Created
September 7, 2020 15:38
-
-
Save tfuji/939768ba662c513a077fae569851e244 to your computer and use it in GitHub Desktop.
Converted the openapi specification from 2.0 to 3.0. https://ddbj.nig.ac.jp/api/apispec/ddbjapi.json
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| openapi: 3.0.0 | |
| info: | |
| title: DDBJ Data Validation API | |
| description: DDBJ Data Validation API | |
| version: 0.9.0 | |
| paths: | |
| /validation: | |
| post: | |
| tags: | |
| - Validation | |
| summary: execute validation | |
| description: Create a new validation job | |
| operationId: validation | |
| requestBody: | |
| content: | |
| multipart/form-data: | |
| schema: | |
| type: object | |
| properties: | |
| submission: | |
| description: Upload DRA submission XML file. | |
| type: string | |
| format: binary | |
| bioproject: | |
| description: Upload BioProject XML file. | |
| type: string | |
| format: binary | |
| biosample: | |
| description: Upload BioSample XML file. | |
| type: string | |
| format: binary | |
| expreriment: | |
| description: Upload DRA expreriment XML file. | |
| type: string | |
| format: binary | |
| run: | |
| description: Upload DRA run XML file. | |
| type: string | |
| format: binary | |
| analysis: | |
| description: Upload DRA analysis XML file. | |
| type: string | |
| format: binary | |
| responses: | |
| "200": | |
| description: Successful Operation | |
| content: | |
| application/json: | |
| schema: | |
| $ref: "#/components/schemas/Status" | |
| ok: | |
| examples: | |
| response: | |
| value: | |
| uuid: 27ca0fbf-88a9-49c5-96f6-f3dfd257888f | |
| status: accepted | |
| start_time: 2017-08-29 21:15:53 +0900 | |
| "400": | |
| description: Bad Request. Invalid input file supplied. | |
| content: | |
| application/json: | |
| schema: | |
| $ref: "#/components/schemas/Error" | |
| invalid file combination: | |
| examples: | |
| response: | |
| value: | |
| status: error | |
| message: Invalid combination of files | |
| "/validation/{uuid}/status": | |
| get: | |
| tags: | |
| - Validation | |
| summary: validation status | |
| description: Get specific validation status | |
| parameters: | |
| - $ref: "#/components/parameters/uuid" | |
| responses: | |
| "200": | |
| description: Successful Operation | |
| content: | |
| application/json: | |
| schema: | |
| $ref: "#/components/schemas/Status" | |
| finished: | |
| examples: | |
| response: | |
| value: | |
| uuid: 27ca0fbf-88a9-49c5-96f6-f3dfd257888f | |
| status: finished | |
| start_time: 2017-08-29 21:15:53 +0900 | |
| end_time: 2017-08-29 21:16:03 +0900 | |
| "400": | |
| description: Bad Request | |
| content: | |
| application/json: | |
| schema: | |
| $ref: "#/components/schemas/Error" | |
| not exist UUID: | |
| examples: | |
| response: | |
| value: | |
| status: error | |
| message: Invalid UUID | |
| "/validation/{uuid}": | |
| get: | |
| tags: | |
| - Validation | |
| summary: validation result | |
| description: Get specific validation result | |
| parameters: | |
| - $ref: "#/components/parameters/uuid" | |
| responses: | |
| "200": | |
| description: Successful Operation | |
| content: | |
| application/json: | |
| schema: | |
| $ref: "#/components/schemas/ValidationResult" | |
| "400": | |
| description: Bad Request | |
| content: | |
| application/json: | |
| schema: | |
| $ref: "#/components/schemas/Error" | |
| error occurred while executing the validation process: | |
| examples: | |
| response: | |
| value: | |
| status: error | |
| message: Failed the sparql query | |
| not exist UUID: | |
| examples: | |
| response: | |
| value: | |
| status: error | |
| message: Invalid UUID | |
| unfinished UUID: | |
| examples: | |
| response: | |
| value: | |
| status: error | |
| message: This validation job has not completed yet | |
| "/validation/{uuid}/{filetype}": | |
| get: | |
| tags: | |
| - Validation | |
| summary: validation original file | |
| description: Get the original file of specific validation | |
| parameters: | |
| - $ref: "#/components/parameters/uuid" | |
| - $ref: "#/components/parameters/filetype" | |
| responses: | |
| "200": | |
| description: An original xml file validated | |
| content: | |
| application/xml: | |
| schema: | |
| type: string | |
| format: binary | |
| "400": | |
| description: Bad Request | |
| content: | |
| application/xml: | |
| schema: | |
| $ref: "#/components/schemas/Error" | |
| not exist UUID: | |
| examples: | |
| response: | |
| value: | |
| status: error | |
| message: Invalid UUID | |
| invalid filetype: | |
| examples: | |
| response: | |
| value: | |
| status: error | |
| message: Invalid or not exist filetype. | |
| "/validation/{uuid}/{filetype}/autocorrect": | |
| get: | |
| tags: | |
| - Validation | |
| summary: validation autocorrected file | |
| description: Get the autocorrected file of specific validation | |
| parameters: | |
| - $ref: "#/components/parameters/uuid" | |
| - $ref: "#/components/parameters/filetype" | |
| responses: | |
| "200": | |
| description: An autocorrected xml file | |
| content: | |
| application/xml: | |
| schema: | |
| type: string | |
| format: binary | |
| "400": | |
| description: Bad Request | |
| content: | |
| application/xml: | |
| schema: | |
| $ref: "#/components/schemas/Error" | |
| not exist UUID: | |
| examples: | |
| response: | |
| value: | |
| status: error | |
| message: Invalid UUID | |
| invalid filetype: | |
| examples: | |
| response: | |
| value: | |
| status: error | |
| message: Invalid or not exist filetype. | |
| no autocorrect fields: | |
| examples: | |
| response: | |
| value: | |
| status: error | |
| message: not exist autocorrect fields on this validation. | |
| "/submission/{filetype}/{submission_id}": | |
| get: | |
| tags: | |
| - Validation | |
| summary: download a submision XML file | |
| description: Get the xml file of specific submission_id. This api for administrator | |
| parameters: | |
| - $ref: "#/components/parameters/filetype" | |
| - $ref: "#/components/parameters/submission_id" | |
| responses: | |
| "200": | |
| description: An xml file of specified submission_id | |
| content: | |
| application/xml: | |
| schema: | |
| type: string | |
| format: binary | |
| "400": | |
| description: Bad Request | |
| content: | |
| application/xml: | |
| schema: | |
| $ref: "#/components/schemas/Error" | |
| not exist UUID: | |
| examples: | |
| response: | |
| value: | |
| status: error | |
| message: Invalid submission_id | |
| invalid filetype: | |
| examples: | |
| response: | |
| value: | |
| status: error | |
| message: Invalid or not exist filetype. | |
| security: | |
| - api_key: [] | |
| servers: | |
| - url: https://ddbj.nig.ac.jp/api | |
| components: | |
| parameters: | |
| uuid: | |
| name: uuid | |
| in: path | |
| description: Unique identifier of Validation Job. | |
| required: true | |
| schema: | |
| type: string | |
| filetype: | |
| name: filetype | |
| in: path | |
| description: filetype e.g., submission, biosample, bioproject, run, | |
| required: true | |
| schema: | |
| type: string | |
| submission_id: | |
| name: submission_id | |
| in: path | |
| description: Unique identifier of Submission. Starts with 'SSUBXXXXXX', 'PSUBXXXXXX' | |
| or 'submitter_id + serial' | |
| required: true | |
| schema: | |
| type: string | |
| securitySchemes: | |
| api_key: | |
| type: apiKey | |
| in: header | |
| name: api_key | |
| schemas: | |
| Status: | |
| type: object | |
| properties: | |
| uuid: | |
| type: string | |
| status: | |
| type: string | |
| description: '"accepted" or "running" or "finished" or "error"' | |
| start_time: | |
| type: string | |
| end_time: | |
| type: string | |
| description: only when status is "finished" | |
| ValidationResult: | |
| type: object | |
| description: validation result file | |
| properties: | |
| uuid: | |
| type: string | |
| status: | |
| type: string | |
| description: only "finished" | |
| start_time: | |
| type: string | |
| end_time: | |
| type: string | |
| result: | |
| type: object | |
| properties: | |
| version: | |
| type: string | |
| description: api version | |
| validity: | |
| type: boolean | |
| description: "true: passed the all validation rules | |
| false: unpassed the | |
| validation | |
| if only warning will return true" | |
| stats: | |
| type: object | |
| description: statistics of validation result | |
| properties: | |
| error_count: | |
| type: integer | |
| warning_count: | |
| type: integer | |
| autocorrect: | |
| type: object | |
| description: true is autocorrect file is exist | |
| messages: | |
| type: array | |
| items: | |
| $ref: "#/components/schemas/ValidationMessages" | |
| example: | |
| uuid: 27ca0fbf-88a9-49c5-96f6-f3dfd257888f | |
| status: finished | |
| start_time: 2017-08-29 21:15:53 +0900 | |
| end_time: 2017-08-29 21:16:03 +0900 | |
| result: | |
| version: 0.9.0 | |
| validity: true | |
| stats: | |
| error_count: 0 | |
| warning_count: 2 | |
| autocorrect: | |
| biosample: true | |
| bioproject: false | |
| messages: | |
| - id: "14" | |
| message: Not predefined attribute name. | |
| level: warning | |
| method: BioSample | |
| object: | |
| - BioSample | |
| source: SSUB001664.xml | |
| annotation: | |
| - key: Sample name | |
| value: DRS000302 | |
| - key: Attribute names | |
| value: sample comment | |
| - id: "7" | |
| message: Invalid date format. An automatically-generated correction will | |
| be applied. | |
| level: warning | |
| method: BioSample | |
| object: | |
| - BioSample | |
| source: SSUB001664.xml | |
| annotation: | |
| - key: Sample name | |
| value: DRS000302 | |
| - key: Attribute | |
| value: collection_date | |
| - key: Attribute value | |
| value: 22-APR-2004 | |
| - key: Suggested value | |
| suggested_value: 2004-04-22 | |
| target_key: Attribute value | |
| location: | |
| - //BioSample[1]/Attributes/Attribute[@attribute_name="collection_date"] | |
| is_auto_annotation: true | |
| ValidationMessages: | |
| type: array | |
| items: | |
| type: object | |
| properties: | |
| method: | |
| type: string | |
| description: rule method | |
| id: | |
| type: integer | |
| description: rule id | |
| message: | |
| type: string | |
| description: error message | |
| level: | |
| type: string | |
| description: '"warning" or "error"' | |
| object: | |
| type: array | |
| items: | |
| type: string | |
| description: related object | |
| source: | |
| type: string | |
| description: validated filename | |
| annotation: | |
| type: array | |
| items: | |
| properties: | |
| key: | |
| type: string | |
| suggested_value: | |
| type: string | |
| is_auto_annotation: | |
| type: boolean | |
| description: if has auto_annotation | |
| target_key: | |
| type: string | |
| description: if has auto_annotation. points other 'key' name | |
| location: | |
| type: array | |
| items: | |
| type: string | |
| description: if has auto_annotation. list of xpath | |
| Error: | |
| type: object | |
| properties: | |
| status: | |
| type: string | |
| message: | |
| type: string |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment