updating tidyUpAnnotation.js to auto-parse annotation.notes into JSON…

… and gracefully handle errors
TeselaGen · Aug 16, 2022 · c8821b9 · c8821b9
1 parent 998a637
commit c8821b9
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Showing 2 changed files with 38 additions and 0 deletions.
diff --git a/src/tidyUpAnnotation.js b/src/tidyUpAnnotation.js
@@ -109,6 +109,17 @@ module.exports = function tidyUpAnnotation(
     );
     annotation.type = "misc_feature";
   }
+  if (annotation.notes && typeof annotation.notes === "string") {
+    try {
+      annotation.notes = JSON.parse(annotation.notes);
+    } catch (error) {
+      console.info(
+        `warning 33y00a0912 - couldn't parse notes for ${annotation.name ||
+          ""} ${annotation.notes}:`,
+        error
+      );
+    }
+  }
 
   if (!annotation.color) {
     annotation.color = featureColors[annotation.type];

diff --git a/src/tidyUpSequenceData.test.js b/src/tidyUpSequenceData.test.js
@@ -211,6 +211,33 @@ describe("tidyUpSequenceData", function() {
     });
     res.features[0].type.should.equal("misc_feature");
   });
+  it("should try to auto-parse annotation.notes into JSON and gracefully handle errors", function() {
+    const res = tidyUpSequenceData({
+      features: [
+        {
+          start: 4,
+          end: 5,
+          notes:
+            '{"gene":["Ampicillin"],"note":["ORF frame 1"],"translation":["MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW*"],"ApEinfo_fwdcolor":["pink"],"ApEinfo_revcolor":["pink"],"ApEinfo_graphicformat":["arrow_data {{0 1 2 0 0 -1} {} 0}"]}'
+        }
+      ]
+    });
+    res.features[0].notes.gene[0].should.equal("Ampicillin");
+    const res2 = tidyUpSequenceData({
+      features: [
+        {
+          start: 4,
+          end: 5,
+          //messed up JSON notes here:
+          notes:
+            '{"gene:["Ampicillin"],"note":["ORF frame 1"],"translation":["MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW*"],"ApEinfo_fwdcolor":["pink"],"ApEinfo_revcolor":["pink"],"ApEinfo_graphicformat":["arrow_data {{0 1 2 0 0 -1} {} 0}"]}'
+        }
+      ]
+    });
+    res2.features[0].notes.should.equal(
+      '{"gene:["Ampicillin"],"note":["ORF frame 1"],"translation":["MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW*"],"ApEinfo_fwdcolor":["pink"],"ApEinfo_revcolor":["pink"],"ApEinfo_graphicformat":["arrow_data {{0 1 2 0 0 -1} {} 0}"]}'
+    );
+  });
   it("should add feature type = misc_feature if an invalid type is provided", function() {
     const res = tidyUpSequenceData({
       features: [{ start: 4, end: 5, type: "idontexist" }]