From bc103fcba5c55e5cbed8c8f5f7011bc405631fde Mon Sep 17 00:00:00 2001 From: David Steinberg Date: Wed, 9 Dec 2015 15:35:57 -0800 Subject: [PATCH] Fix #117 by reproducing Herb's changes on PR #128. Sets the checksum for a SearchReferenceRequest, removes unecessary calls to , and tests to ensure the length of the reference set arrays are equal to 1. Included @calbach's suggestion to simplify getting reference ID using getReferenceSetIdByAssemblyId. --- cts-java/src/test/java/org/ga4gh/cts/api/Utils.java | 11 ++++------- .../ga4gh/cts/api/reads/ReadGroupSetsPagingIT.java | 2 -- .../java/org/ga4gh/cts/api/reads/ReadsSearchIT.java | 6 ++++-- 3 files changed, 8 insertions(+), 11 deletions(-) diff --git a/cts-java/src/test/java/org/ga4gh/cts/api/Utils.java b/cts-java/src/test/java/org/ga4gh/cts/api/Utils.java index 22038b8..835492b 100644 --- a/cts-java/src/test/java/org/ga4gh/cts/api/Utils.java +++ b/cts-java/src/test/java/org/ga4gh/cts/api/Utils.java @@ -117,20 +117,16 @@ public static String randomName() { * @throws AvroRemoteException is the server throws an exception or there's an I/O error */ public static String getValidReferenceId(Client client) throws AvroRemoteException { - final SearchReferenceSetsRequest refSetsReq = SearchReferenceSetsRequest.newBuilder().build(); - final SearchReferenceSetsResponse refSetsResp = client.references.searchReferenceSets(refSetsReq); - - final List refSets = refSetsResp.getReferenceSets(); - final SearchReferencesRequest refsReq = SearchReferencesRequest .newBuilder() - .setReferenceSetId(refSets.get(0).getId()) + .setReferenceSetId(Utils.getReferenceSetIdByAssemblyId(client, TestData.REFERENCESET_ASSEMBLY_ID)) + .setMd5checksum(TestData.REFERENCE_BRCA1_MD5_CHECKSUM) .build(); final SearchReferencesResponse refsResp = client.references.searchReferences(refsReq); assertThat(refsResp).isNotNull(); final List references = refsResp.getReferences(); assertThat(references).isNotNull().isNotEmpty(); - + assertThat(references).hasSize(1); return references.get(0).getId(); } @@ -268,6 +264,7 @@ public static String getReferenceSetIdByAssemblyId(Client client, String assembl client.references.searchReferenceSets(req); final List refSets = resp.getReferenceSets(); assertThat(refSets).isNotNull(); + assertThat(refSets).hasSize(1); final ReferenceSet refSet = refSets.get(0); return refSet.getId(); } diff --git a/cts-java/src/test/java/org/ga4gh/cts/api/reads/ReadGroupSetsPagingIT.java b/cts-java/src/test/java/org/ga4gh/cts/api/reads/ReadGroupSetsPagingIT.java index dd1f170..da945f2 100644 --- a/cts-java/src/test/java/org/ga4gh/cts/api/reads/ReadGroupSetsPagingIT.java +++ b/cts-java/src/test/java/org/ga4gh/cts/api/reads/ReadGroupSetsPagingIT.java @@ -138,8 +138,6 @@ public void checkPagingByRelativelyPrimeChunksOfReadGroupSets() throws AvroRemot @Test public void checkTwoSimultaneousPagingSequencesThroughReadGroupSets() throws AvroRemoteException { - final String referenceId = Utils.getValidReferenceId(client); - final Set setOfReadGroupSets0 = new HashSet<>(); final Set setOfReadGroupSets1 = new HashSet<>(); diff --git a/cts-java/src/test/java/org/ga4gh/cts/api/reads/ReadsSearchIT.java b/cts-java/src/test/java/org/ga4gh/cts/api/reads/ReadsSearchIT.java index e290eb0..488b385 100644 --- a/cts-java/src/test/java/org/ga4gh/cts/api/reads/ReadsSearchIT.java +++ b/cts-java/src/test/java/org/ga4gh/cts/api/reads/ReadsSearchIT.java @@ -40,6 +40,8 @@ public class ReadsSearchIT implements CtkLogs { @Test public void searchReadsWithUninterestingRangeProducesZeroReads() throws AvroRemoteException { + final String refId = Utils.getValidReferenceId(client); + final long emptyRangeStart = 150; final long emptyRangeEnd = 160; @@ -53,7 +55,7 @@ public void searchReadsWithUninterestingRangeProducesZeroReads() throws AvroRemo final SearchReadsRequest srReq = SearchReadsRequest.newBuilder() - .setReferenceId(Utils.getValidReferenceId(client)) + .setReferenceId(refId) .setReadGroupIds(aSingle(Utils.getReadGroupId(client))) .setStart(emptyRangeStart) .setEnd(emptyRangeEnd) @@ -84,7 +86,7 @@ public void searchReadsProducesWellFormedReads() throws AvroRemoteException { final SearchReadsRequest srReq = SearchReadsRequest.newBuilder() - .setReferenceId(Utils.getValidReferenceId(client)) + .setReferenceId(refId) .setReadGroupIds(aSingle(Utils.getReadGroupId(client))) .setStart(start) .setEnd(end)