: 7
- geometryName: geometryName
name: name
type: null
dimensions: 7
simNames:
- - simNames
- simNames
- - simNames
- simNames
publicationInformation:
- vcDocumentType: null
theHashCode: 9
citation: citation
title: title
publicationKey: publicationKey
pubmedid: pubmedid
user:
mySpecials:
- null
- null
userName: userName
key: key
url: url
versionKey: versionKey
authors:
- authors
- authors
doi: doi
pubdate: 2022-03-10T00:00:00.000+00:00
- vcDocumentType: null
theHashCode: 9
citation: citation
title: title
publicationKey: publicationKey
pubmedid: pubmedid
user:
mySpecials:
- null
- null
userName: userName
key: key
url: url
versionKey: versionKey
authors:
- authors
- authors
doi: doi
pubdate: 2022-03-10T00:00:00.000+00:00
version:
date: 2000-01-23T04:56:07.000+00:00
owner:
mySpecials:
- null
- null
userName: userName
key: key
branchID: 0.8008281904610115
flag:
archived: true
current: true
intValue: 1
versionFlag: 6
published: true
groupAccess:
groupid: 5.962133916683182
description: description
name: name
annot: annot
branchPointRefKey: branchPointRefKey
versionKey: versionKey
vCellSoftwareVersion:
vcellSite: null
patchVersion: 4
buildInt: 7
description: description
majorVersion: 3
minorVersion: 2
buildNumber: buildNumber
softwareVersionString: softwareVersionString
versionNumber: versionNumber
properties:
version:
$ref: '#/components/schemas/Version'
summary:
$ref: '#/components/schemas/BioModelChildSummary'
publicationInformation:
items:
$ref: '#/components/schemas/PublicationInfo'
type: array
vCellSoftwareVersion:
$ref: '#/components/schemas/VCellSoftwareVersion'
type: object
BiomodelRef:
example:
bmKey: 5
ownerName: ownerName
name: name
versionFlag: 7
ownerKey: 2
properties:
bmKey:
format: int64
type: integer
name:
type: string
ownerName:
type: string
ownerKey:
format: int64
type: integer
versionFlag:
format: int32
type: integer
type: object
CompositeCurve:
allOf:
- $ref: '#/components/schemas/Curve'
properties:
type:
default: CompositeCurve
type: string
fieldCurves:
items: {}
type: array
curveCount:
format: int32
type: integer
defaultNumSamples:
format: int32
type: integer
segmentCount:
format: int32
type: integer
valid:
type: boolean
required:
- type
type: object
ControlPointCurve:
allOf:
- $ref: '#/components/schemas/Curve'
discriminator:
mapping:
Spline: '#/components/schemas/Spline'
SampledCurve: '#/components/schemas/SampledCurve'
propertyName: type
properties:
type:
default: ControlPointCurve
type: string
controlPoints:
items:
$ref: '#/components/schemas/Coordinate'
type: array
controlPointCount:
format: int32
type: integer
controlPointsVector:
items:
$ref: '#/components/schemas/Coordinate'
type: array
maxControlPoints:
format: int32
type: integer
minControlPoints:
format: int32
type: integer
controlPointAddable:
type: boolean
valid:
type: boolean
required:
- type
type: object
Coordinate:
example:
x: 1.4658129805029452
"y": 5.962133916683182
z: 5.637376656633329
properties:
x:
format: double
type: number
"y":
format: double
type: number
z:
format: double
type: number
type: object
Curve:
discriminator:
mapping:
AnalyticCurve: '#/components/schemas/AnalyticCurve'
CompositeCurve: '#/components/schemas/CompositeCurve'
ControlPointCurve: '#/components/schemas/ControlPointCurve'
propertyName: type
example:
spatialLength: 3.616076749251911
valid: true
bClosed: true
endingCoordinate:
x: 1.4658129805029452
"y": 5.962133916683182
z: 5.637376656633329
description: description
beginningCoordinate:
x: 1.4658129805029452
"y": 5.962133916683182
z: 5.637376656633329
numSamplePoints: 7
closed: true
type: type
defaultNumSamples: 2
segmentCount: 9
properties:
bClosed:
type: boolean
description:
type: string
type:
type: string
beginningCoordinate:
$ref: '#/components/schemas/Coordinate'
defaultNumSamples:
format: int32
type: integer
endingCoordinate:
$ref: '#/components/schemas/Coordinate'
numSamplePoints:
format: int32
type: integer
segmentCount:
format: int32
type: integer
spatialLength:
format: double
type: number
closed:
type: boolean
valid:
type: boolean
required:
- type
type: object
CurveSelectionInfo:
example:
fieldControlPoint: 4
fieldCurve:
spatialLength: 3.616076749251911
valid: true
bClosed: true
endingCoordinate:
x: 1.4658129805029452
"y": 5.962133916683182
z: 5.637376656633329
description: description
beginningCoordinate:
x: 1.4658129805029452
"y": 5.962133916683182
z: 5.637376656633329
numSamplePoints: 7
closed: true
type: type
defaultNumSamples: 2
segmentCount: 9
fieldControlPointExtended: 1
fieldDirectionNegative: true
fieldSegment: 7
fieldUExtended: 1.0246457001441578
fieldType: 2
crossing: true
fieldU: 1.2315135367772556
fieldSegmentExtended: 6
properties:
fieldCurve:
$ref: '#/components/schemas/Curve'
fieldType:
format: int32
type: integer
fieldControlPoint:
format: int32
type: integer
fieldSegment:
format: int32
type: integer
fieldU:
format: double
type: number
fieldUExtended:
format: double
type: number
fieldControlPointExtended:
format: int32
type: integer
fieldSegmentExtended:
format: int32
type: integer
fieldDirectionNegative:
type: boolean
crossing:
type: boolean
type: object
DataIdentifier:
example:
variableType:
defaultUnits: defaultUnits
name: name
typeName: typeName
defaultLabel: defaultLabel
units: units
label: label
type: 0
variableDomain: null
legacyWarn: true
visible: true
displayName: displayName
bFunction: true
domain:
name: name
function: true
name: name
properties:
name:
type: string
displayName:
type: string
variableType:
$ref: '#/components/schemas/VariableType'
domain:
$ref: '#/components/schemas/Domain'
bFunction:
type: boolean
function:
type: boolean
visible:
type: boolean
type: object
Date:
example: 2022-03-10
format: date
type: string
DetailedState:
enum:
- UNKNOWN
- DATAMOVEREVENT_MOVED
- WORKEREVENT_WORKERALIVE
- JOB_WAITING
- JOB_QUEUED
- JOB_QUEUED_RETRY
- JOB_DISPATCHED
- JOB_ACCEPTED
- SOLVER_READY
- SOLVER_STARTING_INIT
- SOLVEREVENT_STARTING_PROC_GEOM
- SOLVEREVENT_STARTING_RESAMPLE_FD
- SOLVER_RUNNING_INIT
- SOLVER_RUNNING_INIT_INPUT_FILE
- SOLVER_RUNNING_INIT_CODEGEN
- SOLVER_RUNNING_INIT_COMPILING
- SOLVER_RUNNING_INIT_COMPILECMD
- SOLVER_RUNNING_INIT_COMPILE_OK
- SOLVER_RUNNING_INIT_LINKING
- SOLVER_RUNNING_INIT_LINKCMD
- SOLVER_RUNNING_INIT_LINK_OK
- SOLVER_RUNNING_INIT_COMPILELINK_OK
- SOLVEREVENT_STARTING_INIT
- SOLVEREVENT_STARTING_CODEGEN
- SOLVEREVENT_STARTING_COMPILELINK
- SOLVEREVENT_STARTING_INPUT_FILE
- SOLVEREVENT_STARTING
- SOLVEREVENT_STARTING_SUBMITTING
- SOLVEREVENT_STARTING_SUBMITTED
- WORKEREVENT_STARTING
- SOLVEREVENT_RUNNING_START
- SOLVER_RUNNING_START
- JOB_RUNNING_UNKNOWN
- SOLVEREVENT_PRINTED
- WORKEREVENT_DATA
- JOB_RUNNING
- SOLVEREVENT_PROGRESS
- WORKEREVENT_PROGRESS
- WORKEREVENT_WORKEREXIT_NORMAL
- WORKEREVENT_WORKEREXIT_ERROR
- SOLVEREVENT_FINISHED
- SOLVER_FINISHED
- WORKEREVENT_COMPLETED
- JOB_COMPLETED
- SOLVER_STOPPED
- JOB_STOPPED
- JOB_FAILED_UNKNOWN
- SOLVER_ABORTED
- WORKEREVENT_FAILURE
- JOB_FAILED
type: string
Domain:
example:
name: name
properties:
name:
type: string
type: object
ExportEvent:
example:
dataKey: dataKey
jobID: 6
dataIdString: dataIdString
format: format
humanReadableData:
numChannels: 5
applicationType: applicationType
differentParameterValues:
- differentParameterValues
- differentParameterValues
serverSavedFileName: serverSavedFileName
subVolume:
key: subVolume
zSlices: 1
simulationName: simulationName
biomodelName: biomodelName
nonSpatial: true
tSlices: 5
applicationName: applicationName
progress: 0.8008281904610115
location: location
eventType: null
user:
mySpecials:
- null
- null
userName: userName
key: key
properties:
eventType:
$ref: '#/components/schemas/ExportProgressType'
progress:
format: double
type: number
format:
type: string
location:
type: string
user:
$ref: '#/components/schemas/User'
jobID:
format: int64
type: integer
dataKey:
type: string
dataIdString:
type: string
humanReadableData:
$ref: '#/components/schemas/HumanReadableExportData'
type: object
ExportProgressType:
enum:
- EXPORT_START
- EXPORT_COMPLETE
- EXPORT_FAILURE
- EXPORT_ASSEMBLING
- EXPORT_PROGRESS
type: string
ExportableDataType:
enum:
- ODE_VARIABLE_DATA
- PDE_VARIABLE_DATA
- PDE_PARTICLE_DATA
type: string
Expression:
type: string
Extent:
example:
x: 7.061401241503109
"y": 9.301444243932576
z: 3.616076749251911
properties:
x:
format: double
type: number
xml:
attribute: true
"y":
format: double
type: number
xml:
attribute: true
z:
format: double
type: number
xml:
attribute: true
type: object
ExternalDataIdentifier:
example:
owner:
mySpecials:
- null
- null
userName: userName
key: key
dataKey: dataKey
simulationKey: simulationKey
jobIndex: 0
name: name
key: key
parameterScanType: true
properties:
key:
type: string
owner:
$ref: '#/components/schemas/User'
name:
type: string
jobIndex:
format: int32
type: integer
simulationKey:
type: string
parameterScanType:
type: boolean
dataKey:
type: string
type: object
FieldData:
example:
extent:
x: 7.061401241503109
"y": 9.301444243932576
z: 3.616076749251911
annotation: annotation
times:
- 1.4658129805029452
- 1.4658129805029452
doubleSpecData:
- - - 6.027456183070403
- 6.027456183070403
- - 6.027456183070403
- 6.027456183070403
- - - 6.027456183070403
- 6.027456183070403
- - 6.027456183070403
- 6.027456183070403
origin:
x: 5.962133916683182
"y": 5.637376656633329
z: 2.3021358869347655
isize:
x: 2
"y": 4
z: 7
name: name
varNames:
- varNames
- varNames
shortSpecData:
- - - 0
- 0
- - 0
- 0
- - - 0
- 0
- - 0
- 0
properties:
shortSpecData:
items:
items:
items:
type: integer
type: array
type: array
type: array
doubleSpecData:
items:
items:
items:
format: double
type: number
type: array
type: array
type: array
varNames:
items:
type: string
type: array
times:
items:
format: double
type: number
type: array
origin:
$ref: '#/components/schemas/Origin'
extent:
$ref: '#/components/schemas/Extent'
isize:
$ref: '#/components/schemas/ISize'
annotation:
type: string
name:
type: string
type: object
FieldDataReference:
example:
annotation: annotation
fieldDataID:
owner:
mySpecials:
- null
- null
userName: userName
key: key
dataKey: dataKey
simulationKey: simulationKey
jobIndex: 0
name: name
key: key
parameterScanType: true
simulationsReferencingThisID:
- null
- null
properties:
fieldDataID:
$ref: '#/components/schemas/ExternalDataIdentifier'
annotation:
type: string
simulationsReferencingThisID:
items:
$ref: '#/components/schemas/KeyValue'
type: array
type: object
FieldDataSavedResults:
example:
fieldDataName: fieldDataName
fieldDataKey: fieldDataKey
properties:
fieldDataName:
type: string
fieldDataKey:
type: string
type: object
FieldDataShape:
example:
extent:
x: 7.061401241503109
"y": 9.301444243932576
z: 3.616076749251911
times:
- 0.8008281904610115
- 0.8008281904610115
origin:
x: 5.962133916683182
"y": 5.637376656633329
z: 2.3021358869347655
isize:
x: 2
"y": 4
z: 7
dataIdentifier:
- variableType:
defaultUnits: defaultUnits
name: name
typeName: typeName
defaultLabel: defaultLabel
units: units
label: label
type: 0
variableDomain: null
legacyWarn: true
visible: true
displayName: displayName
bFunction: true
domain:
name: name
function: true
name: name
- variableType:
defaultUnits: defaultUnits
name: name
typeName: typeName
defaultLabel: defaultLabel
units: units
label: label
type: 0
variableDomain: null
legacyWarn: true
visible: true
displayName: displayName
bFunction: true
domain:
name: name
function: true
name: name
properties:
extent:
$ref: '#/components/schemas/Extent'
origin:
$ref: '#/components/schemas/Origin'
isize:
$ref: '#/components/schemas/ISize'
dataIdentifier:
items:
$ref: '#/components/schemas/DataIdentifier'
type: array
times:
items:
format: double
type: number
type: array
type: object
FunctionCategory:
enum:
- PREDEFINED
- OLDUSERDEFINED
- OUTPUTFUNCTION
- POSTPROCESSFUNCTION
type: string
GIFImage:
example:
size:
x: 2
"y": 4
z: 7
gifEncodedData: ""
properties:
gifEncodedData:
format: binary
type: string
size:
$ref: '#/components/schemas/ISize'
type: object
GeometryMode:
enum:
- GEOMETRY_SELECTIONS
- GEOMETRY_SLICE
- GEOMETRY_FULL
type: string
GeometrySpecDTO:
example:
selections:
- variableType:
defaultUnits: defaultUnits
name: name
typeName: typeName
defaultLabel: defaultLabel
units: units
label: label
type: 0
variableDomain: null
legacyWarn: true
varType:
defaultUnits: defaultUnits
name: name
typeName: typeName
defaultLabel: defaultLabel
units: units
label: label
type: 0
variableDomain: null
legacyWarn: true
smallestMeshCellDimensionLength: 7.457744773683766
closed: true
type: type
point: true
curveSelectionInfo:
fieldControlPoint: 4
fieldCurve:
spatialLength: 3.616076749251911
valid: true
bClosed: true
endingCoordinate:
x: 1.4658129805029452
"y": 5.962133916683182
z: 5.637376656633329
description: description
beginningCoordinate:
x: 1.4658129805029452
"y": 5.962133916683182
z: 5.637376656633329
numSamplePoints: 7
closed: true
type: type
defaultNumSamples: 2
segmentCount: 9
fieldControlPointExtended: 1
fieldDirectionNegative: true
fieldSegment: 7
fieldUExtended: 1.0246457001441578
fieldType: 2
crossing: true
fieldU: 1.2315135367772556
fieldSegmentExtended: 6
- variableType:
defaultUnits: defaultUnits
name: name
typeName: typeName
defaultLabel: defaultLabel
units: units
label: label
type: 0
variableDomain: null
legacyWarn: true
varType:
defaultUnits: defaultUnits
name: name
typeName: typeName
defaultLabel: defaultLabel
units: units
label: label
type: 0
variableDomain: null
legacyWarn: true
smallestMeshCellDimensionLength: 7.457744773683766
closed: true
type: type
point: true
curveSelectionInfo:
fieldControlPoint: 4
fieldCurve:
spatialLength: 3.616076749251911
valid: true
bClosed: true
endingCoordinate:
x: 1.4658129805029452
"y": 5.962133916683182
z: 5.637376656633329
description: description
beginningCoordinate:
x: 1.4658129805029452
"y": 5.962133916683182
z: 5.637376656633329
numSamplePoints: 7
closed: true
type: type
defaultNumSamples: 2
segmentCount: 9
fieldControlPointExtended: 1
fieldDirectionNegative: true
fieldSegment: 7
fieldUExtended: 1.0246457001441578
fieldType: 2
crossing: true
fieldU: 1.2315135367772556
fieldSegmentExtended: 6
sliceNumber: 4
geometryMode: null
axis: 1
properties:
selections:
items:
$ref: '#/components/schemas/SpatialSelection'
type: array
axis:
format: int32
type: integer
sliceNumber:
format: int32
type: integer
geometryMode:
$ref: '#/components/schemas/GeometryMode'
type: object
GeometrySummary:
example:
extent:
x: 7.061401241503109
"y": 9.301444243932576
z: 3.616076749251911
origin:
x: 5.962133916683182
"y": 5.637376656633329
z: 2.3021358869347655
imageRef: imageRef
dimension: 0
version:
date: 2000-01-23T04:56:07.000+00:00
owner:
mySpecials:
- null
- null
userName: userName
key: key
branchID: 0.8008281904610115
flag:
archived: true
current: true
intValue: 1
versionFlag: 6
published: true
groupAccess:
groupid: 5.962133916683182
description: description
name: name
annot: annot
branchPointRefKey: branchPointRefKey
versionKey: versionKey
softwareVersion:
vcellSite: null
patchVersion: 4
buildInt: 7
description: description
majorVersion: 3
minorVersion: 2
buildNumber: buildNumber
softwareVersionString: softwareVersionString
versionNumber: versionNumber
properties:
dimension:
format: int32
type: integer
origin:
$ref: '#/components/schemas/Origin'
extent:
$ref: '#/components/schemas/Extent'
imageRef:
type: string
version:
$ref: '#/components/schemas/Version'
softwareVersion:
$ref: '#/components/schemas/VCellSoftwareVersion'
type: object
GroupAccess:
discriminator:
mapping:
GroupAccessNone: '#/components/schemas/GroupAccessNone'
GroupAccessSome: '#/components/schemas/GroupAccessSome'
GroupAccessAll: '#/components/schemas/GroupAccessAll'
propertyName: type
example:
groupid: 5.962133916683182
description: description
properties:
groupid:
type: number
description:
type: string
required:
- groupid
type: object
GroupAccessAll:
allOf:
- $ref: '#/components/schemas/GroupAccess'
properties:
type:
default: GroupAccessAll
type: string
description:
type: string
required:
- type
type: object
GroupAccessNone:
allOf:
- $ref: '#/components/schemas/GroupAccess'
properties:
type:
default: GroupAccessNone
type: string
description:
type: string
required:
- type
type: object
GroupAccessSome:
allOf:
- $ref: '#/components/schemas/GroupAccess'
properties:
type:
default: GroupAccessSome
type: string
hash:
type: number
groupMembers:
items:
$ref: '#/components/schemas/User'
type: array
hiddenMembers:
items:
type: boolean
type: array
description:
type: string
hiddenGroupMembers:
items:
$ref: '#/components/schemas/User'
type: array
normalGroupMembers:
items:
$ref: '#/components/schemas/User'
type: array
required:
- type
type: object
HelloWorldMessage:
example:
message: message
properties:
message:
type: string
type: object
HtcJobID:
example:
server: server
batchSystemType: null
jobNumber: 0
properties:
jobNumber:
format: int64
type: integer
server:
type: string
batchSystemType:
$ref: '#/components/schemas/BatchSystemType'
type: object
HumanReadableExportData:
example:
numChannels: 5
applicationType: applicationType
differentParameterValues:
- differentParameterValues
- differentParameterValues
serverSavedFileName: serverSavedFileName
subVolume:
key: subVolume
zSlices: 1
simulationName: simulationName
biomodelName: biomodelName
nonSpatial: true
tSlices: 5
applicationName: applicationName
properties:
simulationName:
type: string
biomodelName:
type: string
applicationName:
type: string
differentParameterValues:
items:
type: string
type: array
applicationType:
type: string
serverSavedFileName:
type: string
nonSpatial:
type: boolean
subVolume:
additionalProperties:
type: string
type: object
zSlices:
format: int32
type: integer
tSlices:
format: int32
type: integer
numChannels:
format: int32
type: integer
type: object
ISize:
example:
x: 2
"y": 4
z: 7
properties:
x:
format: int32
type: integer
"y":
format: int32
type: integer
z:
format: int32
type: integer
type: object
Identity:
example:
credentials:
- credentials
- credentials
roles:
- roles
- roles
principal_name: principal_name
attributes:
- attributes
- attributes
properties:
principal_name:
type: string
roles:
items:
type: string
type: array
attributes:
items:
type: string
type: array
credentials:
items:
type: string
type: array
type: object
Instant:
example: 2022-03-10T16:15:50Z
format: date-time
type: string
KeyValue:
type: string
MathModelChildSummary:
example:
simulationAnnotations:
- simulationAnnotations
- simulationAnnotations
simulationNames:
- simulationNames
- simulationNames
geometryName: geometryName
geometryDimension: 0
modelType: null
properties:
modelType:
$ref: '#/components/schemas/MathType'
geometryDimension:
format: int32
type: integer
geometryName:
type: string
simulationAnnotations:
items:
type: string
type: array
simulationNames:
items:
type: string
type: array
type: object
MathModelSummary:
example:
modelInfo:
simulationAnnotations:
- simulationAnnotations
- simulationAnnotations
simulationNames:
- simulationNames
- simulationNames
geometryName: geometryName
geometryDimension: 0
modelType: null
keyValue: keyValue
annotatedFunctions: annotatedFunctions
version:
date: 2000-01-23T04:56:07.000+00:00
owner:
mySpecials:
- null
- null
userName: userName
key: key
branchID: 0.8008281904610115
flag:
archived: true
current: true
intValue: 1
versionFlag: 6
published: true
groupAccess:
groupid: 5.962133916683182
description: description
name: name
annot: annot
branchPointRefKey: branchPointRefKey
versionKey: versionKey
softwareVersion:
vcellSite: null
patchVersion: 4
buildInt: 7
description: description
majorVersion: 3
minorVersion: 2
buildNumber: buildNumber
softwareVersionString: softwareVersionString
versionNumber: versionNumber
publicationInfos:
- vcDocumentType: null
theHashCode: 9
citation: citation
title: title
publicationKey: publicationKey
pubmedid: pubmedid
user:
mySpecials:
- null
- null
userName: userName
key: key
url: url
versionKey: versionKey
authors:
- authors
- authors
doi: doi
pubdate: 2022-03-10T00:00:00.000+00:00
- vcDocumentType: null
theHashCode: 9
citation: citation
title: title
publicationKey: publicationKey
pubmedid: pubmedid
user:
mySpecials:
- null
- null
userName: userName
key: key
url: url
versionKey: versionKey
authors:
- authors
- authors
doi: doi
pubdate: 2022-03-10T00:00:00.000+00:00
properties:
version:
$ref: '#/components/schemas/Version'
keyValue:
type: string
modelInfo:
$ref: '#/components/schemas/MathModelChildSummary'
softwareVersion:
$ref: '#/components/schemas/VCellSoftwareVersion'
publicationInfos:
items:
$ref: '#/components/schemas/PublicationInfo'
type: array
annotatedFunctions:
type: string
type: object
MathType:
enum:
- RuleBased
- Stochastic
- Deterministic
- SpringSaLaD
- Unknown
type: string
MathmodelRef:
example:
ownerName: ownerName
name: name
versionFlag: 2
mmKey: 9
ownerKey: 3
properties:
mmKey:
format: int64
type: integer
name:
type: string
ownerName:
type: string
ownerKey:
format: int64
type: integer
versionFlag:
format: int32
type: integer
type: object
ModelType:
enum:
- BIOMODEL
- MATHMODEL
type: string
N5ExportRequest:
example:
subVolume:
key: subVolume
exportableDataType: null
datasetName: datasetName
standardExportInformation:
contextName: contextName
simulationKey: simulationKey
variableSpecs:
mode: null
variableNames:
- variableNames
- variableNames
simulationName: simulationName
geometrySpecs:
selections:
- variableType:
defaultUnits: defaultUnits
name: name
typeName: typeName
defaultLabel: defaultLabel
units: units
label: label
type: 0
variableDomain: null
legacyWarn: true
varType:
defaultUnits: defaultUnits
name: name
typeName: typeName
defaultLabel: defaultLabel
units: units
label: label
type: 0
variableDomain: null
legacyWarn: true
smallestMeshCellDimensionLength: 7.457744773683766
closed: true
type: type
point: true
curveSelectionInfo:
fieldControlPoint: 4
fieldCurve:
spatialLength: 3.616076749251911
valid: true
bClosed: true
endingCoordinate:
x: 1.4658129805029452
"y": 5.962133916683182
z: 5.637376656633329
description: description
beginningCoordinate:
x: 1.4658129805029452
"y": 5.962133916683182
z: 5.637376656633329
numSamplePoints: 7
closed: true
type: type
defaultNumSamples: 2
segmentCount: 9
fieldControlPointExtended: 1
fieldDirectionNegative: true
fieldSegment: 7
fieldUExtended: 1.0246457001441578
fieldType: 2
crossing: true
fieldU: 1.2315135367772556
fieldSegmentExtended: 6
- variableType:
defaultUnits: defaultUnits
name: name
typeName: typeName
defaultLabel: defaultLabel
units: units
label: label
type: 0
variableDomain: null
legacyWarn: true
varType:
defaultUnits: defaultUnits
name: name
typeName: typeName
defaultLabel: defaultLabel
units: units
label: label
type: 0
variableDomain: null
legacyWarn: true
smallestMeshCellDimensionLength: 7.457744773683766
closed: true
type: type
point: true
curveSelectionInfo:
fieldControlPoint: 4
fieldCurve:
spatialLength: 3.616076749251911
valid: true
bClosed: true
endingCoordinate:
x: 1.4658129805029452
"y": 5.962133916683182
z: 5.637376656633329
description: description
beginningCoordinate:
x: 1.4658129805029452
"y": 5.962133916683182
z: 5.637376656633329
numSamplePoints: 7
closed: true
type: type
defaultNumSamples: 2
segmentCount: 9
fieldControlPointExtended: 1
fieldDirectionNegative: true
fieldSegment: 7
fieldUExtended: 1.0246457001441578
fieldType: 2
crossing: true
fieldU: 1.2315135367772556
fieldSegmentExtended: 6
sliceNumber: 4
geometryMode: null
axis: 1
outputContext:
- functionName: functionName
domain:
name: name
functionType:
defaultUnits: defaultUnits
name: name
typeName: typeName
defaultLabel: defaultLabel
units: units
label: label
type: 0
variableDomain: null
legacyWarn: true
error: error
category: null
functionExpression: functionExpression
- functionName: functionName
domain:
name: name
functionType:
defaultUnits: defaultUnits
name: name
typeName: typeName
defaultLabel: defaultLabel
units: units
label: label
type: 0
variableDomain: null
legacyWarn: true
error: error
category: null
functionExpression: functionExpression
simulationJob: 6
timeSpecs:
mode: null
endTimeIndex: 9
beginTimeIndex: 5
allTimes:
- 9.369310271410669
- 9.369310271410669
properties:
standardExportInformation:
$ref: '#/components/schemas/StandardExportInfo'
subVolume:
additionalProperties:
type: string
type: object
exportableDataType:
$ref: '#/components/schemas/ExportableDataType'
datasetName:
type: string
type: object
Origin:
example:
x: 5.962133916683182
"y": 5.637376656633329
z: 2.3021358869347655
properties:
x:
format: double
type: number
xml:
attribute: true
"y":
format: double
type: number
xml:
attribute: true
z:
format: double
type: number
xml:
attribute: true
type: object
Publication:
example:
date: 2022-03-10T00:00:00.000+00:00
wittid: 5
year: 6
citation: citation
title: title
biomodelRefs:
- bmKey: 5
ownerName: ownerName
name: name
versionFlag: 7
ownerKey: 2
- bmKey: 5
ownerName: ownerName
name: name
versionFlag: 7
ownerKey: 2
pubmedid: pubmedid
url: url
mathmodelRefs:
- ownerName: ownerName
name: name
versionFlag: 2
mmKey: 9
ownerKey: 3
- ownerName: ownerName
name: name
versionFlag: 2
mmKey: 9
ownerKey: 3
pubKey: 0
authors:
- authors
- authors
doi: doi
endnoteid: 1
properties:
pubKey:
format: int64
type: integer
title:
type: string
authors:
items:
type: string
type: array
year:
format: int32
type: integer
citation:
type: string
pubmedid:
type: string
doi:
type: string
endnoteid:
format: int32
type: integer
url:
type: string
wittid:
format: int32
type: integer
biomodelRefs:
items:
$ref: '#/components/schemas/BiomodelRef'
type: array
mathmodelRefs:
items:
$ref: '#/components/schemas/MathmodelRef'
type: array
date:
example: 2022-03-10
format: date
type: string
type: object
PublicationInfo:
example:
vcDocumentType: null
theHashCode: 9
citation: citation
title: title
publicationKey: publicationKey
pubmedid: pubmedid
user:
mySpecials:
- null
- null
userName: userName
key: key
url: url
versionKey: versionKey
authors:
- authors
- authors
doi: doi
pubdate: 2022-03-10T00:00:00.000+00:00
properties:
publicationKey:
type: string
versionKey:
type: string
title:
type: string
authors:
items:
type: string
type: array
citation:
type: string
pubmedid:
type: string
doi:
type: string
url:
type: string
pubdate:
example: 2022-03-10
format: date
type: string
vcDocumentType:
$ref: '#/components/schemas/VCDocumentType'
user:
$ref: '#/components/schemas/User'
theHashCode:
format: int32
type: integer
type: object
SPECIAL_CLAIM:
enum:
- admins
- powerUsers
- publicationEditors
- vcellSupport
type: string
SampledCurve:
allOf:
- $ref: '#/components/schemas/ControlPointCurve'
properties:
type:
default: SampledCurve
type: string
defaultNumSamples:
format: int32
type: integer
maxControlPoints:
format: int32
type: integer
minControlPoints:
format: int32
type: integer
segmentCount:
format: int32
type: integer
spatialLength:
format: double
type: number
required:
- type
type: object
SchedulerStatus:
enum:
- WAITING
- QUEUED
- DISPATCHED
- RUNNING
- COMPLETED
- STOPPED
- FAILED
type: string
SimulationExecutionStatusRecord:
example:
fieldLatestUpdateDate: 2022-03-10T16:15:50Z
fieldHasData: true
fieldStartDate: 2022-03-10T16:15:50Z
fieldEndDate: 2022-03-10T16:15:50Z
fieldComputeHost: fieldComputeHost
fieldHtcJobID:
server: server
batchSystemType: null
jobNumber: 0
properties:
fieldStartDate:
example: 2022-03-10T16:15:50Z
format: date-time
type: string
fieldLatestUpdateDate:
example: 2022-03-10T16:15:50Z
format: date-time
type: string
fieldEndDate:
example: 2022-03-10T16:15:50Z
format: date-time
type: string
fieldComputeHost:
type: string
fieldHasData:
type: boolean
fieldHtcJobID:
$ref: '#/components/schemas/HtcJobID'
type: object
SimulationJobStatusRecord:
example:
fieldSimulationMessage:
htcJobId:
server: server
batchSystemType: null
jobNumber: 0
displayMessage: displayMessage
detailedState: null
message: message
fieldTimeDataStamp: 2022-03-10T16:15:50Z
fieldServerID: fieldServerID
fieldSimulationExecutionStatus:
fieldLatestUpdateDate: 2022-03-10T16:15:50Z
fieldHasData: true
fieldStartDate: 2022-03-10T16:15:50Z
fieldEndDate: 2022-03-10T16:15:50Z
fieldComputeHost: fieldComputeHost
fieldHtcJobID:
server: server
batchSystemType: null
jobNumber: 0
fieldVCSimID:
owner:
mySpecials:
- null
- null
userName: userName
key: key
simulationKey: simulationKey
id: id
fieldTaskID: 6
fieldSimulationQueueEntryStatus:
fieldQueuePriority: 5
fieldQueueID: null
fieldQueueDate: 2022-03-10T16:15:50Z
fieldSubmitDate: 2022-03-10T16:15:50Z
fieldSchedulerStatus: null
fieldJobIndex: 1
properties:
fieldTimeDataStamp:
example: 2022-03-10T16:15:50Z
format: date-time
type: string
fieldVCSimID:
$ref: '#/components/schemas/VCSimulationIdentifier'
fieldSubmitDate:
example: 2022-03-10T16:15:50Z
format: date-time
type: string
fieldSchedulerStatus:
$ref: '#/components/schemas/SchedulerStatus'
fieldSimulationMessage:
$ref: '#/components/schemas/SimulationMessage'
fieldTaskID:
format: int32
type: integer
fieldServerID:
type: string
fieldJobIndex:
format: int32
type: integer
fieldSimulationExecutionStatus:
$ref: '#/components/schemas/SimulationExecutionStatusRecord'
fieldSimulationQueueEntryStatus:
$ref: '#/components/schemas/SimulationQueueEntryStatusRecord'
type: object
SimulationMessage:
example:
htcJobId:
server: server
batchSystemType: null
jobNumber: 0
displayMessage: displayMessage
detailedState: null
message: message
properties:
detailedState:
$ref: '#/components/schemas/DetailedState'
message:
type: string
htcJobId:
$ref: '#/components/schemas/HtcJobID'
displayMessage:
type: string
type: object
SimulationQueueEntryStatusRecord:
example:
fieldQueuePriority: 5
fieldQueueID: null
fieldQueueDate: 2022-03-10T16:15:50Z
properties:
fieldQueuePriority:
format: int32
type: integer
fieldQueueDate:
example: 2022-03-10T16:15:50Z
format: date-time
type: string
fieldQueueID:
$ref: '#/components/schemas/SimulationQueueID'
type: object
SimulationQueueID:
enum:
- QUEUE_ID_WAITING
- QUEUE_ID_SIMULATIONJOB
- QUEUE_ID_NULL
type: string
SimulationStatusPersistentRecord:
example:
hasData: true
details: details
status: null
properties:
status:
$ref: '#/components/schemas/Status'
details:
type: string
hasData:
type: boolean
type: object
SourceModel:
example:
modelID: modelID
modelType: null
properties:
modelID:
type: string
modelType:
$ref: '#/components/schemas/ModelType'
type: object
SpatialSelection:
discriminator:
mapping:
Membrane: '#/components/schemas/SpatialSelectionMembrane'
Contour: '#/components/schemas/SpatialSelectionContour'
Volume: '#/components/schemas/SpatialSelectionVolume'
propertyName: type
example:
variableType:
defaultUnits: defaultUnits
name: name
typeName: typeName
defaultLabel: defaultLabel
units: units
label: label
type: 0
variableDomain: null
legacyWarn: true
varType:
defaultUnits: defaultUnits
name: name
typeName: typeName
defaultLabel: defaultLabel
units: units
label: label
type: 0
variableDomain: null
legacyWarn: true
smallestMeshCellDimensionLength: 7.457744773683766
closed: true
type: type
point: true
curveSelectionInfo:
fieldControlPoint: 4
fieldCurve:
spatialLength: 3.616076749251911
valid: true
bClosed: true
endingCoordinate:
x: 1.4658129805029452
"y": 5.962133916683182
z: 5.637376656633329
description: description
beginningCoordinate:
x: 1.4658129805029452
"y": 5.962133916683182
z: 5.637376656633329
numSamplePoints: 7
closed: true
type: type
defaultNumSamples: 2
segmentCount: 9
fieldControlPointExtended: 1
fieldDirectionNegative: true
fieldSegment: 7
fieldUExtended: 1.0246457001441578
fieldType: 2
crossing: true
fieldU: 1.2315135367772556
fieldSegmentExtended: 6
properties:
curveSelectionInfo:
$ref: '#/components/schemas/CurveSelectionInfo'
varType:
$ref: '#/components/schemas/VariableType'
type:
type: string
smallestMeshCellDimensionLength:
format: double
type: number
variableType:
$ref: '#/components/schemas/VariableType'
closed:
type: boolean
point:
type: boolean
required:
- type
type: object
SpatialSelectionContour:
allOf:
- $ref: '#/components/schemas/SpatialSelection'
properties:
type:
default: Contour
type: string
fieldSampledDataIndexes:
items:
format: int32
type: integer
type: array
indexSamples:
items:
format: int32
type: integer
type: array
sampledDataIndexes:
items:
format: int32
type: integer
type: array
required:
- type
type: object
SpatialSelectionMembrane:
allOf:
- $ref: '#/components/schemas/SpatialSelection'
properties:
type:
default: Membrane
type: string
fieldSampledDataIndexes:
items:
format: int32
type: integer
type: array
selectionSource:
$ref: '#/components/schemas/SampledCurve'
required:
- type
type: object
SpatialSelectionVolume:
allOf:
- $ref: '#/components/schemas/SpatialSelection'
properties:
type:
default: Volume
type: string
symmetric:
type: boolean
required:
- type
type: object
Spline:
allOf:
- $ref: '#/components/schemas/ControlPointCurve'
properties:
type:
default: Spline
type: string
defaultNumSamples:
format: int32
type: integer
maxControlPoints:
format: int32
type: integer
minControlPoints:
format: int32
type: integer
segmentCount:
format: int32
type: integer
required:
- type
type: object
StandardExportInfo:
example:
contextName: contextName
simulationKey: simulationKey
variableSpecs:
mode: null
variableNames:
- variableNames
- variableNames
simulationName: simulationName
geometrySpecs:
selections:
- variableType:
defaultUnits: defaultUnits
name: name
typeName: typeName
defaultLabel: defaultLabel
units: units
label: label
type: 0
variableDomain: null
legacyWarn: true
varType:
defaultUnits: defaultUnits
name: name
typeName: typeName
defaultLabel: defaultLabel
units: units
label: label
type: 0
variableDomain: null
legacyWarn: true
smallestMeshCellDimensionLength: 7.457744773683766
closed: true
type: type
point: true
curveSelectionInfo:
fieldControlPoint: 4
fieldCurve:
spatialLength: 3.616076749251911
valid: true
bClosed: true
endingCoordinate:
x: 1.4658129805029452
"y": 5.962133916683182
z: 5.637376656633329
description: description
beginningCoordinate:
x: 1.4658129805029452
"y": 5.962133916683182
z: 5.637376656633329
numSamplePoints: 7
closed: true
type: type
defaultNumSamples: 2
segmentCount: 9
fieldControlPointExtended: 1
fieldDirectionNegative: true
fieldSegment: 7
fieldUExtended: 1.0246457001441578
fieldType: 2
crossing: true
fieldU: 1.2315135367772556
fieldSegmentExtended: 6
- variableType:
defaultUnits: defaultUnits
name: name
typeName: typeName
defaultLabel: defaultLabel
units: units
label: label
type: 0
variableDomain: null
legacyWarn: true
varType:
defaultUnits: defaultUnits
name: name
typeName: typeName
defaultLabel: defaultLabel
units: units
label: label
type: 0
variableDomain: null
legacyWarn: true
smallestMeshCellDimensionLength: 7.457744773683766
closed: true
type: type
point: true
curveSelectionInfo:
fieldControlPoint: 4
fieldCurve:
spatialLength: 3.616076749251911
valid: true
bClosed: true
endingCoordinate:
x: 1.4658129805029452
"y": 5.962133916683182
z: 5.637376656633329
description: description
beginningCoordinate:
x: 1.4658129805029452
"y": 5.962133916683182
z: 5.637376656633329
numSamplePoints: 7
closed: true
type: type
defaultNumSamples: 2
segmentCount: 9
fieldControlPointExtended: 1
fieldDirectionNegative: true
fieldSegment: 7
fieldUExtended: 1.0246457001441578
fieldType: 2
crossing: true
fieldU: 1.2315135367772556
fieldSegmentExtended: 6
sliceNumber: 4
geometryMode: null
axis: 1
outputContext:
- functionName: functionName
domain:
name: name
functionType:
defaultUnits: defaultUnits
name: name
typeName: typeName
defaultLabel: defaultLabel
units: units
label: label
type: 0
variableDomain: null
legacyWarn: true
error: error
category: null
functionExpression: functionExpression
- functionName: functionName
domain:
name: name
functionType:
defaultUnits: defaultUnits
name: name
typeName: typeName
defaultLabel: defaultLabel
units: units
label: label
type: 0
variableDomain: null
legacyWarn: true
error: error
category: null
functionExpression: functionExpression
simulationJob: 6
timeSpecs:
mode: null
endTimeIndex: 9
beginTimeIndex: 5
allTimes:
- 9.369310271410669
- 9.369310271410669
properties:
outputContext:
items:
$ref: '#/components/schemas/AnnotatedFunctionDTO'
type: array
contextName:
type: string
simulationName:
type: string
simulationKey:
type: string
simulationJob:
format: int32
type: integer
geometrySpecs:
$ref: '#/components/schemas/GeometrySpecDTO'
timeSpecs:
$ref: '#/components/schemas/TimeSpecs'
variableSpecs:
$ref: '#/components/schemas/VariableSpecs'
type: object
Status:
enum:
- UNKNOWN
- NEVER_RAN
- START_REQUESTED
- DISPATCHED
- WAITING
- QUEUED
- RUNNING
- COMPLETED
- FAILED
- STOP_REQUESTED
- STOPPED
- NOT_SAVED
type: string
StatusMessage:
example:
jobStatus:
fieldSimulationMessage:
htcJobId:
server: server
batchSystemType: null
jobNumber: 0
displayMessage: displayMessage
detailedState: null
message: message
fieldTimeDataStamp: 2022-03-10T16:15:50Z
fieldServerID: fieldServerID
fieldSimulationExecutionStatus:
fieldLatestUpdateDate: 2022-03-10T16:15:50Z
fieldHasData: true
fieldStartDate: 2022-03-10T16:15:50Z
fieldEndDate: 2022-03-10T16:15:50Z
fieldComputeHost: fieldComputeHost
fieldHtcJobID:
server: server
batchSystemType: null
jobNumber: 0
fieldVCSimID:
owner:
mySpecials:
- null
- null
userName: userName
key: key
simulationKey: simulationKey
id: id
fieldTaskID: 6
fieldSimulationQueueEntryStatus:
fieldQueuePriority: 5
fieldQueueID: null
fieldQueueDate: 2022-03-10T16:15:50Z
fieldSubmitDate: 2022-03-10T16:15:50Z
fieldSchedulerStatus: null
fieldJobIndex: 1
progress: 5.637376656633329
userName: userName
timepoint: 2.3021358869347655
properties:
jobStatus:
$ref: '#/components/schemas/SimulationJobStatusRecord'
userName:
type: string
progress:
format: double
type: number
timepoint:
format: double
type: number
type: object
TimeMode:
enum:
- TIME_POINT
- TIME_RANGE
type: string
TimeSpecs:
example:
mode: null
endTimeIndex: 9
beginTimeIndex: 5
allTimes:
- 9.369310271410669
- 9.369310271410669
properties:
beginTimeIndex:
format: int32
type: integer
endTimeIndex:
format: int32
type: integer
allTimes:
items:
format: double
type: number
type: array
mode:
$ref: '#/components/schemas/TimeMode'
type: object
User:
example:
mySpecials:
- null
- null
userName: userName
key: key
properties:
userName:
type: string
key:
type: string
mySpecials:
items:
$ref: '#/components/schemas/SPECIAL_CLAIM'
type: array
type: object
UserIdentityJSONSafe:
example:
subject: subject
mapped: true
insertDate: insertDate
id: 0.8008281904610115
userName: userName
properties:
mapped:
type: boolean
userName:
type: string
id:
type: number
subject:
type: string
insertDate:
type: string
type: object
UserLoginInfoForMapping:
example:
password: password
userID: userID
properties:
userID:
type: string
password:
type: string
type: object
UserRegistrationInfo:
example:
emailNotification: true
country: country
organization: organization
title: title
userID: userID
properties:
userID:
type: string
title:
type: string
organization:
type: string
country:
type: string
emailNotification:
type: boolean
type: object
VCDocumentType:
enum:
- BIOMODEL_DOC
- MATHMODEL_DOC
- GEOMETRY_DOC
- EXTERNALFILE_DOC
type: string
VCImageSummary:
example:
extent:
x: 7.061401241503109
"y": 9.301444243932576
z: 3.616076749251911
preview:
size:
x: 2
"y": 4
z: 7
gifEncodedData: ""
size:
x: 2
"y": 4
z: 7
version:
date: 2000-01-23T04:56:07.000+00:00
owner:
mySpecials:
- null
- null
userName: userName
key: key
branchID: 0.8008281904610115
flag:
archived: true
current: true
intValue: 1
versionFlag: 6
published: true
groupAccess:
groupid: 5.962133916683182
description: description
name: name
annot: annot
branchPointRefKey: branchPointRefKey
versionKey: versionKey
softwareVersion:
vcellSite: null
patchVersion: 4
buildInt: 7
description: description
majorVersion: 3
minorVersion: 2
buildNumber: buildNumber
softwareVersionString: softwareVersionString
versionNumber: versionNumber
properties:
size:
$ref: '#/components/schemas/ISize'
extent:
$ref: '#/components/schemas/Extent'
version:
$ref: '#/components/schemas/Version'
preview:
$ref: '#/components/schemas/GIFImage'
softwareVersion:
$ref: '#/components/schemas/VCellSoftwareVersion'
type: object
VCSimulationIdentifier:
example:
owner:
mySpecials:
- null
- null
userName: userName
key: key
simulationKey: simulationKey
id: id
properties:
simulationKey:
type: string
owner:
$ref: '#/components/schemas/User'
id:
type: string
type: object
VCellHTTPError:
properties:
exceptionType:
type: string
message:
type: string
type: object
VCellSite:
enum:
- alpha
- beta
- rel
- other
- unknown
type: string
VCellSoftwareVersion:
example:
vcellSite: null
patchVersion: 4
buildInt: 7
description: description
majorVersion: 3
minorVersion: 2
buildNumber: buildNumber
softwareVersionString: softwareVersionString
versionNumber: versionNumber
properties:
softwareVersionString:
type: string
vcellSite:
$ref: '#/components/schemas/VCellSite'
buildNumber:
type: string
versionNumber:
type: string
majorVersion:
format: int32
type: integer
minorVersion:
format: int32
type: integer
patchVersion:
format: int32
type: integer
buildInt:
format: int32
type: integer
description:
type: string
type: object
VariableDomain:
enum:
- VARIABLEDOMAIN_POSTPROCESSING
- VARIABLEDOMAIN_UNKNOWN
- VARIABLEDOMAIN_VOLUME
- VARIABLEDOMAIN_MEMBRANE
- VARIABLEDOMAIN_CONTOUR
- VARIABLEDOMAIN_NONSPATIAL
- VARIABLEDOMAIN_POINT
type: string
VariableMode:
enum:
- VARIABLE_ONE
- VARIABLE_MULTI
- VARIABLE_ALL
type: string
VariableSpecs:
example:
mode: null
variableNames:
- variableNames
- variableNames
properties:
variableNames:
items:
type: string
type: array
mode:
$ref: '#/components/schemas/VariableMode'
type: object
VariableType:
example:
defaultUnits: defaultUnits
name: name
typeName: typeName
defaultLabel: defaultLabel
units: units
label: label
type: 0
variableDomain: null
legacyWarn: true
properties:
type:
format: int32
type: integer
variableDomain:
$ref: '#/components/schemas/VariableDomain'
name:
type: string
units:
type: string
label:
type: string
legacyWarn:
type: boolean
defaultLabel:
type: string
defaultUnits:
type: string
typeName:
type: string
type: object
Version:
example:
date: 2000-01-23T04:56:07.000+00:00
owner:
mySpecials:
- null
- null
userName: userName
key: key
branchID: 0.8008281904610115
flag:
archived: true
current: true
intValue: 1
versionFlag: 6
published: true
groupAccess:
groupid: 5.962133916683182
description: description
name: name
annot: annot
branchPointRefKey: branchPointRefKey
versionKey: versionKey
properties:
versionKey:
type: string
annot:
type: string
branchID:
type: number
branchPointRefKey:
type: string
date:
format: date-time
type: string
flag:
$ref: '#/components/schemas/VersionFlag'
groupAccess:
$ref: '#/components/schemas/GroupAccess'
name:
type: string
owner:
$ref: '#/components/schemas/User'
type: object
VersionFlag:
example:
archived: true
current: true
intValue: 1
versionFlag: 6
published: true
properties:
versionFlag:
format: int32
type: integer
intValue:
format: int32
type: integer
archived:
type: boolean
current:
type: boolean
published:
type: boolean
type: object
advancedCreate_request:
properties:
file:
format: binary
type: string
fileName:
type: string
extent:
$ref: '#/components/schemas/Extent'
iSize:
$ref: '#/components/schemas/ISize'
channelNames:
items:
type: string
type: array
times:
items:
format: double
type: number
type: array
annotation:
type: string
origin:
$ref: '#/components/schemas/Origin'
type: object
analyzeFile_request:
properties:
file:
format: binary
type: string
fileName:
type: string
type: object
createFromFile_request:
properties:
file:
format: binary
type: string
fieldDataName:
type: string
type: object
createFromSimulation_request:
properties:
simKeyReference:
type: string
jobIndex:
format: int32
type: integer
newFieldDataName:
type: string
type: object
getFVSolverInputFromSBML_request:
properties:
sbmlFile:
format: binary
type: string
duration:
default: 5.0
format: double
type: number
output_time_step:
default: 0.1
format: double
type: number
type: object
getFVSolverInputFromVCML_request:
properties:
vcmlFile:
format: binary
type: string
simulation_name:
type: string
type: object
securitySchemes:
openId:
description: Authentication
openIdConnectUrl: https://dev-dzhx7i2db3x3kkvq.us.auth0.com/.well-known/openid-configuration
type: openIdConnect