@vitessce/vit-s 2.0.3 → 3.0.1

package/src/schemas/obsSets.schema.js

@@ -1,195 +0,0 @@
-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

@@ -1,39 +0,0 @@
-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

@@ -1,121 +0,0 @@
-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;

package/src/schemas/schema-schema.sh

@@ -1,34 +0,0 @@
-#!/usr/bin/env bash
-set -o errexit
-
-die() { set +v; echo "$*" 1>&2 ; exit 1; }
-
-# This is a totally ad-hoc script to ensure some consistency in our schemas.
-# We want to be sure that each "properties" also specifies "additionalProperties" and "required".
-
-FAILURES=$(
-  SCHEMA_DIR=`dirname $0`
-  for SCHEMA in $SCHEMA_DIR/*.schema.json; do
-    export SCHEMA
-    grep -B2 '"properties"' $SCHEMA \
-      | perl -pne 's/\n//; s/\s+/ /g; s/--/\n/;' \
-      | perl -ne 'next unless /properties/; print "$ENV{SCHEMA}: $_" unless /"additionalProperties".*"(required|oneOf|allOf|anyOf)".*"properties"/;'
-  done
-)
-
-if [[ $FAILURES ]]; then
-  die "Check that 'additionalProperties' & 'required' & 'properties' are provided:
-$FAILURES"
-fi
-
-# Check that existing schemas have not changed.
-for SCHEMA in $SCHEMA_DIR/config-*.schema.json; do
-  SCHEMA_NAME=`basename $SCHEMA`
-  SCHEMA_RESPONSE=`curl -s https://raw.githubusercontent.com/vitessce/vitessce/main/src/schemas/$SCHEMA_NAME`
-  if [ "$SCHEMA_RESPONSE" == "404: Not Found" ]; then
-    echo "Schema $SCHEMA is not in production yet."
-  else
-    diff --ignore-all-space $SCHEMA <(echo "$SCHEMA_RESPONSE") \
-      || die "$SCHEMA has changed.  Please do not change existing schema; instead, make a new schema."
-  fi
-done

package/src/schemas/schema.test-old.js

@@ -1,49 +0,0 @@
-// TODO(monorepo)
-/*
-import Ajv from 'ajv';
-import obsSetsSchema from './obsSets.schema';
-import rasterSchema from './raster.schema';
-describe('schemas', () => {
-  [
-    'config-1.0.1',
-    'obsSets',
-    'obsSetsTabular',
-    'raster',
-  ].forEach((type) => {
-    const schemaFile = `${type}.schema.json`;
-    describe(schemaFile, async () => {
-      const schema = await import(`./${schemaFile}`);
-      let validate;
-      if (type === 'config-1.0.1') {
-        const obsSets = obsSetsSchema;
-        const raster = rasterSchema;
-        validate = new Ajv()
-          .addSchema(obsSets)
-          .addSchema(raster)
-          .compile(schema);
-      } else {
-        validate = new Ajv().compile(schema);
-      }
-
-      const [goodFixture, badFixture, badMessage] = [
-        'good', 'bad', 'bad.message',
-      ].map(stem => `${type}.${stem}.json`);
-
-      it(`passes ${goodFixture}`, async () => {
-        const data = await import(`./fixtures/${goodFixture}`);
-        const valid = validate(data);
-        if (!valid) { console.warn(validate.errors); }
-        expect(valid).toEqual(true);
-      });
-
-      it(`fails ${badFixture}`, async () => {
-        const data = await import(`./fixtures/${badFixture}`);
-        const message = await import(`./fixtures/${badMessage}`);
-        const valid = validate(data);
-        expect(valid).toEqual(false);
-        expect(validate.errors).toEqual(message);
-      });
-    });
-  });
-});
-*/