WIP: Unit testing

amphibian-server/pom.xml

@@ -15,6 +15,9 @@
 		<log4j2.version>2.16.0</log4j2.version>
 		<jackson.version>2.11.4</jackson.version>
 		<spring.framework.version>5.2.12.RELEASE</spring.framework.version>
+		<junit.version>4.13.2</junit.version>
+		<hamcrest-library.version>2.2</hamcrest-library.version>
+		<json-path.version>2.6.0</json-path.version>
 	</properties>
 
 	<build>
@@ -173,6 +176,31 @@
 			<artifactId>springfox-swagger-ui</artifactId>
 			<version>2.9.2</version>
 		</dependency>
+
+		<dependency>
+			<groupId>org.springframework</groupId>
+			<artifactId>spring-test</artifactId>
+			<version>${spring.framework.version}</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<version>${junit.version}</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.hamcrest</groupId>
+			<artifactId>hamcrest</artifactId>
+			<version>${hamcrest-library.version}</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>com.jayway.jsonpath</groupId>
+			<artifactId>json-path</artifactId>
+			<version>${json-path.version}</version>
+			<scope>test</scope>
+		</dependency>
 	</dependencies>
 
 	<dependencyManagement>

amphibian-server/src/test/java/org/genesys/amphibian/test/api/PreviewApiTest.java

+package org.genesys.amphibian.test.api;
+
+import com.opencsv.CSVWriter;
+import org.apache.logging.log4j.core.util.StringBuilderWriter;
+import org.apache.poi.ss.usermodel.Cell;
+import org.apache.poi.xssf.usermodel.XSSFRow;
+import org.apache.poi.xssf.usermodel.XSSFSheet;
+import org.apache.poi.xssf.usermodel.XSSFWorkbook;
+import org.genesys.amphibian.api.v0.PreviewApi;
+import org.genesys.amphibian.model.Preview;
+import org.genesys.amphibian.service.PreviewService;
+import org.genesys.amphibian.test.base.AbstractApiTest;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.mock.web.MockMultipartFile;
+
+import java.io.ByteArrayOutputStream;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeMap;
+import java.util.UUID;
+
+import static org.hamcrest.Matchers.*;
+import static org.hamcrest.MatcherAssert.*;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.multipart;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+
+public class PreviewApiTest extends AbstractApiTest {
+
+	@Autowired
+	private PreviewService previewService;
+
+	@Test
+	public void ingestCsvTest() throws Exception {
+		UUID uuid = UUID.randomUUID();
+
+		StringBuilder content = new StringBuilder();
+
+		CSVWriter writer = new CSVWriter(new StringBuilderWriter(content));
+
+		//todo insert data
+		String[] row1 = new String[]{"INSTCODE", "ACCENUMB", "GENUS", "SEEDWGT"};
+		String[] row2 = new String[]{"SYR002", "IG 137552", "Lens", "0.8799999952316284"};
+		List<String[]> rows = new ArrayList<>();
+		rows.add(row1);
+		rows.add(row2);
+		writer.writeAll(rows);
+
+		MockMultipartFile file
+			= new MockMultipartFile(
+			"file",
+			"preview.csv",
+			"text/csv",
+			content.toString().getBytes()
+		);
+
+		/*@formatter:off*/
+		mockMvc
+			.perform(multipart(PreviewApi.CONTROLLER_URL.concat("/ingest/{uuid}"), uuid.toString())
+				.file(file))
+//			.andDo(org.springframework.test.web.servlet.result.MockMvcResultHandlers.print())
+			.andExpect(status().isOk())
+			.andExpect(content().contentType(MediaType.APPLICATION_JSON))
+			.andExpect(jsonPath("$", is(notNullValue())))
+			.andExpect(jsonPath("$.referenceUuid", is(uuid.toString())))
+		;
+		/*@formatter:on*/
+
+		//waiting for data inserting
+		Thread.sleep(500);
+
+		Preview preview = previewService.getPreview(uuid);
+		assertThat(preview, is(notNullValue()));
+		assertThat(preview.getSheets(), hasSize(1));
+		assertThat(preview.getSheets().get(0).rowCount, is(2));
+	}
+
+	@Test
+	public void ingestExelTest() throws Exception {
+		UUID uuid = UUID.randomUUID();
+
+		StringBuilder content = new StringBuilder();
+
+		XSSFWorkbook workbook = new XSSFWorkbook();
+		XSSFSheet spreadsheet = workbook.createSheet("test");
+		XSSFRow row;
+
+		//todo insert data
+		Map<String, Object[]> data = new TreeMap<String, Object[]>();
+
+		data.put("1", new Object[] {"INSTCODE", "ACCENUMB", "GENUS", "SEEDWGT"});
+		data.put("2", new Object[] {"SYR002", "IG 137552", "Lens", "0.8799999952316284"});
+
+		Set<String> keyid = data.keySet();
+
+		int rowid = 0;
+
+		for (String key : keyid) {
+			row = spreadsheet.createRow(rowid++);
+			Object[] objectArr = data.get(key);
+			int cellid = 0;
+			for (Object obj : objectArr) {
+				Cell cell = row.createCell(cellid++);
+				cell.setCellValue((String)obj);
+			}
+		}
+
+		ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
+
+		workbook.write(outputStream);
+
+		MockMultipartFile file
+			= new MockMultipartFile(
+			"file",
+			"preview.exel",
+			"application/vnd.ms-excel",
+			outputStream.toByteArray()
+		);
+
+		/*@formatter:off*/
+		mockMvc
+			.perform(multipart(PreviewApi.CONTROLLER_URL.concat("/ingest/{uuid}"), uuid.toString())
+				.file(file))
+//			.andDo(org.springframework.test.web.servlet.result.MockMvcResultHandlers.print())
+			.andExpect(status().isOk())
+			.andExpect(content().contentType(MediaType.APPLICATION_JSON))
+			.andExpect(jsonPath("$", is(notNullValue())))
+			.andExpect(jsonPath("$.referenceUuid", is(uuid.toString())))
+		;
+		/*@formatter:on*/
+
+		//waiting for data inserting
+		Thread.sleep(500);
+
+		Preview preview = previewService.getPreview(uuid);
+		assertThat(preview, is(notNullValue()));
+		assertThat(preview.getSheets(), hasSize(1));
+		assertThat(preview.getSheets().get(0).rowCount, is(2));
+	}
+}

amphibian-server/src/test/java/org/genesys/amphibian/test/base/AbstractApiTest.java

+/*
+ * Copyright 2021 Global Crop Diversity Trust
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.genesys.amphibian.test.base;
+
+import org.genesys.amphibian.repositories.mongo.DatasetTableRepository;
+import org.genesys.amphibian.repositories.mongo.PreviewRepository;
+import org.genesys.amphibian.repositories.mongo.TableRepository;
+import org.genesys.amphibian.test.config.ApplicationTestConfig;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.ContextHierarchy;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+import org.springframework.test.context.web.WebAppConfiguration;
+import org.springframework.test.web.servlet.MockMvc;
+import org.springframework.test.web.servlet.setup.MockMvcBuilders;
+import org.springframework.transaction.annotation.Transactional;
+import org.springframework.web.context.WebApplicationContext;
+
+@RunWith(SpringJUnit4ClassRunner.class)
+@WebAppConfiguration
+@ContextHierarchy(@ContextConfiguration(name = "api", classes = { ApplicationTestConfig.class }))
+public abstract class AbstractApiTest {
+
+	@Autowired
+	private WebApplicationContext webApplicationContext;
+
+	protected MockMvc mockMvc;
+
+	@Autowired
+	private PreviewRepository previewRepository;
+
+	@Autowired
+	private DatasetTableRepository datasetTableRepository;
+
+	@Autowired
+	private TableRepository tableRepository;
+
+	@After
+	@Transactional
+	public void afterTest() {
+		previewRepository.deleteAll();
+		datasetTableRepository.deleteAll();
+		tableRepository.deleteAll();
+	}
+
+	@Before
+	@Transactional
+	public void beforeTest() throws Exception {
+		mockMvc = MockMvcBuilders.webAppContextSetup(webApplicationContext).build();
+
+	}
+}

amphibian-server/src/test/java/org/genesys/amphibian/test/config/ApplicationTestConfig.java

+/*
+ * Copyright 2021 Global Crop Diversity Trust
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.genesys.amphibian.test.config;
+
+import org.genesys.amphibian.config.SchedulerConfig;
+import org.genesys.amphibian.config.WebConfiguration;
+import org.springframework.context.annotation.ComponentScan;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.EnableAspectJAutoProxy;
+import org.springframework.context.annotation.Import;
+
+@Configuration
+@ComponentScan(basePackages = { "org.genesys.amphibian.service" })
+@Import({ DatabaseConfig.class, SchedulerConfig.class, WebConfiguration.class })
+@EnableAspectJAutoProxy
+public class ApplicationTestConfig {
+
+}

amphibian-server/src/test/java/org/genesys/amphibian/test/config/DatabaseConfig.java

+/*
+ * Copyright 2018 Global Crop Diversity Trust
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.genesys.amphibian.test.config;
+
+import com.mongodb.MongoClient;
+import com.mongodb.MongoClientOptions;
+import com.mongodb.MongoCredential;
+import com.mongodb.ServerAddress;
+import org.genesys.amphibian.config.ApplicationConfig;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.PropertySource;
+import org.springframework.context.annotation.PropertySources;
+import org.springframework.data.mongodb.MongoDbFactory;
+import org.springframework.data.mongodb.MongoTransactionManager;
+import org.springframework.data.mongodb.config.AbstractMongoConfiguration;
+import org.springframework.data.mongodb.config.EnableMongoAuditing;
+import org.springframework.data.mongodb.repository.config.EnableMongoRepositories;
+
+import java.util.ArrayList;
+import java.util.List;
+
+@Configuration
+@PropertySources({ @PropertySource("classpath:/junit.properties") })
+@EnableMongoRepositories(basePackages = { "org.genesys.amphibian.repositories.mongo" })
+@EnableMongoAuditing(modifyOnCreate = true)
+public class DatabaseConfig extends AbstractMongoConfiguration {
+
+	final static Logger LOG = LoggerFactory.getLogger(ApplicationConfig.class);
+
+	@Value("${mongo.hosts}")
+	private String[] dbHosts;
+
+	@Value("${mongo.port}")
+	private Integer dbPort;
+
+	@Value("${mongo.database}")
+	private String dbDatabase;
+
+	@Value("${mongo.username}")
+	private String dbUsername;
+
+	@Value("${mongo.password}")
+	private String dbPassword;
+
+	@Bean
+	MongoTransactionManager transactionManager(MongoDbFactory dbFactory) {
+		return new MongoTransactionManager(dbFactory);
+	}
+
+	@Override
+	protected String getDatabaseName() {
+		return dbDatabase;
+	}
+
+	@Override
+	public MongoClient mongoClient() {
+		MongoCredential credential = MongoCredential.createCredential(dbUsername, dbDatabase, dbPassword.toCharArray());
+		MongoClientOptions options = new MongoClientOptions.Builder().build();
+		List<ServerAddress> servers = new ArrayList<>();
+		for (String dbHost: dbHosts) {
+			LOG.warn("Adding mongo at {}:{}", dbHost, dbPort);
+			servers.add(new ServerAddress(dbHost, dbPort));
+		}
+		MongoClient mongoClient = new MongoClient(servers, credential, options);
+		return mongoClient;
+	}
+}

amphibian-server/src/test/resources/junit.properties

+#-------------------------------------------------------------------------------
+# Copyright 2021 Global Crop Diversity Trust
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# 
+#   http://www.apache.org/licenses/LICENSE-2.0
+# 
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#-------------------------------------------------------------------------------
+
+mongo.hosts=
+mongo.port=
+mongo.database=
+mongo.username=
+mongo.password=
\ No newline at end of file