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package gsrs.substances.tests;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.mockito.Mockito.mock;
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.List;
import java.util.regex.Pattern;
import java.util.stream.Stream;
import javax.persistence.EntityManager;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.extension.RegisterExtension;
import org.quartz.Scheduler;
import org.quartz.SchedulerException;
import org.quartz.impl.StdSchedulerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.autoconfigure.condition.ConditionalOnMissingBean;
import org.springframework.boot.test.autoconfigure.orm.jpa.TestEntityManager;
import org.springframework.boot.test.context.TestConfiguration;
import org.springframework.boot.test.mock.mockito.MockBean;
import org.springframework.boot.test.util.TestPropertyValues;
import org.springframework.context.ApplicationContextInitializer;
import org.springframework.context.ConfigurableApplicationContext;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Import;
import org.springframework.context.annotation.Primary;
import org.springframework.core.io.Resource;
import org.springframework.core.task.TaskExecutor;
import org.springframework.test.context.ActiveProfiles;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.support.TransactionTemplate;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import gov.nih.ncats.common.io.InputStreamSupplier;
import gov.nih.ncats.common.sneak.Sneak;
import gov.nih.ncats.common.yield.Yield;
import gsrs.autoconfigure.GsrsExportConfiguration;
import gsrs.cache.GsrsCache;
import gsrs.controller.GsrsControllerConfiguration;
import gsrs.module.substance.SubstanceEntityService;
import gsrs.module.substance.SubstanceEntityServiceImpl;
import gsrs.module.substance.autoconfigure.GsrsSubstanceModuleAutoConfiguration;
import gsrs.module.substance.repository.SubstanceRepository;
import gsrs.payload.LegacyPayloadConfiguration;
import gsrs.payload.LegacyPayloadService;
import gsrs.payload.PayloadController;
import gsrs.repository.ETagRepository;
import gsrs.repository.EditRepository;
import gsrs.repository.FileDataRepository;
import gsrs.repository.GroupRepository;
import gsrs.repository.PayloadRepository;
import gsrs.service.ExportService;
import gsrs.service.GsrsEntityService;
import gsrs.service.PayloadService;
import gsrs.services.BackupService;
import gsrs.startertests.GsrsEntityTestConfiguration;
import gsrs.startertests.TestEntityProcessorFactory;
import gsrs.startertests.TestGsrsValidatorFactory;
import gsrs.startertests.TestIndexValueMakerFactory;
import gsrs.startertests.jupiter.AbstractGsrsJpaEntityJunit5Test;
import gsrs.startertests.jupiter.ResetAllEntityServicesBeforeEachExtension;
import ix.core.models.Group;
import ix.core.models.Principal;
import ix.core.models.Role;
import ix.core.models.UserProfile;
import ix.core.util.EntityUtils;
import ix.core.validator.ValidationResponse;
import ix.ginas.models.v1.Substance;
/**
* Parent Super-class of that should be used to
* test Substances interacting with a test database.
* Subclasses will have further configurations for different
* granularity tests unit vs end to end etc.
*/
@ActiveProfiles("test")
@ContextConfiguration(classes = { GsrsEntityTestConfiguration.class, GsrsControllerConfiguration.class},
initializers= { AbstractSubstanceJpaEntityTestSuperClass.Initializer.class}
)
//@SpringBootTest
@Import({AbstractSubstanceJpaEntityTest.TestConfig.class, GsrsSubstanceModuleAutoConfiguration.class})
public abstract class AbstractSubstanceJpaEntityTestSuperClass extends AbstractGsrsJpaEntityJunit5Test {
@TestConfiguration
// @AutoConfigureAfter(JpaRepositoriesAutoConfiguration.class)
public static class TestConfig{
@Bean
@Primary
PayloadService payloadService(PayloadRepository payloadRepository, LegacyPayloadConfiguration configuration, FileDataRepository fileDataRepository) throws IOException {
return new LegacyPayloadService(payloadRepository, configuration, fileDataRepository);
}
@Bean
@Primary
TestGsrsValidatorFactory gsrsValidatorFactory(){
return new TestGsrsValidatorFactory();
}
@Bean
SubstanceEntityService substanceEntityService(){
return new SubstanceEntityServiceImpl();
}
@Bean
@Primary
TestIndexValueMakerFactory indexValueMakerFactory(){
return new TestIndexValueMakerFactory();
}
@Bean
@Primary
TestEntityProcessorFactory entityProcessorFactory(){
return new TestEntityProcessorFactory();
}
@Bean
@Primary
public Scheduler getScheduler() throws SchedulerException {
return StdSchedulerFactory.getDefaultScheduler();
}
@Bean
@Primary
public BackupService backupService(){
return new BackupService();
}
@Bean
@ConditionalOnMissingBean
@Primary
public ExportService mockExportService(){
return mock(ExportService.class);
}
@Bean
@ConditionalOnMissingBean
@Primary
protected GsrsExportConfiguration mockGsrsExportConfiguration(){
return mock(GsrsExportConfiguration.class);
}
}
static class Initializer implements ApplicationContextInitializer {
@Override
public void initialize(ConfigurableApplicationContext context) {
TestPropertyValues.of(
"ix.structure.base=" + tempDir+"/structure",
"ix.sequence.base=" + tempDir+"/sequence"
).applyTo(context);
}
}
// @Order(Ordered.HIGHEST_PRECEDENCE)
// @TestConfiguration
// @AutoConfigureAfter(JpaRepositoriesAutoConfiguration.class)
// @ConditionalOnMissingBean(value = ETagRepository.class)
//// @EnableJpaRepositories(basePackages ={"ix","gsrs", "gov.nih.ncats"} )
// public static class JpaScanIfNeededConfiguration{
//
// }
public interface EntityManagerFacade{
T persistAndFlush(T entity);
T persist(T entity);
static EntityManagerFacade wrap(EntityManager em){
return new EntityManagerFacade() {
@Override
public T persistAndFlush(T entity) {
em.persist(entity);
em.flush();
return entity;
}
@Override
public T persist(T entity) {
em.persist(entity);
return entity;
}
};
}
static EntityManagerFacade wrap(TestEntityManager em){
return new EntityManagerFacade() {
@Override
public T persistAndFlush(T entity) {
return em.persistAndFlush(entity);
}
@Override
public T persist(T entity) {
return em.persist(entity);
}
};
}
}
@Autowired
protected SubstanceEntityService substanceEntityService;
@Autowired
protected EditRepository editRepository;
@Autowired
protected SubstanceRepository substanceRepository;
@Autowired
protected GroupRepository groupRepository;
@Autowired
protected PlatformTransactionManager transactionManager;
@Autowired
protected GsrsCache gsrsCache;
@Autowired
protected ExportService mockExportService;
@MockBean
protected TaskExecutor mockTaskExecutor;
@Autowired
protected GsrsExportConfiguration mockGsrsExportConfiguration;
@Autowired
protected ETagRepository eTagRepository;
@MockBean
protected PayloadController payloadController;
@Autowired
@RegisterExtension
protected ResetAllEntityServicesBeforeEachExtension resetAllEntityServicesBeforeEachExtension;
protected abstract EntityManagerFacade getEntityManagerFacade();
private EntityManagerFacade entityManagerFacade;
private final boolean createAdminUserOnInit;
public AbstractSubstanceJpaEntityTestSuperClass(){
this(true);
}
public AbstractSubstanceJpaEntityTestSuperClass(boolean createAdminUserOnInit){
this.createAdminUserOnInit = createAdminUserOnInit;
}
@BeforeEach
public void init(){
entityManagerFacade = getEntityManagerFacade();
if(createAdminUserOnInit) {
TransactionTemplate transactionTemplate = new TransactionTemplate(transactionManager);
// transactionTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
transactionTemplate.executeWithoutResult(s -> {
createUser("admin", Role.values());
//some integration tests will make validation messages which will get assigned an "admin" access group
groupRepository.saveAndFlush(new Group("admin"));
});
}
}
protected Principal createUser(String username, Role... roles){
Principal user = new Principal(username, null);
UserProfile up = new UserProfile();
up.setRoles(Arrays.asList(roles));
up.user= user;
entityManagerFacade.persist(up);
return user;
}
protected TransactionTemplate newTransactionTemplate(){
return new TransactionTemplate(transactionManager);
}
/**
* Load the specially formatted GSRS format file (often with {@code .gsrs} extension although some
* GSRS 1.x verion files have the extension {@code .ginas}. Either way, the file is a GZIPPED
* encoded file of tab delimited text where each row contains the 1 Substance JSON record one line per record along
* with additional metadata.
* @param gsrsFile the GSRS file to load.
* @return a List of {@link gsrs.service.GsrsEntityService.CreationResult}s one per record in the GSRS file.
* @throws IOException if there is a problem parsing the file.
*/
protected List> loadGsrsFile(Resource gsrsFile, Substance.SubstanceClass... substanceClasses) throws IOException {
return loadGsrsFile(gsrsFile.getFile(), substanceClasses);
}
/**
* Load the specially formatted GSRS format file (often with {@code .gsrs} extension although some
* GSRS 1.x verion files have the extension {@code .ginas}. Either way, the file is a GZIPPED
* encoded file of tab delimited text where each row contains the 1 Substance JSON record one line per record along
* with additional metadata.
* @param gsrsFile the GSRS file to load.
* @return a List of {@link gsrs.service.GsrsEntityService.CreationResult}s one per record in the GSRS file.
* @throws IOException if there is a problem parsing the file.
*/
protected List> loadGsrsFile(Resource gsrsFile) throws IOException {
return loadGsrsFile(gsrsFile.getFile());
}
/**
* Load the specially formatted GSRS format file (often with {@code .gsrs} extension although some
* GSRS 1.x verion files have the extension {@code .ginas}. Either way, the file is a GZIPPED
* encoded file of tab delimited text where each row contains the 1 Substance JSON record one line per record along
* with additional metadata.
* @param gsrsFile the GSRS file to load.
* @return a List of {@link gsrs.service.GsrsEntityService.CreationResult}s one per record in the GSRS file.
* @throws IOException if there is a problem parsing the file.
*/
protected List> loadGsrsFile(File gsrsFile) throws IOException {
return loadGsrsFile(gsrsFile, null);
}
/**
* Load the specially formatted GSRS format file (often with {@code .gsrs} extension although some
* GSRS 1.x verion files have the extension {@code .ginas}. Either way, the file is a GZIPPED
* encoded file of tab delimited text where each row contains the 1 Substance JSON record one line per record along
* with additional metadata.
* @param gsrsFile the GSRS file to load.
* @param substanceClasses a list of {@link ix.ginas.models.v1.Substance.SubstanceClass}es to include.
* only the records in the given file of these kinds will be loaded.
* If this var args is empty or null then all records in the file will be loaded.
* @return a List of {@link gsrs.service.GsrsEntityService.CreationResult}s one per record in the GSRS file.
* @throws IOException if there is a problem parsing the file.
*/
protected List> loadGsrsFile(File gsrsFile, Substance.SubstanceClass... substanceClasses) throws IOException {
TransactionTemplate transactionTemplate = new TransactionTemplate(transactionManager);
transactionTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
List> list = new ArrayList<>();
try(Stream stream1 =yieldSubstancesFromGsrsFile(gsrsFile, substanceClasses).stream()){
stream1.forEach(json->{
list.add(transactionTemplate.execute(status ->{
try {
GsrsEntityService.CreationResult result= substanceEntityService.createEntity(json,true);
//full fetch
if(result.isCreated()){
result.getCreatedEntity().toFullJsonNode();
}
return result;
}catch(IOException e){
return Sneak.sneakyThrow(e);
}
}));
});
}catch(Exception e) {
e.printStackTrace();
}
return list;
}
/**
* Parse a Gsrs encoded Spring Resource object and return a {@link Yield}
* for each JsonNode parsed object.
* @param gsrsFile the file to parse.
* @param substanceClasses a list of {@link ix.ginas.models.v1.Substance.SubstanceClass}es to include.
* only the records in the given file of these kinds will be included in the Yield.
* If this var args is empty or null then all records in the file will be included.
* @return a {@link Yield}
* @throws IOException
*/
protected Yield yieldSubstancesFromGsrsFile(Resource gsrsFile,Substance.SubstanceClass... substanceClasses) throws IOException{
return yieldSubstancesFromGsrsFile(gsrsFile.getFile(), substanceClasses);
}
protected Yield yieldSubstancesFromGsrsFile(File gsrsFile, Substance.SubstanceClass... substanceClass){
Yield yield=null;
yield = Yield.create(r->{
String line;
try (BufferedReader reader = new BufferedReader(new InputStreamReader(InputStreamSupplier.forFile(gsrsFile).get()))) {
ObjectMapper mapper = new ObjectMapper();
Pattern gsrsFilePattern = Pattern.compile("\t");
while ((line = reader.readLine()) != null) {
if (line.isEmpty() || line.startsWith("#")) {
//skip
continue;
}
String[] cols = gsrsFilePattern.split(line);
String json = cols[2];
boolean include=true;
if(substanceClass !=null && substanceClass.length >0){
include=false;
for(Substance.SubstanceClass c : substanceClass){
if(json.contains("\"substanceClass\":\""+c.jsonValue()+ "\"")){
include=true;
break;
}
}
}
if(!include){
continue;
}
r.returning(mapper.readTree(json));
}
}catch(IOException e){
Sneak.sneakyThrow(e);
}finally{
r.signalComplete();
}
});
return yield;
}
protected Substance assertCreated(JsonNode json){
TransactionTemplate transactionTemplate = new TransactionTemplate(transactionManager);
transactionTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
return transactionTemplate.execute( status -> {
try {
Substance s= ensurePass(substanceEntityService.createEntity(json));
substanceRepository.flush();
return s;
} catch (Exception e) {
return Sneak.sneakyThrow(e);
}
});
}
protected Substance assertUpdated(JsonNode json){
TransactionTemplate transactionTemplate = new TransactionTemplate(transactionManager);
transactionTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
return transactionTemplate.execute( stauts -> {
try {
Substance s= ensurePass(substanceEntityService.updateEntity(json));
substanceRepository.flush();
return s;
} catch (Exception e) {
return Sneak.sneakyThrow(e);
}
});
}
protected Substance assertCreatedAPI(JsonNode json){
TransactionTemplate transactionTemplate = new TransactionTemplate(transactionManager);
transactionTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
return transactionTemplate.execute( status -> {
try {
Substance s= ensurePass(substanceEntityService.createEntity(json));
substanceRepository.flush();
return s;
} catch (Exception e) {
return Sneak.sneakyThrow(e);
}
});
}
protected Substance assertUpdatedAPI(JsonNode json){
TransactionTemplate transactionTemplate = new TransactionTemplate(transactionManager);
transactionTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
return transactionTemplate.execute( status -> {
try {
Substance s= ensurePass(substanceEntityService.updateEntity(json));
substanceRepository.flush();
return s;
} catch (Exception e) {
return Sneak.sneakyThrow(e);
}
});
}
protected static T ensurePass(GsrsEntityService.UpdateResult updateResult){
ValidationResponse resp = updateResult.getValidationResponse();
assertTrue(resp.isValid(), ()->"response is not valid "+ resp.getValidationMessages());
assertTrue(!resp.hasError(), ()->"response has error "+ resp.getValidationMessages());
assertEquals(GsrsEntityService.UpdateResult.STATUS.UPDATED, updateResult.getStatus(), ()->"was not updated "+ resp.getValidationMessages());
return updateResult.getUpdatedEntity();
}
protected static T ensurePass(GsrsEntityService.CreationResult creationResult){
ValidationResponse resp = creationResult.getValidationResponse();
assertTrue(resp.isValid(), ()->"response is not valid "+ resp.getValidationMessages());
assertTrue(!resp.hasError(), ()->"response has error "+ resp.getValidationMessages());
assertTrue(creationResult.isCreated(), ()->"was not created "+ resp.getValidationMessages());
T sub= creationResult.getCreatedEntity();
EntityUtils.EntityWrapper.of(sub).toFullJson();
return sub;
}
protected static Collection> ensurePass(Collection> creationResults){
for(GsrsEntityService.CreationResult creationResult: creationResults) {
ValidationResponse resp = creationResult.getValidationResponse();
assertTrue(resp.isValid(), () -> "response is not valid " + resp.getValidationMessages());
assertTrue(!resp.hasError(), () -> "response has error " + resp.getValidationMessages());
assertTrue(creationResult.isCreated(), () -> "was not created " + resp.getValidationMessages());
T sub = creationResult.getCreatedEntity();
}
return creationResults;
}
}
