@vitessce/vit-s 3.0.0 → 3.0.1

package/src/schemas/config-1.0.2.schema.json

@@ -1,911 +0,0 @@
-{
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "$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" },
-                "spatialRotationX": { "type": "string" },
-                "spatialRotationY": { "type": "string" },
-                "spatialRotationZ": { "type": "string" },
-                "spatialRotationOrbit": { "type": "string" },
-                "spatialOrbitAxis": { "type": "string" },
-                "spatialAxisFixed": { "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" },
-                "spatialRasterLayers": { "type": "string" },
-                "spatialCellsLayer": { "type": "string" },
-                "spatialMoleculesLayer": { "type": "string" },
-                "spatialNeighborhoodsLayer": { "type": "string" },
-                "genomicZoomX": { "type": "string" },
-                "genomicZoomY": { "type": "string" },
-                "genomicTargetX": { "type": "string" },
-                "genomicTargetY": { "type": "string" },
-                "additionalCellSets": { "type": "string" },
-                "moleculeHighlight": { "type": "string" }
-              }
-            }
-          }
-        }
-      },
-      "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"],
-        "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."
-          },
-          "opacity": {
-            "type": "number"
-          },
-          "modelMatrix": {
-            "oneOf": [
-              {
-                "type": "array",
-                "minItems": 16,
-                "maxItems": 16,
-                "description": "transformation matrix for this layer"
-              },
-              {
-                "type": "null",
-                "description": "Use no transformation."
-              }
-            ]
-          },
-          "domainType": {
-            "type": "string",
-            "enum": ["Full", "Min/Max"],
-            "description": "Determines the extent of the channel slider input element in the layer controller."
-          },
-          "resolution": {
-            "type": "number",
-            "description": "Resolution of 3D volumetric rendering"
-          },
-          "xSlice": {
-            "oneOf": [
-              {
-                "type": "array",
-                "minItems": 2,
-                "maxItems": 2,
-                "description": "Slice bounds"
-              },
-              {
-                "type": "null",
-                "description": "No slicing"
-              }
-            ]
-          },
-          "renderingMode": {
-            "type": "string",
-             "description": "Rendering mode of 3D volumetric rendering"
-          },
-          "ySlice": {
-            "oneOf": [
-              {
-                "type": "array",
-                "minItems": 2,
-                "maxItems": 2,
-                "description": "Slice bounds"
-              },
-              {
-                "type": "null",
-                "description": "No slicing"
-              }
-            ]
-          },
-          "zSlice": {
-            "oneOf": [
-              {
-                "type": "array",
-                "minItems": 2,
-                "maxItems": 2,
-                "description": "Slice bounds"
-              },
-              {
-                "type": "null",
-                "description": "No slicing"
-              }
-            ]
-          },
-          "type": {
-            "type": "string",
-            "enum": ["raster", "bitmask"]
-          },
-          "use3d": {
-            "type": "boolean"
-          },
-          "visible": {
-            "type": "boolean",
-            "description": "Determines whether this entire layer will be rendered in the spatial component."
-          }
-        }
-      },
-      "moleculesLayer": {
-        "type": "object",
-        "description": "The properties of this object are the rendering settings for the molecules layer.",
-        "additionalProperties": false,
-        "required": ["visible", "radius", "opacity"],
-        "properties": {
-          "visible": {
-            "type": "boolean"
-          },
-          "radius": {
-            "type": "number"
-          },
-          "opacity": {
-            "type": "number"
-          }
-        }
-      },
-      "cellsLayer": {
-        "type": "object",
-        "description": "The properties of this object are the rendering settings for the cells layer.",
-        "additionalProperties": false,
-        "required": ["visible", "stroked", "radius", "opacity"],
-        "properties": {
-          "visible": {
-            "type": "boolean"
-          },
-          "stroked": {
-            "type": "boolean"
-          },
-          "radius": {
-            "type": "number"
-          },
-          "opacity": {
-            "type": "number"
-          }
-        }
-      },
-      "neighborhoodsLayer": {
-        "type": "object",
-        "description": "The properties of this object are the rendering settings for the neighborhoods layer.",
-        "additionalProperties": false,
-        "required": ["visible"],
-        "properties": {
-          "visible": {
-            "type": "boolean"
-          }
-        }
-      },
-      "spatialRasterLayers": {
-        "type": "array",
-        "description": "Array of Spatial Layers",
-        "items": {
-          "$ref": "#/definitions/rasterLayer"
-        }
-      }
-    },
-    "additionalProperties": false,
-    "required": ["version", "name", "datasets", "layout", "initStrategy"],
-    "properties": {
-      "name": { "type": "string" },
-      "public": { "type": "boolean" },
-      "description": { "type": "string" },
-      "datasets": {
-        "type": "array",
-        "description": "The datasets array defines groups of files, where the files within each dataset reference the same entities (cells, genes, cell sets, etc).",
-        "items": {
-          "type": "object",
-          "additionalProperties": false,
-          "required": ["uid", "files"],
-          "properties": {
-            "uid": { "type": "string" },
-            "name": { "type": "string" },
-            "description": { "type": "string" },
-            "files": {
-              "type": "array",
-              "items": {
-                "type": "object",
-                "additionalProperties": false,
-                "required": ["fileType"],
-                "properties": {
-                  "name": { "type": "string" },
-                  "type": { "type": "string" },
-                  "fileType": { "type": "string" },
-                  "url": { "type": "string" },
-                  "options": { "oneOf": [
-                    { "type": "object" },
-                    { "type": "array" }
-                  ] },
-                  "requestInit": { "$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": {
-              ".":  { "oneOf": [
-                  {
-                    "type": "null",
-                    "description": "If null is provided, value will be automatically set."
-                  },
-                  { "type": "number" }
-                ]
-              }
-            }
-          },
-          "spatialRotationX": {
-            "type": "object",
-            "patternProperties": {
-              ".": {
-                "oneOf": [
-                  {
-                    "type": "null",
-                    "description": "If null is provided, value will be automatically set. Only useful for 3D viewing."
-                  },
-                  { "type": "number" }
-                ]
-              }
-            }
-          },
-          "spatialRotationY": {
-            "type": "object",
-            "patternProperties": {
-              ".": {
-                "oneOf": [
-                  {
-                    "type": "null",
-                    "description": "If null is provided, value will be automatically set. Only useful for 3D viewing."
-                  },
-                  { "type": "number" }
-                ]
-              }
-            }
-          },
-          "spatialRotationZ": {
-            "type": "object",
-            "patternProperties": {
-              ".": {
-                "oneOf": [
-                  {
-                    "type": "null",
-                    "description": "If null is provided, value will be automatically set. Only useful for 3D viewing."
-                  },
-                  { "type": "number" }
-                ]
-              }
-            }
-          },
-           "spatialRotationOrbit": {
-            "type": "object",
-            "patternProperties": {
-              ".": {
-                "oneOf": [
-                  {
-                    "type": "null",
-                    "description": "If null is provided, value will be automatically set. Only useful for 3D viewing."
-                  },
-                  { "type": "number" }
-                ]
-              }
-            }
-          },
-          "spatialOrbitAxis": {
-            "type": "object",
-            "patternProperties": {
-              ".": {
-                "oneOf": [
-                  {
-                    "type": "null",
-                    "description": "If null is provided, value will be automatically set. Only useful for 3D viewing."
-                  },
-                  { "type": "string" }
-                ]
-              }
-            }
-          },
-          "spatialAxisFixed": {
-            "type": "object",
-            "patternProperties": {
-              ".": {
-                "oneOf": [
-                  {
-                    "type": "null",
-                    "description": "Whether or not to have a fixed axis for the camera. Only useful for 3D viewing."
-                  },
-                  { "type": "boolean" }
-                ]
-              }
-            }
-          },
-          "spatialRasterLayers": {
-            "type": "object",
-            "patternProperties": {
-              ".": {
-                "oneOf": [
-                  {
-                    "type": "null",
-                    "description": "If null is provided and auto layer initialization is enabled, layers will be automatically initialized."
-                  },
-                  { "$ref": "#/definitions/spatialRasterLayers" }
-                ]
-              }
-            }
-          },
-          "spatialCellsLayer": {
-            "type": "object",
-            "patternProperties": {
-              ".": {
-                "oneOf": [
-                  {
-                    "type": "null",
-                    "description": "If null is provided and auto layer initialization is enabled, layers will be automatically initialized."
-                  },
-                  { "$ref": "#/definitions/cellsLayer" }
-                ]
-              }
-            }
-          },
-          "spatialNeighborhoodsLayer": {
-            "type": "object",
-            "patternProperties": {
-              ".": {
-                "oneOf": [
-                  {
-                    "type": "null",
-                    "description": "If null is provided and auto layer initialization is enabled, layers will be automatically initialized."
-                  },
-                  { "$ref": "#/definitions/neighborhoodsLayer" }
-                ]
-              }
-            }
-          },
-          "spatialMoleculesLayer": {
-            "type": "object",
-            "patternProperties": {
-              ".": {
-                "oneOf": [
-                  {
-                    "type": "null",
-                    "description": "If null is provided and auto layer initialization is enabled, layers will be automatically initialized."
-                  },
-                  { "$ref": "#/definitions/moleculesLayer" }
-                ]
-              }
-            }
-          },
-          "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": ["1.0.2"],
-        "description": "The schema version for the view config."
-      }
-    }
-  }
-