add file cleanup to test

EBIvariation · Jun 20, 2024 · 95dfa93 · 95dfa93
1 parent 01aec6a
commit 95dfa93
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Showing 2 changed files with 12 additions and 3 deletions.
diff --git a/...onfiguration/batch/jobs/CreateSeveralIntervalsOfSubsnpAccessionsJobConfigurationTest.java b/...onfiguration/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/...cession/pipeline/configuration/batch/jobs/CreateSubsnpAccessionsJobConfigurationTest.java b/...cession/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