@vitessce/config 3.4.12 → 3.5.0

package/dist/index.js

@@ -19,6 +19,9 @@ const FileType = {
   // OME-Zarr
   IMAGE_OME_ZARR: "image.ome-zarr",
   OBS_SEGMENTATIONS_OME_ZARR: "obsSegmentations.ome-zarr",
+  // OME-Zarr - Zipped
+  IMAGE_OME_ZARR_ZIP: "image.ome-zarr.zip",
+  OBS_SEGMENTATIONS_OME_ZARR_ZIP: "obsSegmentations.ome-zarr.zip",
   // AnnData
   OBS_FEATURE_MATRIX_ANNDATA_ZARR: "obsFeatureMatrix.anndata.zarr",
   OBS_FEATURE_COLUMNS_ANNDATA_ZARR: "obsFeatureColumns.anndata.zarr",
@@ -814,7 +817,7 @@ class VitessceConfigView {
    * @param {number} w The width of the view in the layout.
    * @param {number} h The height of the view in the layout.
    */
-  constructor(component, coordinationScopes, x, y, w, h) {
+  constructor(component, coordinationScopes, x, y, w, h, uid) {
     this.view = {
       component,
       coordinationScopes,
@@ -823,7 +826,8 @@ class VitessceConfigView {
       x,
       y,
       w,
-      h
+      h,
+      uid
     };
   }
   /**
@@ -1107,6 +1111,7 @@ class VitessceConfig {
       y = 0,
       w = 1,
       h = 1,
+      uid = void 0,
       mapping = null
     } = options || {};
     const datasetMatches = this.config.coordinationSpace[CoordinationType.DATASET] ? Object.entries(this.config.coordinationSpace[CoordinationType.DATASET]).filter(([scopeName, datasetScope2]) => datasetScope2.cValue === dataset.dataset.uid).map(([scopeName]) => scopeName) : [];
@@ -1119,7 +1124,7 @@ class VitessceConfig {
     const coordinationScopes = {
       [CoordinationType.DATASET]: datasetScope
     };
-    const newView = new VitessceConfigView(component, coordinationScopes, x, y, w, h);
+    const newView = new VitessceConfigView(component, coordinationScopes, x, y, w, h, uid);
     if (mapping) {
       const [etScope] = this.addCoordination(CoordinationType.EMBEDDING_TYPE);
       etScope.setValue(mapping);
@@ -1137,9 +1142,20 @@ class VitessceConfig {
   addCoordination(...args) {
     const cTypes = args;
     const result = [];
-    cTypes.forEach((cType) => {
-      const prevScopes = this.config.coordinationSpace[cType] ? Object.keys(this.config.coordinationSpace[cType]) : [];
-      const scope = new VitessceConfigCoordinationScope(cType, this.getNextScope(prevScopes));
+    cTypes.forEach((cTypeOrObj) => {
+      let cType;
+      let cScope;
+      let cValue;
+      if (typeof cTypeOrObj === "string") {
+        cType = cTypeOrObj;
+        const prevScopes = this.config.coordinationSpace[cType] ? Object.keys(this.config.coordinationSpace[cType]) : [];
+        cScope = this.getNextScope(prevScopes);
+      } else {
+        cType = cTypeOrObj.cType;
+        cScope = cTypeOrObj.cScope;
+        cValue = cTypeOrObj.cValue;
+      }
+      const scope = new VitessceConfigCoordinationScope(cType, cScope, cValue);
       if (!this.config.coordinationSpace[scope.cType]) {
         this.config.coordinationSpace[scope.cType] = {};
       }
@@ -1393,7 +1409,15 @@ class VitessceConfig {
       }
     });
     config.layout.forEach((c) => {
-      const newView = new VitessceConfigView(c.component, c.coordinationScopes, c.x, c.y, c.w, c.h);
+      const newView = new VitessceConfigView(
+        c.component,
+        c.coordinationScopes,
+        c.x,
+        c.y,
+        c.w,
+        c.h,
+        c.uid
+      );
       vc.config.layout.push(newView);
     });
     return vc;

package/dist-tsc/VitessceConfig.d.ts

@@ -96,7 +96,7 @@ export class VitessceConfigView {
      * @param {number} w The width of the view in the layout.
      * @param {number} h The height of the view in the layout.
      */
-    constructor(component: string, coordinationScopes: object, x: number, y: number, w: number, h: number);
+    constructor(component: string, coordinationScopes: object, x: number, y: number, w: number, h: number, uid: any);
     view: {
         component: string;
         coordinationScopes: object;
@@ -105,6 +105,7 @@ export class VitessceConfigView {
         y: number;
         w: number;
         h: number;
+        uid: any;
     };
     /**
      * Attach coordination scopes to this view.

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

@@ -1 +1 @@
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+{"version":3,"file":"VitessceConfig.d.ts","sourceRoot":"","sources":["../src/VitessceConfig.js"],"names":[],"mappings":"AA2XA;;;;;GAKG;AACH,kCAJe,CAAC,kBAAkB,GAAC,yBAAyB,GAAC,yBAAyB,CAAC,EAAA,GAE1E,yBAAyB,CAKrC;AAED;;;;;GAKG;AACH,kCAJe,CAAC,kBAAkB,GAAC,yBAAyB,GAAC,yBAAyB,CAAC,EAAA,GAE1E,yBAAyB,CAKrC;AAsBD,kDAEC;AAgmBD;;;;EAiBC;AAphCD;;GAEG;AACH;IACE;;;;;;;;OAQG;IACH,iBAPW,MAAM,YAEN,MAAM,oCACN,MAAM,GAAC,KAAK,GAAC,IAAI,EAW3B;IANC;;;;;MAKC;IAGH;;OAEG;IACH,UAFa,MAAM,CAIlB;CACF;AAED;;GAEG;AACH;IACE;;;;;OAKG;IACH,iBAJW,MAAM,QACN,MAAM,eACN,MAAM,EAShB;IANC;;;;;MAKC;IAGH;;;;;;;;;;OAUG;IACH,gBARG;QAAiC,GAAG,EAA5B,MAAM,GAAC,SAAS;QACD,QAAQ,EAAvB,MAAM;QACmB,kBAAkB,EAA3C,MAAM,GAAC,SAAS;QACe,OAAO,EAAtC,MAAM,GAAC,KAAK,GAAC,SAAS;KAG9B,mBAAU,qBAAqB,CA6BjC;IAED;;OAEG;IACH,UAFa,MAAM,CAOlB;CACF;AA0ID;;GAEG;AACH;IACE;;;;;;;;;OASG;IACH,uBARW,MAAM,sBACN,MAAM,KAEN,MAAM,KACN,MAAM,KACN,MAAM,KACN,MAAM,YAahB;IAVC;;;;;;;;;MASC;IAGH;;;;;OAKG;IACH,yBAJe,+BAA+B,EAAA,GAEjC,kBAAkB,CAQ9B;IAED;;;;;OAKG;IACH,gCAJW,MAAM,GAEJ,kBAAkB,CAiB9B;IAED;;;;OAIG;IACH,+BAHW,mCAAmC,GACjC,kBAAkB,CAe9B;IAED;;;;;;;QAOI;IACJ,WANY,MAAM,KACN,MAAM,KACN,MAAM,KACN,MAAM,GACJ,kBAAkB,CAS/B;IAED;;;OAGG;IACH,sBAFa,kBAAkB,CAQ9B;IAED;;OAEG;IACH,UAFa,MAAM,CAIlB;CACF;AAED;;GAEG;AACH;IACE,wBAEC;IADC,WAAkB;CAErB;AAED;;GAEG;AACH;IACE,wBAEC;IADC,WAAkB;CAErB;AAgDD;;GAEG;AACH;IACE;;;;;OAKG;IACH,mBAJW,MAAM,UACN,MAAM,WACN,CAAC,GAAG,CAAC,EAMf;IAHC,cAAkB;IAClB,eAAoB;IACpB,cAAoB;IAGtB;;;;OAIG;IACH,iBAHW,GAAG,GACD,+BAA+B,CAK3C;CACF;AAED;;;;GAIG;AACH;IACE;;;;OAIG;IACH,uBAHW,MAAM,eACN,MAAM,EAWhB;IARC,2CAGC;IACD,6CAGC;IAGH;;;;;OAKG;IACH,yBAJe,+BAA+B,EAAA,GAEjC,mCAAmC,CAU/C;IAED;;;;;;OAMG;IACH,gCAJW,MAAM,GAEJ,kBAAkB,CAiB9B;CACF;AAED;;GAEG;AACH;IAsdE;;;;;;OAMG;IACH,wBAJW,MAAM,GACJ,cAAc,CAmC1B;IA5fD;;;;;;OAMG;IACH,oBAJG;QAAuB,aAAa,EAA5B,MAAM;QACS,IAAI,EAAnB,MAAM;QACmB,WAAW,EAApC,MAAM,GAAC,SAAS;KAC1B,kBAmCA;IAVC;;;;;;;;MAQC;IACD,kBAAgC;IAGlC;;;;;;;;OAQG;IACH,kBAPW,MAAM,gBACN,MAAM,YAEd;QAAwB,GAAG,EAAnB,MAAM;KAEd,GAAU,qBAAqB,CAWjC;IAED;;;;;;;;;;;;;OAaG;IACH,iBAZW,qBAAqB,aAErB,MAAM,WAEd;QAAwB,CAAC,EAAjB,MAAM;QACU,CAAC,EAAjB,MAAM;QACU,CAAC,EAAjB,MAAM;QACU,CAAC,EAAjB,MAAM;QACU,OAAO,EAAvB,MAAM;KAEd,GAAU,kBAAkB,CAoC9B;IAED;;;;;OAKG;IACH,yBAHc,MAAM,EAAA,GACP,+BAA+B,EAAE,CAkC7C;IAED;;;;OAIG;IACH,uBAFa,mCAAmC,CA4B/C;IAED;;;;;;;;;;;;OAYG;IACH,+BATW,MAAM,GAKJ,MAAM,CAuIlB;IAED;;;;;;;OAOG;IACH,iBANW,kBAAkB,EAAE,UACpB,MAAM,EAAE,YACR,GAAG,EAAE,GAEH,cAAc,CAe1B;IAED;;;;;;;;;;;;;;;OAeG;IACH,yBAbW,kBAAkB,EAAE,SACpB,MAAM,YAKN,MAAM,GAAC,IAAI,GAKT,cAAc,CAyB1B;IAED;;;;;;;;OAQG;IACH,4BALW,MAAM,UACN,MAAM,UACN,GAAG,GACD,+BAA+B,CAS3C;IAED;;;;;OAKG;IACH,mBAJW,kBAAkB,GAAC,yBAAyB,GAAC,yBAAyB,GAEpE,cAAc,CA0B1B;IAED;;;OAGG;IACH,UAFa,MAAM,CAmBlB;CA0CF;AAlnBD;IACE,wBAGC;IAFC,WAAkB;IAClB,iBAAuB;IAGzB,qCAEC;IAED,iBAEC;IAED,oBAEC;CACF"}

package/dist-tsc/VitessceConfig.js

@@ -236,7 +236,7 @@ export class VitessceConfigView {
      * @param {number} w The width of the view in the layout.
      * @param {number} h The height of the view in the layout.
      */
-    constructor(component, coordinationScopes, x, y, w, h) {
+    constructor(component, coordinationScopes, x, y, w, h, uid) {
         this.view = {
             component,
             coordinationScopes,
@@ -245,6 +245,7 @@ export class VitessceConfigView {
             y,
             w,
             h,
+            uid,
         };
     }
     /**
@@ -543,7 +544,7 @@ export class VitessceConfig {
      * @returns {VitessceConfigView} A new view instance.
      */
     addView(dataset, component, options) {
-        const { x = 0, y = 0, w = 1, h = 1, mapping = null, } = options || {};
+        const { x = 0, y = 0, w = 1, h = 1, uid = undefined, mapping = null, } = options || {};
         const datasetMatches = (this.config.coordinationSpace[CoordinationType.DATASET]
             ? Object.entries(this.config.coordinationSpace[CoordinationType.DATASET])
                 // eslint-disable-next-line no-unused-vars
@@ -560,7 +561,7 @@ export class VitessceConfig {
         const coordinationScopes = {
             [CoordinationType.DATASET]: datasetScope,
         };
-        const newView = new VitessceConfigView(component, coordinationScopes, x, y, w, h);
+        const newView = new VitessceConfigView(component, coordinationScopes, x, y, w, h, uid);
         if (mapping) {
             const [etScope] = this.addCoordination(CoordinationType.EMBEDDING_TYPE);
             etScope.setValue(mapping);
@@ -578,11 +579,27 @@ export class VitessceConfig {
     addCoordination(...args) {
         const cTypes = args;
         const result = [];
-        cTypes.forEach((cType) => {
-            const prevScopes = (this.config.coordinationSpace[cType]
-                ? Object.keys(this.config.coordinationSpace[cType])
-                : []);
-            const scope = new VitessceConfigCoordinationScope(cType, this.getNextScope(prevScopes));
+        cTypes.forEach((cTypeOrObj) => {
+            let cType;
+            let cScope;
+            let cValue;
+            if (typeof cTypeOrObj === 'string') {
+                cType = cTypeOrObj;
+                const prevScopes = (this.config.coordinationSpace[cType]
+                    ? Object.keys(this.config.coordinationSpace[cType])
+                    : []);
+                cScope = this.getNextScope(prevScopes);
+            }
+            else {
+                // If not a string, assume it is an object like { cType: string, cScope: string }.
+                // eslint-disable-next-line prefer-destructuring
+                cType = cTypeOrObj.cType;
+                // eslint-disable-next-line prefer-destructuring
+                cScope = cTypeOrObj.cScope;
+                // eslint-disable-next-line prefer-destructuring
+                cValue = cTypeOrObj.cValue;
+            }
+            const scope = new VitessceConfigCoordinationScope(cType, cScope, cValue);
             if (!this.config.coordinationSpace[scope.cType]) {
                 this.config.coordinationSpace[scope.cType] = {};
             }
@@ -925,7 +942,7 @@ export class VitessceConfig {
             }
         });
         config.layout.forEach((c) => {
-            const newView = new VitessceConfigView(c.component, c.coordinationScopes, c.x, c.y, c.w, c.h);
+            const newView = new VitessceConfigView(c.component, c.coordinationScopes, c.x, c.y, c.w, c.h, c.uid);
             vc.config.layout.push(newView);
         });
         return vc;

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@vitessce/config",
-  "version": "3.4.12",
-  "author": "Gehlenborg Lab",
+  "version": "3.5.0",
+  "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
     "type": "git",
@@ -16,8 +16,8 @@
     "dist-tsc"
   ],
   "dependencies": {
-    "@vitessce/constants-internal": "3.4.12",
-    "@vitessce/utils": "3.4.12"
+    "@vitessce/constants-internal": "3.5.0",
+    "@vitessce/utils": "3.5.0"
   },
   "scripts": {
     "bundle": "pnpm exec vite build -c ../../scripts/vite.config.js",

package/src/VitessceConfig.js

@@ -252,7 +252,7 @@ export class VitessceConfigView {
    * @param {number} w The width of the view in the layout.
    * @param {number} h The height of the view in the layout.
    */
-  constructor(component, coordinationScopes, x, y, w, h) {
+  constructor(component, coordinationScopes, x, y, w, h, uid) {
     this.view = {
       component,
       coordinationScopes,
@@ -261,6 +261,7 @@ export class VitessceConfigView {
       y,
       w,
       h,
+      uid,
     };
   }
 
@@ -599,6 +600,7 @@ export class VitessceConfig {
       y = 0,
       w = 1,
       h = 1,
+      uid = undefined,
       mapping = null,
     } = options || {};
     const datasetMatches = (
@@ -618,7 +620,7 @@ export class VitessceConfig {
     const coordinationScopes = {
       [CoordinationType.DATASET]: datasetScope,
     };
-    const newView = new VitessceConfigView(component, coordinationScopes, x, y, w, h);
+    const newView = new VitessceConfigView(component, coordinationScopes, x, y, w, h, uid);
     if (mapping) {
       const [etScope] = this.addCoordination(CoordinationType.EMBEDDING_TYPE);
       etScope.setValue(mapping);
@@ -637,13 +639,28 @@ export class VitessceConfig {
   addCoordination(...args) {
     const cTypes = args;
     const result = [];
-    cTypes.forEach((cType) => {
-      const prevScopes = (
-        this.config.coordinationSpace[cType]
-          ? Object.keys(this.config.coordinationSpace[cType])
-          : []
-      );
-      const scope = new VitessceConfigCoordinationScope(cType, this.getNextScope(prevScopes));
+    cTypes.forEach((cTypeOrObj) => {
+      let cType;
+      let cScope;
+      let cValue;
+      if (typeof cTypeOrObj === 'string') {
+        cType = cTypeOrObj;
+        const prevScopes = (
+          this.config.coordinationSpace[cType]
+            ? Object.keys(this.config.coordinationSpace[cType])
+            : []
+        );
+        cScope = this.getNextScope(prevScopes);
+      } else {
+        // If not a string, assume it is an object like { cType: string, cScope: string }.
+        // eslint-disable-next-line prefer-destructuring
+        cType = cTypeOrObj.cType;
+        // eslint-disable-next-line prefer-destructuring
+        cScope = cTypeOrObj.cScope;
+        // eslint-disable-next-line prefer-destructuring
+        cValue = cTypeOrObj.cValue;
+      }
+      const scope = new VitessceConfigCoordinationScope(cType, cScope, cValue);
       if (!this.config.coordinationSpace[scope.cType]) {
         this.config.coordinationSpace[scope.cType] = {};
       }
@@ -1002,7 +1019,9 @@ export class VitessceConfig {
       }
     });
     config.layout.forEach((c) => {
-      const newView = new VitessceConfigView(c.component, c.coordinationScopes, c.x, c.y, c.w, c.h);
+      const newView = new VitessceConfigView(
+        c.component, c.coordinationScopes, c.x, c.y, c.w, c.h, c.uid,
+      );
       vc.config.layout.push(newView);
     });
     return vc;