---
swagger: "2.0"
info:
  description: "API to support pVacSeq user interface for generating reports on pipeline\
    \ results"
  version: "1.0.0"
  title: "pVacSeq UI"
host: "localhost"
basePath: "/q"
schemes:
- "https"
produces:
- "application/json"
- "text/html"
paths:
  /api/v1/processes/{id}/results:
    get:
      tags:
      - "results"
      summary: "Get available output files"
      description: "The results endpoint returns a list of available pipeline data\
        \ files for generating reports. The response includes an array of objects\
        \ containing a \n"
      operationId: "pvacseq.server.controllers.default_controller.results_get"
      parameters:
      - name: "id"
        in: "path"
        description: "Process ID from which to fetch results"
        required: true
        type: "integer"
      - name: "count"
        in: "query"
        description: "Number of results to return"
        required: false
        type: "integer"
        default: 10
      - name: "page"
        in: "query"
        description: "Page number of results to return"
        required: false
        type: "integer"
        default: 1
      responses:
        200:
          description: "An array of results"
          schema:
            type: "array"
            items:
              $ref: "#/definitions/Result"
        default:
          description: "Unexpected error"
          schema:
            $ref: "#/definitions/Error"
      x-tags:
      - tag: "results"
  /api/v1/processes/{id}/results/{fileID}:
    get:
      tags:
      - "file"
      summary: "Get pipeline output data"
      description: "This endpoint returns raw data from the requested output file \n"
      operationId: "pvacseq.server.controllers.default_controller.results_getfile"
      parameters:
      - name: "id"
        in: "path"
        description: "Process ID from which to read results"
        required: true
        type: "integer"
      - name: "count"
        in: "query"
        description: "Number of results to return"
        required: false
        type: "integer"
        default: 10
      - name: "page"
        in: "query"
        description: "Page number of results to return"
        required: false
        type: "integer"
        default: 1
      - name: "fileID"
        in: "path"
        description: "File id from which to read data"
        required: true
        type: "integer"
      responses:
        200:
          description: "An array of entries"
          schema:
            type: "array"
            items: {
              type: "object"
            }
        default:
          description: "Unexpected error"
          schema:
            $ref: "#/definitions/Error"
      x-tags:
      - tag: "file"
  /api/v1/processes/{id}/results/{fileID}/cols:
    get:
      tags:
      - "columns"
      summary: "Get column mappings"
      description: "This endpoint returns mappings from standardized column names\
        to their names as they appear in the source data \n"
      operationId: "pvacseq.server.controllers.default_controller.results_getcols"
      parameters:
      - name: "id"
        in: "path"
        description: "Process ID from which to read results"
        required: true
        type: "integer"
      - name: "fileID"
        in: "path"
        description: "File id from which to read data"
        required: true
        type: "integer"
      responses:
        200:
          description: "An object mapping the columns"
          schema:
            type: "object"
        default:
          description: "Unexpected error"
          schema:
            $ref: "#/definitions/Error"
      x-tags:
      - tag: "cols"
  /api/v1/start:
    post:
      tags:
      - "start"
      summary: "Start a new pVAC-Seq run"
      description: "This endpoint initiates a new pVAC-Seq run\n"
      operationId: "pvacseq.server.controllers.default_controller.start"
      parameters:
      - name: "input"
        in: "formData"
        description: "Input VCF file"
        required: true
        type: "string"
      - name: "samplename"
        in: "formData"
        description: "Sample Name"
        required: true
        type: "string"
      - name: "alleles"
        in: "formData"
        description: "A comma-separated list of alleles to run the sequences against"
        required: true
        type: "string"
      - name: "epitope_lengths"
        in: "formData"
        description: "A comma-separated list of epitope lengths to produce"
        required: false
        type: "string"
        default: "10"
      - name: "prediction_algorithms"
        in: "formData"
        description: "A comma-separated list of prediction algorithms to use"
        required: true
        type: "string"
      - name: "output"
        in: "formData"
        description: "The directory to write output to"
        required: true
        type: "string"
      - name: "peptide_sequence_length"
        in: "formData"
        description: "Length of the peptide sequences to produce in the FASTA"
        type: "integer"
        default: 21
      - name: "gene_expn_file"
        in: "formData"
        description: "genes.fpkm_tracking file from Cufflinks"
        type: "string"
        default: ""
      - name: "transcript_expn_file"
        in: "formData"
        description: "isoforms.fpkm_tracking file from Cufflinks"
        type: "string"
        default: ""
      - name: "net_chop_method"
        in: "formData"
        description: "Run NetChop using the specified method"
        type: "string"
        enum: ["cterm", "20s"]
      - name: "netmhc_stab"
        in: "formData"
        description: "Run NetMHCStabPan at the end of the pipeline"
        type: "boolean"
        default: false
      - name: "top_result_per_mutation"
        in: "formData"
        description: "Output top scoring candidate per allele-length per mutation"
        type: "boolean"
        default: false
      - name: "top_score_metric"
        in: "formData"
        description: "ic50 metric for choosing best epitopes during binding filtering"
        type: "string"
        enum: ["lowest", "median"]
        default: "median"
      - name: "binding_threshold"
        in: "formData"
        description: "Report only epitopes with a predicted binding score below this value"
        type: "integer"
        default: 500
      - name: "minimum_fold_change"
        in: "formData"
        description: "Report only epitopes with a fold change between the mutant and wildtype sequences above this value"
        type: "integer"
        default: 0
      - name: "expn_val"
        in: "formData"
        description: "Gene expression cutoff"
        type: "integer"
        default: 1
      - name: "net_chop_threshold"
        in: "formData"
        description: "NetChop prediction threshold"
        type: "number"
        default: 0.5
      - name: "fasta_size"
        in: "formData"
        description: "Number of entries submitted to IEDB in each request.  Must be an even number"
        type: "integer"
        default: 200
      - name: "keep_tmp_files"
        in: "formData"
        description: "Keep temporary files in the output directory after completion"
        type: "boolean"
        default: false
      responses:
        200:
          description: "Returns the process ID of the newly started pVAC-Seq run"
          schema:
            type: "integer"
        default:
          description: "Unexpected error"
          schema:
            $ref: "#/definitions/Error"
      x-tags:
      - tag: "test"
  /api/v1/processes:
    get:
      tags:
        - "processes"
      summary: "Get list of running processes"
      description: "This endpoint returns a list of active pvacseq runs\n"
      operationId: "pvacseq.server.controllers.default_controller.processes"
      responses:
        200:
          description: "A list of active processes"
          schema:
            type: "array"
            items: {
              type: "integer"
            }
        default:
          description: "Unexpected error"
          schema:
            $ref: "#/definitions/Error"
  /api/v1/processes/{id}:
    get:
      tags:
        - "processes"
      summary: "Get info about a specific process"
      description: "This endpoint returns data about a currently running process\n"
      operationId: "pvacseq.server.controllers.default_controller.process_info"
      parameters:
      - name: "id"
        in: "path"
        description: "Process id of an active pVAC-Seq run"
        required: true
        type: "integer"
      responses:
        200:
          description: "A list of active processes"
          schema:
            $ref: "#/definitions/Process"
        default:
          description: "Unexpected error"
          schema:
            $ref: "#/definitions/Error"
  /api/v1/shutdown:
    get:
      tags:
        - "shutdown"
      summary: "Terminate any running processes then shutdown the server"
      description: "This endpoint handles the cleanup for closing any active \
        pvacseq runs, then shutsdown the server\n"
      operationId: "pvacseq.server.controllers.default_controller.shutdown"
      responses:
        200:
          description: "This endpoint does not actually return anything"
          schema:
            type: "object"
        default:
          description: "Unexpected error"
          schema:
            $ref: "#/definitions/Error"
  # /api/v1/stop/{id}:
  #   get:
  #     tags:
  #       - "stop"
  #     summary: "Terminate the specified process"
  #     description: "This endpoint closes the requested process if it is still running. /
  #       id must refer to a valid process id started by the current user"
  #     operationId: "pvacseq.server.controllers.default_controller.stop"
  #     parameters:
  #     - name: "id"
  #       in: "path"
  #       description: "Process id of an active pVAC-Seq run"
  #       required: true
  #       type: "integer"
  #     responses:
  #       200:
  #         description: "Returns the status of the process just before termination"
  #         schema:
  #           $ref: "#/definitions/Process"
  #       default:
  #         description: "Unexpected error"
  #         schema:
  #           $ref: "#/definitions/Error"
definitions:
  Process:
    type: "object"
    properties:
      pid:
        type: "integer"
        description: "Actual pid assigned by the OS for this pVAC-Seq run"
      id:
        type: "integer"
        description: "Unique process ID"
      command:
        type: "string"
        description: "The shell command issued to start this pVAC-Seq run"
      status:
        type: "string"
        description: "The most recent message sent by pVAC-Seq"
      log:
        type: "string"
        description: "The full output transcript from pVAC-Seq"
      output:
        type: "string"
        description: "The output folder of the specified process"
      running:
        type: "boolean"
        description: "Indicates whether or not the process is still running"
  Result:
    type: "object"
    properties:
      id:
        type: "integer"
        description: "Unique identifier of the result file."
      description:
        type: "string"
        description: "Description of result file"
      display_name:
        type: "string"
        description: "Display name of result file (try to keep under 32 chars or so)"
      url:
        type: "string"
        description: "URL of results file"
      size:
        type: "string"
        description: "Size of data file, in bytes"
  Error:
    type: "object"
    properties:
      code:
        type: "integer"
        format: "int32"
      message:
        type: "string"
      fields:
        type: "string"