{
  "$schema": "http://json-schema.org/draft-07/schema#",
  "$id": "https://github.com/vitessce/vitessce/#dataset",
  "title": "Vitessce data set",
  "type": "object",
  "definitions": {
    "components": {
      "description": "The layout array defines the views, or components, rendered in the grid.",
      "type": "array",
      "items": {
        "type": "object",
        "additionalProperties": false,
        "required": ["component", "x", "y"],
        "properties": {
          "component": {
            "type": "string",
            "description": "Specify a component using a name defined in the component registry."
          },
          "props": {
            "type": "object",
            "description": "Extra prop values for the component."
          },
          "x": { "type": "integer" },
          "y": { "type": "integer" },
          "w": { "type": "integer" },
          "h": { "type": "integer" },
          "coordinationScopes": {
            "type": "object",
            "description": "Component-level coordination scope mappings define which coordination object values a particular component can read and write, for each coordination type.",
            "additionalProperties": false,
            "required": [],
            "properties": {
              "dataset": { "type": "string" },
              "embeddingType": { "type": "string" },
              "embeddingZoom": { "type": "string" },
              "embeddingRotation": { "type": "string" },
              "embeddingTargetX": { "type": "string" },
              "embeddingTargetY": { "type": "string" },
              "embeddingTargetZ": { "type": "string" },
              "embeddingCellSetPolygonsVisible": { "type": "string" },
              "embeddingCellSetLabelsVisible": { "type": "string" },
              "embeddingCellSetLabelSize": { "type": "string" },
              "embeddingCellRadius": { "type": "string" },
              "spatialZoom": { "type": "string" },
              "spatialRotation": { "type": "string" },
              "spatialTargetX": { "type": "string" },
              "spatialTargetY": { "type": "string" },
              "spatialTargetZ": { "type": "string" },
              "heatmapZoomX": { "type": "string" },
              "heatmapZoomY": { "type": "string" },
              "heatmapTargetX": { "type": "string" },
              "heatmapTargetY": { "type": "string" },
              "cellFilter": { "type": "string" },
              "cellHighlight": { "type": "string" },
              "cellSetSelection": { "type": "string" },
              "cellSetHighlight": { "type": "string" },
              "cellSetColor": { "type": "string" },
              "geneFilter": { "type": "string" },
              "geneHighlight": { "type": "string" },
              "geneSelection": { "type": "string" },
              "geneExpressionTransform": { "type": "string" },
              "geneExpressionColormap": { "type": "string" },
              "geneExpressionColormapRange": { "type": "string" },
              "cellColorEncoding": { "type": "string" },
              "spatialLayers": { "type": "string" },
              "genomicZoomX": { "type": "string" },
              "genomicZoomY": { "type": "string" },
              "genomicTargetX": { "type": "string" },
              "genomicTargetY": { "type": "string" },
              "additionalCellSets": { "type": "string" },
              "moleculeHighlight": { "type": "string" }
            }
          }
        }
      }
    },
    "annDataCellSets": {
      "type": "array",
      "description": "Array of cell set configuration, following closely the conventions of the tabular schema",
      "items": {
        "type": "object",
        "additionalProperties": false,
        "required": ["groupName", "setName"],
        "properties": {
          "groupName": {
            "type": "string",
            "description": "The display name for the set, like 'Cell Type' or 'Louvain.'"
          },
          "setName": {
            "type": "string",
            "description": "The location in the AnnData store for the set, like 'obs/louvain' or 'obs/celltype.'"
          }
        }
      }
    },
    "annDataCells": {
      "type": "object",
      "description": "The properties of this object are the configuration for how to layout scatterplots and spatial information",
      "minProperties": 1,
      "additionalProperties": false,
      "required": [],
      "properties": {
        "xy": {
          "type": "string",
          "description": "The location in the AnnData store of cell centroids, like 'obsm/X_centroids.'"
        },
        "poly": {
          "type": "string",
          "description": "The location in the AnnData store of cell polygon outlines, like 'obsm/X_polygons.'"
        },
        "factors": {
          "type": "array",
          "description": "List of locations in the AnnData store of cell sets, like 'obs/louvain'",
          "items": {
            "type": "string"
          }
        },
        "mappings": {
          "patternProperties": {
            ".": {
              "type": "object",
              "description": "An object containing key-values for mappings like { UMAP: { key: 'obsm/X_umap', dims: [0, 1] } }.",
              "additionalProperties": false,
              "required": ["key"],
              "properties": {
                "key": {
                  "type": "string",
                  "description": "Where to look in the AnnData store for this mapping, like 'obsm/X_umap.'"
                },
                "dims": {
                  "type": "array",
                  "description": "Which indices of the obsm object to take for a scatterplot, allowing for, for example, different PCs from obsm/X_pca",
                  "minItems": 2,
                  "maxItems": 2,
                  "items": { "type": "number" }
                }
              }
            }
          }
        }
      }
    },
    "annDataExpressionMatrix": {
      "type": "object",
      "description": "The properties of this object are the configuration for how to fetch the cell x genes matrix",
      "additionalProperties": false,
      "required": ["matrix"],
      "properties": {
        "matrix": {
          "type": "string",
           "description": "The location in the AnnData store of the cell x gene matrix, like 'obsm/hvg_subset.' or 'X'"
        },
        "geneFilter": {
          "type": "string",
           "description": "The location in the AnnData store of a filter for the genes if using a subset of the data, like 'var.highly_variable.' if the matrix comes from 'obsm/hvg_subset.'"
        },
        "matrixGeneFilter": {
          "type": "string",
           "description": "The location in the AnnData store of a filter for the matrix data (used in heatmap and histogram), like 'var.highly_variable.''"
        }
      }
    },
    "requestInit": {
      "type": "object",
      "description": "The properties of this object correspond to the parameters of the JavaScript fetch() function.",
      "additionalProperties": false,
      "required": [],
      "properties": {
        "method": {
          "type": "string"
        },
        "headers": {
          "type": "object"
        },
        "body": {
          "type": "string"
        },
        "mode": {
          "type": "string"
        },
        "credentials": {
          "type": "string"
        },
        "cache": {
          "type": "string"
        },
        "redirect": {
          "type": "string"
        },
        "referrer": {
          "type": "string"
        },
        "integrity": {
          "type": "string"
        }
      }
    },
    "rasterLayer": {
      "description": "The properties of this object are the rendering settings for the raster layer.",
      "additionalProperties": false,
      "required": ["channels", "colormap", "index", "opacity", "type"],
      "properties": {
        "channels": {
          "type": "array",
          "items": {
            "type": "object",
            "additionalProperties": false,
            "required": ["selection"],
            "properties": {
              "color": {
                "type": "array",
                "items": { "type": "number" },
                "description": "The color to use when rendering this channel under the null colormap."
              },
              "selection": {
                "type": "object",
                "description": "Determines the channel selection, e.g. some Z and time slice."
              },
              "slider": {
                "type": "array",
                "items": { "type": "number" },
                "description": "Determines the range for color mapping."
              },
              "visible": {
                "type": "boolean",
                "description": "Determines whether this channel of the layer will be rendered in the spatial component."
              }
            }
          }
        },
        "colormap": {
          "oneOf": [
            {
              "type": "string",
              "description": "The name of the colormap to use for this layer."
            },
            {
              "type": "null",
              "description": "Use the solid color definitions."
            }
          ]
        },
        "transparentColor": {
          "oneOf": [
            {
              "type": "array",
              "minItems": 3,
              "maxItems": 3,
              "items": { 
                "type": "number",
                "description": "One of R G or B (0 - 255)." 
              },
              "description": "Determines the color to be set to opacity 0"
            },
            {
              "type": "null",
              "description": "No selection."
            }
          ]
        },
        "index": {
          "type": "number",
          "description": "The index of the layer among the array of layers available in the image file."
        },
        "modelMatrix": {
          "oneOf": [
            {
              "type": "array",
              "minItems": 16,
              "maxItems": 16,
              "description": "transformation matrix for this layer"
            },
            {
              "type": "null",
              "description": "Use no transformation."
            }
          ]
        },
        "opacity": {
          "type": "number"
        },
        "domainType": {
          "type": "string",
          "enum": ["Full", "Min/Max"],
          "description": "Determines the extent of the channel slider input element in the layer controller."
        },
        "type": {
          "type": "string",
          "enum": ["raster"]
        }
      }
    },
    "moleculesLayer": {
      "description": "The properties of this object are the rendering settings for the molecules layer.",
      "additionalProperties": false,
      "required": ["visible", "radius", "opacity", "type"],
      "properties": {
        "visible": {
          "type": "boolean"
        },
        "radius": {
          "type": "number"
        },
        "opacity": {
          "type": "number"
        },
        "type": {
          "type": "string",
          "enum": ["molecules"]
        }
      }
    },
    "cellsLayer": {
      "description": "The properties of this object are the rendering settings for the cells layer.",
      "additionalProperties": false,
      "required": ["visible", "stroked", "radius", "opacity", "type"],
      "properties": {
        "visible": {
          "type": "boolean"
        },
        "stroked": {
          "type": "boolean"
        },
        "radius": {
          "type": "number"
        },
        "opacity": {
          "type": "number"
        },
        "type": {
          "type": "string",
          "enum": ["cells"]
        }
      }
    },
    "neighborhoodsLayer": {
      "description": "The properties of this object are the rendering settings for the neighborhoods layer.",
      "additionalProperties": false,
      "required": ["visible", "type"],
      "properties": {
        "visible": {
          "type": "boolean"
        },
        "type": {
          "type": "string",
          "enum": ["neighborhoods"]
        }
      }
    },
    "spatialLayers": {
      "type": "array",
      "description": "Array of Spatial Layers",
      "items": {
        "oneOf": [
          {
            "$ref": "#/definitions/rasterLayer"
          },
          {
            "$ref": "#/definitions/cellsLayer"
          },
          {
            "$ref": "#/definitions/moleculesLayer"
          },
          {
            "$ref": "#/definitions/neighborhoodsLayer"
          }
        ]
      }
    }
  },
  "additionalProperties": false,
  "required": ["version", "name", "datasets", "layout", "initStrategy"],
  "properties": {
    "name": { "type": "string" },
    "public": { "type": "boolean" },
    "description": { "type": "string" },
    "datasets": {
      "type": "array",
      "description": "The datasets array defines groups of files, where the files within each dataset reference the same entities (cells, genes, cell sets, etc).",
      "items": {
        "type": "object",
        "additionalProperties": false,
        "required": ["uid", "files"],
        "properties": {
          "uid": { "type": "string" },
          "name": { "type": "string" },
          "description": { "type": "string" },
          "files": {
            "type": "array",
            "items": {
              "type": "object",
              "additionalProperties": false,
              "required": ["type", "fileType"],
              "properties": {
                "name": { "type": "string" },
                "type": { "type": "string" },
                "fileType": { "type": "string" },
                "url": { "type": "string" },
                "options": { "oneOf": [{ "$ref": "#/definitions/annDataCellSets" }, { "$ref": "https://github.com/vitessce/vitessce/#raster" }, { "$ref": "#/definitions/annDataCells" }, { "$ref": "#/definitions/annDataExpressionMatrix" }] },
                "requestInit": { "$ref": "#/definitions/requestInit" }
              }
            }
          }
        }
      }
    },
    "coordinationSpace": {
      "type": "object",
      "description": "The coordination space stores the values for each scope of each coordination object.",
      "additionalProperties": false,
      "required": [],
      "properties": {
        "dataset": {
          "type": "object",
          "patternProperties": {
            ".": { "type": "string" }
          }
        },
        "embeddingZoom": {
          "type": "object",
          "patternProperties": {
            ".": { "oneOf": [
                {
                  "type": "null",
                  "description": "If null is provided, value will be automatically set."
                },
                { "type": "number" }
              ]
            }
          }
        },
        "embeddingRotation": {
          "type": "object",
          "patternProperties": {
            ".": { "type": "number" }
          }
        },
        "embeddingTargetX": {
          "type": "object",
          "patternProperties": {
            ".": { "oneOf": [
                {
                  "type": "null",
                  "description": "If null is provided, value will be automatically set."
                },
                { "type": "number" }
              ]
            }
          }
        },
        "embeddingTargetY": {
          "type": "object",
          "patternProperties": {
            ".":  { "oneOf": [
                {
                  "type": "null",
                  "description": "If null is provided, value will be automatically set."
                },
                { "type": "number" }
              ]
            }
          }
        },
        "embeddingTargetZ": {
          "type": "object",
          "patternProperties": {
            ".": { "type": "number" }
          }
        },
        "embeddingType": {
          "type": "object",
          "patternProperties": {
            ".": { "type": "string" }
          }
        },
        "embeddingCellSetPolygonsVisible": {
          "type": "object",
          "patternProperties": {
            ".": { "type": "boolean" }
          }
        },
        "embeddingCellSetLabelsVisible": {
          "type": "object",
          "patternProperties": {
            ".": { "type": "boolean" }
          }
        },
        "embeddingCellSetLabelSize": {
          "type": "object",
          "patternProperties": {
            ".": { "type": "number" }
          }
        },
        "embeddingCellRadius": {
          "type": "object",
          "patternProperties": {
            ".": { "type": "number" }
          }
        },
        "spatialZoom": {
          "type": "object",
          "patternProperties": {
            ".":  { "oneOf": [
                {
                  "type": "null",
                  "description": "If null is provided, value will be automatically set."
                },
                { "type": "number" }
              ]
            }
          }
        },
        "spatialRotation": {
          "type": "object",
          "patternProperties": {
            ".": { "type": "number" }
          }
        },
        "spatialTargetX": {
          "type": "object",
          "patternProperties": {
            ".":  { "oneOf": [
                {
                  "type": "null",
                  "description": "If null is provided, value will be automatically set."
                },
                { "type": "number" }
              ]
            }
          }
        },
        "spatialTargetY": {
          "type": "object",
          "patternProperties": {
            ".":  { "oneOf": [
                {
                  "type": "null",
                  "description": "If null is provided, value will be automatically set."
                },
                { "type": "number" }
              ]
            }
          }
        },
        "spatialTargetZ": {
          "type": "object",
          "patternProperties": {
            ".": { "type": "number" }
          }
        },
        "spatialLayers": {
          "type": "object",
          "patternProperties": {
            ".": {
              "oneOf": [
                {
                  "type": "null",
                  "description": "If null is provided and auto layer initialization is enabled, layers will be automatically initialized."
                },
                { "$ref": "#/definitions/spatialLayers" }
              ]
            }
          }
        },
        "heatmapZoomX": {
          "type": "object",
          "patternProperties": {
            ".": { "type": "number" }
          }
        },
        "heatmapZoomY": {
          "type": "object",
          "patternProperties": {
            ".": { "type": "number" }
          }
        },
        "heatmapTargetX": {
          "type": "object",
          "patternProperties": {
            ".": { "type": "number" }
          }
        },
        "heatmapTargetY": {
          "type": "object",
          "patternProperties": {
            ".": { "type": "number" }
          }
        },
        "cellFilter": {
          "type": "object",
          "patternProperties": {
            ".": {
              "oneOf": [
                {
                  "type": "null",
                  "description": "If null is provided, no cells will be filtered out initially."
                },
                { "type": "array", "items": { "type": "string" } }
              ]
            }
          }
        },
        "cellHighlight": {
          "type": "object",
          "patternProperties": {
            ".": {
              "oneOf": [
                {
                  "type": "null",
                  "description": "If null is provided, no cell will be highlighted initially."
                },
                { "type": "string" }
              ]
            }
          }
        },
        "cellSetSelection": {
          "type": "object",
          "patternProperties": {
            ".": {
              "oneOf": [
                {
                  "type": "null",
                  "description": "If null is provided and auto cell set initialization is enabled, cell set selections will be automatically initialized."
                },
                { "type": "array" }
              ]
            }
          }
        },
        "cellSetHighlight": {
          "type": "object",
          "patternProperties": {
            ".": {
              "oneOf": [
                {
                  "type": "null",
                  "description": "If null is provided, no cell sets will be highlighted initially."
                },
                { "type": "string" }
              ]
            }
          }
        },
        "cellSetColor": {
          "type": "object",
          "patternProperties": {
            ".": {
              "oneOf": [
                {
                  "type": "null",
                  "description": "If null is provided, cell set colors will be automatically initialized."
                },
                {
                  "type": "array",
                  "items": {
                    "type": "object",
                    "additionalProperties": false,
                    "required": ["path", "color"],
                    "properties": {
                      "path": {
                        "type": "array",
                        "items": { "type": "string" }
                      },
                      "color": {
                        "type": "array",
                        "items": { "type": "number" }
                      }
                    }
                  }
                }
              ]
            }
          }
        },
        "cellColorEncoding": {
          "type": "object",
          "patternProperties": {
            ".": { "type": "string" }
          }
        },
        "geneFilter": {
          "type": "object",
          "patternProperties": {
            ".": {
              "oneOf": [
                {
                  "type": "null",
                  "description": "If null is provided, no genes will be filtered out initially."
                },
                { "type": "array", "items": { "type": "string" } }
              ]
            }
          }
        },
        "geneHighlight": {
          "type": "object",
          "patternProperties": {
            ".": {
              "oneOf": [
                {
                  "type": "null",
                  "description": "If null is provided, no genes will be highlighted initially."
                },
                { "type": "string" }
              ]
            }
          }
        },
        "geneSelection": {
          "type": "object",
          "patternProperties": {
            ".": {
              "oneOf": [
                {
                  "type": "null"
                },
                { "type": "array", "items": { "type": "string" } }
              ]
            }
          }
        },
        "geneExpressionTransform": {
          "type": "object",
          "patternProperties": {
            ".": {
              "oneOf": [
                {
                  "type": "null"
                },
                { "type": "string", "pattern": "log1p" }
              ]
            }
          }
        },
        "geneExpressionColormap": {
          "type": "object",
          "patternProperties": {
            ".": { "type": "string" }
          }
        },
        "geneExpressionColormapRange": {
          "type": "object",
          "patternProperties": {
            ".": { "type": "array", "items": { "type": "number" } }
          }
        },
        "genomicZoomX": {
          "type": "object",
          "patternProperties": {
            ".": { "type": "number" }
          }
        },
        "genomicZoomY": {
          "type": "object",
          "patternProperties": {
            ".": { "type": "number" }
          }
        },
        "genomicTargetX": {
          "type": "object",
          "patternProperties": {
            ".": { "type": "number" }
          }
        },
        "genomicTargetY": {
          "type": "object",
          "patternProperties": {
            ".": { "type": "number" }
          }
        },
        "additionalCellSets": {
          "type": "object",
          "patternProperties": {
            ".": {
              "oneOf": [
                {
                  "type": "null",
                  "description": "If null is provided, no cell will be highlighted initially."
                },
                {
                  "$ref": "https://github.com/vitessce/vitessce/#cell-sets"
                }
              ]
            }
          }
        },
        "moleculeHighlight": {
          "type": "object",
          "patternProperties": {
            ".": {
              "oneOf": [
                {
                  "type": "null",
                  "description": "If null is provided, no molecule will be highlighted initially."
                },
                { "type": "string" }
              ]
            }
          }
        }
      }
    },
    "layout": { "$ref": "#/definitions/components" },
    "initStrategy": {
      "type": "string",
      "enum": ["none", "auto"],
      "description": "The initialization strategy determines how missing coordination objects and coordination scope mappings are initially filled in."
    },
    "version": {
      "type": "string",
      "enum": ["1.0.0"],
      "description": "The schema version for the view config."
    }
  }
}