Galatea Bio

Galatea Bio Data API

The data API from Galatea Bio — 12 operation(s) for data.

GitHub OpenAPI

Operations 13

GET /data/files Data files list #
POST /data/files/upload Data files upload create #
PUT /data/files/{source_file_id} Data files update #
DELETE /data/files/{source_file_id} Data files delete #
GET /data/files/{source_file_id}/download Data files download list #
GET /data/pdfdata Data pdfdata list #
GET /data/prsdata Data prsdata list #
POST /data/results/pdf_report/{pdf_request_id}/change_notice Data results pdf report change notice create #
POST /data/results/upload Data results upload create #
GET /data/results/{exec_order_id}/download Data results download list #
GET /data/results/{exec_order_id}/json Data results json list #
GET /data/results/{exec_order_id}/pdf_report Data results pdf report list #
POST /data/results/{exec_order_id}/request_pdf Data results request pdf create #

Documentation

📖
Documentation
https://docs.galatea.bio/
📖
APIReference
https://docs.galatea.bio/#api-reference-contents
📖
Authentication
https://artifacts.apis.io/galatea-bio/authentication/galatea-bio-authentication.yml

Specifications

⚙
OpenAPI
https://artifacts.apis.io/galatea-bio/openapi/galatea-bio-data-api-openapi.yml

Other Resources

🔗
Swagger
https://api.galatea.bio/swagger/
🔗
Conventions
https://artifacts.apis.io/galatea-bio/conventions/galatea-bio-conventions.yml
🔗
ErrorCatalog
https://artifacts.apis.io/galatea-bio/errors/galatea-bio-problem-types.yml
🔗
DataModel
https://artifacts.apis.io/galatea-bio/data-model/galatea-bio-data-model.yml
🔗
Webhooks
https://artifacts.apis.io/galatea-bio/asyncapi/galatea-bio-octopod-webhooks.yml
🔗
Sandbox
https://artifacts.apis.io/galatea-bio/sandbox/galatea-bio-sandbox.yml

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OpenAPI Specification

galatea-bio-data-api-openapi.yml Raw ↑ 
openapi: 3.2.0
info:
  title: Octopod Data API
  version: v1
servers:
- url: https://api.galatea.bio/api/v1
security:
- Bearer: []
tags:
- name: Data
paths:
  /data/files:
    parameters: []
    get:
      operationId: data_files_list
      description: Get source files with pagination
      parameters:
      - name: page
        in: query
        description: A page number within the paginated result set.
        required: false
        schema:
          type: integer
      - name: page_size
        in: query
        description: Number of results to return per page.
        required: false
        schema:
          type: integer
      - name: file
        in: query
        description: Search by id or filename
        required: false
        schema:
          type: string
      - name: only_acceptable
        in: query
        description: Search in not deleted and acceptable files
        required: false
        schema:
          type: boolean
      - name: org_names
        in: query
        description: Search by organizations names
        required: false
        schema:
          type: array
          items:
            type: string
      - name: min_date
        in: query
        description: Search by date range
        required: false
        example: '2000-01-01'
        schema:
          type: string
          format: date
          pattern: YYYY-MM-DD
      - name: max_date
        in: query
        description: Search by date range
        required: false
        example: '2000-01-01'
        schema:
          type: string
          format: date
          pattern: YYYY-MM-DD
      - name: show_virtual
        in: query
        description: Show virtual/external source files
        required: false
        schema:
          type: boolean
      - name: files_ids
        in: query
        description: List of File IDs for search
        required: false
        schema:
          type: array
          items:
            type: string
      responses:
        '401':
          description: unauthorized
        '403':
          description: forbidden
        '200':
          description: Paginated entity list
          content:
            application/json:
              schema:
                required:
                - count
                - results
                type: object
                properties:
                  count:
                    type: integer
                  next:
                    type:
                    - string
                    - 'null'
                    format: uri
                  previous:
                    type:
                    - string
                    - 'null'
                    format: uri
                  results:
                    type: array
                    items:
                      required:
                      - id
                      - src_file_name
                      - file_size_bytes
                      type: object
                      properties:
                        id:
                          title: Id
                          type: string
                          format: uuid
                        status:
                          title: Status
                          type: string
                          readOnly: true
                        src_file_name:
                          title: Src file name
                          type: string
                          maxLength: 190
                          minLength: 1
                        src_short_file_path:
                          title: Src short file path
                          type: string
                          readOnly: true
                        file_size_bytes:
                          title: File size bytes
                          type: integer
                          maximum: 9223372036854775807
                          minimum: -9223372036854775808
                        created_at:
                          title: Created at
                          type: string
                          format: date-time
                          readOnly: true
                        check_sum:
                          title: Check sum
                          type:
                          - string
                          - 'null'
                          maxLength: 128
                          minLength: 1
                        acceptable:
                          title: Acceptable
                          type: boolean
                        purged_from_storage:
                          title: Purged from storage
                          type: boolean
                        orders_count:
                          title: Orders count
                          type: integer
                          readOnly: true
                          default: 0
                        genome_type:
                          title: Genome type
                          type: string
                          enum:
                          - GNT
                          - WGS
                        amount_of_samples:
                          title: Amount of samples
                          type: integer
                          maximum: 2147483647
                          minimum: -2147483648
                        deleted_at:
                          title: Deleted at
                          type:
                          - string
                          - 'null'
                          format: date-time
                        org_name:
                          title: Org name
                          type: string
                          readOnly: true
                        check_completed:
                          title: Check completed
                          type: boolean
                        sample_alias:
                          title: Sample alias
                          type: string
                          readOnly: true
                        check_information:
                          title: Check information
                          type:
                          - string
                          - 'null'
                          maxLength: 1000
                        virtual:
                          title: Virtual
                          type: boolean
      tags:
      - Data
      summary: Data files list
      x-summary-source: derived
  /data/files/upload:
    parameters: []
    post:
      operationId: data_files_upload_create
      description: Upload source file
      responses:
        '401':
          description: unauthorized
        '403':
          description: forbidden
        '201':
          description: Source file
          content:
            application/json:
              schema:
                required:
                - id
                - src_file_name
                - file_size_bytes
                type: object
                properties:
                  id:
                    title: Id
                    type: string
                    format: uuid
                  status:
                    title: Status
                    type: string
                    readOnly: true
                  src_file_name:
                    title: Src file name
                    type: string
                    maxLength: 190
                    minLength: 1
                  src_short_file_path:
                    title: Src short file path
                    type: string
                    readOnly: true
                  file_size_bytes:
                    title: File size bytes
                    type: integer
                    maximum: 9223372036854775807
                    minimum: -9223372036854775808
                  created_at:
                    title: Created at
                    type: string
                    format: date-time
                    readOnly: true
                  check_sum:
                    title: Check sum
                    type:
                    - string
                    - 'null'
                    maxLength: 128
                    minLength: 1
                  acceptable:
                    title: Acceptable
                    type: boolean
                  purged_from_storage:
                    title: Purged from storage
                    type: boolean
                  orders_count:
                    title: Orders count
                    type: integer
                    readOnly: true
                    default: 0
                  genome_type:
                    title: Genome type
                    type: string
                    enum:
                    - GNT
                    - WGS
                  amount_of_samples:
                    title: Amount of samples
                    type: integer
                    maximum: 2147483647
                    minimum: -2147483648
                  deleted_at:
                    title: Deleted at
                    type:
                    - string
                    - 'null'
                    format: date-time
                  org_name:
                    title: Org name
                    type: string
                    readOnly: true
                  check_completed:
                    title: Check completed
                    type: boolean
                  sample_alias:
                    title: Sample alias
                    type: string
                    readOnly: true
                  check_information:
                    title: Check information
                    type:
                    - string
                    - 'null'
                    maxLength: 1000
                  virtual:
                    title: Virtual
                    type: boolean
      tags:
      - Data
      requestBody:
        content:
          multipart/form-data:
            schema:
              type: object
              properties:
                file:
                  type: string
                  description: Source file
                  format: binary
              required:
              - file
          application/x-www-form-urlencoded:
            schema:
              type: object
              properties:
                file:
                  type: string
                  description: Source file
                  format: binary
              required:
              - file
      summary: Data files upload create
      x-summary-source: derived
  /data/files/{source_file_id}:
    parameters:
    - name: source_file_id
      in: path
      required: true
      schema:
        type: string
    put:
      operationId: data_files_update
      description: Update source file
      parameters:
      - name: source_file_id
        in: path
        description: Id of source file
        required: true
        schema:
          type: string
      responses:
        '401':
          description: unauthorized
        '403':
          description: forbidden
        '404':
          description: not found
        '201':
          description: Source file
          content:
            application/json:
              schema:
                required:
                - id
                - src_file_name
                - file_size_bytes
                type: object
                properties:
                  id:
                    title: Id
                    type: string
                    format: uuid
                  status:
                    title: Status
                    type: string
                    readOnly: true
                  src_file_name:
                    title: Src file name
                    type: string
                    maxLength: 190
                    minLength: 1
                  src_short_file_path:
                    title: Src short file path
                    type: string
                    readOnly: true
                  file_size_bytes:
                    title: File size bytes
                    type: integer
                    maximum: 9223372036854775807
                    minimum: -9223372036854775808
                  created_at:
                    title: Created at
                    type: string
                    format: date-time
                    readOnly: true
                  check_sum:
                    title: Check sum
                    type:
                    - string
                    - 'null'
                    maxLength: 128
                    minLength: 1
                  acceptable:
                    title: Acceptable
                    type: boolean
                  purged_from_storage:
                    title: Purged from storage
                    type: boolean
                  orders_count:
                    title: Orders count
                    type: integer
                    readOnly: true
                    default: 0
                  genome_type:
                    title: Genome type
                    type: string
                    enum:
                    - GNT
                    - WGS
                  amount_of_samples:
                    title: Amount of samples
                    type: integer
                    maximum: 2147483647
                    minimum: -2147483648
                  deleted_at:
                    title: Deleted at
                    type:
                    - string
                    - 'null'
                    format: date-time
                  org_name:
                    title: Org name
                    type: string
                    readOnly: true
                  check_completed:
                    title: Check completed
                    type: boolean
                  sample_alias:
                    title: Sample alias
                    type: string
                    readOnly: true
                  check_information:
                    title: Check information
                    type:
                    - string
                    - 'null'
                    maxLength: 1000
                  virtual:
                    title: Virtual
                    type: boolean
      tags:
      - Data
      requestBody:
        content:
          application/json:
            schema:
              type: object
              properties:
                sample_alias:
                  title: Sample alias
                  type:
                  - string
                  - 'null'
        required: true
      summary: Data files update
      x-summary-source: derived
    delete:
      operationId: data_files_delete
      description: Delete source file
      parameters:
      - name: source_file_id
        in: path
        description: Id of source file
        required: true
        schema:
          type: string
      responses:
        '401':
          description: unauthorized
        '403':
          description: forbidden
        '404':
          description: not found
        '200':
          description: ok
      tags:
      - Data
      summary: Data files delete
      x-summary-source: derived
  /data/files/{source_file_id}/download:
    parameters:
    - name: source_file_id
      in: path
      required: true
      schema:
        type: string
    get:
      operationId: data_files_download_list
      description: Download source file
      parameters:
      - name: source_file_id
        in: path
        description: Id of source file
        required: true
        schema:
          type: string
      responses:
        '401':
          description: unauthorized
        '403':
          description: forbidden
        '404':
          description: not found
        '200':
          description: Source file stream
      tags:
      - Data
      summary: Data files download list
      x-summary-source: derived
  /data/pdfdata:
    parameters: []
    get:
      operationId: data_pdfdata_list
      description: test view
      parameters:
      - name: order_id
        in: query
        description: Id of order
        required: true
        schema:
          type: string
      - name: result_id
        in: query
        description: Id of sample result
        required: true
        schema:
          type: string
      responses:
        '400':
          description: '{"detail": "Bad request"}'
        '401':
          description: '{"detail": "Unauthorized request"}'
        '403':
          description: '{"detail": "Forbidden"}'
        '404':
          description: '{"detail": "Not found data"}'
        '200':
          description: '{"detail": "Data for PDF report"}'
      tags:
      - Data
      summary: Data pdfdata list
      x-summary-source: derived
  /data/prsdata:
    parameters: []
    get:
      operationId: data_prsdata_list
      description: test view
      parameters:
      - name: order_id
        in: query
        description: Id of order
        required: true
        schema:
          type: string
      - name: result_id
        in: query
        description: Id of sample result
        required: true
        schema:
          type: string
      - name: report_type
        in: query
        description: report type
        required: false
        schema:
          type: string
      responses:
        '400':
          description: '{"detail": "Bad request"}'
        '401':
          description: '{"detail": "Unauthorized request"}'
        '403':
          description: '{"detail": "Forbidden"}'
        '404':
          description: '{"detail": "Not found data"}'
        '200':
          description: '{"detail": "Data for PDF report"}'
      tags:
      - Data
      summary: Data prsdata list
      x-summary-source: derived
  /data/results/pdf_report/{pdf_request_id}/change_notice:
    parameters:
    - name: pdf_request_id
      in: path
      required: true
      schema:
        type: string
    post:
      operationId: data_results_pdf_report_change_notice_create
      description: ''
      responses:
        '201':
          description: ''
      tags:
      - Data
      summary: Data results pdf report change notice create
      x-summary-source: derived
  /data/results/upload:
    parameters: []
    post:
      operationId: data_results_upload_create
      description: Upload result file
      responses:
        '401':
          description: unauthorized
        '403':
          description: forbidden
        '201':
          description: ok
      tags:
      - Data
      requestBody:
        content:
          multipart/form-data:
            schema:
              type: object
              properties:
                file:
                  type: string
                  description: Result file
                  format: binary
                model_api_name:
                  type: string
                  enum:
                  - skywalker
                  - hutt
                  - palpatine
                  - vader
                  - mysterio
                  description: Model API name
              required:
              - file
              - model_api_name
          application/x-www-form-urlencoded:
            schema:
              type: object
              properties:
                file:
                  type: string
                  description: Result file
                  format: binary
                model_api_name:
                  type: string
                  enum:
                  - skywalker
                  - hutt
                  - palpatine
                  - vader
                  - mysterio
                  description: Model API name
              required:
              - file
              - model_api_name
      summary: Data results upload create
      x-summary-source: derived
  /data/results/{exec_order_id}/download:
    parameters:
    - name: exec_order_id
      in: path
      required: true
      schema:
        type: string
    get:
      operationId: data_results_download_list
      description: Download result file
      parameters:
      - name: exec_order_id
        in: path
        description: Id of order
        required: true
        schema:
          type: string
      - name: result_type
        in: query
        description: Type of result file
        required: true
        schema:
          type: string
          enum:
          - SUMMARY_SUPERSET
          - SUMMARY_CHROMS
          - DETAILED_SUPERSET
          - DETAILED_CHROMS
          - PDF_REPORT
          - PRS_JSON_DATA
          - PRS_IMAGES
          - EXEC_ERRORS
      - name: pdf_request_id
        in: query
        description: PDF request id
        required: false
        schema:
          type: string
      responses:
        '401':
          description: unauthorized
        '403':
          description: forbidden
        '404':
          description: not found
        '200':
          description: Result file stream
      tags:
      - Data
      summary: Data results download list
      x-summary-source: derived
  /data/results/{exec_order_id}/json:
    parameters:
    - name: exec_order_id
      in: path
      required: true
      schema:
        type: string
    get:
      operationId: data_results_json_list
      description: Get result as json
      parameters:
      - name: exec_order_id
        in: path
        description: Id of order
        required: true
        schema:
          type: string
      - name: result_type
        in: query
        description: Type of result file
        required: true
        schema:
          type: string
          enum:
          - SUMMARY_CHROMS
          - SUMMARY_SUPERSET
          - DETAILED_CHROMS
          - DETAILED_SUPERSET
      responses:
        '401':
          description: unauthorized
        '403':
          description: forbidden
        '404':
          description: not found
        '200':
          description: Result file stream
      tags:
      - Data
      summary: Data results json list
      x-summary-source: derived
  /data/results/{exec_order_id}/pdf_report:
    parameters:
    - name: exec_order_id
      in: path
      required: true
      schema:
        type: string
    get:
      operationId: data_results_pdf_report_list
      description: Get pdf reports with pagination
      parameters:
      - name: page
        in: query
        description: A page number within the paginated result set.
        required: false
        schema:
          type: integer
      - name: page_size
        in: query
        description: Number of results to return per page.
        required: false
        schema:
          type: integer
      - name: exec_order_id
        in: path
        description: Search by id or order
        required: true
        schema:
          type: string
      - name: request_version
        in: query
        description: Search report request version
        required: false
        schema:
          type: integer
      - name: report_version
        in: query
        description: Search by report version
        required: false
        schema:
          type: string
      - name: sample_id
        in: query
        description: Search by sample id
        required: false
        schema:
          type: string
      - name: latest
        in: query
        description: Search by latest report request version
        required: false
        schema:
          type: boolean
      - name: report_type
        in: query
        description: Report type
        required: true
        schema:
          type: string
          enum:
          - PRS_RUO_CARDIO
          - PRS_RUO_CANCER
          - PRS_CLINICAL_CARDIO
          - PRS_CLINICAL_CANCER
          - ANCESTRY
      responses:
        '401':
          description: unauthorized
        '403':
          description: forbidden
        '422':
          description: unprocessable
        '200':
          description: Paginated entity list
          content:
            application/json:
              schema:
                required:
                - count
                - results
                type: object
                properties:
                  count:
                    type: integer
                  next:
                    type:
                    - string
                    - 'null'
                    format: uri
                  previous:
                    type:
                    - string
                    - 'null'
                    format: uri
                  results:
                    type: array
                    items:
                      required:
                      - id
                      type: object
                      properties:
                        id:
                          title: Id
                          type: string
                          format: uuid
                        status:
                          title: Status
                          type: string
                          enum:
                          - PENDING
                          - COMPLETED
                          - FAILED
                          - QC_FAILED
                        sample_id:
                          title: Sample id
                          type:
                          - string
                          - 'null'
                          maxLength: 300
                        order_id:
                          title: Order id
                          type: string
                          readOnly: true
                        result_id:
                          title: Result id
                          type: string
                          readOnly: true
                        org_name:
                          title: Org name
                          type: string
                          readOnly: true
                        report_type:
                          title: Report type
                          type: string
                          enum:
                          - ANCESTRY
                          - PRS_RUO_CARDIO
                          - PRS_RUO_CANCER
                          - PRS_CLINICAL
                          - PRS_CLINICAL_CARDIO
                          - PRS_CLINICAL_CANCER
                        request_type:
                          title: Request type
                          type: string
                          enum:
                          - ORDER
                          - SAMPLE
                        request_version:
                          title: Request version
                          type: integer
                          maximum: 32767
                          minimum: -32768
                        report_version:
                          title: Report version
                          type:
                          - string
                          - 'null'
                          maxLength: 300
                        pdf_file_name:
                          title: Pdf file name
                          type:
                          - string
                          - 'null'
                          maxLength: 260
                        file_size_bytes:
                          title: File size bytes
                          type:
                          - integer
                          - 'null'
                          maximum: 9223372036854775807
                          minimum: -9223372036854775808
                        check_sum:
                          title: Check sum
                          type:
                          - string
                          - 'null'
                          maxLength: 128
                          minLength: 1
                        started_at:
                          title: Started at
                          type: string
                          readOnly: true
                        completed_at:
                          title: Completed at
                          type:
                          - string
                          - 'null'
                          format: date-time
                        is_signed_by_deprecated_director:
                          title: Is signed by deprecated director
                          type: boolean
                        notice:
                          title: Notice
                          type: string
                          readOnly: true
      tags:
      - Data
      summary: Data results pdf report list
      x-summary-source: derived
  /data/results/{exec_order_id}/request_pdf:
    parameters:
    - name: exec_order_id
      in: path
      required: true
      schema:
        type: string
    post:
      operationId: data_results_request_pdf_create
      description: Request regenerate PDF report for order if reports are failed.
      responses:
        '400':
          description: bad request
        '401':
          description: unauthorized
        '403':
          description: forbidden
        '422':
          description: unprocessable
        '200':
          description: Request PDF report for order_id
      tags:
      - Data
      summary: Data results request pdf create
      x-summary-source: derived
components:
  securitySchemes:
    Bearer:
      type: apiKey
      name: Authorization
      in: header