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TASK-7549 - Include new annotation data: ACMG and variant context #728

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Merged
jtarraga merged 17 commits into from
Nov 5, 2025
Merged

TASK-7549 - Include new annotation data: ACMG and variant context #728

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f7ecf88
lib: add ACMG annotation, #TASK-7626, #TASK-7549
jtarraga Apr 24, 2025
809ba1f
lib: include genomic sequence context for INDELs, #TASK-7627, #TASK-7549
jtarraga Apr 25, 2025
d0c8e80
lib: fix checkstyle, #TASK-7549
jtarraga May 29, 2025
c9bf7f4
Merge branch 'release-6.x.x' into TASK-7549
ifiancu Jun 26, 2025
0e7adfd
Merge branch 'release-6.x.x' into TASK-7549
juanfeSanahuja Jun 27, 2025
ad2788c
Added org param in docker build #TASK-7549
juanfeSanahuja Jun 27, 2025
7bb887d
Merge branch 'release-6.x.x' into TASK-7549
juanfeSanahuja Jun 27, 2025
ee9470b
pom: upgrade biodata and java-commons-lib versions, #TASK-7549
jtarraga Jul 11, 2025
8876b74
Merge branch 'release-6.x.x' into TASK-7549
jtarraga Jul 11, 2025
1931420
Merge branch 'TASK-7549' of https://github.com/opencb/cellbase into T…
jtarraga Jul 11, 2025
1777480
lib: fix the position 'end' for the genomic sequence context, #TASK-7…
jtarraga Sep 10, 2025
fa77559
Merge branch 'release-6.x.x' into TASK-7549
jtarraga Sep 10, 2025
cf07116
lib: check genomic context ranges, and minor improvements, #TASK-7627…
jtarraga Sep 10, 2025
19c5f33
lib: add the include value 'genomicContext', #TASK-7627, #TASK-7549
jtarraga Sep 11, 2025
76a6f36
cicd: Fix task name workflow #TASK-7549
juanfeSanahuja Oct 30, 2025
0d48166
tests: fix JUnit tests by using a LTS version (CellBase 5.8), #TASK-…
jtarraga Oct 31, 2025
9ba7ead
Merge branch 'TASK-7549' of https://github.com/opencb/cellbase into T…
jtarraga Oct 31, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/task.yml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
name: CellBase Develop workflow
name: CellBase task workflow

on:
push:
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12 changes: 6 additions & 6 deletions cellbase-client/src/test/java/org/opencb/cellbase/client/rest/VariantClientTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -154,14 +154,14 @@ public void testSearchSnpBydbSnpId() throws Exception {
int dataRelease = 7;
ClientConfiguration clientConfiguration = new ClientConfiguration()
.setDefaultSpecies("hsapiens")
.setVersion("v5.8.3-SNAPSHOT")
.setVersion("v5.8")
.setRest(new RestConfig(Collections.singletonList("https://ws.zettagenomics.com/cellbase"), 2000));

CellBaseClient client = new CellBaseClient(clientConfiguration);

// Assumptions before running the test
ObjectMap result = client.getMetaClient().about().firstResult();
Assumptions.assumeTrue(VersionUtils.isMinVersion("5.8.3-SNAPSHOT", result.getString("Version")));
Assumptions.assumeTrue(VersionUtils.isMinVersion("5.8", result.getString("Version")));
CellBaseDataResponse<DataRelease> dataReleaseResponse = client.getMetaClient().dataReleases();
Assumptions.assumeTrue(dataReleaseResponse.getResponses().get(0).getResults().stream().map(DataRelease::getRelease).collect(Collectors.toList()).contains(dataRelease));

Expand All @@ -180,14 +180,14 @@ public void testSearchSnpByPosition() throws Exception {
int dataRelease = 7;
ClientConfiguration clientConfiguration = new ClientConfiguration()
.setDefaultSpecies("hsapiens")
.setVersion("v5.8.3-SNAPSHOT")
.setVersion("v5.8")
.setRest(new RestConfig(Collections.singletonList("https://ws.zettagenomics.com/cellbase"), 2000));

CellBaseClient client = new CellBaseClient(clientConfiguration);

// Assumptions before running the test
ObjectMap result = client.getMetaClient().about().firstResult();
Assumptions.assumeTrue(VersionUtils.isMinVersion("5.8.3-SNAPSHOT", result.getString("Version")));
Assumptions.assumeTrue(VersionUtils.isMinVersion("5.8", result.getString("Version")));
CellBaseDataResponse<DataRelease> dataReleaseResponse = client.getMetaClient().dataReleases();
Assumptions.assumeTrue(dataReleaseResponse.getResponses().get(0).getResults().stream().map(DataRelease::getRelease).collect(Collectors.toList()).contains(dataRelease));

Expand All @@ -211,14 +211,14 @@ public void testStarsWithSnp() throws Exception {
int dataRelease = 7;
ClientConfiguration clientConfiguration = new ClientConfiguration()
.setDefaultSpecies("hsapiens")
.setVersion("v5.8.3-SNAPSHOT")
.setVersion("v5.8")
.setRest(new RestConfig(Collections.singletonList("https://ws.zettagenomics.com/cellbase"), 2000));

CellBaseClient client = new CellBaseClient(clientConfiguration);

// Assumptions before running the test
ObjectMap result = client.getMetaClient().about().firstResult();
Assumptions.assumeTrue(VersionUtils.isMinVersion("5.8.3-SNAPSHOT", result.getString("Version")));
Assumptions.assumeTrue(VersionUtils.isMinVersion("5.8", result.getString("Version")));
CellBaseDataResponse<DataRelease> dataReleaseResponse = client.getMetaClient().dataReleases();
Assumptions.assumeTrue(dataReleaseResponse.getResponses().get(0).getResults().stream().map(DataRelease::getRelease).collect(Collectors.toList()).contains(dataRelease));

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