From 95dfa93be14deb69f92f3ea334b1ab113d3dbd08 Mon Sep 17 00:00:00 2001 From: April Shen Date: Thu, 20 Jun 2024 13:49:14 +0100 Subject: [PATCH] add file cleanup to test --- ...alIntervalsOfSubsnpAccessionsJobConfigurationTest.java | 8 ++++++-- .../jobs/CreateSubsnpAccessionsJobConfigurationTest.java | 7 ++++++- 2 files changed, 12 insertions(+), 3 deletions(-) diff --git a/eva-accession-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/configuration/batch/jobs/CreateSeveralIntervalsOfSubsnpAccessionsJobConfigurationTest.java b/eva-accession-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/configuration/batch/jobs/CreateSeveralIntervalsOfSubsnpAccessionsJobConfigurationTest.java index 1efdf3cf8..e0c56c850 100644 --- a/eva-accession-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/configuration/batch/jobs/CreateSeveralIntervalsOfSubsnpAccessionsJobConfigurationTest.java +++ b/eva-accession-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/configuration/batch/jobs/CreateSeveralIntervalsOfSubsnpAccessionsJobConfigurationTest.java @@ -100,6 +100,7 @@ public class CreateSeveralIntervalsOfSubsnpAccessionsJobConfigurationTest { @Before public void setUp() throws Exception { + this.cleanSlate(); mongoTemplate.dropCollection(SubmittedVariantEntity.class); mockServer = MockRestServiceServer.createServer(restTemplate); mockServer.expect(ExpectedCount.manyTimes(), requestTo(new URI(countServiceParameters.getUrl() + URL_PATH_SAVE_COUNT))) @@ -109,12 +110,15 @@ public void setUp() throws Exception { @After public void tearDown() throws Exception { + this.cleanSlate(); + mongoTemplate.dropCollection(SubmittedVariantEntity.class); + } + + public void cleanSlate() throws Exception { Files.deleteIfExists(Paths.get(inputParameters.getOutputVcf())); Files.deleteIfExists(Paths.get(inputParameters.getOutputVcf() + AccessionReportWriter.VARIANTS_FILE_SUFFIX)); Files.deleteIfExists(Paths.get(inputParameters.getOutputVcf() + AccessionReportWriter.CONTIGS_FILE_SUFFIX)); - Files.deleteIfExists(Paths.get(inputParameters.getOutputVcf())); Files.deleteIfExists(Paths.get(inputParameters.getFasta() + ".fai")); - mongoTemplate.dropCollection(SubmittedVariantEntity.class); } @Test diff --git a/eva-accession-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/configuration/batch/jobs/CreateSubsnpAccessionsJobConfigurationTest.java b/eva-accession-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/configuration/batch/jobs/CreateSubsnpAccessionsJobConfigurationTest.java index 12966f77e..0e35e0f44 100644 --- a/eva-accession-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/configuration/batch/jobs/CreateSubsnpAccessionsJobConfigurationTest.java +++ b/eva-accession-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/configuration/batch/jobs/CreateSubsnpAccessionsJobConfigurationTest.java @@ -99,6 +99,7 @@ public class CreateSubsnpAccessionsJobConfigurationTest { @Before public void setUp() throws Exception { + this.cleanSlate(); mongoTemplate.dropCollection(SubmittedVariantEntity.class); mockServer = MockRestServiceServer.createServer(restTemplate); mockServer.expect(ExpectedCount.manyTimes(), requestTo(new URI(countServiceParameters.getUrl() + URL_PATH_SAVE_COUNT))) @@ -108,11 +109,15 @@ public void setUp() throws Exception { @After public void tearDown() throws Exception { + this.cleanSlate(); + mongoTemplate.dropCollection(SubmittedVariantEntity.class); + } + + public void cleanSlate() throws Exception { Files.deleteIfExists(Paths.get(inputParameters.getOutputVcf())); Files.deleteIfExists(Paths.get(inputParameters.getOutputVcf() + AccessionReportWriter.VARIANTS_FILE_SUFFIX)); Files.deleteIfExists(Paths.get(inputParameters.getOutputVcf() + AccessionReportWriter.CONTIGS_FILE_SUFFIX)); Files.deleteIfExists(Paths.get(inputParameters.getFasta() + ".fai")); - mongoTemplate.dropCollection(SubmittedVariantEntity.class); } @Test