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BuwujiuBuwujiu
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Merge pull request #761 from overture-stack/rc/4.10.0
Release Candidate 4.10.0
2 parents ea623c3 + 2abfd74 commit 59b018e

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12 files changed

+175
-18
lines changed

12 files changed

+175
-18
lines changed

‎pom.xml

+1-1
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@@ -21,7 +21,7 @@
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<groupId>bio.overture</groupId>
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<artifactId>song</artifactId>
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<packaging>pom</packaging>
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<version>4.9.0</version>
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<version>4.10.0</version>
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<modules>
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<module>song-core</module>
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<module>song-java-sdk</module>

‎song-client/pom.xml

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@@ -18,7 +18,7 @@
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<parent>
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<artifactId>song</artifactId>
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<groupId>bio.overture</groupId>
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<version>4.9.0</version>
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<version>4.10.0</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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@@ -35,12 +35,12 @@
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<dependency>
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<groupId>bio.overture</groupId>
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<artifactId>song-java-sdk</artifactId>
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<version>4.9.0</version>
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<version>4.10.0</version>
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</dependency>
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<dependency>
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<groupId>bio.overture</groupId>
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<artifactId>song-core</artifactId>
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<version>4.9.0</version>
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<version>4.10.0</version>
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</dependency>
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<!-- CLI -->

‎song-core/pom.xml

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@@ -19,7 +19,7 @@
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<parent>
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<artifactId>song</artifactId>
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<groupId>bio.overture</groupId>
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<version>4.9.0</version>
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<version>4.10.0</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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‎song-java-sdk/pom.xml

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@@ -18,7 +18,7 @@
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<parent>
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<artifactId>song</artifactId>
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<groupId>bio.overture</groupId>
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<version>4.9.0</version>
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<version>4.10.0</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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‎song-server/pom.xml

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@@ -19,7 +19,7 @@
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<parent>
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<artifactId>song</artifactId>
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<groupId>bio.overture</groupId>
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<version>4.9.0</version>
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<version>4.10.0</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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@@ -37,7 +37,7 @@
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<dependency>
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<groupId>bio.overture</groupId>
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<artifactId>song-core</artifactId>
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<version>4.9.0</version>
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<version>4.10.0</version>
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</dependency>
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<!-- Spring -->

‎song-server/src/main/java/bio/overture/song/server/service/analysis/AnalysisServiceImpl.java

-1
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@@ -128,7 +128,6 @@ public Analysis create(@NonNull String studyId, @NonNull Payload payload) {
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analysisData.setAnalysis(a);
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saveCompositeEntities(studyId, analysisId, a.getSamples());
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saveFiles(analysisId, studyId, a.getFiles());
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‎song-server/src/main/resources/schemas/analysis/analysisBase.json

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@@ -234,12 +234,36 @@
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}
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},
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"then": {
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"properties": {
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"matchedNormalSubmitterSampleId": {
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"$ref": "#/definitions/common/submitterId"
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"if": {
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"properties": {
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"sampleType": {
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"pattern": "\\b(RNA)\\b"
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}
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}
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},
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"required": ["matchedNormalSubmitterSampleId"]
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"then": {
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"properties": {
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"matchedNormalSubmitterSampleId": {
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"oneOf": [
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{
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"const": null
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},
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{
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"$ref": "#/definitions/common/submitterId"
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}
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]
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}
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},
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"required": ["matchedNormalSubmitterSampleId"]
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},
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"else": {
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"properties": {
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"matchedNormalSubmitterSampleId": {
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"$ref": "#/definitions/common/submitterId"
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}
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},
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"required": ["matchedNormalSubmitterSampleId"]
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}
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},
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"else": {
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"properties": {

‎song-server/src/test/java/bio/overture/song/server/controller/EnforcedSubmitControllerTest.java

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@@ -162,6 +162,18 @@ public void matchedNormalFieldInclusionValidation_NormalAndNull_Success() {
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runMatchedNormalTest("variantcall-normal-valid.json");
163163
}
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165+
// Test for RNA payload:
166+
@Test
167+
public void matchedNormalFieldInclusionValidation_RNATumourNull_Success() {
168+
runMatchedNormalTest("seq-exp-RNA-tumour-null-valid.json");
169+
}
170+
171+
@Test
172+
public void matchedNormalFieldInclusionValidation_RNATumour_NonNull_Success() {
173+
runMatchedNormalTest("seq-exp-RNA-tumour-empty-id.json",
174+
"#/samples/0/matchedNormalSubmitterSampleId: ,#/samples/0/matchedNormalSubmitterSampleId: string [] does not match pattern");
175+
}
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@Test
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@SneakyThrows
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public void testInvalidSample() {

‎song-server/src/test/resources/documents/validation/dynamic-analysis-type/rendered-schema.json

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@@ -241,12 +241,36 @@
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}
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},
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"then": {
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"properties": {
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"matchedNormalSubmitterSampleId": {
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"$ref": "#/definitions/common/submitterId"
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"if": {
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"properties": {
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"sampleType": {
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"pattern": "\\b(RNA)\\b"
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}
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}
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},
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"required": ["matchedNormalSubmitterSampleId"]
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"then": {
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"properties": {
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"matchedNormalSubmitterSampleId": {
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"oneOf": [
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{
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"const": null
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},
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{
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"$ref": "#/definitions/common/submitterId"
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}
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]
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}
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},
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"required": ["matchedNormalSubmitterSampleId"]
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},
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"else": {
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"properties": {
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"matchedNormalSubmitterSampleId": {
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"$ref": "#/definitions/common/submitterId"
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}
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},
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"required": ["matchedNormalSubmitterSampleId"]
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}
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},
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"else": {
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"properties": {

‎song-server/src/test/resources/documents/validation/seq-exp-RNA-tumour-empty-id.json

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@@ -0,0 +1,49 @@
1+
{
2+
"studyId": "ABC123",
3+
"analysisType": {
4+
"name": "variantCall",
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"version": 1
6+
},
7+
"experiment": {
8+
"variantCallingTool": "silver bullet",
9+
"matchedNormalSampleSubmitterId": "sample-x24-11a"
10+
},
11+
"samples": [
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{
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"submitterSampleId": "internal_sample_98024759826836",
14+
"sampleType": "Total RNA",
15+
"matchedNormalSubmitterSampleId": "",
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"specimen": {
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"submitterSpecimenId": "internal_specimen_9b73gk8s02dk",
18+
"tumourNormalDesignation": "Tumour",
19+
"specimenTissueSource": "Solid tissue",
20+
"specimenType": "Primary tumour"
21+
},
22+
"donor": {
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"submitterDonorId": "internal_donor_123456789-00",
24+
"gender": "Female"
25+
}
26+
}
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],
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"files": [
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{
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"fileName": "a3bc0998a-3521-43fd-fa10-a834f3874e46.MUSE_1-0rc-vcf.20170711.somatic.snv_mnv.vcf.gz",
31+
"dataType": "SOME_DATA_TYPE",
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"fileSize": 376953,
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"fileMd5sum": "61a91c4bf04ac2bd3795254104f75ad3",
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"fileAccess": "open",
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"fileType": "VCF"
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},
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{
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"fileName": "a3bc0998a-3521-43fd-fa10-a834f3874e46.MUSE_1-0rc-vcf.20170711.somatic.snv_mnv.vcf.gz.idx",
39+
"dataType": "SOME_DATA_TYPE",
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"fileSize": 4840,
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"fileMd5sum": "61a91c4bf04bb54d3795254104f75ad3",
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"fileAccess": "open",
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"fileType": "IDX"
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}
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],
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"info": {
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"description": "This is extra info in a JSON format"
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}
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}

‎song-server/src/test/resources/documents/validation/seq-exp-RNA-tumour-null-valid.json

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@@ -0,0 +1,49 @@
1+
{
2+
"studyId": "ABC123",
3+
"analysisType": {
4+
"name": "variantCall",
5+
"version": 1
6+
},
7+
"experiment": {
8+
"variantCallingTool": "silver bullet",
9+
"matchedNormalSampleSubmitterId": "sample-x24-11a"
10+
},
11+
"samples": [
12+
{
13+
"submitterSampleId": "internal_sample_98024759826836",
14+
"sampleType": "Total RNA",
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"matchedNormalSubmitterSampleId": null,
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"specimen": {
17+
"submitterSpecimenId": "internal_specimen_9b73gk8s02dk",
18+
"tumourNormalDesignation": "Tumour",
19+
"specimenTissueSource": "Solid tissue",
20+
"specimenType": "Primary tumour"
21+
},
22+
"donor": {
23+
"submitterDonorId": "internal_donor_123456789-00",
24+
"gender": "Female"
25+
}
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}
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],
28+
"files": [
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{
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"fileName": "a3bc0998a-3521-43fd-fa10-a834f3874e46.MUSE_1-0rc-vcf.20170711.somatic.snv_mnv.vcf.gz",
31+
"dataType": "SOME_DATA_TYPE",
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"fileSize": 376953,
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"fileMd5sum": "61a91c4bf04ac2bd3795254104f75ad3",
34+
"fileAccess": "open",
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"fileType": "VCF"
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},
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{
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"fileName": "a3bc0998a-3521-43fd-fa10-a834f3874e46.MUSE_1-0rc-vcf.20170711.somatic.snv_mnv.vcf.gz.idx",
39+
"dataType": "SOME_DATA_TYPE",
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"fileSize": 4840,
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"fileMd5sum": "61a91c4bf04bb54d3795254104f75ad3",
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"fileAccess": "open",
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"fileType": "IDX"
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}
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],
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"info": {
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"description": "This is extra info in a JSON format"
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}
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}

‎song-server/src/test/resources/documents/validation/variantcall-tumour-null-invalid.json

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"samples": [
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{
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"submitterSampleId": "internal_sample_98024759826836",
14-
"sampleType": "Total RNA",
14+
"sampleType": "Total DNA",
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"matchedNormalSubmitterSampleId": null,
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"specimen": {
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"submitterSpecimenId": "internal_specimen_9b73gk8s02dk",

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