diff --git a/.circleci/config.yml b/.circleci/config.yml index 263ed2c..7a3bec4 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -1,11 +1,11 @@ defaults: &defaults docker: - - image: cimg/openjdk:8.0.275 + - image: cimg/openjdk:21.0 version: 2.1 orbs: - maven: circleci/maven@1.0.3 + maven: circleci/maven@1.4.1 jobs: run_checkstyle: @@ -25,7 +25,7 @@ jobs: git checkout ${SMILE_COMMONS_VERSION} - run: name: "Build project..." - command: mvn clean install + command: mvn clean install -U - run: name: "Run checkstyle plugin..." command: mvn checkstyle:checkstyle diff --git a/Dockerfile b/Dockerfile index 59299ea..b4f525f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,9 +1,9 @@ -FROM maven:3.6.1-jdk-11-slim +FROM maven:3.8.8 RUN mkdir /request-filter ADD . /request-filter WORKDIR /request-filter RUN mvn clean install -FROM openjdk:11-slim +FROM openjdk:21 COPY --from=0 /request-filter/target/smile_request_filter.jar /request-filter/smile_request_filter.jar ENTRYPOINT ["java"] diff --git a/jitpack.yml b/jitpack.yml new file mode 100644 index 0000000..9d14120 --- /dev/null +++ b/jitpack.yml @@ -0,0 +1,9 @@ +jdk: + - openjdk21 + +before_install: + - sdk install maven 3.8.8 + - sdk use maven 3.8.8 + - sdk install java 21.0.2-open + - sdk use java 21.0.2-open + - sdk update diff --git a/pom.xml b/pom.xml index 0cfb00c..1ea6d6e 100644 --- a/pom.xml +++ b/pom.xml @@ -11,7 +11,7 @@ org.springframework.boot spring-boot-starter-parent - 2.3.3.RELEASE + 3.3.3 @@ -29,18 +29,17 @@ - 1.8 - 1.8 - 5.2.6.RELEASE - 2.3.3.RELEASE - 1.7.30 - 2.11.2 + 21 + 3.11.0 + 6.1.12 + 3.3.3 + 2.17.2 com.github.mskcc - 1.4.1.RELEASE + java-v21-beta-RC-4 com.github.mskcc - 1.4.1.RELEASE + java-v21-beta-RC-4 @@ -58,20 +57,15 @@ - junit - junit - test - - - org.springframework - spring-test - ${spring.version} + org.springframework.boot + spring-boot-test + ${spring.boot.version} test + jar org.mockito mockito-core - 3.3.3 test jar @@ -85,19 +79,19 @@ org.skyscreamer jsonassert - 1.5.0 + 1.5.3 - - com.google.guava - guava - 19.0 - jar + commons-logging + commons-logging + 1.3.4 - org.apache.commons - commons-lang3 - 3.11 + org.junit.jupiter + junit-jupiter-api + 5.10.3 + test + jar @@ -130,10 +124,10 @@ org.apache.maven.plugins maven-compiler-plugin - 3.6.1 + ${maven.compiler.version} - ${maven.compiler.version} - ${maven.compiler.version} + ${java.version} + ${java.version} -Xlint:deprecation diff --git a/src/main/java/org/mskcc/smile/service/impl/PromotedRequestMsgHandlingServiceImpl.java b/src/main/java/org/mskcc/smile/service/impl/PromotedRequestMsgHandlingServiceImpl.java index 808b650..825eb68 100644 --- a/src/main/java/org/mskcc/smile/service/impl/PromotedRequestMsgHandlingServiceImpl.java +++ b/src/main/java/org/mskcc/smile/service/impl/PromotedRequestMsgHandlingServiceImpl.java @@ -2,7 +2,6 @@ import com.fasterxml.jackson.databind.ObjectMapper; import io.nats.client.Message; -import java.io.IOException; import java.nio.charset.StandardCharsets; import java.util.Map; import java.util.concurrent.BlockingQueue; @@ -29,16 +28,16 @@ @Service public class PromotedRequestMsgHandlingServiceImpl implements PromotedRequestMsgHandlingService { - @Value("${igo.validate_promoted_request_topic}") + @Value("${igo.validate_promoted_request_topic:}") private String VALIDATE_PROMOTED_REQUEST_TOPIC; - @Value("${igo.cmo_promoted_label_topic}") + @Value("${igo.cmo_promoted_label_topic:}") private String CMO_PROMOTED_LABEL_TOPIC; - @Value("${igo.promoted_request_topic}") + @Value("${igo.promoted_request_topic:}") private String IGO_PROMOTED_REQUEST_TOPIC; - @Value("${num.promoted_request_handler_threads}") + @Value("${num.promoted_request_handler_threads:1}") private int NUM_PROMOTED_REQUEST_HANDLERS; @Autowired diff --git a/src/main/java/org/mskcc/smile/service/impl/RequestFilterMsgHandlingServiceIml.java b/src/main/java/org/mskcc/smile/service/impl/RequestFilterMsgHandlingServiceIml.java index 300dde0..711931a 100644 --- a/src/main/java/org/mskcc/smile/service/impl/RequestFilterMsgHandlingServiceIml.java +++ b/src/main/java/org/mskcc/smile/service/impl/RequestFilterMsgHandlingServiceIml.java @@ -2,7 +2,6 @@ import com.fasterxml.jackson.databind.ObjectMapper; import io.nats.client.Message; -import java.io.IOException; import java.nio.charset.StandardCharsets; import java.util.concurrent.BlockingQueue; import java.util.concurrent.CountDownLatch; @@ -28,16 +27,16 @@ @Service public class RequestFilterMsgHandlingServiceIml implements RequestFilterMessageHandlingService { - @Value("${igo.request_filter_topic}") + @Value("${igo.request_filter_topic:}") private String IGO_REQUEST_FILTER_TOPIC; - @Value("${igo.cmo_label_generator_topic}") + @Value("${igo.cmo_label_generator_topic:}") private String CMO_LABEL_GENERATOR_TOPIC; - @Value("${igo.new_request_topic}") + @Value("${igo.new_request_topic:}") private String IGO_NEW_REQUEST_TOPIC; - @Value("${num.new_request_handler_threads}") + @Value("${num.new_request_handler_threads:1}") private int NUM_NEW_REQUEST_HANDLERS; @Autowired diff --git a/src/main/java/org/mskcc/smile/service/impl/ValidRequestCheckerImpl.java b/src/main/java/org/mskcc/smile/service/impl/ValidRequestCheckerImpl.java index 6613147..5321653 100644 --- a/src/main/java/org/mskcc/smile/service/impl/ValidRequestCheckerImpl.java +++ b/src/main/java/org/mskcc/smile/service/impl/ValidRequestCheckerImpl.java @@ -13,13 +13,11 @@ import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; -import org.apache.logging.log4j.util.Strings; import org.mskcc.smile.commons.enums.CmoSampleClass; import org.mskcc.smile.commons.enums.SampleOrigin; import org.mskcc.smile.commons.enums.SampleType; import org.mskcc.smile.commons.enums.SpecimenType; import org.mskcc.smile.service.ValidRequestChecker; -import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.stereotype.Component; @@ -611,7 +609,7 @@ private Boolean requestHasSamples(String requestJson) throws JsonProcessingExcep } private Boolean isBlank(String value) { - return (Strings.isBlank(value) || value.equals("null")); + return (StringUtils.isBlank(value) || value.equals("null")); } @Override diff --git a/src/main/java/org/mskcc/smile/service/impl/ValidateUpdatesMsgHandlingServiceImpl.java b/src/main/java/org/mskcc/smile/service/impl/ValidateUpdatesMsgHandlingServiceImpl.java index 6baebc9..b7954f9 100644 --- a/src/main/java/org/mskcc/smile/service/impl/ValidateUpdatesMsgHandlingServiceImpl.java +++ b/src/main/java/org/mskcc/smile/service/impl/ValidateUpdatesMsgHandlingServiceImpl.java @@ -23,22 +23,22 @@ @Service public class ValidateUpdatesMsgHandlingServiceImpl implements ValidateUpdatesMessageHandlingService { - @Value("${igo.validate_request_update_topic}") + @Value("${igo.validate_request_update_topic:}") private String VALIDATOR_REQUEST_UPDATE_TOPIC; - @Value("${igo.validate_sample_update_topic}") + @Value("${igo.validate_sample_update_topic:}") private String VALIDATOR_SAMPLE_UPDATE_TOPIC; - @Value("${igo.cmo_label_update_topic}") + @Value("${igo.cmo_label_update_topic:}") private String CMO_LABEL_UPDATE_TOPIC; - @Value("${smile.request_update_topic}") + @Value("${smile.request_update_topic:}") private String SERVER_REQUEST_UPDATE_TOPIC; - @Value("${smile.sample_update_topic}") + @Value("${smile.sample_update_topic:}") private String SERVER_SAMPLE_UPDATE_TOPIC; - @Value("${num.new_request_handler_threads}") + @Value("${num.new_request_handler_threads:1}") private int NUM_NEW_REQUEST_HANDLERS; @Autowired diff --git a/src/test/java/org/mskcc/smile/SmileRequestFilterTestApp.java b/src/test/java/org/mskcc/smile/SmileRequestFilterTestApp.java new file mode 100644 index 0000000..aac4669 --- /dev/null +++ b/src/test/java/org/mskcc/smile/SmileRequestFilterTestApp.java @@ -0,0 +1,30 @@ +package org.mskcc.smile; + +import org.mskcc.cmo.messaging.Gateway; +import org.mskcc.smile.service.impl.PromotedRequestMsgHandlingServiceImpl; +import org.mskcc.smile.service.impl.ValidRequestCheckerImpl; +import org.mskcc.smile.service.impl.ValidateUpdatesMsgHandlingServiceImpl; +import org.springframework.boot.autoconfigure.SpringBootApplication; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.context.annotation.Bean; + +/** + * + * @author laptop + */ +@SpringBootApplication(scanBasePackages = {"org.mskcc.smile.service", "org.mskcc.smile.commons.*"}) +public class SmileRequestFilterTestApp { + @Bean + public ValidRequestCheckerImpl validRequestCheckerImpl() { + return new ValidRequestCheckerImpl(); + } + + @MockBean + public Gateway messagingGateway; + + @MockBean + public PromotedRequestMsgHandlingServiceImpl promotedRequestMsgHandlingService; + + @MockBean + public ValidateUpdatesMsgHandlingServiceImpl validateUpdatesMsgHandlingService; +} diff --git a/src/test/java/org/mskcc/smile/ValidRequestCheckerTest.java b/src/test/java/org/mskcc/smile/ValidRequestCheckerTest.java index 4d67c98..5d819d1 100644 --- a/src/test/java/org/mskcc/smile/ValidRequestCheckerTest.java +++ b/src/test/java/org/mskcc/smile/ValidRequestCheckerTest.java @@ -3,20 +3,17 @@ import com.fasterxml.jackson.databind.ObjectMapper; import java.util.Map; import org.apache.commons.lang3.StringUtils; -import org.junit.Assert; -import org.junit.Test; -import org.junit.runner.RunWith; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; import org.mskcc.smile.config.MockDataConfig; import org.mskcc.smile.model.MockJsonTestData; import org.mskcc.smile.service.ValidRequestChecker; import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.context.annotation.ComponentScan; -import org.springframework.test.context.ContextConfiguration; -import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.context.annotation.Import; -@ContextConfiguration(classes = MockDataConfig.class) -@RunWith(SpringJUnit4ClassRunner.class) -@ComponentScan("org.mskcc.smile.service") +@SpringBootTest(classes = SmileRequestFilterTestApp.class) +@Import(MockDataConfig.class) public class ValidRequestCheckerTest { private ObjectMapper mapper = new ObjectMapper(); @@ -31,7 +28,7 @@ public class ValidRequestCheckerTest { */ @Test public void testMockedRequestJsonDataLoading() { - Assert.assertNotNull(mockedRequestJsonDataMap); + Assertions.assertNotNull(mockedRequestJsonDataMap); } /** @@ -46,14 +43,14 @@ public void testValidRequestJson() throws Exception { .getFilteredValidRequestJson(requestJson.getJsonString()); Map requestJsonMap = mapper.readValue(modifiedRequestJson, Map.class); Map requestStatus = mapper.convertValue(requestJsonMap.get("status"), Map.class); - Assert.assertTrue((Boolean) requestStatus.get("validationStatus")); + Assertions.assertTrue((Boolean) requestStatus.get("validationStatus")); Object[] sampleList = mapper.convertValue(requestJsonMap.get("samples"), Object[].class); for (Object sample: sampleList) { Map sampleMap = mapper.convertValue(sample, Map.class); Map sampleStatus = mapper.convertValue(sampleMap.get("status"), Map.class); - Assert.assertTrue((Boolean) sampleStatus.get("validationStatus")); + Assertions.assertTrue((Boolean) sampleStatus.get("validationStatus")); } } @@ -68,14 +65,14 @@ public void testNullJsonFieldHandlingInRequestJson() throws Exception { .getFilteredValidRequestJson(requestJson.getJsonString()); Map requestJsonMap = mapper.readValue(modifiedRequestJson, Map.class); Map requestStatus = mapper.convertValue(requestJsonMap.get("status"), Map.class); - Assert.assertTrue((Boolean) requestStatus.get("validationStatus")); + Assertions.assertTrue((Boolean) requestStatus.get("validationStatus")); Object[] sampleList = mapper.convertValue(requestJsonMap.get("samples"), Object[].class); for (Object sample: sampleList) { Map sampleMap = mapper.convertValue(sample, Map.class); Map sampleStatus = mapper.convertValue(sampleMap.get("status"), Map.class); - Assert.assertTrue((Boolean) sampleStatus.get("validationStatus")); + Assertions.assertTrue((Boolean) sampleStatus.get("validationStatus")); } } @@ -90,14 +87,14 @@ public void testSingleNullSampleManifestInRequestJson() throws Exception { .getFilteredValidRequestJson(requestJson.getJsonString()); Map requestJsonMap = mapper.readValue(modifiedRequestJson, Map.class); Map requestStatus = mapper.convertValue(requestJsonMap.get("status"), Map.class); - Assert.assertFalse((Boolean) requestStatus.get("validationStatus")); + Assertions.assertFalse((Boolean) requestStatus.get("validationStatus")); Object[] sampleList = mapper.convertValue(requestJsonMap.get("samples"), Object[].class); for (Object sample: sampleList) { Map sampleMap = mapper.convertValue(sample, Map.class); Map sampleStatus = mapper.convertValue(sampleMap.get("status"), Map.class); - Assert.assertFalse((Boolean) sampleStatus.get("validationStatus")); + Assertions.assertFalse((Boolean) sampleStatus.get("validationStatus")); } } @@ -112,14 +109,14 @@ public void testNullBaitSetInSampleManifestInRequestJson() throws Exception { .getFilteredValidRequestJson(requestJson.getJsonString()); Map requestJsonMap = mapper.readValue(modifiedRequestJson, Map.class); Map requestStatus = mapper.convertValue(requestJsonMap.get("status"), Map.class); - Assert.assertFalse((Boolean) requestStatus.get("validationStatus")); + Assertions.assertFalse((Boolean) requestStatus.get("validationStatus")); Object[] sampleList = mapper.convertValue(requestJsonMap.get("samples"), Object[].class); for (Object sample: sampleList) { Map sampleMap = mapper.convertValue(sample, Map.class); Map sampleStatus = mapper.convertValue(sampleMap.get("status"), Map.class); - Assert.assertFalse((Boolean) sampleStatus.get("validationStatus")); + Assertions.assertFalse((Boolean) sampleStatus.get("validationStatus")); } } @@ -134,19 +131,19 @@ public void testRequestJsonWithNoValidSamples() throws Exception { .getFilteredValidRequestJson(requestJson.getJsonString()); Map requestJsonMap = mapper.readValue(modifiedRequestJson, Map.class); Map requestStatus = mapper.convertValue(requestJsonMap.get("status"), Map.class); - Assert.assertFalse((Boolean) requestStatus.get("validationStatus")); + Assertions.assertFalse((Boolean) requestStatus.get("validationStatus")); Object[] sampleList = mapper.convertValue(requestJsonMap.get("samples"), Object[].class); for (Object sample: sampleList) { Map sampleMap = mapper.convertValue(sample, Map.class); Map sampleStatus = mapper.convertValue(sampleMap.get("status"), Map.class); - Assert.assertFalse((Boolean) sampleStatus.get("validationStatus")); + Assertions.assertFalse((Boolean) sampleStatus.get("validationStatus")); } String ddogValidationReport = validRequestChecker.generateValidationReport(requestJson.getJsonString(), modifiedRequestJson); - Assert.assertFalse(StringUtils.isBlank(ddogValidationReport)); + Assertions.assertFalse(StringUtils.isBlank(ddogValidationReport)); } /** @@ -159,11 +156,11 @@ public void testRequestJsonWithTwoInvalidSamples() throws Exception { .get("mockRequest1dJsonDataWithMFS"); String modifiedRequestJson = validRequestChecker .getFilteredValidRequestJson(requestJson.getJsonString()); - Assert.assertNotSame(modifiedRequestJson, requestJson.getJsonString()); + Assertions.assertNotSame(modifiedRequestJson, requestJson.getJsonString()); String ddogValidationReport = validRequestChecker.generateValidationReport(requestJson.getJsonString(), modifiedRequestJson); - Assert.assertFalse(StringUtils.isBlank(ddogValidationReport)); + Assertions.assertFalse(StringUtils.isBlank(ddogValidationReport)); } /** @@ -176,11 +173,11 @@ public void testRequestJsonWithMissingFieldsUsedForSTA() throws Exception { .get("mockRequest1aJsonDataWithSTA"); String modifiedRequestJson = validRequestChecker .getFilteredValidRequestJson(requestJson.getJsonString()); - Assert.assertNotNull(modifiedRequestJson); + Assertions.assertNotNull(modifiedRequestJson); String ddogValidationReport = validRequestChecker.generateValidationReport(requestJson.getJsonString(), modifiedRequestJson); - Assert.assertTrue(StringUtils.isBlank(ddogValidationReport)); + Assertions.assertTrue(StringUtils.isBlank(ddogValidationReport)); } /** @@ -193,11 +190,11 @@ public void testRequestJsonWithMissingFieldsUsedForNAA() throws Exception { .get("mockRequest1bJsonDataWithNAA"); String modifiedRequestJson = validRequestChecker .getFilteredValidRequestJson(requestJson.getJsonString()); - Assert.assertNotNull(modifiedRequestJson); + Assertions.assertNotNull(modifiedRequestJson); String ddogValidationReport = validRequestChecker.generateValidationReport(requestJson.getJsonString(), modifiedRequestJson); - Assert.assertTrue(StringUtils.isBlank(ddogValidationReport)); + Assertions.assertTrue(StringUtils.isBlank(ddogValidationReport)); } @Test @@ -205,19 +202,19 @@ public void testGetRequestIdMissingRequestId() throws Exception { String requestJson = "{\"smileRequestId\": \"smileRequestIdValue\", \"igoProjectId\": \"MOCKREQUEST1\"}"; String requestId = validRequestChecker.getRequestId(requestJson); - Assert.assertNull(requestId); + Assertions.assertNull(requestId); } @Test public void testGetRequestIdWithNullJson() throws Exception { String requestId = validRequestChecker.getRequestId(null); - Assert.assertNull(requestId); + Assertions.assertNull(requestId); } @Test public void testGetRequestIdWithEmptyJsonString() throws Exception { String requestId = validRequestChecker.getRequestId(""); - Assert.assertNull(requestId); + Assertions.assertNull(requestId); } @Test @@ -228,11 +225,11 @@ public void testValidPromotedRequest() throws Exception { validRequestChecker.generatePromotedRequestValidationMap(requestJson); Map requestStatus = mapper.convertValue(promotedRequestJsonMap.get("status"), Map.class); - Assert.assertTrue((Boolean) requestStatus.get("validationStatus")); + Assertions.assertTrue((Boolean) requestStatus.get("validationStatus")); String ddogValidationReport = validRequestChecker.generateValidationReport(requestJson, mapper.writeValueAsString(promotedRequestJsonMap)); - Assert.assertTrue(StringUtils.isBlank(ddogValidationReport)); + Assertions.assertTrue(StringUtils.isBlank(ddogValidationReport)); } @Test @@ -243,11 +240,11 @@ public void testValidPromotedRequestFailedSample() throws Exception { validRequestChecker.generatePromotedRequestValidationMap(requestJson); Map requestStatus = mapper.convertValue(promotedRequestJsonMap.get("status"), Map.class); - Assert.assertFalse((Boolean) requestStatus.get("validationStatus")); + Assertions.assertFalse((Boolean) requestStatus.get("validationStatus")); String ddogValidationReport = validRequestChecker.generateValidationReport(requestJson, mapper.writeValueAsString(promotedRequestJsonMap)); - Assert.assertFalse(StringUtils.isBlank(ddogValidationReport)); + Assertions.assertFalse(StringUtils.isBlank(ddogValidationReport)); } @Test @@ -258,11 +255,11 @@ public void testValidPromotedRequestUniversalSchema() throws Exception { validRequestChecker.generatePromotedRequestValidationMap(requestJson); Map requestStatus = mapper.convertValue(promotedRequestJsonMap.get("status"), Map.class); - Assert.assertTrue((Boolean) requestStatus.get("validationStatus")); + Assertions.assertTrue((Boolean) requestStatus.get("validationStatus")); String ddogValidationReport = validRequestChecker.generateValidationReport(requestJson, mapper.writeValueAsString(promotedRequestJsonMap)); - Assert.assertTrue(StringUtils.isBlank(ddogValidationReport)); + Assertions.assertTrue(StringUtils.isBlank(ddogValidationReport)); } @Test @@ -273,11 +270,11 @@ public void testValidPromotedRequestMissingProjectId() throws Exception { validRequestChecker.generatePromotedRequestValidationMap(requestJson); Map requestStatus = mapper.convertValue(promotedRequestJsonMap.get("status"), Map.class); - Assert.assertTrue((Boolean) requestStatus.get("validationStatus")); + Assertions.assertTrue((Boolean) requestStatus.get("validationStatus")); String ddogValidationReport = validRequestChecker.generateValidationReport(requestJson, mapper.writeValueAsString(promotedRequestJsonMap)); - Assert.assertTrue(StringUtils.isBlank(ddogValidationReport)); + Assertions.assertTrue(StringUtils.isBlank(ddogValidationReport)); } @Test @@ -288,11 +285,11 @@ public void testValidPromotedRequestMissingRequestId() throws Exception { validRequestChecker.generatePromotedRequestValidationMap(requestJson); Map requestStatus = mapper.convertValue(promotedRequestJsonMap.get("status"), Map.class); - Assert.assertFalse((Boolean) requestStatus.get("validationStatus")); + Assertions.assertFalse((Boolean) requestStatus.get("validationStatus")); String ddogValidationReport = validRequestChecker.generateValidationReport(requestJson, mapper.writeValueAsString(promotedRequestJsonMap)); - Assert.assertFalse(StringUtils.isBlank(ddogValidationReport)); + Assertions.assertFalse(StringUtils.isBlank(ddogValidationReport)); } @Test @@ -304,11 +301,11 @@ public void testValidPromotedSampleWithNormPatientId() throws Exception { validRequestChecker.generatePromotedRequestValidationMap(requestJson); Map requestStatus = mapper.convertValue(promotedRequestJsonMap.get("status"), Map.class); - Assert.assertTrue((Boolean) requestStatus.get("validationStatus")); + Assertions.assertTrue((Boolean) requestStatus.get("validationStatus")); String ddogValidationReport = validRequestChecker.generateValidationReport(requestJson, mapper.writeValueAsString(promotedRequestJsonMap)); - Assert.assertTrue(StringUtils.isBlank(ddogValidationReport)); + Assertions.assertTrue(StringUtils.isBlank(ddogValidationReport)); } /** @@ -322,11 +319,11 @@ public void testRequestJsonWithSamplesMissingFastqs() throws Exception { .get("mockRequest1SamplesMissingFastQs"); String modifiedRequestJson = validRequestChecker .getFilteredValidRequestJson(requestJson.getJsonString()); - Assert.assertNotNull(modifiedRequestJson); + Assertions.assertNotNull(modifiedRequestJson); String ddogValidationReport = validRequestChecker.generateValidationReport(requestJson.getJsonString(), modifiedRequestJson); - Assert.assertFalse(StringUtils.isBlank(ddogValidationReport)); + Assertions.assertFalse(StringUtils.isBlank(ddogValidationReport)); } /** @@ -342,19 +339,19 @@ public void testRequestJsonWithAllSamplesMissingFastqs() throws Exception { .getFilteredValidRequestJson(requestJson.getJsonString()); Map requestJsonMap = mapper.readValue(modifiedRequestJson, Map.class); Map requestStatus = mapper.convertValue(requestJsonMap.get("status"), Map.class); - Assert.assertFalse((Boolean) requestStatus.get("validationStatus")); + Assertions.assertFalse((Boolean) requestStatus.get("validationStatus")); Object[] sampleList = mapper.convertValue(requestJsonMap.get("samples"), Object[].class); for (Object sample: sampleList) { Map sampleMap = mapper.convertValue(sample, Map.class); Map sampleStatus = mapper.convertValue(sampleMap.get("status"), Map.class); - Assert.assertFalse((Boolean) sampleStatus.get("validationStatus")); + Assertions.assertFalse((Boolean) sampleStatus.get("validationStatus")); } String ddogValidationReport = validRequestChecker.generateValidationReport(requestJson.getJsonString(), modifiedRequestJson); - Assert.assertFalse(StringUtils.isBlank(ddogValidationReport)); + Assertions.assertFalse(StringUtils.isBlank(ddogValidationReport)); } /** @@ -371,22 +368,22 @@ public void testRequestSamplesMissingPatientIds() throws Exception { // assert sample list is empty in the modified request json Object[] sampleList = mapper.convertValue(requestJsonMap.get("samples"), Object[].class); - Assert.assertTrue(sampleList.length == 1); + Assertions.assertTrue(sampleList.length == 1); // assert request validation status is true since there's at least one valid sample Map requestStatus = mapper.convertValue(requestJsonMap.get("status"), Map.class); - Assert.assertTrue((Boolean) requestStatus.get("validationStatus")); + Assertions.assertTrue((Boolean) requestStatus.get("validationStatus")); // assert request validation report has 'samples' and length is 4 Map validationReport = mapper.convertValue(requestStatus.get("validationReport"), Map.class); Object[] failedSamplesList = mapper.convertValue(validationReport.get("samples"), Object[].class); - Assert.assertTrue(failedSamplesList.length == 3); + Assertions.assertTrue(failedSamplesList.length == 3); String ddogValidationReport = validRequestChecker.generateValidationReport(requestJson.getJsonString(), modifiedRequestJson); - Assert.assertFalse(StringUtils.isBlank(ddogValidationReport)); + Assertions.assertFalse(StringUtils.isBlank(ddogValidationReport)); } /** @@ -400,7 +397,7 @@ public void testRequestJsonWithSamplesHavingFalseIgoComplete() throws Exception String modifiedRequestJson = validRequestChecker .getFilteredValidRequestJson(requestJson.getJsonString()); - Assert.assertNotNull(modifiedRequestJson); + Assertions.assertNotNull(modifiedRequestJson); Map requestJsonMap = mapper.readValue(modifiedRequestJson, Map.class); Object[] sampleList = mapper.convertValue(requestJsonMap.get("samples"), @@ -408,13 +405,13 @@ public void testRequestJsonWithSamplesHavingFalseIgoComplete() throws Exception for (Object sample: sampleList) { Map sampleMap = mapper.convertValue(sample, Map.class); Map sampleStatus = mapper.convertValue(sampleMap.get("status"), Map.class); - if (!Boolean.valueOf(sampleMap.get("igoComplete").toString())) { - Assert.assertFalse((Boolean) sampleStatus.get("validationStatus")); + if (!Boolean.parseBoolean(sampleMap.get("igoComplete").toString())) { + Assertions.assertFalse((Boolean) sampleStatus.get("validationStatus")); } } String ddogValidationReport = validRequestChecker.generateValidationReport(requestJson.getJsonString(), modifiedRequestJson); - Assert.assertFalse(StringUtils.isBlank(ddogValidationReport)); + Assertions.assertFalse(StringUtils.isBlank(ddogValidationReport)); } } diff --git a/src/test/java/org/mskcc/smile/config/MockDataConfig.java b/src/test/java/org/mskcc/smile/config/MockDataConfig.java index 5f20eae..a6a12e8 100644 --- a/src/test/java/org/mskcc/smile/config/MockDataConfig.java +++ b/src/test/java/org/mskcc/smile/config/MockDataConfig.java @@ -10,18 +10,14 @@ import java.util.HashMap; import java.util.List; import java.util.Map; -import org.mockito.Mockito; import org.mskcc.smile.commons.FileUtil; import org.mskcc.smile.model.MockJsonTestData; -import org.mskcc.smile.service.impl.ValidRequestCheckerImpl; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.context.annotation.Bean; -import org.springframework.context.annotation.ComponentScan; import org.springframework.context.annotation.Configuration; import org.springframework.core.io.ClassPathResource; @Configuration -@ComponentScan(basePackages = "org.mskcc.smile.commons.*") public class MockDataConfig { private final ObjectMapper mapper = new ObjectMapper(); private final String MOCKED_REQUEST_DATA_DETAILS_FILEPATH = "data/mocked_request_data_details.txt"; @@ -42,11 +38,6 @@ public FileUtil fileUtil() { return fileUtil; } - @Bean - public ValidRequestCheckerImpl validRequestCheckerImpl() { - return new ValidRequestCheckerImpl(); - } - private Map mockedRequestJsonDataMap; /**