basic integration tests for the API's endpoints

src/main/resources/application.properties

@@ -24,7 +24,7 @@ server.port=8081
 [email protected]@
 [email protected]@
 
-config.scaffolds.enabled = @contig-alias.scaffolds-enabled@
+config.scaffolds.enabled=@contig-alias.scaffolds-enabled@
 
 asm.file.download.dir=/tmp
 service.info.file.path=src/main/resources/static/service-info.json

src/test/java/uk/ac/ebi/eva/evaseqcol/controller/AdminControllerIntegrationTest.java

@@ -0,0 +1,92 @@
+package uk.ac.ebi.eva.evaseqcol.controller;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.test.web.server.LocalServerPort;
+import org.springframework.http.client.support.BasicAuthenticationInterceptor;
+import org.springframework.test.context.DynamicPropertyRegistry;
+import org.springframework.test.context.DynamicPropertySource;
+import org.springframework.transaction.annotation.Transactional;
+import org.springframework.web.client.RestTemplate;
+import org.testcontainers.containers.PostgreSQLContainer;
+import org.testcontainers.junit.jupiter.Container;
+import org.testcontainers.junit.jupiter.Testcontainers;
+
+import uk.ac.ebi.eva.evaseqcol.entities.SeqColLevelOneEntity;
+import uk.ac.ebi.eva.evaseqcol.entities.SeqColLevelTwoEntity;
+import uk.ac.ebi.eva.evaseqcol.service.SeqColService;
+
+import java.util.Optional;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT)
+@Testcontainers
+public class AdminControllerIntegrationTest {
+
+    @LocalServerPort
+    private int port;
+
+    private String baseUrl = "http://localhost";
+
+    @Value("${server.servlet.context-path}")
+    private String contextPath;
+
+    @Value("${controller.auth.admin.username}")
+    private String USERNAME_ADMIN;
+
+    @Value("${controller.auth.admin.password}")
+    private String PASSWORD_ADMIN;
+
+    private final String ADMIN_PATH = "/admin/seqcols";
+
+    private final String ASM_ACCESSION = "GCA_000146045.2";
+
+    private final String insertedSeqColDigest = "3mTg0tAA3PS-R1TzelLVWJ2ilUzoWfVq"; // The digest of the seqCol that will be inserted by the PUT method
+
+    private static RestTemplate restTemplate;
+
+    @Autowired
+    private SeqColService seqColService;
+
+    @Container
+    static PostgreSQLContainer<?> postgreSQLContainer = new PostgreSQLContainer<>("postgres:14.0");
+
+    @DynamicPropertySource
+    static void dataSourceProperties(DynamicPropertyRegistry registry) {
+        registry.add("spring.datasource.url", postgreSQLContainer::getJdbcUrl);
+        registry.add("spring.datasource.username", postgreSQLContainer::getUsername);
+        registry.add("spring.datasource.password", postgreSQLContainer::getPassword);
+        registry.add("spring.jpa.hibernate.ddl-auto", () -> "update");
+    }
+
+    @BeforeEach
+    void setUp() {
+        restTemplate = new RestTemplate();
+        restTemplate.getInterceptors().add(
+                new BasicAuthenticationInterceptor(USERNAME_ADMIN, PASSWORD_ADMIN)
+        );
+        baseUrl = baseUrl + ":" + port + contextPath + ADMIN_PATH;
+    }
+
+    @Test
+    @Transactional
+    /**
+     * Ingest all possible seqCol objects given the assembly accession*/
+    void ingestSeqColsTest() {
+        String finalRequest = baseUrl + "/{asmAccession}";
+        restTemplate.put(finalRequest, null, ASM_ACCESSION);
+        Optional<SeqColLevelOneEntity> levelOneEntity = (Optional<SeqColLevelOneEntity>)
+                seqColService.getSeqColByDigestAndLevel(insertedSeqColDigest, 1);
+        Optional<SeqColLevelTwoEntity> levelTwoEntity = (Optional<SeqColLevelTwoEntity>)
+                seqColService.getSeqColByDigestAndLevel(insertedSeqColDigest, 2);
+        assertTrue(levelOneEntity.isPresent());
+        assertTrue(levelTwoEntity.isPresent());
+        assertEquals(insertedSeqColDigest,levelOneEntity.get().getDigest());
+        assertNotNull(levelTwoEntity.get().getLengths());
+    }
+
+}

src/test/java/uk/ac/ebi/eva/evaseqcol/controller/SeqColComparisonControllerIntegrationTest.java

@@ -0,0 +1,103 @@
+package uk.ac.ebi.eva.evaseqcol.controller;
+
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.test.web.server.LocalServerPort;
+import org.springframework.test.context.DynamicPropertyRegistry;
+import org.springframework.test.context.DynamicPropertySource;
+import org.springframework.web.client.RestTemplate;
+import org.testcontainers.containers.PostgreSQLContainer;
+import org.testcontainers.junit.jupiter.Container;
+import org.testcontainers.junit.jupiter.Testcontainers;
+
+import uk.ac.ebi.eva.evaseqcol.entities.SeqColLevelTwoEntity;
+import uk.ac.ebi.eva.evaseqcol.io.SeqColGenerator;
+import uk.ac.ebi.eva.evaseqcol.io.SeqColWriter;
+
+import java.io.IOException;
+import java.util.Map;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT)
+@Testcontainers
+public class SeqColComparisonControllerIntegrationTest {
+
+    @LocalServerPort
+    private int port;
+
+    private String baseUrl = "http://localhost";
+
+    @Value("${server.servlet.context-path}")
+    private String contextPath;
+
+    private final String COMPARISON_PATH = "/comparison";
+
+    private final String SEQCOL_A_DIGEST = "3mTg0tAA3PS-R1TzelLVWJ2ilUzoWfVq"; // seqCol test digest
+
+    private final String SEQCOL_B_DIGEST = "rkTW1yZ0e22IN8K-0frqoGOMT8dynNyE";
+
+    @Autowired
+    private SeqColWriter seqColWriter;
+
+    @Autowired
+    private SeqColGenerator seqColGenerator;
+
+    private static RestTemplate restTemplate;
+
+    @Container
+    static PostgreSQLContainer<?> postgreSQLContainer = new PostgreSQLContainer<>("postgres:14.0");
+
+    @DynamicPropertySource
+    static void dataSourceProperties(DynamicPropertyRegistry registry) {
+        registry.add("spring.datasource.url", postgreSQLContainer::getJdbcUrl);
+        registry.add("spring.datasource.username", postgreSQLContainer::getUsername);
+        registry.add("spring.datasource.password", postgreSQLContainer::getPassword);
+        registry.add("spring.jpa.hibernate.ddl-auto", () -> "update");
+    }
+
+    @BeforeAll
+    static void init() {
+        restTemplate = new RestTemplate();
+    }
+
+    @BeforeEach
+    void setUp() throws IOException {
+        seqColWriter.write(); // Save some seqCol objects into the database
+        baseUrl = baseUrl + ":" + port + contextPath + COMPARISON_PATH;
+    }
+
+    @AfterEach
+    void tearDown() {
+        seqColWriter.clearData();
+    }
+
+    @Test
+    void compareLocalSeqColsTest() {
+        String finalRequest = baseUrl + "/" + SEQCOL_A_DIGEST + "/" + SEQCOL_B_DIGEST;
+        Map<String, Object> comparisonResult = restTemplate.getForObject(finalRequest, Map.class);
+        assertNotNull(comparisonResult);
+        assertNotNull(comparisonResult.get("digests"));
+        assertNotNull(comparisonResult.get("arrays"));
+        assertNotNull(comparisonResult.get("elements"));
+    }
+
+    @Test
+    /**
+     * Compare a local seqCol object (identified by digest) with a user provided one,
+     * provided in the body of the POST request*/
+    void compareALocalSeqColWithProvidedOneTest() {
+        String finlRequest = baseUrl + "/" + SEQCOL_A_DIGEST;
+        SeqColLevelTwoEntity seqColLevelTwoPostBody = seqColGenerator.generateLevelTwoEntity();
+        Map<String, Object> comparisonResult = restTemplate.postForObject(finlRequest, seqColLevelTwoPostBody, Map.class);
+        assertNotNull(comparisonResult);
+        assertNotNull(comparisonResult.get("digests"));
+        assertNotNull(comparisonResult.get("arrays"));
+        assertNotNull(comparisonResult.get("elements"));
+    }
+}

src/test/java/uk/ac/ebi/eva/evaseqcol/controller/SeqColControllerIntegrationTest.java

@@ -0,0 +1,98 @@
+package uk.ac.ebi.eva.evaseqcol.controller;
+
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.test.web.server.LocalServerPort;
+import org.springframework.test.context.DynamicPropertyRegistry;
+import org.springframework.test.context.DynamicPropertySource;
+import org.springframework.web.client.RestTemplate;
+import org.testcontainers.containers.PostgreSQLContainer;
+import org.testcontainers.junit.jupiter.Container;
+import org.testcontainers.junit.jupiter.Testcontainers;
+
+import uk.ac.ebi.eva.evaseqcol.io.SeqColWriter;
+
+import java.io.IOException;
+import java.util.List;
+import java.util.Map;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT)
+@Testcontainers
+public class SeqColControllerIntegrationTest {
+
+    @LocalServerPort
+    private int port;
+
+    private String baseUrl = "http://localhost";
+
+    private final String RETRIEVAL_PATH = "/collection";
+
+    private final String SEQCOL_DIGEST = "3mTg0tAA3PS-R1TzelLVWJ2ilUzoWfVq"; // seqCol test digest
+
+    private final String SERVICE_INFO_PATH = "/service-info";
+
+    @Value("${server.servlet.context-path}")
+    private String contextPath;
+
+    private static RestTemplate restTemplate;
+
+
+    @Autowired
+    private SeqColWriter seqColWriter;
+
+    @Container
+    static PostgreSQLContainer<?> postgreSQLContainer = new PostgreSQLContainer<>("postgres:14.0");
+
+    @DynamicPropertySource
+    static void dataSourceProperties(DynamicPropertyRegistry registry) {
+        registry.add("spring.datasource.url", postgreSQLContainer::getJdbcUrl);
+        registry.add("spring.datasource.username", postgreSQLContainer::getUsername);
+        registry.add("spring.datasource.password", postgreSQLContainer::getPassword);
+        registry.add("spring.jpa.hibernate.ddl-auto", () -> "update");
+    }
+
+    @BeforeAll
+     static void init() {
+        restTemplate = new RestTemplate();
+     }
+
+     @BeforeEach
+     void setUp() throws IOException {
+        seqColWriter.write(); // Save some seqCol objects into the database
+        baseUrl = baseUrl + ":" + port + contextPath ;
+     }
+
+    @AfterEach
+    void tearDown() {
+        seqColWriter.clearData();
+    }
+
+    @Test
+    void getSeqColByDigestTest() {
+        String level_1_path = "?level=1"; // can be left to default
+        String level_2_path = "?level=2";
+        String finalRequest = baseUrl + RETRIEVAL_PATH + "/" + SEQCOL_DIGEST;
+        Map<String, Object> levelOneEntity = restTemplate.getForObject(finalRequest + level_1_path, Map.class);
+        Map<String, List<String>> levelTwoEntity = restTemplate.getForObject(finalRequest + level_2_path, Map.class);
+        assertNotNull(levelOneEntity);
+        assertNotNull(levelTwoEntity);
+        assertNotNull(levelOneEntity.get("digest"));
+        assertNotNull(levelTwoEntity.get("sequences"));
+    }
+
+    @Test
+    void getServiceInfoTest() {
+        String finalRequest = baseUrl + SERVICE_INFO_PATH;
+        Map<String, Object> serviceInfoMap = restTemplate.getForObject(finalRequest, Map.class);
+        assertNotNull(serviceInfoMap);
+        assertNotNull(serviceInfoMap.get("id"));
+    }
+}
+