<commit_before># this is an example of the Uber API
# as a demonstration of an API spec in YAML
swagger: '2.0'
info:
  title: AVE REST API
  description: Allelic Variation Explorer REST API, Serving variant, annotation and genome data for AVE visualisation.
  version: "0.0.2"
# the domain of the service
host: {{HOSTPORT}}
# array of all schemes that your API supports
schemes:
  - {{SCHEME}}
# will be prefixed to all paths
basePath: /api/
produces:
  - application/json
  - application/problem+json
paths:
  /species:
    get:
      operationId: avedata.api.species.all
      summary: List of species
      description: |
        Fetch list of the species with available data.
      tags:
        - Species
      responses:
        200:
          description: Array of the speecies names
          schema:
            type: array
            items:
              $ref: '#/definitions/Species'
        default:
          description: Unexpected error
          schema:
            $ref: '#/definitions/Error'
  # /species/{species_id}/genomes:
  #   get:
  #     operationId: avedata.api.species.genomes
  #     summary: Genomes of selected species
  #     description: |
  #       List of genomes available for this species id
  #     parameters:
  #       - name: species_id
  #         in: path
  #         description: Species identifier
  #         required: true
  #         type: string
  #     tags:
  #       - Species
  #     responses:
  #       200:
  #         schema:
  #           type: array
  #           items:
  #             $ref: '#/definitions/Genome'
  #       default:
  #         description: Unexpected error
  #         schema:
  #           $ref: '#/definitions/Error'
  # /genomes/{genome_id}:
  #   get:
  #     operationId: avedata.api.genomes.get
  #     summary: Genome information of selected genome
  #     description: |
  #       Genome information for selected genome
  #     parameters:
  #       - name: genome_id
  #         in: path
  #         description: Genome id
  #         required: true
  #         type: string
  #     tags:
  #       - Genomes
  #     responses:
  #       200:
  #         description: Array of genomic features for selected genome id
  #         schema:
  #           $ref: '#/definitions/Genome'
  /genomes/{genome_id}/chromosomes/{chrom_id}/start/{start_position}/end/{end_position}/genes:
    get:
      operationId: avedata.api.genomes.genes
      summary: Genomic features of the genomic region
      description: |
        Genomic features of genomic region of selected genome, chromosome from start position to end position
      parameters:
        - name: genome_id
          in: path
          description: Genome id
          required: true
          type: string
        - name: chrom_id
          in: path
          description: Chromosome id
          required: true
          type: string
        - name: start_position
          in: path
          description: Start Position
          required: true
          type: integer
        - name: end_position
          in: path
          description: End Position
          required: true
          type: integer
      tags:
        - Genomes
      responses:
        200:
          description: Array of genomic features for selected genome id
          schema:
            type: array
            items:
              $ref: '#/definitions/Annotation'
        default:
          description: Unexpected error
          schema:
            $ref: '#/definitions/Error'
  /genomes/{genome_id}/chromosomes/{chrom_id}/start/{start_position}/end/{end_position}/annotations:
    get:
      operationId: avedata.api.genomes.annotations
      summary: Genomic features of the genomic region
      description: |
        Genomic features of genomic region of selected genome, chromosome from start position to end position
      parameters:
        - name: genome_id
          in: path
          description: Genome id
          required: true
          type: string
        - name: chrom_id
          in: path
          description: Chromosome id
          required: true
          type: string
        - name: start_position
          in: path
          description: Start Position
          required: true
          type: integer
        - name: end_position
          in: path
          description: End Position
          required: true
          type: integer
      tags:
        - Genomes
      responses:
        200:
          description: Array of genomic features for selected genome id
          schema:
            type: array
            items:
              $ref: '#/definitions/Annotation'
        default:
          description: Unexpected error
          schema:
            $ref: '#/definitions/Error'

  # /genomes/{genome_id}/chromosomes/{chrom_id}/start/{start_position}/end/{end_position}/haplotypes:
  #   get:
  #     summary: Genomic variants of the genomic region
  #     description: |
  #       Genomic variants of genomic region of selected genome, chromosome from start position to end position
  #     parameters:
  #       - name: genome_id
  #         in: path
  #         description: Genome id
  #         required: true
  #         type: string
  #       - name: chrom_id
  #         in: path
  #         description: Chromosome id
  #         required: true
  #         type: string
  #       - name: start_position
  #         in: path
  #         description: Start Position
  #         required: true
  #         type: integer
  #       - name: end_position
  #         in: path
  #         description: End Position
  #         required: true
  #         type: integer
  #     tags:
  #       - Genomes
  #     responses:
  #       200:
  #         description: Array of genomic variants for selected genome id
  #         schema:
  #           $ref: '#/definitions/Haplotypes'
  #       default:
  #         description: Unexpected error
  #         schema:
  #           $ref: '#/definitions/Error'
definitions:
  Error:
    type: object
    description: >-<commit_msg>Comment in/out parts of swagger specification<commit_after># this is an example of the Uber API
# as a demonstration of an API spec in YAML
swagger: '2.0'
info:
  title: AVE REST API
  description: Allelic Variation Explorer REST API, Serving variant, annotation and genome data for AVE visualisation.
  version: "0.0.2"
# the domain of the service
host: {{HOSTPORT}}
# array of all schemes that your API supports
schemes:
  - {{SCHEME}}
# will be prefixed to all paths
basePath: /api/
produces:
  - application/json
  - application/problem+json
paths:
  /species:
    get:
      operationId: avedata.api.species.all
      summary: List of species
      description: |
        Fetch list of the species with available data.
      tags:
        - Species
      responses:
        200:
          description: Array of the speecies names
          schema:
            type: array
            items:
              $ref: '#/definitions/Species'
        default:
          description: Unexpected error
          schema:
            $ref: '#/definitions/Error'
  # /species/{species_id}/genomes:
  #   get:
  #     operationId: avedata.api.species.genomes
  #     summary: Genomes of selected species
  #     description: |
  #       List of genomes available for this species id
  #     parameters:
  #       - name: species_id
  #         in: path
  #         description: Species identifier
  #         required: true
  #         type: string
  #     tags:
  #       - Species
  #     responses:
  #       200:
  #         schema:
  #           type: array
  #           items:
  #             $ref: '#/definitions/Genome'
  #       default:
  #         description: Unexpected error
  #         schema:
  #           $ref: '#/definitions/Error'
  # /genomes/{genome_id}:
  #   get:
  #     operationId: avedata.api.genomes.get
  #     summary: Genome information of selected genome
  #     description: |
  #       Genome information for selected genome
  #     parameters:
  #       - name: genome_id
  #         in: path
  #         description: Genome id
  #         required: true
  #         type: string
  #     tags:
  #       - Genomes
  #     responses:
  #       200:
  #         description: Array of genomic features for selected genome id
  #         schema:
  #           $ref: '#/definitions/Genome'
  /genomes/{genome_id}/chromosomes/{chrom_id}/start/{start_position}/end/{end_position}/genes:
    get:
      operationId: avedata.api.genomes.genes
      summary: Genomic features of the genomic region
      description: |
        Genomic features of genomic region of selected genome, chromosome from start position to end position
      parameters:
        - name: genome_id
          in: path
          description: Genome id
          required: true
          type: string
        - name: chrom_id
          in: path
          description: Chromosome id
          required: true
          type: string
        - name: start_position
          in: path
          description: Start Position
          required: true
          type: integer
        - name: end_position
          in: path
          description: End Position
          required: true
          type: integer
      tags:
        - Genomes
      responses:
        200:
          description: Array of genomic features for selected genome id
          schema:
            type: array
            items:
              $ref: '#/definitions/Annotation'
        default:
          description: Unexpected error
          schema:
            $ref: '#/definitions/Error'
  /genomes/{genome_id}/chromosomes/{chrom_id}/start/{start_position}/end/{end_position}/annotations:
    get:
      operationId: avedata.api.genomes.annotations
      summary: Genomic features of the genomic region
      description: |
        Genomic features of genomic region of selected genome, chromosome from start position to end position
      parameters:
        - name: genome_id
          in: path
          description: Genome id
          required: true
          type: string
        - name: chrom_id
          in: path
          description: Chromosome id
          required: true
          type: string
        - name: start_position
          in: path
          description: Start Position
          required: true
          type: integer
        - name: end_position
          in: path
          description: End Position
          required: true
          type: integer
      tags:
        - Genomes
      responses:
        200:
          description: Array of genomic features for selected genome id
          schema:
            type: array
            items:
              $ref: '#/definitions/Annotation'
        default:
          description: Unexpected error
          schema:
            $ref: '#/definitions/Error'

  # /genomes/{genome_id}/chromosomes/{chrom_id}/start/{start_position}/end/{end_position}/haplotypes:
  #   get:
  #     summary: Genomic variants of the genomic region
  #     description: |
  #       Genomic variants of genomic region of selected genome, chromosome from start position to end position
  #     parameters:
  #       - name: genome_id
  #         in: path
  #         description: Genome id
  #         required: true
  #         type: string
  #       - name: chrom_id
  #         in: path
  #         description: Chromosome id
  #         required: true
  #         type: string
  #       - name: start_position
  #         in: path
  #         description: Start Position
  #         required: true
  #         type: integer
  #       - name: end_position
  #         in: path
  #         description: End Position
  #         required: true
  #         type: integer
  #       - name: accessions
  #         description: Calculate haplotypes on subset of accessions
  #         in: query
  #         type: array
  #         items:
  #           type: string
  #         minItems: 0
  #     tags:
  #       - Genomes
  #     responses:
  #       200:
  #         description: Array of genomic variants for selected genome id
  #         schema:
  #           $ref: '#/definitions/Haplotypes'
  #       default:
  #         description: Unexpected error
  #         schema:
  #           $ref: '#/definitions/Error'
definitions:
  Error:
    type: object
    description: >-
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