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 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 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