Merge pull request #413 from ga4gh/issue-408

Add tests for ComposedSequenceExpression (#408)
ga4gh · Jan 16, 2023 · 09f3276 · 09f3276
2 parents a8c8c90 + 5e6976b
commit 09f3276
Showing 1 changed file with 94 additions and 0 deletions.
diff --git a/validation/models.yaml b/validation/models.yaml
@@ -169,6 +169,38 @@ RepeatedSequenceExpression:
       type: RepeatedSequenceExpression
     out:
       ga4gh_serialize: '{"count":{"comparator":">=","type":"IndefiniteRange","value":6},"seq_expr":{"location":"QrRSuBj-VScAGV_gEdxNgsnh41jYH1Kg","reverse_complement":false,"type":"DerivedSequenceExpression"},"type":"RepeatedSequenceExpression"}'
+ComposedSequenceExpression:
+  - name: "Composed Sequence Expression w/ order 1"
+    in:
+      components:
+        - type: LiteralSequenceExpression
+          sequence: CGC
+        - type: RepeatedSequenceExpression
+          seq_expr:
+            type: LiteralSequenceExpression
+            sequence: CGA
+          count:
+            type: Number
+            value: 3
+      type: ComposedSequenceExpression
+    out:
+      ga4gh_serialize: '{"components":[{"sequence":"CGC","type":"LiteralSequenceExpression"},{"count":{"type":"Number","value":3},"seq_expr":{"sequence":"CGA","type":"LiteralSequenceExpression"},"type":"RepeatedSequenceExpression"}],"type":"ComposedSequenceExpression"}'
+ComposedSequenceExpression:
+  - name: "Composed Sequence Expression w/ order 2"
+    in:
+      components:
+        - type: RepeatedSequenceExpression
+          seq_expr:
+            type: LiteralSequenceExpression
+            sequence: CGA
+          count:
+            type: Number
+            value: 3
+        - type: LiteralSequenceExpression
+          sequence: CGC
+      type: ComposedSequenceExpression
+    out:
+      ga4gh_serialize: '{"components":[{"count":{"type":"Number","value":3},"seq_expr":{"sequence":"CGA","type":"LiteralSequenceExpression"},"type":"RepeatedSequenceExpression"},{"sequence":"CGC","type":"LiteralSequenceExpression"}],"type":"ComposedSequenceExpression"}'
 Allele:
   - name: "rs7412@GRCh38>T w/SequenceState"
     in:
@@ -213,6 +245,68 @@ Allele:
       ga4gh_digest: CxiA_hvYbkD8Vqwjhx5AYuyul4mtlkpD
       ga4gh_identify: ga4gh:VA.CxiA_hvYbkD8Vqwjhx5AYuyul4mtlkpD
       ga4gh_serialize: '{"location":"QrRSuBj-VScAGV_gEdxNgsnh41jYH1Kg","state":{"sequence":"T","type":"LiteralSequenceExpression"},"type":"Allele"}'
+Allele:
+  - name: "Allele w/ Composed Sequence Expression w/ order 1"
+    in:
+      location:
+        interval:
+          end:
+            type: Number
+            value: 44908822
+          start:
+            type: Number
+            value: 44908821
+          type: SequenceInterval
+        sequence_id: ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl
+        type: SequenceLocation
+      state:
+        components:
+          - type: LiteralSequenceExpression
+            sequence: CGC
+          - type: RepeatedSequenceExpression
+            seq_expr:
+              type: LiteralSequenceExpression
+              sequence: CGA
+            count:
+              type: Number
+              value: 3
+        type: ComposedSequenceExpression
+      type: Allele
+    out:
+      ga4gh_digest: obWIAB54mfRE2HAwQiIzKZeIx0REPG-8
+      ga4gh_identify: ga4gh:VA.obWIAB54mfRE2HAwQiIzKZeIx0REPG-8
+      ga4gh_serialize: '{"location":"QrRSuBj-VScAGV_gEdxNgsnh41jYH1Kg","state":{"components":[{"sequence":"CGC","type":"LiteralSequenceExpression"},{"count":{"type":"Number","value":3},"seq_expr":{"sequence":"CGA","type":"LiteralSequenceExpression"},"type":"RepeatedSequenceExpression"}],"type":"ComposedSequenceExpression"},"type":"Allele"}'
+Allele:
+  - name: "Allele w/ Composed Sequence Expression w/ order 2"
+    in:
+      location:
+        interval:
+          end:
+            type: Number
+            value: 44908822
+          start:
+            type: Number
+            value: 44908821
+          type: SequenceInterval
+        sequence_id: ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl
+        type: SequenceLocation
+      state:
+        components:
+          - type: RepeatedSequenceExpression
+            seq_expr:
+              type: LiteralSequenceExpression
+              sequence: CGA
+            count:
+              type: Number
+              value: 3
+          - type: LiteralSequenceExpression
+            sequence: CGC
+        type: ComposedSequenceExpression
+      type: Allele
+    out:
+      ga4gh_digest: KDrbvmR-Y2dccsgckQnpEsQuLMq4p10d
+      ga4gh_identify: ga4gh:VA.KDrbvmR-Y2dccsgckQnpEsQuLMq4p10d
+      ga4gh_serialize: '{"location":"QrRSuBj-VScAGV_gEdxNgsnh41jYH1Kg","state":{"components":[{"count":{"type":"Number","value":3},"seq_expr":{"sequence":"CGA","type":"LiteralSequenceExpression"},"type":"RepeatedSequenceExpression"},{"sequence":"CGC","type":"LiteralSequenceExpression"}],"type":"ComposedSequenceExpression"},"type":"Allele"}'
 Haplotype:
   - name: "APOE1 on GRCh38, inline"
     in: