One Codex Alignments API

openapi: 3.1.0
info:
  description: The One Codex API (v1) -- programmatic access to One Codex's suite of microbial genomics data storage, analysis, and query tools.
  title: One Codex API (v1) Account Alignments API
  version: v1
servers:
- url: https://app.onecodex.com
security:
- apiKeyAuth: []
tags:
- name: Alignments
paths:
  /api/v1/alignments:
    get:
      operationId: get_alignments_instances
      parameters:
      - description: Page number. Defaults to 1. See Pagination for more details.
        in: query
        name: page
        required: false
        schema:
          default: 1
          format: int32
          type: integer
      - description: Number of requested paginated records. Defaults to 50. See Pagination for more details.
        in: query
        name: per_page
        required: false
        schema:
          default: 50
          format: int32
          type: integer
      - description: 'Optional Mongo-style JSON sort clause, e.g., `sort={"created_at": true}` to sort by created_at (descending)'
        in: query
        name: sort
        required: false
        schema:
          anyOf:
          - type: string
          - type: 'null'
          default: null
      - description: 'Optional Mongo-style JSON filter clause, e.g., `where={"$uri": {"$eq": "/api/v1/samples/0ee172af60e84f61"}}`'
        in: query
        name: where
        required: false
        schema:
          anyOf:
          - type: string
          - type: 'null'
          default: null
      responses:
        '200':
          content:
            application/json:
              schema:
                items:
                  $ref: '#/components/schemas/alignments'
                type: array
          description: OK
      summary: GET alignments instances
      tags:
      - Alignments
  /api/v1/alignments/public:
    get:
      operationId: get_alignments_instances_public
      parameters:
      - description: Page number. Defaults to 1. See Pagination for more details.
        in: query
        name: page
        required: false
        schema:
          default: 1
          format: int32
          type: integer
      - description: Number of requested paginated records. Defaults to 50. See Pagination for more details.
        in: query
        name: per_page
        required: false
        schema:
          default: 50
          format: int32
          type: integer
      - description: 'Optional Mongo-style JSON sort clause, e.g., `sort={"created_at": true}` to sort by created_at (descending)'
        in: query
        name: sort
        required: false
        schema:
          anyOf:
          - type: string
          - type: 'null'
          default: null
      - description: 'Optional Mongo-style JSON filter clause, e.g., `where={"$uri": {"$eq": "/api/v1/samples/0ee172af60e84f61"}}`'
        in: query
        name: where
        required: false
        schema:
          anyOf:
          - type: string
          - type: 'null'
          default: null
      responses:
        '200':
          content:
            application/json:
              schema:
                items:
                  $ref: '#/components/schemas/alignments'
                type: array
          description: OK
      summary: GET alignments instances_public
      tags:
      - Alignments
  /api/v1/alignments/{id}:
    get:
      operationId: get_alignments_self
      parameters:
      - in: path
        name: id
        required: true
        schema:
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/alignments'
          description: OK
      summary: GET alignments
      tags:
      - Alignments
  /api/v1/alignments/{id}/cancel:
    post:
      operationId: post_alignments_cancel
      parameters:
      - in: path
        name: id
        required: true
        schema:
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/alignments'
          description: OK
      summary: POST alignments cancel
      tags:
      - Alignments
  /api/v1/alignments/{id}/file_details:
    get:
      operationId: get_alignments_file_details
      parameters:
      - in: path
        name: id
        required: true
        schema:
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                properties:
                  files:
                    description: A list of output files.
                    items:
                      properties:
                        filename:
                          description: The filename of the output file.
                          title: Filename
                          type: string
                        filepath:
                          description: The full file path.
                          title: Filepath
                          type: string
                        size:
                          description: File size in bytes.
                          minimum: 0
                          title: Size
                          type: integer
                        url:
                          description: Pre-signed download URL.
                          title: Url
                          type: string
                      required:
                      - filename
                      - filepath
                      - size
                      - url
                      title: AnalysisFileDetailsSchema
                      type: object
                    title: Files
                    type: array
                required:
                - files
                title: AnalysisFileDetailsResponse
                type: object
          description: OK
      summary: GET alignments file_details
      tags:
      - Alignments
  /api/v1/alignments/{id}/files:
    delete:
      operationId: delete_alignments_files
      parameters:
      - in: path
        name: id
        required: true
        schema:
          type: string
      responses:
        '204':
          description: No Content
      summary: DELETE alignments files
      tags:
      - Alignments
    get:
      operationId: get_alignments_files
      parameters:
      - in: path
        name: id
        required: true
        schema:
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                description: A mapping of filenames to download URLs.
                type: object
          description: OK
      summary: GET alignments files
      tags:
      - Alignments
  /api/v1/alignments/{id}/logs:
    get:
      operationId: get_alignments_logs
      parameters:
      - in: path
        name: id
        required: true
        schema:
          type: string
      - in: query
        name: tail
        required: false
        schema:
          anyOf:
          - minimum: 1
            type: integer
          - type: 'null'
          default: null
      responses:
        '200':
          description: OK
      summary: GET alignments logs
      tags:
      - Alignments
  /api/v1/alignments/{id}/rerun:
    post:
      operationId: post_alignments_rerun
      parameters:
      - in: path
        name: id
        required: true
        schema:
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/alignments'
          description: OK
      summary: POST alignments rerun
      tags:
      - Alignments
  /api/v1/alignments/{id}/results:
    get:
      operationId: get_alignments_results
      parameters:
      - in: path
        name: id
        required: true
        schema:
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                properties:
                  assembly_accession:
                    anyOf:
                    - type: string
                    - type: 'null'
                    default: null
                    title: Assembly Accession
                  assembly_id:
                    title: Assembly Id
                    type: string
                  average_coverage:
                    title: Average Coverage
                    type: number
                  average_identity:
                    title: Average Identity
                    type: number
                  coverage:
                    properties:
                      binned_depths:
                        items:
                          properties:
                            contig_id:
                              title: Contig Id
                              type: string
                            depths:
                              items:
                                type: integer
                              title: Depths
                              type: array
                            length:
                              minimum: 1
                              title: Length
                              type: integer
                          required:
                          - contig_id
                          - depths
                          - length
                          title: _BinnedDepth
                          type: object
                        title: Binned Depths
                        type: array
                      binned_window_width:
                        title: Binned Window Width
                        type: string
                    required:
                    - binned_depths
                    - binned_window_width
                    title: _Coverage
                    type: object
                  genome_id:
                    anyOf:
                    - type: string
                    - type: 'null'
                    default: null
                    title: Genome Id
                  genome_name:
                    anyOf:
                    - type: string
                    - type: 'null'
                    default: null
                    title: Genome Name
                  genome_taxon_id:
                    anyOf:
                    - type: string
                    - type: 'null'
                    default: null
                    title: Genome Taxon Id
                  genome_taxon_name:
                    anyOf:
                    - type: string
                    - type: 'null'
                    default: null
                    title: Genome Taxon Name
                  median_depth:
                    title: Median Depth
                    type: number
                  n_mapped:
                    anyOf:
                    - type: integer
                    - type: 'null'
                    default: null
                    title: N Mapped
                  n_reads:
                    anyOf:
                    - type: integer
                    - type: 'null'
                    default: null
                    title: N Reads
                required:
                - assembly_id
                - average_coverage
                - average_identity
                - coverage
                - median_depth
                title: AlignmentResultsResponse
                type: object
          description: OK
      summary: GET alignments results
      tags:
      - Alignments
components:
  schemas:
    alignments:
      properties:
        $uri:
          example: /api/v1/alignments/0d77065796f8d173
          pattern: ^/api/v1/alignments/[a-f0-9]{16}$
          readOnly: true
          title: $Uri
          type: string
        complete:
          default: false
          title: Complete
          type: boolean
        created_at:
          description: Timestamp for when the object was created on the One Codex platform, encoded as a [RFC 3339](https://www.ietf.org/rfc/rfc3339.txt) timestamp.
          format: date-time
          title: Created At
          type: string
        error_msg:
          anyOf:
          - maxLength: 255
            type: string
          - type: 'null'
          default: null
          description: The error message from the analysis, if it failed.
          title: Error Msg
        job:
          description: 'A reference to the versioned job underlying the analysis, e.g., `{"$ref": "/api/v1/jobs/d512cb556241440f"}`.'
          properties:
            $ref:
              example: /api/v1/jobs/a1b2c3d4e5f67890
              format: uri
              pattern: ^/api/v1/jobs/[a-f0-9]{16}$
              type: string
          title: jobs
          type: object
        job_args:
          additionalProperties: true
          default: {}
          description: The arguments passed into this analysis (can be `null`).
          title: Job Args
          type: object
        sample:
          description: 'A reference to the sample underlying the analysis, e.g., `{"$ref": "/api/v1/sample/0ee172af60e84f61"}`.'
          properties:
            $ref:
              example: /api/v1/samples/a1b2c3d4e5f67890
              format: uri
              pattern: ^/api/v1/samples/[a-f0-9]{16}$
              type: string
          title: samples
          type: object
        success:
          default: false
          title: Success
          type: boolean
        updated_at:
          anyOf:
          - format: date-time
            type: string
          - type: 'null'
          default: null
          description: Timestamp for when the object was last updated on the One Codex platform, encoded as a [RFC 3339](https://www.ietf.org/rfc/rfc3339.txt) timestamp.
          title: Updated At
      required:
      - $uri
      - created_at
      - job
      - sample
      title: alignments
      type: object
  securitySchemes:
    apiKeyAuth:
      in: header
      name: X-API-Key
      type: apiKey