Added SRA (and SRP* accessions) as a possible data source.

ArtifactDB · Dec 18, 2023 · 4a5d0d0 · 4a5d0d0
1 parent 12171f1
commit 4a5d0d0
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Showing 2 changed files with 8 additions and 1 deletion.
diff --git a/schemas/bioconductor.json b/schemas/bioconductor.json
@@ -65,7 +65,7 @@
                     "provider": {
                         "type": "string",
                         "description": "Name of the data provider.",
-                        "enum": [ "GEO", "ArrayExpress", "PubMed", "DOI", "other" ]
+                        "enum": [ "GEO", "SRA", "ArrayExpress", "PubMed", "DOI", "other" ]
                     },
                     "id": {
                         "type": "string",
@@ -79,6 +79,10 @@
                         "if": { "properties": { "provider": { "const": "GEO" } } },
                         "then": { "properties": { "id": { "type": "string", "pattern": "^GSE[0-9]+$" } } }
                     },
+                    {
+                        "if": { "properties": { "provider": { "const": "SRA" } } },
+                        "then": { "properties": { "id": { "type": "string", "pattern": "^SRP[0-9]+$" } } }
+                    },
                     {
                         "if": { "properties": { "provider": { "const": "ArrayExpress" } } },
                         "then": { "properties": { "id": { "type": "string", "pattern": "^E-MTAB-[0-9]+$" } } }

diff --git a/tests/schemas/bioconductor.test.js b/tests/schemas/bioconductor.test.js
@@ -21,6 +21,7 @@ test("Bioconductor schema behaves as expected", () => {
         genome: [ "GRCm38" ],
         sources: [
             { provider: "GEO", id: "GSE12345" },
+            { provider: "SRA", id: "SRP12345" },
             { provider: "ArrayExpress", id: "E-MTAB-12345" },
             { provider: "PubMed", id: "12332423" },
             { provider: "DOI", id: "123.13/231.23" },
@@ -86,6 +87,8 @@ test("Bioconductor schema behaves as expected", () => {
 
     obj.sources = [{ provider: "GEO", id: "foo" }];
     expect(() => validate(obj)).toThrow("pattern");
+    obj.sources = [{ provider: "SRA", id: "foo" }];
+    expect(() => validate(obj)).toThrow("pattern");
     obj.sources = [{ provider: "ArrayExpress", id: "foo" }];
     expect(() => validate(obj)).toThrow("pattern");
     obj.sources = [{ provider: "PubMed", id: "foo" }];