api.raml

#%RAML 1.0 Extension

extends: https://raw.githubusercontent.com/VEuPathDB/docs-api-schema/v2.0.2/libraries/base-service.raml

title: EDA Workspace Data Service API
version: v1.0.0
mediaType: application/json

uses:
  error: https://raw.githubusercontent.com/VEuPathDB/docs-api-schema/v2.0.2/libraries/errors.raml
  lib: schema/library.raml

securitySchemes:
  header-auth:
    description: Authentication based on a WDK auth cookie.
    type:
      x-custom
    describedBy:
      headers:
        Auth_Key:
          description: Authorization header.
          type: string

####################################
# Data Service Specific Endpoints
####################################

/filter-aware-metadata/continuous-variable:
  post:
    description: Returns equal interval, quantile and standard deviation based bin ranges and/or the median for a continuous variable over a specified range.
    body:
      application/json:
        type: lib.ContinuousVariableMetadataPostRequest
    responses:
      200:
        body:
          application/json:
            type: lib.ContinuousVariableMetadataPostResponse

/apps:
  displayName: Available Apps
  get:
    responses:
      200:
        body:
          application/json:
            type: lib.AppsGetResponse

  /standalone-map/visualizations:
    displayName: Available visualizations for the Standalone Map application

    /map-markers:
      post:
        description: Returns data required to make Standalone Map markers
        body:
          application/json:
            type: lib.StandaloneMapMarkersPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.StandaloneMapMarkersPostResponse

      /bubbles:
        post:
          description: |
            Returns data required to make bubble markers.
          body:
            application/json:
              type: lib.StandaloneMapBubblesPostRequest
          responses:
            200:
              body:
                application/json:
                  type: lib.StandaloneMapBubblesPostResponse

        /legend:
          post:
            description: Returns data required to make bubble marker legends
            body:
              application/json:
                type: lib.StandaloneMapBubblesLegendPostRequest
            responses:
              200:
                body:
                  application/json:
                    type: lib.StandaloneMapBubblesLegendPostResponse
      /collections:
        post:
          description: |
            Map marker endpoint for collection variables.
          body:
            application/json:
              type: lib.StandaloneCollectionMapMarkerPostRequest
          responses:
            200:
              body:
                application/json:
                  type: lib.StandaloneCollectionMapMarkerPostResponse


  /standalone-map-xyrelationships/visualizations:
    displayName: Available visualizations for the Standalone Map application

    /scatterplot:
      post:
        description: Returns data required to create a floating scatterplot visualization in the Standalone Map
        body:
          application/json:
            type: lib.FloatingScatterplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.FloatingScatterplotPostResponse

    /lineplot:
      post:
        description: Returns data required to create a floating lineplot visualization in the Standalone Map
        body:
          application/json:
            type: lib.FloatingLineplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.FloatingLineplotPostResponse

    /timeseries:
      post:
        description: Returns data required to create a floating time series visualization in the Standalone Map
        body:
          application/json:
            type: lib.FloatingLineplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.FloatingLineplotPostResponse

  /standalone-map-distributions/visualizations:
    displayName: Available visualizations for the Standalone Map application

    /histogram:
      post:
        description: Returns data required to create a floating histogram visualization in the Standalone Map
        body:
          application/json:
            type: lib.FloatingHistogramPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.FloatingHistogramPostResponse

    /boxplot:
      post:
        description: Returns data required to create a floating boxplot visualization in the Standalone Map
        body:
          application/json:
            type: lib.FloatingBoxplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.FloatingBoxplotPostResponse

  /standalone-map-countsandproportions/visualizations:
    displayName: Available visualizations for the Standalone Map application

    /barplot:
      post:
        description: Returns data required to create a floating bar plot visualization in the Standalone Map
        body:
          application/json:
            type: lib.FloatingBarplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.FloatingBarplotPostResponse

    /conttable:
      post:
        description: Returns data required to create a floating RxC mosaic plot visualization in the Standalone Map
        body:
          application/json:
            type: lib.FloatingContTablePostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.FloatingContTablePostResponse

  /standalone-map-continuous-collections/visualizations:
    displayName: Available visualizations for the Standalone Map application

    /lineplot:
      post:
        description: Returns data required to create a floating line plot visualization for continuous variable collections in the Standalone Map
        body:
          application/json:
            type: lib.CollectionFloatingLineplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.FloatingLineplotPostResponse

    /timeseries:
      post:
        description: Returns data required to create a floating time series visualization for continuous variable collections in the Standalone Map
        body:
          application/json:
            type: lib.CollectionFloatingLineplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.FloatingLineplotPostResponse

    /boxplot:
      post:
        description: Returns data required to create a floating box plot visualization for continuous variable collections in the Standalone Map
        body:
          application/json:
            type: lib.CollectionFloatingBoxplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.FloatingBoxplotPostResponse

    /histogram:
      post:
        description: Returns data required to create a floating histogram visualization for continuous variable collections in the Standalone Map
        body:
          application/json:
            type: lib.CollectionFloatingHistogramPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.FloatingHistogramPostResponse

  /standalone-map-categorical-collections/visualizations:
    displayName: Available visualizations for the Standalone Map application

    /lineplot:
      post:
        description: Returns data required to create a floating line plot visualization for categorical variable collections in the Standalone Map
        body:
          application/json:
            type: lib.CollectionFloatingLineplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.FloatingLineplotPostResponse


    /barplot:
      post:
        description: Returns data required to create a floating bar plot visualization for categorical variable collections in the Standalone Map
        body:
          application/json:
            type: lib.CollectionFloatingBarplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.FloatingBarplotPostResponse

    /conttable:
      post:
        description: Returns data required to create a floating RxC mosaic plot visualization for categorical variable collections in the Standalone Map
        body:
          application/json:
            type: lib.CollectionFloatingContTablePostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.FloatingContTablePostResponse

  /pass/visualizations:
    displayName: Available visualizations for the null/ pass-through app

    /map-markers:
      post:
        description: Returns data required to make MapVeu markers <br> Java impl- working <br> R impl- NA
        body:
          application/json:
            type: lib.MapPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.MapPostResponse

    /table:
      post:
        description: Return a tabular report of one or more variables. In the request, `filters` must be a subclass of [Filter](#type:lib.Filter)
        body:
          application/json:
            type: lib.TablePostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.TablePostResponse

    /scatterplot:
      post:
        description: Returns data required to create a scatterplot visualization <br> Java impl- NA <br> R impl- working
        body:
          application/json:
            type: lib.ScatterplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.ScatterplotPostResponse


    /densityplot:
      post:
        description: Returns data required to create a densityplot visualization <br> Java impl- NA <br> R impl- drafted, passing unit tests, not confirmed working
        body:
          application/json:
            type: lib.DensityplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.DensityplotPostResponse

    /timeseries:
      post:
        description: Returns data required to create a Time Series visualization <br> Java impl- NA <br> R impl- working
        body:
          application/json:
            type: lib.LineplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.LineplotPostResponse

    /lineplot:
      post:
        description: Returns data required to create a lineplot visualization <br> Java impl- NA <br> R impl- working
        body:
          application/json:
            type: lib.LineplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.LineplotPostResponse

    /histogram:
      post:
        description: Returns data required to create a histogram visualization. <br> Java impl- NA <br> R impl- working
        body:
          application/json:
            type: lib.HistogramPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.HistogramPostResponse

    /boxplot:
      post:
        description: Returns data required to create a boxplot visualization <br> Java impl- NA <br> R impl- working
        body:
          application/json:
            type: lib.BoxplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.BoxplotPostResponse

    /heatmap:
      post:
        description: Returns data required to create a heatmap visualization <br> Java impl- NA <br> R impl- drafted
        body:
          application/json:
            type: lib.HeatmapPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.HeatmapPostResponse

    /barplot:
      post:
        description: Returns data required to create a bar plot visualization <br> Java impl- drafted, not working <br> R impl- working
        body:
          application/json:
            type: lib.BarplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.BarplotPostResponse

    /map-markers-overlay:
      post:
        description: Returns data required to create a pie plot visualization <br> Java impl- NA <br> R impl- working
        body:
          application/json:
            type: lib.MapMarkersOverlayPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.MapMarkersOverlayPostResponse

    /twobytwo:
      post:
        description: Returns data required to create a mosaic plot visualization <br> Java impl- NA <br> R impl- working
        body:
          application/json:
            type: lib.TwoByTwoPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.TwoByTwoPostResponse

    /conttable:
      post:
        description: Returns data required to create a mosaic plot visualization <br> Java impl- NA <br> R impl- drafted
        body:
          application/json:
            type: lib.MosaicPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.ContTablePostResponse

  /alphadiv/visualizations:
    displayName: Visualizations for assessing internal sample diversity (alpha diversity).

    /boxplot:
      post:
        description: Returns data required to create a box plot with alpha diversity as dependent axis <br> Java impl- NA <br> R impl- NA
        body:
          application/json:
            type: lib.AlphaDivBoxplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.BoxplotPostResponse

    /scatterplot:
        post:
          description: Returns data required to create a scatterplot that explores the relationship between a continuous variable and alpha diversity <br> Java impl- NA <br> R impl- NA
          body:
            application/json:
              type: lib.AlphaDivScatterplotPostRequest
          responses:
            200:
              body:
                application/json:
                  type: lib.ScatterplotPostResponse

  /abundance/visualizations:
    displayName: Visualizations for assessing abundance data in a collection of samples.

    /boxplot:
      post:
        description: Returns data required to create a box plot with abundance as dependent axis <br> Java impl- NA <br> R impl- NA
        body:
          application/json:
            type: lib.AbundanceBoxplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.BoxplotPostResponse

    /scatterplot:
      post:
        description: Returns data required to create a scatterplot that explores the relationship between a continuous variable and alpha diversity <br> Java impl- NA <br> R impl- NA
        body:
          application/json:
            type: lib.AbundanceScatterplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.ScatterplotPostResponse

  /betadiv/visualizations:
    displayName: Visualizations for exploring the diversity between samples (beta diversity).

    /scatterplot:
      post:
        description: Returns data required to create a scatterplot that explores the differences between samples in a dataset as described by beta diversity <br> Java impl- NA <br> R impl- NA
        body:
          application/json:
            type: lib.BetaDivScatterplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.ScatterplotPostResponse

  /differentialabundance/visualizations:
    displayName: Visualizations for interrogating differentially abundant taxa, genes, or pathways

    /volcanoplot:
      post:
        description: Returns data required to create a volcanoplot from a differential abundance analysis.
        body:
          application/json:
            type: lib.DifferentialAbundanceVolcanoplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.DifferentialAbundanceStatsResponse

  /correlationassayassay/visualizations:
    displayName: Visualizations for discovering correlations between various assay data

    /bipartitenetwork:
      post:
        description: Returns data required to create a bipartite network from a correlation matrix.
        body:
          application/json:
            type: lib.CorrelationAssayAssayBipartitenetworkPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.CorrelationBipartiteNetworkPostResponse

  /correlationassaymetadata/visualizations:
    displayName: Visualizations for discovering corrleations between assay data and sample metadata

    /bipartitenetwork:
      post:
        description: Returns data required to create a bipartite network from a correlation matrix.
        body:
          application/json:
            type: lib.CorrelationAssayMetadataBipartitenetworkPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.CorrelationBipartiteNetworkPostResponse

  /correlationassayself/visualizations:
    displayName: Visualizations for discovering correlations between variables within an assay

    /unipartitenetwork:
      post:
        description: Returns data required to create a unipartite network from a correlation matrix.
        body:
          application/json:
            type: lib.CorrelationAssaySelfUnipartitenetworkPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.CorrelationNetworkPostResponse

  /distributions/visualizations:
    displayName: Visualizations for exploring distributions of data.

    /histogram:
      post:
        description: Returns data required to create a histogram visualization. <br> Java impl- NA <br> R impl- working
        body:
          application/json:
            type: lib.HistogramPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.HistogramPostResponse

    /boxplot:
      post:
        description: Returns data required to create a boxplot visualization <br> Java impl- NA <br> R impl- working
        body:
          application/json:
            type: lib.BoxplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.BoxplotPostResponse

  /countsandproportions/visualizations:
    displayName: Visualizations for exploring quantities and relative sizes of data.

    /barplot:
      post:
        description: Returns data required to create a bar or pie plot visualization <br> Java impl- drafted, not working <br> R impl- working
        body:
          application/json:
            type: lib.BarplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.BarplotPostResponse

    /twobytwo:
      post:
        description: Returns data required to create a mosaic plot visualization <br> Java impl- NA <br> R impl- working
        body:
          application/json:
            type: lib.TwoByTwoPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.TwoByTwoPostResponse

    /conttable:
      post:
        description: Returns data required to create a mosaic plot visualization <br> Java impl- NA <br> R impl- drafted
        body:
          application/json:
            type: lib.MosaicPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.ContTablePostResponse

  /xyrelationships/visualizations:
    displayName: Visualizations for exploring relationships between two continuous variables.

    /scatterplot:
      post:
        description: Returns data required to create a scatterplot visualization <br> Java impl- NA <br> R impl- working
        body:
          application/json:
            type: lib.ScatterplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.ScatterplotPostResponse

    /lineplot:
      post:
        description: Returns data required to create a lineplot visualization <br> Java impl- NA <br> R impl- working
        body:
          application/json:
            type: lib.LineplotPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.LineplotPostResponse

  /sample/visualizations:
    displayName: Sample visualizations demonstrating/testing service capabilities

    /record-count:
      post:
        description: Returns a count of the records in the subset
        body:
          application/json:
            type: lib.RecordCountPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.RecordCountPostResponse

    /multi-stream:
      post:
        description: Returns a stream of records with its first two attributes (combined from parallel streams)
        body:
          application/json:
            type: lib.MultiStreamPostRequest
        responses:
          200:
            body:
              text/plain:
                type: lib.EntityTabularPostResponse

    /collections-test:
      post:
        description: Returns a tabular response for the subset with all vars in the requested collection
        body:
          application/json:
            type: lib.TestCollectionsPostRequest
        responses:
          200:
            body:
              text/plain:
                type: lib.EntityTabularPostResponse

    /categorical-distribution:
      post:
        description: Returns a set of count and proportion distributions for a native categorical variable
        body:
          application/json:
            type: lib.CategoricalDistributionPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.CategoricalDistributionPostResponse

  /samplewithcompute/visualizations:
    displayName: Sample visualizations with computes demonstrating/testing service capabilities

    /viz-with-compute:
      post:
        description: Sample visualization plugin that uses data from a compute
        body:
          application/json:
            type: lib.ExampleComputeVizPostRequest
        responses:
          200:
            body:
              application/json:
                type: lib.ExampleComputeVizPostResponse