@vitessce/vit-s 2.0.0-beta.0

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Files changed (91) hide show
  1. package/LICENSE +21 -0
  2. package/dist/CallbackPublisher.js +68 -0
  3. package/dist/LoadingIndicator.js +27 -0
  4. package/dist/TitleInfo.js +151 -0
  5. package/dist/VitS.js +113 -0
  6. package/dist/Vitessce.integration.test.js +36 -0
  7. package/dist/Vitessce.js +101 -0
  8. package/dist/VitessceGrid.js +55 -0
  9. package/dist/VitessceGrid.test.js +36 -0
  10. package/dist/Warning.js +45 -0
  11. package/dist/classNames.js +8 -0
  12. package/dist/component-registry.js +16 -0
  13. package/dist/data/AbstractLoader.js +35 -0
  14. package/dist/data/AbstractTwoStepLoader.js +7 -0
  15. package/dist/data/LoaderResult.js +7 -0
  16. package/dist/data/index.js +3 -0
  17. package/dist/data/loader-registry.js +15 -0
  18. package/dist/data-hook-utils.js +175 -0
  19. package/dist/data-hooks.js +241 -0
  20. package/dist/errors/AbstractLoaderError.js +13 -0
  21. package/dist/errors/DataSourceFetchError.js +13 -0
  22. package/dist/errors/DatasetNotFoundError.js +17 -0
  23. package/dist/errors/LoaderNotFoundError.js +17 -0
  24. package/dist/errors/LoaderValidationError.js +15 -0
  25. package/dist/errors/OptionsValidationError.js +15 -0
  26. package/dist/errors/index.js +6 -0
  27. package/dist/export-utils.js +70 -0
  28. package/dist/export-utils.test.js +66 -0
  29. package/dist/file-options-schemas-legacy.js +136 -0
  30. package/dist/file-options-schemas-legacy.test.js +126 -0
  31. package/dist/file-options-schemas.js +322 -0
  32. package/dist/file-options-schemas.test.js +23 -0
  33. package/dist/hooks.js +215 -0
  34. package/dist/index.js +18 -0
  35. package/dist/joint-file-types-legacy.js +278 -0
  36. package/dist/joint-file-types-legacy.test.js +400 -0
  37. package/dist/joint-file-types.js +148 -0
  38. package/dist/joint-file-types.test.js +139 -0
  39. package/dist/loader-registry.js +98 -0
  40. package/dist/plugins.js +154 -0
  41. package/dist/plugins.test.fixtures.js +76 -0
  42. package/dist/plugins.test.js +30 -0
  43. package/dist/schemas/PrettyJsonSchema.js +34 -0
  44. package/dist/schemas/config-0.1.0.schema.json +84 -0
  45. package/dist/schemas/config-1.0.0.schema.json +733 -0
  46. package/dist/schemas/config-1.0.1.schema.json +909 -0
  47. package/dist/schemas/config-1.0.10.schema.json +969 -0
  48. package/dist/schemas/config-1.0.11.schema.json +990 -0
  49. package/dist/schemas/config-1.0.12.schema.json +997 -0
  50. package/dist/schemas/config-1.0.13.schema.json +1013 -0
  51. package/dist/schemas/config-1.0.14.schema.json +1048 -0
  52. package/dist/schemas/config-1.0.15.schema.json +1048 -0
  53. package/dist/schemas/config-1.0.15.schema.test.js +22 -0
  54. package/dist/schemas/config-1.0.2.schema.json +910 -0
  55. package/dist/schemas/config-1.0.3.schema.json +910 -0
  56. package/dist/schemas/config-1.0.4.schema.json +949 -0
  57. package/dist/schemas/config-1.0.5.schema.json +949 -0
  58. package/dist/schemas/config-1.0.6.schema.json +949 -0
  59. package/dist/schemas/config-1.0.7.schema.json +949 -0
  60. package/dist/schemas/config-1.0.8.schema.json +965 -0
  61. package/dist/schemas/config-1.0.9.schema.json +965 -0
  62. package/dist/schemas/obsSets.schema.js +195 -0
  63. package/dist/schemas/obsSets.schema.json +194 -0
  64. package/dist/schemas/obsSetsTabular.schema.js +38 -0
  65. package/dist/schemas/obsSetsTabular.schema.json +37 -0
  66. package/dist/schemas/raster.schema.js +120 -0
  67. package/dist/schemas/raster.schema.json +119 -0
  68. package/dist/schemas/schema.test-old.js +50 -0
  69. package/dist/schemas/schema.test.js +46 -0
  70. package/dist/schemas.js +4 -0
  71. package/dist/shared-mui/components.js +35 -0
  72. package/dist/shared-mui/container.js +211 -0
  73. package/dist/shared-mui/styles.js +63 -0
  74. package/dist/shared-plot-options/CellColorEncodingOption.js +18 -0
  75. package/dist/shared-plot-options/OptionSelect.js +12 -0
  76. package/dist/shared-plot-options/OptionsContainer.js +12 -0
  77. package/dist/shared-plot-options/index.js +4 -0
  78. package/dist/shared-plot-options/styles.js +48 -0
  79. package/dist/state/hooks.js +550 -0
  80. package/dist/view-config-upgraders.js +525 -0
  81. package/dist/view-config-utils.js +286 -0
  82. package/dist/view-config-utils.test.fixtures.js +765 -0
  83. package/dist/view-config-utils.test.js +66 -0
  84. package/dist/view-config-versions.js +47 -0
  85. package/dist/vitessce-grid-layout/VitessceGridLayout.js +96 -0
  86. package/dist/vitessce-grid-layout/VitessceGridLayout.test.js +40 -0
  87. package/dist/vitessce-grid-layout/index.js +1 -0
  88. package/dist/vitessce-grid-layout/layout-utils.js +61 -0
  89. package/dist/vitessce-grid-layout/layout-utils.test.js +146 -0
  90. package/dist/vitessce-grid-utils.js +140 -0
  91. package/package.json +43 -0
package/dist/schemas/obsSets.schema.js ADDED
@@ -0,0 +1,195 @@
1
+ const schema = {
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+ $schema: 'http://json-schema.org/draft-07/schema#',
3
+ $id: 'https://github.com/vitessce/vitessce/#cell-sets',
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+ title: 'Vitessce obs sets data',
5
+ type: 'object',
6
+ definitions: {
7
+ stringArray: {
8
+ type: 'array',
9
+ items: {
10
+ type: 'string',
11
+ },
12
+ },
13
+ stringProbabilityTupleArray: {
14
+ type: 'array',
15
+ items: {
16
+ type: 'array',
17
+ additionalItems: false,
18
+ items: [
19
+ {
20
+ type: 'string',
21
+ },
22
+ {
23
+ oneOf: [
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+ {
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+ type: 'number',
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+ minimum: 0.0,
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+ maximum: 1.0,
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+ },
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+ {
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+ type: 'null',
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+ },
32
+ ],
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+ },
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+ ],
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+ },
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+ },
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+ colorArray: {
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+ type: 'array',
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+ items: {
40
+ type: 'integer',
41
+ minimum: 0,
42
+ maximum: 255,
43
+ },
44
+ minItems: 3,
45
+ maxItems: 3,
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+ },
47
+ treeNodeLeaf: {
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+ type: 'object',
49
+ additionalProperties: false,
50
+ required: ['name'],
51
+ properties: {
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+ name: {
53
+ type: 'string',
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+ },
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+ color: {
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+ $ref: '#/definitions/colorArray',
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+ },
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+ set: {
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+ $ref: '#/definitions/stringArray',
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+ },
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+ },
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+ },
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+ treeNodeNonLeaf: {
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+ type: 'object',
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+ additionalProperties: false,
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+ required: ['name'],
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+ properties: {
68
+ name: {
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+ type: 'string',
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+ },
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+ color: {
72
+ $ref: '#/definitions/colorArray',
73
+ },
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+ children: {
75
+ type: 'array',
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+ items: {
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+ $ref: '#/definitions/treeNode',
78
+ },
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+ },
80
+ },
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+ },
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+ treeNode: {
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+ oneOf: [
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+ {
85
+ $ref: '#/definitions/treeNodeNonLeaf',
86
+ },
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+ {
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+ $ref: '#/definitions/treeNodeLeaf',
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+ },
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+ ],
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+ },
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+ 'version0.1.2': {
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+ type: 'object',
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+ additionalProperties: false,
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+ required: ['version', 'datatype', 'tree'],
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+ properties: {
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+ dataset: {
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+ type: 'string',
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+ },
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+ version: {
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+ type: 'string',
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+ enum: ['0.1.2'],
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+ },
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+ datatype: {
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+ type: 'string',
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+ enum: ['cell', 'obs'],
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+ },
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+ tree: {
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+ type: 'array',
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+ items: {
111
+ $ref: '#/definitions/treeNodeNonLeaf',
112
+ },
113
+ },
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+ },
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+ },
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+ treeNodeLeafProbabilistic: {
117
+ type: 'object',
118
+ additionalProperties: false,
119
+ required: ['name'],
120
+ properties: {
121
+ name: {
122
+ type: 'string',
123
+ },
124
+ color: {
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+ $ref: '#/definitions/colorArray',
126
+ },
127
+ set: {
128
+ $ref: '#/definitions/stringProbabilityTupleArray',
129
+ },
130
+ },
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+ },
132
+ treeNodeNonLeafProbabilistic: {
133
+ type: 'object',
134
+ additionalProperties: false,
135
+ required: ['name'],
136
+ properties: {
137
+ name: {
138
+ type: 'string',
139
+ },
140
+ color: {
141
+ $ref: '#/definitions/colorArray',
142
+ },
143
+ children: {
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+ type: 'array',
145
+ items: {
146
+ $ref: '#/definitions/treeNodeProbabilistic',
147
+ },
148
+ },
149
+ },
150
+ },
151
+ treeNodeProbabilistic: {
152
+ oneOf: [
153
+ {
154
+ $ref: '#/definitions/treeNodeNonLeafProbabilistic',
155
+ },
156
+ {
157
+ $ref: '#/definitions/treeNodeLeafProbabilistic',
158
+ },
159
+ ],
160
+ },
161
+ 'version0.1.3': {
162
+ type: 'object',
163
+ additionalProperties: false,
164
+ required: ['version', 'datatype', 'tree'],
165
+ properties: {
166
+ dataset: {
167
+ type: 'string',
168
+ },
169
+ version: {
170
+ type: 'string',
171
+ enum: ['0.1.3'],
172
+ },
173
+ datatype: {
174
+ type: 'string',
175
+ enum: ['cell', 'obs'],
176
+ },
177
+ tree: {
178
+ type: 'array',
179
+ items: {
180
+ $ref: '#/definitions/treeNodeNonLeafProbabilistic',
181
+ },
182
+ },
183
+ },
184
+ },
185
+ },
186
+ oneOf: [
187
+ {
188
+ $ref: '#/definitions/version0.1.2',
189
+ },
190
+ {
191
+ $ref: '#/definitions/version0.1.3',
192
+ },
193
+ ],
194
+ };
195
+ export default schema;
package/dist/schemas/obsSets.schema.json ADDED
@@ -0,0 +1,194 @@
1
+ {
2
+ "$schema": "http://json-schema.org/draft-07/schema#",
3
+ "$id": "https://github.com/vitessce/vitessce/#cell-sets",
4
+ "title": "Vitessce obs sets data",
5
+ "type": "object",
6
+ "definitions": {
7
+ "stringArray": {
8
+ "type": "array",
9
+ "items": {
10
+ "type": "string"
11
+ }
12
+ },
13
+ "stringProbabilityTupleArray": {
14
+ "type": "array",
15
+ "items": {
16
+ "type": "array",
17
+ "additionalItems": false,
18
+ "items": [
19
+ {
20
+ "type": "string"
21
+ },
22
+ {
23
+ "oneOf": [
24
+ {
25
+ "type": "number",
26
+ "minimum": 0.0,
27
+ "maximum": 1.0
28
+ },
29
+ {
30
+ "type": "null"
31
+ }
32
+ ]
33
+ }
34
+ ]
35
+ }
36
+ },
37
+ "colorArray": {
38
+ "type": "array",
39
+ "items": {
40
+ "type": "integer",
41
+ "minimum": 0,
42
+ "maximum": 255
43
+ },
44
+ "minItems": 3,
45
+ "maxItems": 3
46
+ },
47
+ "treeNodeLeaf": {
48
+ "type": "object",
49
+ "additionalProperties": false,
50
+ "required": ["name"],
51
+ "properties": {
52
+ "name": {
53
+ "type": "string"
54
+ },
55
+ "color": {
56
+ "$ref": "#/definitions/colorArray"
57
+ },
58
+ "set": {
59
+ "$ref": "#/definitions/stringArray"
60
+ }
61
+ }
62
+ },
63
+ "treeNodeNonLeaf": {
64
+ "type": "object",
65
+ "additionalProperties": false,
66
+ "required": ["name"],
67
+ "properties": {
68
+ "name": {
69
+ "type": "string"
70
+ },
71
+ "color": {
72
+ "$ref": "#/definitions/colorArray"
73
+ },
74
+ "children": {
75
+ "type": "array",
76
+ "items": {
77
+ "$ref": "#/definitions/treeNode"
78
+ }
79
+ }
80
+ }
81
+ },
82
+ "treeNode": {
83
+ "oneOf": [
84
+ {
85
+ "$ref": "#/definitions/treeNodeNonLeaf"
86
+ },
87
+ {
88
+ "$ref": "#/definitions/treeNodeLeaf"
89
+ }
90
+ ]
91
+ },
92
+ "version0.1.2": {
93
+ "type": "object",
94
+ "additionalProperties": false,
95
+ "required": ["version", "datatype", "tree"],
96
+ "properties": {
97
+ "dataset": {
98
+ "type": "string"
99
+ },
100
+ "version": {
101
+ "type": "string",
102
+ "enum": ["0.1.2"]
103
+ },
104
+ "datatype": {
105
+ "type": "string",
106
+ "enum": ["cell", "obs"]
107
+ },
108
+ "tree": {
109
+ "type": "array",
110
+ "items": {
111
+ "$ref": "#/definitions/treeNodeNonLeaf"
112
+ }
113
+ }
114
+ }
115
+ },
116
+ "treeNodeLeafProbabilistic": {
117
+ "type": "object",
118
+ "additionalProperties": false,
119
+ "required": ["name"],
120
+ "properties": {
121
+ "name": {
122
+ "type": "string"
123
+ },
124
+ "color": {
125
+ "$ref": "#/definitions/colorArray"
126
+ },
127
+ "set": {
128
+ "$ref": "#/definitions/stringProbabilityTupleArray"
129
+ }
130
+ }
131
+ },
132
+ "treeNodeNonLeafProbabilistic": {
133
+ "type": "object",
134
+ "additionalProperties": false,
135
+ "required": ["name"],
136
+ "properties": {
137
+ "name": {
138
+ "type": "string"
139
+ },
140
+ "color": {
141
+ "$ref": "#/definitions/colorArray"
142
+ },
143
+ "children": {
144
+ "type": "array",
145
+ "items": {
146
+ "$ref": "#/definitions/treeNodeProbabilistic"
147
+ }
148
+ }
149
+ }
150
+ },
151
+ "treeNodeProbabilistic": {
152
+ "oneOf": [
153
+ {
154
+ "$ref": "#/definitions/treeNodeNonLeafProbabilistic"
155
+ },
156
+ {
157
+ "$ref": "#/definitions/treeNodeLeafProbabilistic"
158
+ }
159
+ ]
160
+ },
161
+ "version0.1.3": {
162
+ "type": "object",
163
+ "additionalProperties": false,
164
+ "required": ["version", "datatype", "tree"],
165
+ "properties": {
166
+ "dataset": {
167
+ "type": "string"
168
+ },
169
+ "version": {
170
+ "type": "string",
171
+ "enum": ["0.1.3"]
172
+ },
173
+ "datatype": {
174
+ "type": "string",
175
+ "enum": ["cell", "obs"]
176
+ },
177
+ "tree": {
178
+ "type": "array",
179
+ "items": {
180
+ "$ref": "#/definitions/treeNodeNonLeafProbabilistic"
181
+ }
182
+ }
183
+ }
184
+ }
185
+ },
186
+ "oneOf": [
187
+ {
188
+ "$ref": "#/definitions/version0.1.2"
189
+ },
190
+ {
191
+ "$ref": "#/definitions/version0.1.3"
192
+ }
193
+ ]
194
+ }
package/dist/schemas/obsSetsTabular.schema.js ADDED
@@ -0,0 +1,38 @@
1
+ const schema = {
2
+ $schema: 'http://json-schema.org/draft-07/schema#',
3
+ $id: 'https://github.com/vitessce/vitessce/#obsSetsTabular',
4
+ title: 'Vitessce obs sets data, tabular format',
5
+ definitions: {
6
+ colorArray: {
7
+ type: 'array',
8
+ items: { type: 'integer', minimum: 0, maximum: 255 },
9
+ minItems: 3,
10
+ maxItems: 3,
11
+ },
12
+ },
13
+ type: 'array',
14
+ items: {
15
+ type: 'object',
16
+ additionalProperties: false,
17
+ required: ['groupName', 'setName', 'obsId'],
18
+ properties: {
19
+ groupName: { type: 'string' },
20
+ setName: { type: 'string' },
21
+ setColor: { $ref: '#/definitions/colorArray' },
22
+ obsId: { type: 'string' },
23
+ predictionScore: {
24
+ oneOf: [
25
+ {
26
+ type: 'number',
27
+ minimum: 0.0,
28
+ maximum: 1.0,
29
+ },
30
+ {
31
+ type: 'null',
32
+ },
33
+ ],
34
+ },
35
+ },
36
+ },
37
+ };
38
+ export default schema;
package/dist/schemas/obsSetsTabular.schema.json ADDED
@@ -0,0 +1,37 @@
1
+ {
2
+ "$schema": "http://json-schema.org/draft-07/schema#",
3
+ "$id": "https://github.com/vitessce/vitessce/#obsSetsTabular",
4
+ "title": "Vitessce obs sets data, tabular format",
5
+ "definitions": {
6
+ "colorArray": {
7
+ "type": "array",
8
+ "items": { "type": "integer", "minimum": 0, "maximum": 255 },
9
+ "minItems": 3,
10
+ "maxItems": 3
11
+ }
12
+ },
13
+ "type": "array",
14
+ "items": {
15
+ "type": "object",
16
+ "additionalProperties": false,
17
+ "required": ["groupName", "setName", "obsId"],
18
+ "properties": {
19
+ "groupName": { "type": "string" },
20
+ "setName": { "type": "string" },
21
+ "setColor": { "$ref": "#/definitions/colorArray" },
22
+ "obsId": { "type": "string" },
23
+ "predictionScore": {
24
+ "oneOf": [
25
+ {
26
+ "type": "number",
27
+ "minimum": 0.0,
28
+ "maximum": 1.0
29
+ },
30
+ {
31
+ "type": "null"
32
+ }
33
+ ]
34
+ }
35
+ }
36
+ }
37
+ }
package/dist/schemas/raster.schema.js ADDED
@@ -0,0 +1,120 @@
1
+ const schema = {
2
+ $schema: 'http://json-schema.org/draft-07/schema#',
3
+ $id: 'https://github.com/vitessce/vitessce/#raster',
4
+ title: 'Vitessce image data',
5
+ type: 'object',
6
+ definitions: {
7
+ transform: {
8
+ type: 'object',
9
+ additionalProperties: false,
10
+ oneOf: [{ required: ['scale', 'translate'] }, { required: ['matrix'] }],
11
+ properties: {
12
+ scale: { type: 'number' },
13
+ translate: {
14
+ type: 'object',
15
+ additionalProperties: false,
16
+ required: ['y', 'x'],
17
+ properties: {
18
+ y: { type: 'number' },
19
+ x: { type: 'number' },
20
+ },
21
+ },
22
+ matrix: {
23
+ type: 'array',
24
+ items: { type: 'number' },
25
+ minItems: 16,
26
+ maxItems: 16,
27
+ },
28
+ },
29
+ },
30
+ dimensions: {
31
+ type: 'array',
32
+ items: {
33
+ type: 'object',
34
+ additionalProperties: false,
35
+ required: ['field', 'type', 'values'],
36
+ properties: {
37
+ field: { type: 'string' },
38
+ type: {
39
+ type: 'string',
40
+ enum: ['quantitative', 'nominal', 'ordinal', 'temporal'],
41
+ },
42
+ values: {
43
+ type: ['array', 'null'],
44
+ items: { type: 'string' },
45
+ },
46
+ },
47
+ },
48
+ },
49
+ metadata: {
50
+ type: 'object',
51
+ additionalProperties: false,
52
+ anyOf: [{ required: ['dimensions', 'isPyramid'] }, { required: ['transform'] }, { required: ['omeTiffOffsetsUrl'] }, { required: ['isBitmask'] }],
53
+ properties: {
54
+ dimensions: { $ref: '#/definitions/dimensions' },
55
+ isPyramid: { type: 'boolean' },
56
+ transform: { $ref: '#/definitions/transform' },
57
+ isBitmask: { type: 'boolean' },
58
+ omeTiffOffsetsUrl: { type: 'string', format: 'uri' },
59
+ },
60
+ },
61
+ requestInit: {
62
+ type: 'object',
63
+ additionalProperties: false,
64
+ required: [],
65
+ properties: {
66
+ method: {
67
+ type: 'string',
68
+ },
69
+ headers: {
70
+ type: 'object',
71
+ },
72
+ body: {
73
+ type: 'string',
74
+ },
75
+ mode: {
76
+ type: 'string',
77
+ },
78
+ credentials: {
79
+ type: 'string',
80
+ },
81
+ cache: {
82
+ type: 'string',
83
+ },
84
+ redirect: {
85
+ type: 'string',
86
+ },
87
+ referrer: {
88
+ type: 'string',
89
+ },
90
+ integrity: {
91
+ type: 'string',
92
+ },
93
+ },
94
+ },
95
+ image: {
96
+ type: 'object',
97
+ additionalProperties: false,
98
+ required: ['name', 'url', 'type'],
99
+ properties: {
100
+ name: { type: 'string' },
101
+ url: { type: 'string', format: 'uri' },
102
+ type: { type: 'string' },
103
+ metadata: { $ref: '#/definitions/metadata' },
104
+ requestInit: { $ref: '#/definitions/requestInit' },
105
+ },
106
+ },
107
+ },
108
+ additionalProperties: false,
109
+ required: ['schemaVersion', 'images'],
110
+ properties: {
111
+ schemaVersion: { type: 'string' },
112
+ usePhysicalSizeScaling: { type: 'boolean', description: 'Default is false: passing true in will infer scaling from the reported physcial size' },
113
+ renderLayers: { type: 'array', items: { type: 'string' } },
114
+ images: {
115
+ type: 'array',
116
+ items: { $ref: '#/definitions/image' },
117
+ },
118
+ },
119
+ };
120
+ export default schema;