@vitessce/constants-internal 3.4.14 → 3.5.0

package/dist/index.js

@@ -15,7 +15,8 @@ const ViewType = {
   OBS_SET_FEATURE_VALUE_DISTRIBUTION: "obsSetFeatureValueDistribution",
   FEATURE_VALUE_HISTOGRAM: "featureValueHistogram",
   DOT_PLOT: "dotPlot",
-  FEATURE_BAR_PLOT: "featureBarPlot"
+  FEATURE_BAR_PLOT: "featureBarPlot",
+  BIOMARKER_SELECT: "biomarkerSelect"
 };
 const DataType = {
   OBS_LABELS: "obsLabels",
@@ -33,6 +34,24 @@ const DataType = {
   SAMPLE_SETS: "sampleSets",
   SAMPLE_EDGES: "sampleEdges"
 };
+const AsyncFunctionType = {
+  // String input (rather than Node input)
+  AUTOCOMPLETE_FEATURE: "autocompleteFeature",
+  // (partial: string, targetModality: null | 'gene' | 'protein' | 'genomic-region' | 'cell-type') -> list of feature nodes
+  TRANSFORM_FEATURE: "transformFeature",
+  // (featureNode, targetModality) -> list of feature nodes from target modality
+  RELATED_FEATURES: "relatedFeatures",
+  // (featureNode) -> list of related feature nodes
+  FEATURE_TO_URL: "featureToUrl",
+  // (featureNode) -> URL
+  FEATURE_TO_INTERVAL: "featureToInterval",
+  // (featureNode) -> genomic interval { chr, start, end }
+  // Cell2Sentence/LLM-based?
+  OBS_SET_TO_FEATURES: "obsSetToFeatures",
+  // (cell type node) -> list of feature nodes
+  FEATURES_TO_OBS_SET: "featuresToObsSet"
+  // (list of feature nodes) -> cell type node
+};
 const FileType = {
   // Joint file types
   ANNDATA_ZARR: "anndata.zarr",
@@ -896,13 +915,18 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType.OBS_SET_COLOR,
     CoordinationType.OBS_COLOR_ENCODING,
     CoordinationType.ADDITIONAL_OBS_SETS
+  ],
+  [ViewType.BIOMARKER_SELECT]: [
+    CoordinationType.FEATURE_SELECTION,
+    CoordinationType.SAMPLE_SET_SELECTION
+    // TODO: create coordination types for internal state of the biomarker selection view?
   ]
 };
 const note = "This file is autogenerated by .changeset/post-changelog.mjs.";
-const version = "3.4.14";
-const date = "2024-10-07";
+const version = "3.5.0";
+const date = "2024-11-01";
 const branch = "changeset-release/main";
-const hash = "f416e01c";
+const hash = "1eb007aa";
 const version$1 = {
   note,
   version,
@@ -913,6 +937,7 @@ const version$1 = {
 export {
   ALT_ZARR_STORE_TYPES,
   AUTO_INDEPENDENT_COORDINATION_TYPES,
+  AsyncFunctionType,
   COMPONENT_COORDINATION_TYPES,
   CoordinationType,
   DATA_TYPE_COORDINATION_VALUE_USAGE,

package/dist-tsc/constants.d.ts

@@ -21,6 +21,7 @@ export declare const ViewType: {
     FEATURE_VALUE_HISTOGRAM: string;
     DOT_PLOT: string;
     FEATURE_BAR_PLOT: string;
+    BIOMARKER_SELECT: string;
 };
 export declare const DataType: {
     OBS_LABELS: string;
@@ -39,8 +40,10 @@ export declare const DataType: {
     SAMPLE_EDGES: string;
 };
 export declare const AsyncFunctionType: {
-    FEATURE_METADATA: string;
-    FEATURE_EDGES: string;
+    AUTOCOMPLETE_FEATURE: string;
+    TRANSFORM_FEATURE: string;
+    RELATED_FEATURES: string;
+    FEATURE_TO_URL: string;
     FEATURE_TO_INTERVAL: string;
     OBS_SET_TO_FEATURES: string;
     FEATURES_TO_OBS_SET: string;

package/dist-tsc/constants.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"constants.d.ts","sourceRoot":"","sources":["../src/constants.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AACH,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;;;;CAkBpB,CAAC;AAEF,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;CAepB,CAAC;AAEF,eAAO,MAAM,iBAAiB;;;;;;CAM7B,CAAC;AAGF,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAwHpB,CAAC;AAEF;;;GAGG;AACH,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAsH5B,CAAC;AAEF,eAAO,MAAM,MAAM;;;;CAIlB,CAAC;AAEF,eAAO,MAAM,eAAe;;;CAG3B,CAAC;AAEF;;;GAGG;AACH,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;CAgB3B,CAAC"}
+{"version":3,"file":"constants.d.ts","sourceRoot":"","sources":["../src/constants.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AACH,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;;;;;CAmBpB,CAAC;AAEF,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;CAepB,CAAC;AAEF,eAAO,MAAM,iBAAiB;;;;;;;;CAY7B,CAAC;AAEF,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAwHpB,CAAC;AAEF;;;GAGG;AACH,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAsH5B,CAAC;AAEF,eAAO,MAAM,MAAM;;;;CAIlB,CAAC;AAEF,eAAO,MAAM,eAAe;;;CAG3B,CAAC;AAEF;;;GAGG;AACH,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;CAgB3B,CAAC"}

package/dist-tsc/constants.js

@@ -21,6 +21,7 @@ export const ViewType = {
     FEATURE_VALUE_HISTOGRAM: 'featureValueHistogram',
     DOT_PLOT: 'dotPlot',
     FEATURE_BAR_PLOT: 'featureBarPlot',
+    BIOMARKER_SELECT: 'biomarkerSelect',
 };
 export const DataType = {
     OBS_LABELS: 'obsLabels',
@@ -39,11 +40,15 @@ export const DataType = {
     SAMPLE_EDGES: 'sampleEdges',
 };
 export const AsyncFunctionType = {
-    FEATURE_METADATA: 'featureMetadata', // (featureName, featureType) -> metadata object
-    FEATURE_EDGES: 'featureEdges', // (featureName, featureType, targetFeatureType) -> list of features from target modality
-    FEATURE_TO_INTERVAL: 'featureToInterval', // (featureName, featureType) -> genomic interval { chr, start, end }
-    OBS_SET_TO_FEATURES: 'obsSetToFeatures', // (cell type name) -> list of feature names
-    FEATURES_TO_OBS_SET: 'featuresToObsSet', // (list of feature names) -> cell type name
+    // String input (rather than Node input)
+    AUTOCOMPLETE_FEATURE: 'autocompleteFeature', // (partial: string, targetModality: null | 'gene' | 'protein' | 'genomic-region' | 'cell-type') -> list of feature nodes
+    TRANSFORM_FEATURE: 'transformFeature', // (featureNode, targetModality) -> list of feature nodes from target modality
+    RELATED_FEATURES: 'relatedFeatures', // (featureNode) -> list of related feature nodes
+    FEATURE_TO_URL: 'featureToUrl', // (featureNode) -> URL
+    FEATURE_TO_INTERVAL: 'featureToInterval', // (featureNode) -> genomic interval { chr, start, end }
+    // Cell2Sentence/LLM-based?
+    OBS_SET_TO_FEATURES: 'obsSetToFeatures', // (cell type node) -> list of feature nodes
+    FEATURES_TO_OBS_SET: 'featuresToObsSet', // (list of feature nodes) -> cell type node
 };
 export const FileType = {
     // Joint file types

package/dist-tsc/coordination.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"coordination.d.ts","sourceRoot":"","sources":["../src/coordination.ts"],"names":[],"mappings":"AASA,eAAO,MAAM,mCAAmC,UAc/C,CAAC;AAEF;;;;;;;KAOK;AACL,eAAO,MAAM,4BAA4B;;;CAgaxC,CAAC"}
+{"version":3,"file":"coordination.d.ts","sourceRoot":"","sources":["../src/coordination.ts"],"names":[],"mappings":"AASA,eAAO,MAAM,mCAAmC,UAc/C,CAAC;AAEF;;;;;;;KAOK;AACL,eAAO,MAAM,4BAA4B;;;CAqaxC,CAAC"}

package/dist-tsc/coordination.js

@@ -445,4 +445,9 @@ export const COMPONENT_COORDINATION_TYPES = {
         CoordinationType.OBS_COLOR_ENCODING,
         CoordinationType.ADDITIONAL_OBS_SETS,
     ],
+    [ViewType.BIOMARKER_SELECT]: [
+        CoordinationType.FEATURE_SELECTION,
+        CoordinationType.SAMPLE_SET_SELECTION,
+        // TODO: create coordination types for internal state of the biomarker selection view?
+    ],
 };

package/dist-tsc/index.d.ts

@@ -1,5 +1,5 @@
-export { ViewType, DataType, FileType, CoordinationType, STATUS, ViewHelpMapping, DescriptionType, } from './constants.js';
+export { ViewType, DataType, FileType, CoordinationType, AsyncFunctionType, ViewHelpMapping, DescriptionType, STATUS, } from './constants.js';
 export { FILE_TYPE_DATA_TYPE_MAPPING, DATA_TYPE_COORDINATION_VALUE_USAGE, ALT_ZARR_STORE_TYPES, } from './constant-relationships.js';
-export { AUTO_INDEPENDENT_COORDINATION_TYPES, COMPONENT_COORDINATION_TYPES } from './coordination.js';
+export { AUTO_INDEPENDENT_COORDINATION_TYPES, COMPONENT_COORDINATION_TYPES, } from './coordination.js';
 export { default as META_VERSION } from './version.json';
 //# sourceMappingURL=index.d.ts.map

package/dist-tsc/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,QAAQ,EAAE,QAAQ,EAAE,QAAQ,EAAE,gBAAgB,EAAE,MAAM,EAAE,eAAe,EAAE,eAAe,GACzF,MAAM,gBAAgB,CAAC;AACxB,OAAO,EACL,2BAA2B,EAC3B,kCAAkC,EAClC,oBAAoB,GACrB,MAAM,6BAA6B,CAAC;AACrC,OAAO,EAAE,mCAAmC,EAAE,4BAA4B,EAAE,MAAM,mBAAmB,CAAC;AACtG,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,QAAQ,EACR,QAAQ,EACR,QAAQ,EACR,gBAAgB,EAChB,iBAAiB,EACjB,eAAe,EACf,eAAe,EACf,MAAM,GACP,MAAM,gBAAgB,CAAC;AACxB,OAAO,EACL,2BAA2B,EAC3B,kCAAkC,EAClC,oBAAoB,GACrB,MAAM,6BAA6B,CAAC;AACrC,OAAO,EACL,mCAAmC,EACnC,4BAA4B,GAC7B,MAAM,mBAAmB,CAAC;AAC3B,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAC"}

package/dist-tsc/index.js

@@ -1,4 +1,4 @@
-export { ViewType, DataType, FileType, CoordinationType, STATUS, ViewHelpMapping, DescriptionType, } from './constants.js';
+export { ViewType, DataType, FileType, CoordinationType, AsyncFunctionType, ViewHelpMapping, DescriptionType, STATUS, } from './constants.js';
 export { FILE_TYPE_DATA_TYPE_MAPPING, DATA_TYPE_COORDINATION_VALUE_USAGE, ALT_ZARR_STORE_TYPES, } from './constant-relationships.js';
-export { AUTO_INDEPENDENT_COORDINATION_TYPES, COMPONENT_COORDINATION_TYPES } from './coordination.js';
+export { AUTO_INDEPENDENT_COORDINATION_TYPES, COMPONENT_COORDINATION_TYPES, } from './coordination.js';
 export { default as META_VERSION } from './version.json';

package/dist-tsc/version.json

@@ -1,7 +1,7 @@
 {
     "note": "This file is autogenerated by .changeset/post-changelog.mjs.",
-    "version": "3.4.14",
-    "date": "2024-10-07",
+    "version": "3.5.0",
+    "date": "2024-11-01",
     "branch": "changeset-release/main",
-    "hash": "f416e01c"
+    "hash": "1eb007aa"
 }

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@vitessce/constants-internal",
-  "version": "3.4.14",
-  "author": "Gehlenborg Lab",
+  "version": "3.5.0",
+  "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
     "type": "git",

package/src/constants.ts

@@ -21,6 +21,7 @@ export const ViewType = {
   FEATURE_VALUE_HISTOGRAM: 'featureValueHistogram',
   DOT_PLOT: 'dotPlot',
   FEATURE_BAR_PLOT: 'featureBarPlot',
+  BIOMARKER_SELECT: 'biomarkerSelect',
 };
 
 export const DataType = {
@@ -41,13 +42,18 @@ export const DataType = {
 };
 
 export const AsyncFunctionType = {
-  FEATURE_METADATA: 'featureMetadata', // (featureName, featureType) -> metadata object
-  FEATURE_EDGES: 'featureEdges', // (featureName, featureType, targetFeatureType) -> list of features from target modality
-  FEATURE_TO_INTERVAL: 'featureToInterval', // (featureName, featureType) -> genomic interval { chr, start, end }
-  OBS_SET_TO_FEATURES: 'obsSetToFeatures', // (cell type name) -> list of feature names
-  FEATURES_TO_OBS_SET: 'featuresToObsSet', // (list of feature names) -> cell type name
-};
+  // String input (rather than Node input)
+  AUTOCOMPLETE_FEATURE: 'autocompleteFeature', // (partial: string, targetModality: null | 'gene' | 'protein' | 'genomic-region' | 'cell-type') -> list of feature nodes
+
+  TRANSFORM_FEATURE: 'transformFeature', // (featureNode, targetModality) -> list of feature nodes from target modality
+  RELATED_FEATURES: 'relatedFeatures', // (featureNode) -> list of related feature nodes
+  FEATURE_TO_URL: 'featureToUrl', // (featureNode) -> URL
+  FEATURE_TO_INTERVAL: 'featureToInterval', // (featureNode) -> genomic interval { chr, start, end }
 
+  // Cell2Sentence/LLM-based?
+  OBS_SET_TO_FEATURES: 'obsSetToFeatures', // (cell type node) -> list of feature nodes
+  FEATURES_TO_OBS_SET: 'featuresToObsSet', // (list of feature nodes) -> cell type node
+};
 
 export const FileType = {
   // Joint file types

package/src/coordination.ts

@@ -447,4 +447,9 @@ export const COMPONENT_COORDINATION_TYPES = {
     CoordinationType.OBS_COLOR_ENCODING,
     CoordinationType.ADDITIONAL_OBS_SETS,
   ],
+  [ViewType.BIOMARKER_SELECT]: [
+    CoordinationType.FEATURE_SELECTION,
+    CoordinationType.SAMPLE_SET_SELECTION,
+    // TODO: create coordination types for internal state of the biomarker selection view?
+  ],
 };

package/src/index.ts

@@ -1,10 +1,20 @@
 export {
-  ViewType, DataType, FileType, CoordinationType, STATUS, ViewHelpMapping, DescriptionType,
+  ViewType,
+  DataType,
+  FileType,
+  CoordinationType,
+  AsyncFunctionType,
+  ViewHelpMapping,
+  DescriptionType,
+  STATUS,
 } from './constants.js';
 export {
   FILE_TYPE_DATA_TYPE_MAPPING,
   DATA_TYPE_COORDINATION_VALUE_USAGE,
   ALT_ZARR_STORE_TYPES,
 } from './constant-relationships.js';
-export { AUTO_INDEPENDENT_COORDINATION_TYPES, COMPONENT_COORDINATION_TYPES } from './coordination.js';
+export {
+  AUTO_INDEPENDENT_COORDINATION_TYPES,
+  COMPONENT_COORDINATION_TYPES,
+} from './coordination.js';
 export { default as META_VERSION } from './version.json';

package/src/version.json

@@ -1,7 +1,7 @@
 {
   "note": "This file is autogenerated by .changeset/post-changelog.mjs.",
-  "version": "3.4.14",
-  "date": "2024-10-07",
+  "version": "3.5.0",
+  "date": "2024-11-01",
   "branch": "changeset-release/main",
-  "hash": "f416e01c"
+  "hash": "1eb007aa"
 }