syndb_openapi.yaml

openapi: 3.0.2
info:
  title: Synapse DB
  version: 0.4.1
paths:
  /user/auth/jwt/login:
    post:
      tags:
      - user
      - jwt
      - auth
      summary: Auth:Jwt.Login
      operationId: auth_jwt_login_user_auth_jwt_login_post
      requestBody:
        content:
          application/x-www-form-urlencoded:
            schema:
              $ref: '#/components/schemas/Body_auth_jwt_login_user_auth_jwt_login_post'
        required: true
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BearerResponse'
              example:
                access_token: eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJ1c2VyX2lkIjoiOTIyMWZmYzktNjQwZi00MzcyLTg2ZDMtY2U2NDJjYmE1NjAzIiwiYXVkIjoiZmFzdGFwaS11c2VyczphdXRoIiwiZXhwIjoxNTcxNTA0MTkzfQ.M10bjOe45I5Ncu_uXvOmVV8QxnL-nZfcH96U90JaocI
                token_type: bearer
        '404':
          description: Not found
        '400':
          description: Bad Request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ErrorModel'
              examples:
                LOGIN_BAD_CREDENTIALS:
                  summary: Bad credentials or the user is inactive.
                  value:
                    detail: LOGIN_BAD_CREDENTIALS
                LOGIN_USER_NOT_VERIFIED:
                  summary: The user is not verified.
                  value:
                    detail: LOGIN_USER_NOT_VERIFIED
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /user/auth/jwt/logout:
    post:
      tags:
      - user
      - jwt
      - auth
      summary: Auth:Jwt.Logout
      operationId: auth_jwt_logout_user_auth_jwt_logout_post
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema: {}
        '404':
          description: Not found
        '401':
          description: Missing token or inactive user.
      security:
      - APIKeyCookie: []
      - OAuth2PasswordBearer: []
  /user/auth/database/login:
    post:
      tags:
      - user
      - database
      - auth
      summary: Auth:Database.Login
      operationId: auth_database_login_user_auth_database_login_post
      requestBody:
        content:
          application/x-www-form-urlencoded:
            schema:
              $ref: '#/components/schemas/Body_auth_database_login_user_auth_database_login_post'
        required: true
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema: {}
        '404':
          description: Not found
        '400':
          description: Bad Request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ErrorModel'
              examples:
                LOGIN_BAD_CREDENTIALS:
                  summary: Bad credentials or the user is inactive.
                  value:
                    detail: LOGIN_BAD_CREDENTIALS
                LOGIN_USER_NOT_VERIFIED:
                  summary: The user is not verified.
                  value:
                    detail: LOGIN_USER_NOT_VERIFIED
        '204':
          description: No Content
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /user/auth/database/logout:
    post:
      tags:
      - user
      - database
      - auth
      summary: Auth:Database.Logout
      operationId: auth_database_logout_user_auth_database_logout_post
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema: {}
        '404':
          description: Not found
        '401':
          description: Missing token or inactive user.
      security:
      - APIKeyCookie: []
      - OAuth2PasswordBearer: []
  /user/register:
    post:
      tags:
      - user
      summary: Register:Register
      operationId: register_register_user_register_post
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/UserCreate'
        required: true
      responses:
        '201':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/UserRead'
        '404':
          description: Not found
        '400':
          description: Bad Request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ErrorModel'
              examples:
                REGISTER_USER_ALREADY_EXISTS:
                  summary: A user with this email already exists.
                  value:
                    detail: REGISTER_USER_ALREADY_EXISTS
                REGISTER_INVALID_PASSWORD:
                  summary: Password validation failed.
                  value:
                    detail:
                      code: REGISTER_INVALID_PASSWORD
                      reason: Password should beat least 3 characters
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /user/request-verify-token:
    post:
      tags:
      - user
      summary: Verify:Request-Token
      operationId: verify_request_token_user_request_verify_token_post
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/Body_verify_request_token_user_request_verify_token_post'
        required: true
      responses:
        '202':
          description: Successful Response
          content:
            application/json:
              schema: {}
        '404':
          description: Not found
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /user/verify:
    post:
      tags:
      - user
      summary: Verify:Verify
      operationId: verify_verify_user_verify_post
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/Body_verify_verify_user_verify_post'
        required: true
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/UserRead'
        '404':
          description: Not found
        '400':
          description: Bad Request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ErrorModel'
              examples:
                VERIFY_USER_BAD_TOKEN:
                  summary: Bad token, not existing user ornot the e-mail currently
                    set for the user.
                  value:
                    detail: VERIFY_USER_BAD_TOKEN
                VERIFY_USER_ALREADY_VERIFIED:
                  summary: The user is already verified.
                  value:
                    detail: VERIFY_USER_ALREADY_VERIFIED
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /user/profile.json:
    get:
      tags:
      - user
      summary: User Profile
      operationId: user_profile_user_profile_json_get
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/UserRead'
        '404':
          description: Not found
      security:
      - APIKeyCookie: []
      - OAuth2PasswordBearer: []
  /stargate/neurodata/stargate/upload/existing/{dataset_id}:
    get:
      tags:
      - stargate
      summary: Upload Existing Dataset
      operationId: upload_existing_dataset_stargate_neurodata_stargate_upload_existing__dataset_id__get
      parameters:
      - required: true
        schema:
          title: Dataset Id
          type: string
          format: uuid
        name: dataset_id
        in: path
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema: {}
        '404':
          description: Not found
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
      security:
      - APIKeyCookie: []
      - OAuth2PasswordBearer: []
  /stargate/neurodata/stargate/upload/new:
    post:
      tags:
      - stargate
      summary: Upload New Dataset
      operationId: upload_new_dataset_stargate_neurodata_stargate_upload_new_post
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/CreateDataset'
        required: true
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema: {}
        '404':
          description: Not found
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
      security:
      - APIKeyCookie: []
      - OAuth2PasswordBearer: []
  /stargate/neurodata/stargate/read_neuro_data.json:
    get:
      tags:
      - stargate
      summary: Read Neuro Data
      operationId: read_neuro_data_stargate_neurodata_stargate_read_neuro_data_json_get
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema: {}
        '404':
          description: Not found
      security:
      - APIKeyCookie: []
      - OAuth2PasswordBearer: []
  /stargate/neurodata/stargate/jwks.json:
    get:
      tags:
      - stargate
      summary: Jwks
      operationId: jwks_stargate_neurodata_stargate_jwks_json_get
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema: {}
        '404':
          description: Not found
  /stargate/neurodata/dataset/my_datasets:
    get:
      tags:
      - stargate
      - data
      summary: User Datasets
      operationId: user_datasets_stargate_neurodata_dataset_my_datasets_get
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/syndb_api.neurodata.models.Dataset.leaf_list'
        '404':
          description: Not found
      security:
      - APIKeyCookie: []
      - OAuth2PasswordBearer: []
  /stargate/neurodata/dataset/my_projects:
    get:
      tags:
      - stargate
      - data
      summary: User Projects
      operationId: user_projects_stargate_neurodata_dataset_my_projects_get
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema: {}
        '404':
          description: Not found
      security:
      - APIKeyCookie: []
      - OAuth2PasswordBearer: []
  /:
    get:
      summary: Redirect
      operationId: redirect__get
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema: {}
components:
  schemas:
    BearerResponse:
      title: BearerResponse
      required:
      - access_token
      - token_type
      type: object
      properties:
        access_token:
          title: Access Token
          type: string
        token_type:
          title: Token Type
          type: string
    Body_auth_database_login_user_auth_database_login_post:
      title: Body_auth_database_login_user_auth_database_login_post
      required:
      - username
      - password
      type: object
      properties:
        grant_type:
          title: Grant Type
          pattern: password
          type: string
        username:
          title: Username
          type: string
        password:
          title: Password
          type: string
        scope:
          title: Scope
          type: string
          default: ''
        client_id:
          title: Client Id
          type: string
        client_secret:
          title: Client Secret
          type: string
    Body_auth_jwt_login_user_auth_jwt_login_post:
      title: Body_auth_jwt_login_user_auth_jwt_login_post
      required:
      - username
      - password
      type: object
      properties:
        grant_type:
          title: Grant Type
          pattern: password
          type: string
        username:
          title: Username
          type: string
        password:
          title: Password
          type: string
        scope:
          title: Scope
          type: string
          default: ''
        client_id:
          title: Client Id
          type: string
        client_secret:
          title: Client Secret
          type: string
    Body_verify_request_token_user_request_verify_token_post:
      title: Body_verify_request_token_user_request_verify_token_post
      required:
      - email
      type: object
      properties:
        email:
          title: Email
          type: string
          format: email
    Body_verify_verify_user_verify_post:
      title: Body_verify_verify_user_verify_post
      required:
      - token
      type: object
      properties:
        token:
          title: Token
          type: string
    CreateDataset:
      title: ReadOnlyDataset
      required:
      - dataset_size
      type: object
      properties:
        upload_complete:
          title: Upload Complete
          type: boolean
          default: false
        dataset_size:
          title: Dataset Size
          maximum: 9.223372036854776e+18
          minimum: -9.223372036854776e+18
          type: integer
        label:
          title: Label
          maxLength: 50
          type: string
        notes:
          title: Notes
          type: string
          nullable: true
        project:
          $ref: '#/components/schemas/syndb_api.neurodata.models.Project.leaf'
        animal:
          $ref: '#/components/schemas/syndb_api.neurodata.models.Animal.leaf'
        brain_structure:
          $ref: '#/components/schemas/syndb_api.neurodata.models.BrainStructure.leaf'
        targeted_mutation:
          $ref: '#/components/schemas/syndb_api.neurodata.models.TargetedMutation.leaf'
        microscopy_method:
          $ref: '#/components/schemas/syndb_api.neurodata.models.MicroscopyMethod.leaf'
      additionalProperties: false
    ErrorModel:
      title: ErrorModel
      required:
      - detail
      type: object
      properties:
        detail:
          title: Detail
          anyOf:
          - type: string
          - type: object
            additionalProperties:
              type: string
    HTTPValidationError:
      title: HTTPValidationError
      type: object
      properties:
        detail:
          title: Detail
          type: array
          items:
            $ref: '#/components/schemas/ValidationError'
    UserCreate:
      title: UserCreate
      required:
      - email
      - password
      type: object
      properties:
        email:
          title: Email
          type: string
          format: email
        password:
          title: Password
          type: string
        is_active:
          title: Is Active
          type: boolean
          default: true
        is_superuser:
          title: Is Superuser
          type: boolean
          default: false
        is_verified:
          title: Is Verified
          type: boolean
          default: false
    UserRead:
      title: UserRead
      required:
      - email
      type: object
      properties:
        id:
          title: Id
        email:
          title: Email
          type: string
          format: email
        is_active:
          title: Is Active
          type: boolean
          default: true
        is_superuser:
          title: Is Superuser
          type: boolean
          default: false
        is_verified:
          title: Is Verified
          type: boolean
          default: false
      description: Base User model.
    ValidationError:
      title: ValidationError
      required:
      - loc
      - msg
      - type
      type: object
      properties:
        loc:
          title: Location
          type: array
          items:
            type: string
        msg:
          title: Message
          type: string
        type:
          title: Error Type
          type: string
    syndb_api.neurodata.models.Animal.leaf:
      title: Animal
      required:
      - species
      type: object
      properties:
        species:
          title: Species
          maxLength: 200
          type: string
      additionalProperties: false
    syndb_api.neurodata.models.BrainStructure.leaf:
      title: BrainStructure
      required:
      - name
      type: object
      properties:
        name:
          title: Name
          maxLength: 200
          type: string
      additionalProperties: false
    syndb_api.neurodata.models.Dataset.leaf:
      title: Dataset
      required:
      - dataset_size
      - animal_species
      - targeted_mutation_names
      - microscopy_method_name
      - brain_structure_name
      type: object
      properties:
        id:
          title: Id
          type: string
          format: uuid
        upload_complete:
          title: Upload Complete
          type: boolean
          default: false
        dataset_size:
          title: Dataset Size
          maximum: 9.223372036854776e+18
          minimum: -9.223372036854776e+18
          type: integer
        label:
          title: Label
          maxLength: 50
          type: string
        notes:
          title: Notes
          type: string
          nullable: true
        animal_species:
          title: Animal Species
          type: string
        targeted_mutation_names:
          title: Targeted Mutation Names
          type: array
          items:
            type: string
        microscopy_method_name:
          title: Microscopy Method Name
          type: string
        brain_structure_name:
          title: Brain Structure Name
          type: string
      additionalProperties: false
    syndb_api.neurodata.models.Dataset.leaf_list:
      title: Dataset_list
      type: array
      items:
        $ref: '#/components/schemas/syndb_api.neurodata.models.Dataset.leaf'
    syndb_api.neurodata.models.MicroscopyMethod.leaf:
      title: MicroscopyMethod
      required:
      - name
      type: object
      properties:
        name:
          title: Name
          maxLength: 200
          type: string
      additionalProperties: false
    syndb_api.neurodata.models.Project.leaf:
      title: Project
      type: object
      properties:
        id:
          title: Id
          type: string
          format: uuid
        doi:
          title: Doi
          maxLength: 200
          type: string
          nullable: true
        label:
          title: Label
          maxLength: 50
          type: string
        notes:
          title: Notes
          type: string
          nullable: true
      additionalProperties: false
    syndb_api.neurodata.models.TargetedMutation.leaf:
      title: TargetedMutation
      required:
      - gene
      - method
      type: object
      properties:
        gene:
          title: Gene
          maxLength: 80
          type: string
        is_knock_in:
          title: Is Knock In
          type: boolean
          default: false
        method:
          title: Method
          maxLength: 200
          type: string
      additionalProperties: false
  securitySchemes:
    APIKeyCookie:
      type: apiKey
      in: cookie
      name: fastapiusersauth
    OAuth2PasswordBearer:
      type: oauth2
      flows:
        password:
          scopes: {}
          tokenUrl: auth/jwt/login