From 2cac0d40bf1c71e80cfd8950450ea1d2af4d1411 Mon Sep 17 00:00:00 2001
From: Sehi L'Yi <sehilyi@gmail.com>
Date: Thu, 7 Jul 2022 13:01:37 -0400
Subject: [PATCH 1/2] chore: add entry point for using plugin data fetchers

---
 schema/gosling.schema.json     | 27 +++++++++++++++++++++++++++
 src/core/gosling-to-higlass.ts | 33 +++++++++++++++------------------
 src/core/gosling.schema.ts     | 15 ++++++++++++++-
 3 files changed, 56 insertions(+), 19 deletions(-)

diff --git a/schema/gosling.schema.json b/schema/gosling.schema.json
index 017e24572..9e8303589 100644
--- a/schema/gosling.schema.json
+++ b/schema/gosling.schema.json
@@ -534,6 +534,9 @@
         },
         {
           "$ref": "#/definitions/VCFData"
+        },
+        {
+          "$ref": "#/definitions/PluginData"
         }
       ]
     },
@@ -5562,6 +5565,30 @@
       },
       "type": "object"
     },
+    "PluginData": {
+      "additionalProperties": false,
+      "description": "A data spec to use plugin data fetcher that are defined externally",
+      "properties": {
+        "name": {
+          "description": "The name of the plugin data that should match the `type` of a plugin data fetcher",
+          "type": "string"
+        },
+        "options": {
+          "description": "All custom options used in the plugin data fetcher",
+          "type": "object"
+        },
+        "type": {
+          "const": "experimentalPlugin",
+          "type": "string"
+        }
+      },
+      "required": [
+        "type",
+        "name",
+        "options"
+      ],
+      "type": "object"
+    },
     "PredefinedColors": {
       "enum": [
         "viridis",
diff --git a/src/core/gosling-to-higlass.ts b/src/core/gosling-to-higlass.ts
index 0711a6c0c..5d9e2fcd4 100644
--- a/src/core/gosling-to-higlass.ts
+++ b/src/core/gosling-to-higlass.ts
@@ -109,24 +109,21 @@ export function goslingToHiGlass(
             }
         };
 
-        if (
-            firstResolvedSpec.data &&
-            IsDataDeep(firstResolvedSpec.data) &&
-            (firstResolvedSpec.data.type === 'csv' ||
-                firstResolvedSpec.data.type === 'json' ||
-                firstResolvedSpec.data.type === 'bigwig' ||
-                firstResolvedSpec.data.type === 'bam' ||
-                firstResolvedSpec.data.type === 'vcf')
-        ) {
-            // use gosling's custom data fetchers
-            hgTrack.data = {
-                ...firstResolvedSpec.data,
-                // Additionally, add assembly, otherwise, a default genome build is used
-                assembly
-                // TODO: should look all sub tracks' `dataTransform` and apply OR operation.
-                // Add a data transformation spec so that the fetcher can properly sample datasets
-                // filter: (firstResolvedSpec as any).dataTransform?.filter((f: DataTransform) => f.type === 'filter')
-            };
+        if (firstResolvedSpec.data && IsDataDeep(firstResolvedSpec.data)) {
+            const dataType = firstResolvedSpec.data.type;
+            if (
+                dataType === 'csv' ||
+                dataType === 'json' ||
+                dataType === 'bigwig' ||
+                dataType === 'bam' ||
+                dataType === 'vcf'
+            ) {
+                // This means, we are using custom data fetchers defined internally
+                hgTrack.data = { ...firstResolvedSpec.data, assembly };
+            } else if (dataType === 'experimentalPlugin') {
+                // This means, we are using external data fetchers that the user implemented
+                hgTrack.data = { ...firstResolvedSpec.data.options, type: firstResolvedSpec.data.name, assembly };
+            }
         }
 
         // We use higlass 'heatmap' track instead of 'gosling-track' for rendering performance.
diff --git a/src/core/gosling.schema.ts b/src/core/gosling.schema.ts
index d140d3380..ea20235b8 100644
--- a/src/core/gosling.schema.ts
+++ b/src/core/gosling.schema.ts
@@ -759,7 +759,8 @@ export type DataDeep =
     | VectorData
     | MatrixData
     | BAMData
-    | VCFData;
+    | VCFData
+    | PluginData;
 
 /** Values in the form of JSON. */
 export interface Datum {
@@ -1058,6 +1059,18 @@ export interface MatrixData {
     binSize?: number;
 }
 
+/** A data spec to use plugin data fetcher that are defined externally */
+export interface PluginData {
+    // TODO (7-Jul-2022): change to 'plugin' for official support
+    type: 'experimentalPlugin';
+
+    /** The name of the plugin data that should match the `type` of a plugin data fetcher */
+    name: string;
+
+    /** All custom options used in the plugin data fetcher */
+    options: Record<string, any>;
+}
+
 /* ----------------------------- DATA TRANSFORM ----------------------------- */
 
 export type DataTransform =

From 41ec318773ae003c402f5c53bb1e3df3f2388674 Mon Sep 17 00:00:00 2001
From: Sehi L'Yi <sehilyi@gmail.com>
Date: Thu, 7 Jul 2022 14:50:36 -0400
Subject: [PATCH 2/2] chore: comment statements

---
 src/core/gosling-to-higlass.ts | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/core/gosling-to-higlass.ts b/src/core/gosling-to-higlass.ts
index 5d9e2fcd4..ed5dc5e2b 100644
--- a/src/core/gosling-to-higlass.ts
+++ b/src/core/gosling-to-higlass.ts
@@ -118,10 +118,10 @@ export function goslingToHiGlass(
                 dataType === 'bam' ||
                 dataType === 'vcf'
             ) {
-                // This means, we are using custom data fetchers defined internally
+                // This means we use data fetchers that are implemented in Gosling
                 hgTrack.data = { ...firstResolvedSpec.data, assembly };
             } else if (dataType === 'experimentalPlugin') {
-                // This means, we are using external data fetchers that the user implemented
+                // This means we use an external data fetcher that a user implemented
                 hgTrack.data = { ...firstResolvedSpec.data.options, type: firstResolvedSpec.data.name, assembly };
             }
         }