gosling.js 0.16.0 → 1.0.0

package/README.md

@@ -6,9 +6,6 @@
 
 <img width="1549" alt="teaser" src="https://user-images.githubusercontent.com/9922882/109852545-e05f3400-7c22-11eb-90f3-7371e4ddeb42.png">
 
-> [!WARNING]
-> Please be aware that the grammar of Gosling.js is subject to change before the v1.0.0 release.
-
 ## Why Gosling?
 
 The Gosling's key features compared to existing visualization libraries and grammars are as follows:
@@ -23,27 +20,20 @@ The Gosling's key features compared to existing visualization libraries and gram
 
 -   [Documentation](http://gosling-lang.org/)
 -   [Gosling.js Editor](https://gosling.js.org/)
--   [Roadmap](https://github.com/gosling-lang/gosling.js/projects/1)
+-   [Gallery Examples](https://gosling-lang.org/examples/)
+-   [How-to & Tutorials](https://gosling-lang.org/tutorials/)
 
-## Contributing to Gosling.js
+## Contribute to Gosling.js
 
 We welcome and greatly appreciate your contribution to this project! Please read [CONTRIBUTING.md](/CONTRIBUTING.md) to find guidelines.
 
 ## Contact
 
--   Open [Github Issues](https://github.com/gosling-lang/gosling.js/issues/) to ask questions or request features.
-
-## Team
-
--   Sehi L'Yi ([@sehi_lyi](https://twitter.com/sehi_lyi) | <sehi_lyi@hms.harvard.edu>)
--   Qianwen Wang ([@WangQianwenToo](https://twitter.com/WangQianwenToo) | <qianwen_wang@hms.harvard.edu>)
--   Fritz Lekschas ([@flekschas](https://twitter.com/flekschas) | [lekschas.de](https://lekschas.de))
--   Trevor Manz ([@trevmanz](https://twitter.com/trevmanz) | <trevor_manz@g.harvard.edu>)
--   Nils Gehlenborg ([@ngehlenborg](https://twitter.com/ngehlenborg) | <nils@hms.harvard.edu>)
+Open [Github Issues](https://github.com/gosling-lang/gosling.js/issues/) to ask questions or request features.
 
 ## Citation
 
-[L'Yi et al., 2021. “Gosling: A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization.”](https://osf.io/6evmb)
+[L'Yi et al., 2021. “Gosling: A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization.”](https://pmc.ncbi.nlm.nih.gov/articles/PMC8826597/)
 
 ```bib
 @article{lyi2021gosling,

package/dist/editor/example/json-spec/mouse-event.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"mouse-event.d.ts","sourceRoot":"","sources":["../../../../editor/example/json-spec/mouse-event.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,WAAW,EAAE,WAAW,EAAE,MAAM,8BAA8B,CAAC;AAI7E,eAAO,MAAM,GAAG,EAAE,WA6BjB,CAAC;AAEF,eAAO,MAAM,mBAAmB,EAAE,WA+LjC,CAAC"}
+{"version":3,"file":"mouse-event.d.ts","sourceRoot":"","sources":["../../../../editor/example/json-spec/mouse-event.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,WAAW,EAAE,WAAW,EAAE,MAAM,8BAA8B,CAAC;AAI7E,eAAO,MAAM,GAAG,EAAE,WA6BjB,CAAC;AAEF,eAAO,MAAM,mBAAmB,EAAE,WAqLjC,CAAC"}

package/dist/{exported-utils-ac60e3c5.js → exported-utils-51b5f19f.js}

@@ -2751,7 +2751,7 @@ function drawPostEmbellishment(HGC, trackInfo, tile, model, theme) {
   drawColorLegend(HGC, trackInfo, tile, model, theme);
 }
 function resolveSuperposedTracks(track) {
-  if (IsDataTrack(track) || IsDummyTrack(track)) {
+  if (IsTemplateTrack(track) || IsDummyTrack(track)) {
     return [];
   }
   if (!IsOverlaidTrack(track)) {
@@ -2787,7 +2787,7 @@ function resolveSuperposedTracks(track) {
 function spreadTracksByData(tracks) {
   return [].concat(
     ...tracks.map((t) => {
-      if (IsDataTrack(t) || !IsOverlaidTrack(t) || t._overlay.length <= 1) {
+      if (!IsOverlaidTrack(t) || t._overlay.length <= 1) {
         return [t];
       }
       if (t._overlay.filter((s) => s.data).length === 0) {
@@ -2880,15 +2880,9 @@ function IsOverlaidTracks(_) {
 function IsStackedTracks(_) {
   return !IsFlatTracks(_) && !IsOverlaidTracks(_);
 }
-function IsDataTrack(_) {
-  return !IsOverlaidTrack(_) && "data" in _ && !("mark" in _);
-}
 function IsDummyTrack(_) {
   return "type" in _ && _.type == "dummy-track";
 }
-function IsDataTemplate(_) {
-  return !!("data" in _ && "overrideTemplate" in _ && _.overrideTemplate);
-}
 function IsDataDeep(data2) {
   return typeof data2 === "object";
 }
@@ -9475,86 +9469,6 @@ function traverseToFixSpecDownstream(spec, parentDef) {
     });
   }
 }
-function getVectorTemplate(column, value) {
-  return {
-    data: {
-      type: "vector",
-      url: "",
-      column,
-      value
-    },
-    mark: "bar",
-    x: { field: column, type: "genomic", axis: "top" },
-    y: { field: value, type: "quantitative" },
-    width: 400,
-    height: 100
-  };
-}
-function getMultivecTemplate(row, column, value, categories) {
-  return categories && categories.length < 10 ? {
-    data: {
-      type: "multivec",
-      url: "",
-      row,
-      column,
-      value,
-      categories
-    },
-    mark: "bar",
-    x: { field: column, type: "genomic", axis: "top" },
-    y: { field: value, type: "quantitative" },
-    row: { field: row, type: "nominal", legend: true },
-    color: { field: row, type: "nominal" },
-    width: 400,
-    height: 100
-  } : {
-    data: {
-      type: "multivec",
-      url: "",
-      row,
-      column,
-      value,
-      categories
-    },
-    mark: "rect",
-    x: { field: column, type: "genomic", axis: "top" },
-    row: { field: row, type: "nominal", legend: true },
-    color: { field: value, type: "quantitative" },
-    width: 400,
-    height: 100
-  };
-}
-function overrideDataTemplates(spec) {
-  traverseTracks(spec, (t, i, ts) => {
-    var _a, _b, _c, _d, _e;
-    if (!("data" in t) || !t.data || !IsDataDeepTileset(t.data)) {
-      return;
-    }
-    if ("alignment" in t) {
-      return;
-    }
-    if (!IsDataTemplate(t)) {
-      return;
-    }
-    switch (t.data.type) {
-      case "vector":
-      case "bigwig":
-        ts[i] = Object.assign(getVectorTemplate((_a = t.data.column) != null ? _a : "position", (_b = t.data.value) != null ? _b : "value"), t);
-        break;
-      case "multivec":
-        ts[i] = Object.assign(
-          getMultivecTemplate(
-            (_c = t.data.row) != null ? _c : "category",
-            (_d = t.data.column) != null ? _d : "position",
-            (_e = t.data.value) != null ? _e : "value",
-            t.data.categories
-          ),
-          t
-        );
-        break;
-    }
-  });
-}
 const CHROM_SIZE_HG38 = {
   chr1: 248956422,
   chr2: 242193529,
@@ -9839,17 +9753,27 @@ const CRHOM_SIZES = Object.freeze({
     // just to ensure this does not make crash
   }
 });
-function getAutoCompleteId(assembly) {
+function getAutoCompleteObject(assembly = "hg38") {
+  const base = {
+    autocompleteServer: "https://server.gosling-lang.org/api/v1",
+    chromInfoServer: "https://server.gosling-lang.org/api/v1",
+    chromInfoId: assembly
+  };
   switch (assembly) {
     case "hg19":
-      return "OHJakQICQD6gTD7skx4EWA";
+      return { ...base, autocompleteId: "gene-annotation-hg19" };
     case "mm10":
-      return "QDutvmyiSrec5nX4pA5WGQ";
+      return { ...base, autocompleteId: "gene-annotation-mm10" };
     case "mm9":
-      return "GUm5aBiLRCyz2PsBea7Yzg";
+      return {
+        ...base,
+        autocompleteServer: "https://higlass.io/api/v1",
+        chromInfoServer: "https://higlass.io/api/v1",
+        autocompleteId: "GUm5aBiLRCyz2PsBea7Yzg"
+      };
     case "hg38":
     default:
-      return "P0PLbQMwTYGy-5uPIQid7A";
+      return { ...base, autocompleteId: "gene-annotation" };
   }
 }
 function getChromInterval(chromSize) {
@@ -10009,15 +9933,14 @@ export {
   IsHiGlassMatrix as a4,
   getHiGlassColorRange as a5,
   DEFAULT_TEXT_STYLE as a6,
-  overrideDataTemplates as a7,
-  traverseToFixSpecDownstream as a8,
-  GenomicPositionHelper as a9,
-  isObject as aa,
-  getChromInterval as ab,
-  getChromTotalSize as ac,
-  parseGenomicPosition as ad,
-  convertToFlatTracks as ae,
-  spreadTracksByData as af,
+  traverseToFixSpecDownstream as a7,
+  GenomicPositionHelper as a8,
+  isObject as a9,
+  getChromInterval as aa,
+  getChromTotalSize as ab,
+  parseGenomicPosition as ac,
+  convertToFlatTracks as ad,
+  spreadTracksByData as ae,
   cartesianToPolar as b,
   computeChromSizes as c,
   commonjsGlobal as d,
@@ -10040,8 +9963,8 @@ export {
   uuid as u,
   valueToRadian as v,
   insertItemToArray as w,
-  getAutoCompleteId as x,
+  getAutoCompleteObject as x,
   IsChannelValue as y,
   getValueUsingChannel as z
 };
-//# sourceMappingURL=exported-utils-ac60e3c5.js.map
+//# sourceMappingURL=exported-utils-51b5f19f.js.map