Add jsonParse to jexl

GMOD · Mar 12, 2024 · 49098e6 · 49098e6
1 parent 94dfbd9
commit 49098e6
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Showing 4 changed files with 53 additions and 1 deletion.
diff --git a/packages/core/util/jexl.ts b/packages/core/util/jexl.ts
@@ -75,6 +75,7 @@ export default function (/* config?: any*/): JexlNonBuildable {
   )
   j.addFunction('toLowerCase', (s: string) => s.toLowerCase())
   j.addFunction('toUpperCase', (s: string) => s.toUpperCase())
+  j.addFunction('jsonParse', (s: string) => JSON.parse(s))
   j.addFunction('trim', (s: string) => s.trim())
   j.addFunction('trimEnd', (s: string) => s.trimEnd())
   j.addFunction('trimStart', (s: string) => s.trimStart())

diff --git a/products/jbrowse-web/src/__snapshots__/jbrowseModel.test.ts.snap b/products/jbrowse-web/src/__snapshots__/jbrowseModel.test.ts.snap
@@ -2106,6 +2106,39 @@ exports[`JBrowse model creates with non-empty snapshot 1`] = `
       "trackId": "volvox_sv",
       "type": "AlignmentsTrack",
     },
+    {
+      "adapter": {
+        "gffLocation": {
+          "internetAccountId": undefined,
+          "internetAccountPreAuthorization": undefined,
+          "locationType": "UriLocation",
+          "uri": "volvox.sort.gff3",
+        },
+        "type": "Gff3Adapter",
+      },
+      "assemblyNames": [
+        "volvox",
+      ],
+      "category": [
+        "Miscellaneous",
+      ],
+      "displays": [
+        {
+          "displayId": "gff3_genes-LinearBasicDisplay",
+          "type": "LinearBasicDisplay",
+        },
+        {
+          "displayId": "gff3_genes-LinearArcDisplay",
+          "type": "LinearArcDisplay",
+        },
+      ],
+      "formatDetails": {
+        "feature": "jexl:{table:jsonParse(feature.table)}",
+      },
+      "name": "GFF3 genes",
+      "trackId": "gff3_genes",
+      "type": "FeatureTrack",
+    },
     {
       "adapter": {
         "gffGzLocation": {

diff --git a/test_data/volvox/config.json b/test_data/volvox/config.json
@@ -1076,6 +1076,24 @@
         }
       }
     },
+    {
+      "type": "FeatureTrack",
+      "trackId": "gff3_genes",
+      "assemblyNames": ["volvox"],
+      "name": "GFF3 genes",
+      "formatDetails": {
+        "feature": "jexl:{table:jsonParse(feature.table)}"
+      },
+      "category": ["Miscellaneous"],
+      "adapter": {
+        "type": "Gff3Adapter",
+        "gffLocation": {
+          "uri": "volvox.sort.gff3",
+          "locationType": "UriLocation"
+        }
+      }
+    },
+
     {
       "type": "FeatureTrack",
       "trackId": "gff3tabix_genes",

diff --git a/test_data/volvox/volvox.sort.gff3 b/test_data/volvox/volvox.sort.gff3
@@ -2,7 +2,7 @@
 # multi-exon gene - several linked CDSs
 # single exon gene - one CDS only
 ##gff-version 3
-ctgA	example	contig	1	50001	.	.	.	Name=ctgA;multivalue=val1,val2,val3
+ctgA	example	contig	1	50001	.	.	.	Name=ctgA;multivalue=val1,val2,val3;table=%5B%7B%22name%22%3A%22hello1%22%2C%22value%22%3A1%7D%2C%7B%22name%22%3A%22hello2%22%2C%22value%22%3A2%7D%2C%7B%22name%22%3A%22hello3%22%2C%22value%22%3A3%7D%2C%7B%22name%22%3A%22hello4%22%2C%22value%22%3A4%7D%2C%7B%22name%22%3A%22hello5%22%2C%22value%22%3A5%7D%5D
 ctgA	example	BAC	1000	20000	.	.	.	ID=b101.2;Name=b101.2;Note=Fingerprinted BAC with end reads
 ctgA	example	SNP	1000	1000	0.987	.	.	ID=FakeSNP1;Name=FakeSNP;Note=This is a fake SNP that should appear at 1000 with length 1
 ctgA	example	clone_start	1000	1500	.	+	.	Parent=b101.2