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