@vitessce/vit-s 2.0.3-beta.0 → 3.0.0

package/src/schemas/fixtures/cellSets.good.json

@@ -0,0 +1,16 @@
+{
+    "version": "0.1.2",
+    "datatype": "cell",
+    "tree": [
+        {
+            "name": "Clustering Algorithm",
+            "children": [
+                {
+                    "name": "Cluster A",
+                    "color": [255, 0, 0],
+                    "set": ["cell_243", "cell_271", "cell_247", "cell_248"]
+                }
+            ]
+        }
+    ]
+}

package/src/schemas/fixtures/config-1.0.1.bad.json

@@ -0,0 +1 @@
+[]

package/src/schemas/fixtures/config-1.0.1.bad.message.json

@@ -0,0 +1,11 @@
+[
+  {
+    "dataPath": "",
+    "keyword": "type",
+    "message": "should be object",
+    "params": {
+      "type": "object"
+    },
+    "schemaPath": "#/type"
+  }
+]

package/src/schemas/fixtures/config-1.0.1.good.json

@@ -0,0 +1,37 @@
+{
+  "name": "fake view config",
+  "description": "Spatial organization of the somatosensory cortex",
+  "datasets": [
+    {
+      "uid": "fake-dataset",
+      "name": "Fake Dataset",
+      "files": [
+        {
+          "type": "fake",
+          "fileType": "fake.json",
+          "url": "http://example.com",
+          "requestInit": {
+            "method": "POST",
+            "headers": {"x-foo": "bar"},
+            "body": "Body only valid with POSTs.",
+            "mode": "cors",
+            "credentials": "omit",
+            "cache": "no-store",
+            "redirect": "error",
+            "referrer": "foo-bar",
+            "integrity": "foo"
+          }
+        }
+      ]
+    }
+  ],
+  "coordinationSpace": {
+
+  },
+  "layout": [
+    { "component": "FooBar", "x": 0, "y": 0, "w": 1, "h": 1  },
+    { "component": "FooBar", "props": { "foo": "bar" }, "x": 1, "y": 1, "w": 1, "h": 1 }
+  ],
+  "initStrategy": "auto",
+  "version": "1.0.1"
+}

package/src/schemas/fixtures/config-1.0.2.bad.json

@@ -0,0 +1 @@
+[]

package/src/schemas/fixtures/config-1.0.2.bad.message.json

@@ -0,0 +1,11 @@
+[
+  {
+    "dataPath": "",
+    "keyword": "type",
+    "message": "should be object",
+    "params": {
+      "type": "object"
+    },
+    "schemaPath": "#/type"
+  }
+]

package/src/schemas/fixtures/config-1.0.2.good.json

@@ -0,0 +1,38 @@
+{
+    "name": "fake view config",
+    "description": "Spatial organization of the somatosensory cortex",
+    "datasets": [
+      {
+        "uid": "fake-dataset",
+        "name": "Fake Dataset",
+        "files": [
+          {
+            "type": "fake",
+            "fileType": "fake.json",
+            "url": "http://example.com",
+            "requestInit": {
+              "method": "POST",
+              "headers": {"x-foo": "bar"},
+              "body": "Body only valid with POSTs.",
+              "mode": "cors",
+              "credentials": "omit",
+              "cache": "no-store",
+              "redirect": "error",
+              "referrer": "foo-bar",
+              "integrity": "foo"
+            }
+          }
+        ]
+      }
+    ],
+    "coordinationSpace": {
+  
+    },
+    "layout": [
+      { "component": "FooBar", "x": 0, "y": 0, "w": 1, "h": 1  },
+      { "component": "FooBar", "props": { "foo": "bar" }, "x": 1, "y": 1, "w": 1, "h": 1 }
+    ],
+    "initStrategy": "auto",
+    "version": "1.0.2"
+  }
+  

package/src/schemas/fixtures/config-1.0.3.bad.json

@@ -0,0 +1 @@
+[]

package/src/schemas/fixtures/config-1.0.3.bad.message.json

@@ -0,0 +1,11 @@
+[
+  {
+    "dataPath": "",
+    "keyword": "type",
+    "message": "should be object",
+    "params": {
+      "type": "object"
+    },
+    "schemaPath": "#/type"
+  }
+]

package/src/schemas/fixtures/config-1.0.3.good.json

@@ -0,0 +1,38 @@
+{
+    "name": "fake view config",
+    "description": "Spatial organization of the somatosensory cortex",
+    "datasets": [
+      {
+        "uid": "fake-dataset",
+        "name": "Fake Dataset",
+        "files": [
+          {
+            "type": "fake",
+            "fileType": "fake.json",
+            "url": "http://example.com",
+            "requestInit": {
+              "method": "POST",
+              "headers": {"x-foo": "bar"},
+              "body": "Body only valid with POSTs.",
+              "mode": "cors",
+              "credentials": "omit",
+              "cache": "no-store",
+              "redirect": "error",
+              "referrer": "foo-bar",
+              "integrity": "foo"
+            }
+          }
+        ]
+      }
+    ],
+    "coordinationSpace": {
+  
+    },
+    "layout": [
+      { "component": "FooBar", "x": 0, "y": 0, "w": 1, "h": 1  },
+      { "component": "FooBar", "props": { "foo": "bar" }, "x": 1, "y": 1, "w": 1, "h": 1 }
+    ],
+    "initStrategy": "auto",
+    "version": "1.0.3"
+  }
+  

package/src/schemas/fixtures/obsSets.bad.json

@@ -0,0 +1 @@
+[]

package/src/schemas/fixtures/obsSets.bad.message.json

@@ -0,0 +1,11 @@
+[
+    {
+      "dataPath": "",
+      "keyword": "type",
+      "message": "should be object",
+      "params": {
+        "type": "object"
+      },
+      "schemaPath": "#/type"
+    }
+  ]

package/src/schemas/fixtures/obsSets.good.json

@@ -0,0 +1,16 @@
+{
+    "version": "0.1.2",
+    "datatype": "obs",
+    "tree": [
+        {
+            "name": "Clustering Algorithm",
+            "children": [
+                {
+                    "name": "Cluster A",
+                    "color": [255, 0, 0],
+                    "set": ["cell_243", "cell_271", "cell_247", "cell_248"]
+                }
+            ]
+        }
+    ]
+}

package/src/schemas/fixtures/obsSetsTabular.bad.json

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+{}

package/src/schemas/fixtures/obsSetsTabular.bad.message.json

@@ -0,0 +1,11 @@
+[
+    {
+      "dataPath": "",
+      "keyword": "type",
+      "message": "should be array",
+      "params": {
+        "type": "array"
+      },
+      "schemaPath": "#/type"
+    }
+  ]

package/src/schemas/fixtures/obsSetsTabular.good.json

@@ -0,0 +1,26 @@
+[
+    {
+        "groupName": "Clustering Algorithm",
+        "setName": "Cluster A",
+        "setColor": [255, 0, 0],
+        "obsId": "cell_243"
+    },
+    {
+        "groupName": "Clustering Algorithm",
+        "setName": "Cluster A",
+        "setColor": [255, 0, 0],
+        "obsId": "cell_271"
+    },
+    {
+        "groupName": "Clustering Algorithm",
+        "setName": "Cluster A",
+        "setColor": [255, 0, 0],
+        "obsId": "cell_247"
+    },
+    {
+        "groupName": "Clustering Algorithm",
+        "setName": "Cluster A",
+        "setColor": [255, 0, 0],
+        "obsId": "cell_248"
+    }
+]

package/src/schemas/fixtures/raster.bad.json

@@ -0,0 +1 @@
+[]

package/src/schemas/fixtures/raster.bad.message.json

@@ -0,0 +1,11 @@
+[
+  {
+    "dataPath": "",
+    "keyword": "type",
+    "message": "should be object",
+    "params": {
+      "type": "object"
+    },
+    "schemaPath": "#/type"
+  }
+]

package/src/schemas/fixtures/raster.good.json

@@ -0,0 +1,39 @@
+{
+  "schemaVersion": "0.0.2",
+  "images": [
+    {
+      "name": "Some Image",
+      "url": "https://vitessce-data.storage.googleapis.com/0.0.25/master_release/test.zarr",
+      "type": "zarr",
+      "metadata": {
+        "dimensions": [
+          {
+            "field": "channel",
+            "type": "nominal",
+            "values": [
+              "A", "B", "C"
+            ]
+          },
+          {
+            "field": "y",
+            "type": "quantitative",
+            "values": null
+          },
+          {
+            "field": "x",
+            "type": "quantitative",
+            "values": null
+          }
+        ],
+        "isPyramid": false,
+        "transform": {
+          "scale": 20.0,
+          "translate": {
+            "y": 200,
+            "x": 200
+          }
+        }
+      }
+    }
+  ]
+}

package/src/schemas/obsSets.schema.js

@@ -0,0 +1,195 @@
+const schema = {
+  $schema: 'http://json-schema.org/draft-07/schema#',
+  $id: 'https://github.com/vitessce/vitessce/#cell-sets',
+  title: 'Vitessce obs sets data',
+  type: 'object',
+  definitions: {
+    stringArray: {
+      type: 'array',
+      items: {
+        type: 'string',
+      },
+    },
+    stringProbabilityTupleArray: {
+      type: 'array',
+      items: {
+        type: 'array',
+        additionalItems: false,
+        items: [
+          {
+            type: 'string',
+          },
+          {
+            oneOf: [
+              {
+                type: 'number',
+                minimum: 0.0,
+                maximum: 1.0,
+              },
+              {
+                type: 'null',
+              },
+            ],
+          },
+        ],
+      },
+    },
+    colorArray: {
+      type: 'array',
+      items: {
+        type: 'integer',
+        minimum: 0,
+        maximum: 255,
+      },
+      minItems: 3,
+      maxItems: 3,
+    },
+    treeNodeLeaf: {
+      type: 'object',
+      additionalProperties: false,
+      required: ['name'],
+      properties: {
+        name: {
+          type: 'string',
+        },
+        color: {
+          $ref: '#/definitions/colorArray',
+        },
+        set: {
+          $ref: '#/definitions/stringArray',
+        },
+      },
+    },
+    treeNodeNonLeaf: {
+      type: 'object',
+      additionalProperties: false,
+      required: ['name'],
+      properties: {
+        name: {
+          type: 'string',
+        },
+        color: {
+          $ref: '#/definitions/colorArray',
+        },
+        children: {
+          type: 'array',
+          items: {
+            $ref: '#/definitions/treeNode',
+          },
+        },
+      },
+    },
+    treeNode: {
+      oneOf: [
+        {
+          $ref: '#/definitions/treeNodeNonLeaf',
+        },
+        {
+          $ref: '#/definitions/treeNodeLeaf',
+        },
+      ],
+    },
+    'version0.1.2': {
+      type: 'object',
+      additionalProperties: false,
+      required: ['version', 'datatype', 'tree'],
+      properties: {
+        dataset: {
+          type: 'string',
+        },
+        version: {
+          type: 'string',
+          enum: ['0.1.2'],
+        },
+        datatype: {
+          type: 'string',
+          enum: ['cell', 'obs'],
+        },
+        tree: {
+          type: 'array',
+          items: {
+            $ref: '#/definitions/treeNodeNonLeaf',
+          },
+        },
+      },
+    },
+    treeNodeLeafProbabilistic: {
+      type: 'object',
+      additionalProperties: false,
+      required: ['name'],
+      properties: {
+        name: {
+          type: 'string',
+        },
+        color: {
+          $ref: '#/definitions/colorArray',
+        },
+        set: {
+          $ref: '#/definitions/stringProbabilityTupleArray',
+        },
+      },
+    },
+    treeNodeNonLeafProbabilistic: {
+      type: 'object',
+      additionalProperties: false,
+      required: ['name'],
+      properties: {
+        name: {
+          type: 'string',
+        },
+        color: {
+          $ref: '#/definitions/colorArray',
+        },
+        children: {
+          type: 'array',
+          items: {
+            $ref: '#/definitions/treeNodeProbabilistic',
+          },
+        },
+      },
+    },
+    treeNodeProbabilistic: {
+      oneOf: [
+        {
+          $ref: '#/definitions/treeNodeNonLeafProbabilistic',
+        },
+        {
+          $ref: '#/definitions/treeNodeLeafProbabilistic',
+        },
+      ],
+    },
+    'version0.1.3': {
+      type: 'object',
+      additionalProperties: false,
+      required: ['version', 'datatype', 'tree'],
+      properties: {
+        dataset: {
+          type: 'string',
+        },
+        version: {
+          type: 'string',
+          enum: ['0.1.3'],
+        },
+        datatype: {
+          type: 'string',
+          enum: ['cell', 'obs'],
+        },
+        tree: {
+          type: 'array',
+          items: {
+            $ref: '#/definitions/treeNodeNonLeafProbabilistic',
+          },
+        },
+      },
+    },
+  },
+  oneOf: [
+    {
+      $ref: '#/definitions/version0.1.2',
+    },
+    {
+      $ref: '#/definitions/version0.1.3',
+    },
+  ],
+};
+export default schema;

package/src/schemas/obsSetsTabular.schema.js

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+const schema = {
+  $schema: 'http://json-schema.org/draft-07/schema#',
+  $id: 'https://github.com/vitessce/vitessce/#obsSetsTabular',
+  title: 'Vitessce obs sets data, tabular format',
+  definitions: {
+    colorArray: {
+      type: 'array',
+      items: { type: 'integer', minimum: 0, maximum: 255 },
+      minItems: 3,
+      maxItems: 3,
+    },
+  },
+  type: 'array',
+  items: {
+    type: 'object',
+    additionalProperties: false,
+    required: ['groupName', 'setName', 'obsId'],
+    properties: {
+      groupName: { type: 'string' },
+      setName: { type: 'string' },
+      setColor: { $ref: '#/definitions/colorArray' },
+      obsId: { type: 'string' },
+      predictionScore: {
+        oneOf: [
+          {
+            type: 'number',
+            minimum: 0.0,
+            maximum: 1.0,
+          },
+          {
+            type: 'null',
+          },
+        ],
+      },
+    },
+  },
+};
+
+export default schema;

package/src/schemas/raster.schema.js

@@ -0,0 +1,121 @@
+const schema = {
+  $schema: 'http://json-schema.org/draft-07/schema#',
+  $id: 'https://github.com/vitessce/vitessce/#raster',
+  title: 'Vitessce image data',
+  type: 'object',
+  definitions: {
+    transform: {
+      type: 'object',
+      additionalProperties: false,
+      oneOf: [{ required: ['scale', 'translate'] }, { required: ['matrix'] }],
+      properties: {
+        scale: { type: 'number' },
+        translate: {
+          type: 'object',
+          additionalProperties: false,
+          required: ['y', 'x'],
+          properties: {
+            y: { type: 'number' },
+            x: { type: 'number' },
+          },
+        },
+        matrix: {
+          type: 'array',
+          items: { type: 'number' },
+          minItems: 16,
+          maxItems: 16,
+        },
+      },
+    },
+    dimensions: {
+      type: 'array',
+      items: {
+        type: 'object',
+        additionalProperties: false,
+        required: ['field', 'type', 'values'],
+        properties: {
+          field: { type: 'string' },
+          type: {
+            type: 'string',
+            enum: ['quantitative', 'nominal', 'ordinal', 'temporal'],
+          },
+          values: {
+            type: ['array', 'null'],
+            items: { type: 'string' },
+          },
+        },
+      },
+    },
+    metadata: {
+      type: 'object',
+      additionalProperties: false,
+      anyOf: [{ required: ['dimensions', 'isPyramid'] }, { required: ['transform'] }, { required: ['omeTiffOffsetsUrl'] }, { required: ['isBitmask'] }],
+      properties: {
+        dimensions: { $ref: '#/definitions/dimensions' },
+        isPyramid: { type: 'boolean' },
+        transform: { $ref: '#/definitions/transform' },
+        isBitmask: { type: 'boolean' },
+        omeTiffOffsetsUrl: { type: 'string', format: 'uri' },
+      },
+    },
+    requestInit: {
+      type: 'object',
+      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',
+        },
+      },
+    },
+    image: {
+      type: 'object',
+      additionalProperties: false,
+      required: ['name', 'url', 'type'],
+      properties: {
+        name: { type: 'string' },
+        url: { type: 'string', format: 'uri' },
+        type: { type: 'string' },
+        metadata: { $ref: '#/definitions/metadata' },
+        requestInit: { $ref: '#/definitions/requestInit' },
+      },
+    },
+  },
+  additionalProperties: false,
+  required: ['schemaVersion', 'images'],
+  properties: {
+    schemaVersion: { type: 'string' },
+    usePhysicalSizeScaling: { type: 'boolean', description: 'Default is false: passing true in will infer scaling from the reported physcial size' },
+    renderLayers: { type: 'array', items: { type: 'string' } },
+    images: {
+      type: 'array',
+      items: { $ref: '#/definitions/image' },
+    },
+  },
+};
+
+export default schema;