#5275

Committed 23 Aug 2024 03:02PM UTC coverage: 77.59% (+0.4%) from 77.22%

Build # #5275

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Commit Message

DCJ-626: Code Cleanup (#2382)

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/src/main/java/org/broadinstitute/consent/http/ConsentModule.java

package org.broadinstitute.consent.http;

import com.google.inject.AbstractModule;
import com.google.inject.Inject;
import com.google.inject.Provides;
import io.dropwizard.client.JerseyClientBuilder;
import io.dropwizard.core.Configuration;
import io.dropwizard.core.setup.Environment;
import io.dropwizard.jdbi3.JdbiFactory;
import jakarta.ws.rs.client.Client;
import org.broadinstitute.consent.http.authentication.OAuthAuthenticator;
import org.broadinstitute.consent.http.cloudstore.GCSService;
import org.broadinstitute.consent.http.configurations.ConsentConfiguration;
import org.broadinstitute.consent.http.db.AcknowledgementDAO;
import org.broadinstitute.consent.http.db.CounterDAO;
import org.broadinstitute.consent.http.db.DAOContainer;
import org.broadinstitute.consent.http.db.DaaDAO;
import org.broadinstitute.consent.http.db.DacDAO;
import org.broadinstitute.consent.http.db.DarCollectionDAO;
import org.broadinstitute.consent.http.db.DarCollectionSummaryDAO;
import org.broadinstitute.consent.http.db.DataAccessRequestDAO;
import org.broadinstitute.consent.http.db.DatasetAssociationDAO;
import org.broadinstitute.consent.http.db.DatasetDAO;
import org.broadinstitute.consent.http.db.ElectionDAO;
import org.broadinstitute.consent.http.db.FileStorageObjectDAO;
import org.broadinstitute.consent.http.db.InstitutionDAO;
import org.broadinstitute.consent.http.db.LibraryCardDAO;
import org.broadinstitute.consent.http.db.MailMessageDAO;
import org.broadinstitute.consent.http.db.MatchDAO;
import org.broadinstitute.consent.http.db.OidcAuthorityDAO;
import org.broadinstitute.consent.http.db.SamDAO;
import org.broadinstitute.consent.http.db.StudyDAO;
import org.broadinstitute.consent.http.db.UserDAO;
import org.broadinstitute.consent.http.db.UserPropertyDAO;
import org.broadinstitute.consent.http.db.UserRoleDAO;
import org.broadinstitute.consent.http.db.VoteDAO;
import org.broadinstitute.consent.http.mail.SendGridAPI;
import org.broadinstitute.consent.http.mail.freemarker.FreeMarkerTemplateHelper;
import org.broadinstitute.consent.http.service.AcknowledgementService;
import org.broadinstitute.consent.http.service.CounterService;
import org.broadinstitute.consent.http.service.DaaService;
import org.broadinstitute.consent.http.service.DacService;
import org.broadinstitute.consent.http.service.DarCollectionService;
import org.broadinstitute.consent.http.service.DataAccessRequestService;
import org.broadinstitute.consent.http.service.DatasetRegistrationService;
import org.broadinstitute.consent.http.service.DatasetService;
import org.broadinstitute.consent.http.service.ElasticSearchService;
import org.broadinstitute.consent.http.service.ElectionService;
import org.broadinstitute.consent.http.service.EmailService;
import org.broadinstitute.consent.http.service.FileStorageObjectService;
import org.broadinstitute.consent.http.service.InstitutionService;
import org.broadinstitute.consent.http.service.LibraryCardService;
import org.broadinstitute.consent.http.service.MatchService;
import org.broadinstitute.consent.http.service.MetricsService;
import org.broadinstitute.consent.http.service.NihService;
import org.broadinstitute.consent.http.service.OidcService;
import org.broadinstitute.consent.http.service.OntologyService;
import org.broadinstitute.consent.http.service.ResearcherService;
import org.broadinstitute.consent.http.service.SupportRequestService;
import org.broadinstitute.consent.http.service.UseRestrictionConverter;
import org.broadinstitute.consent.http.service.UserService;
import org.broadinstitute.consent.http.service.VoteService;
import org.broadinstitute.consent.http.service.dao.DaaServiceDAO;
import org.broadinstitute.consent.http.service.dao.DacServiceDAO;
import org.broadinstitute.consent.http.service.dao.DarCollectionServiceDAO;
import org.broadinstitute.consent.http.service.dao.DataAccessRequestServiceDAO;
import org.broadinstitute.consent.http.service.dao.DatasetServiceDAO;
import org.broadinstitute.consent.http.service.dao.NihServiceDAO;
import org.broadinstitute.consent.http.service.dao.UserServiceDAO;
import org.broadinstitute.consent.http.service.dao.VoteServiceDAO;
import org.broadinstitute.consent.http.service.ontology.ElasticSearchSupport;
import org.broadinstitute.consent.http.service.sam.SamService;
import org.broadinstitute.consent.http.util.HttpClientUtil;
import org.broadinstitute.consent.http.util.gson.GsonUtil;
import org.jdbi.v3.core.Jdbi;
import org.jdbi.v3.gson2.Gson2Config;
import org.jdbi.v3.gson2.Gson2Plugin;
import org.jdbi.v3.guava.GuavaPlugin;
import org.jdbi.v3.sqlobject.SqlObjectPlugin;

public class ConsentModule extends AbstractModule {

  @Inject
  private final ConsentConfiguration config;
  @Inject
  private final Environment environment;

  private final Client client;
  private final Jdbi jdbi;
  private final CounterDAO counterDAO;
  private final ElectionDAO electionDAO;
  private final VoteDAO voteDAO;
  private final StudyDAO studyDAO;
  private final DatasetDAO datasetDAO;
  private final DatasetAssociationDAO datasetAssociationDAO;
  private final DaaDAO daaDAO;
  private final DacDAO dacDAO;
  private final UserDAO userDAO;
  private final UserRoleDAO userRoleDAO;
  private final MatchDAO matchDAO;
  private final MailMessageDAO mailMessageDAO;
  private final UserPropertyDAO userPropertyDAO;
  private final DataAccessRequestDAO dataAccessRequestDAO;
  private final DarCollectionDAO darCollectionDAO;
  private final DarCollectionSummaryDAO darCollectionSummaryDAO;
  private final InstitutionDAO institutionDAO;
  private final LibraryCardDAO libraryCardDAO;
  private final FileStorageObjectDAO fileStorageObjectDAO;
  private final AcknowledgementDAO acknowledgementDAO;

  public static final String DB_ENV = "postgresql";

  ConsentModule(ConsentConfiguration consentConfiguration, Environment environment) {
    this.config = consentConfiguration;
    this.environment = environment;
    this.client = new JerseyClientBuilder(environment)
        .using(config.getJerseyClientConfiguration())
        .build(this.getClass().getName());

    this.jdbi = new JdbiFactory().build(environment, config.getDataSourceFactory(), DB_ENV);
    jdbi.installPlugin(new SqlObjectPlugin());
    jdbi.installPlugin(new Gson2Plugin());
    jdbi.installPlugin(new GuavaPlugin());
    jdbi.getConfig().get(Gson2Config.class).setGson(GsonUtil.buildGson());

    this.counterDAO = this.jdbi.onDemand(CounterDAO.class);
    this.electionDAO = this.jdbi.onDemand(ElectionDAO.class);
    this.voteDAO = this.jdbi.onDemand(VoteDAO.class);
    this.studyDAO = this.jdbi.onDemand(StudyDAO.class);
    this.datasetDAO = this.jdbi.onDemand(DatasetDAO.class);
    this.datasetAssociationDAO = this.jdbi.onDemand(DatasetAssociationDAO.class);
    this.daaDAO = this.jdbi.onDemand(DaaDAO.class);
    this.dacDAO = this.jdbi.onDemand(DacDAO.class);
    this.userDAO = this.jdbi.onDemand(UserDAO.class);
    this.userRoleDAO = this.jdbi.onDemand(UserRoleDAO.class);
    this.matchDAO = this.jdbi.onDemand(MatchDAO.class);
    this.mailMessageDAO = this.jdbi.onDemand(MailMessageDAO.class);
    this.userPropertyDAO = this.jdbi.onDemand(UserPropertyDAO.class);
    this.dataAccessRequestDAO = this.jdbi.onDemand(DataAccessRequestDAO.class);
    this.darCollectionDAO = this.jdbi.onDemand(DarCollectionDAO.class);
    this.darCollectionSummaryDAO = this.jdbi.onDemand(DarCollectionSummaryDAO.class);
    this.institutionDAO = this.jdbi.onDemand((InstitutionDAO.class));
    this.libraryCardDAO = this.jdbi.onDemand((LibraryCardDAO.class));
    this.fileStorageObjectDAO = this.jdbi.onDemand((FileStorageObjectDAO.class));
    this.acknowledgementDAO = this.jdbi.onDemand((AcknowledgementDAO.class));
  }

  @Override
  protected void configure() {
    bind(Configuration.class).toInstance(config);
    bind(Environment.class).toInstance(environment);
  }

  @Provides
  public DAOContainer providesDAOContainer() {
    DAOContainer container = new DAOContainer();
    container.setCounterDAO(providesCounterDAO());
    container.setDacDAO(providesDacDAO());
    container.setDataAccessRequestDAO(providesDataAccessRequestDAO());
    container.setDarCollectionDAO(providesDARCollectionDAO());
    container.setDarCollectionSummaryDAO(providesDarCollectionSummaryDAO());
    container.setDatasetAssociationDAO(providesDatasetAssociationDAO());
    container.setDatasetDAO(providesDatasetDAO());
    container.setElectionDAO(providesElectionDAO());
    container.setMailMessageDAO(providesMailMessageDAO());
    container.setMatchDAO(providesMatchDAO());
    container.setUserPropertyDAO(providesUserPropertyDAO());
    container.setUserDAO(providesUserDAO());
    container.setUserRoleDAO(providesUserRoleDAO());
    container.setVoteDAO(providesVoteDAO());
    container.setStudyDAO(providesStudyDAO());
    container.setInstitutionDAO(providesInstitutionDAO());
    container.setFileStorageObjectDAO(providesFileStorageObjectDAO());
    container.setAcknowledgementDAO(providesAcknowledgementDAO());
    return container;
  }

  @Provides
  Client providesClient() {
    return client;
  }

  @Provides
  HttpClientUtil providesHttpClientUtil() {
    return new HttpClientUtil(config.getServicesConfiguration());
  }

  @Provides
  Jdbi providesJdbi() {
    return jdbi;
  }

  @Provides
  UseRestrictionConverter providesUseRestrictionConverter() {
    return new UseRestrictionConverter(providesClient(), config.getServicesConfiguration());
  }

  @Provides
  OntologyService providesOntologyService() {
    return new OntologyService(providesClient(), config.getServicesConfiguration());
  }

  @Provides
  OAuthAuthenticator providesOAuthAuthenticator() {
    return new OAuthAuthenticator(providesSamService());
  }

  @Provides
  DarCollectionService providesDarCollectionService() {
    return new DarCollectionService(
        providesDARCollectionDAO(),
        providesDarCollectionServiceDAO(),
        providesDatasetDAO(),
        providesElectionDAO(),
        providesDataAccessRequestDAO(),
        providesEmailService(),
        providesVoteDAO(),
        providesMatchDAO(),
        providesDarCollectionSummaryDAO()
    );
  }

  @Provides
  FileStorageObjectService providesFileStorageObjectService() {
    return new FileStorageObjectService(
        providesFileStorageObjectDAO(),
        providesGCSService()
    );
  }

  @Provides
  GCSService providesGCSService() {
    return new GCSService(config.getCloudStoreConfiguration());
  }

  @Provides
  CounterDAO providesCounterDAO() {
    return counterDAO;
  }

  @Provides
  CounterService providesCounterService() {
    return new CounterService(providesCounterDAO());
  }

  @Provides
  DataAccessRequestService providesDataAccessRequestService() {
    return new DataAccessRequestService(
        providesCounterService(),
        providesDAOContainer(),
        providesDacService(),
        providesDataAccessRequestServiceDAO(),
        providesUseRestrictionConverter()
    );
  }

  @Provides
  DatasetServiceDAO providesDatasetServiceDAO() {
    return new DatasetServiceDAO(
        jdbi,
        providesDatasetDAO(),
        providesStudyDAO());
  }

  @Provides
  DatasetService providesDatasetService() {
    return new DatasetService(
        providesDatasetDAO(),
        providesDaaDAO(),
        providesDacDAO(),
        providesEmailService(),
        providesOntologyService(),
        providesStudyDAO(),
        providesDatasetServiceDAO(),
        providesUserDAO());
  }

  @Provides
  ElectionService providesElectionService() {
    return new ElectionService(
        providesElectionDAO()
    );
  }

  @Provides
  FreeMarkerTemplateHelper providesFreeMarkerTemplateHelper() {
    return new FreeMarkerTemplateHelper(config.getFreeMarkerConfiguration());
  }

  @Provides
  EmailService providesEmailService() {
    return new EmailService(
        providesDARCollectionDAO(),
        providesVoteDAO(),
        providesElectionDAO(),
        providesUserDAO(),
        providesMailMessageDAO(),
        providesDatasetDAO(),
        providesDacDAO(),
        providesSendGridAPI(),
        providesFreeMarkerTemplateHelper(),
        config.getServicesConfiguration().getLocalURL()
    );
  }

  @Provides
  SendGridAPI providesSendGridAPI() {
    return new SendGridAPI(
        config.getMailConfiguration(),
        providesUserDAO());
  }

  @Provides
  DataAccessRequestDAO providesDataAccessRequestDAO() {
    return dataAccessRequestDAO;
  }

  @Provides
  DarCollectionDAO providesDARCollectionDAO() {
    return darCollectionDAO;
  }

  @Provides
  DarCollectionSummaryDAO providesDarCollectionSummaryDAO() {
    return darCollectionSummaryDAO;
  }

  @Provides
  DarCollectionServiceDAO providesDarCollectionServiceDAO() {
    return new DarCollectionServiceDAO(
        providesDatasetDAO(),
        providesElectionDAO(),
        providesJdbi(),
        providesUserDAO());
  }

  @Provides
  DataAccessRequestServiceDAO providesDataAccessRequestServiceDAO() {
    return new DataAccessRequestServiceDAO(
        providesDataAccessRequestDAO(),
        providesJdbi(),
        providesDARCollectionDAO()
    );
  }

  @Provides
  ElectionDAO providesElectionDAO() {
    return electionDAO;
  }

  @Provides
  VoteDAO providesVoteDAO() {
    return voteDAO;
  }

  @Provides
  StudyDAO providesStudyDAO() {
    return studyDAO;
  }

  @Provides
  VoteServiceDAO providesVoteServiceDAO() {
    return new VoteServiceDAO(
        providesJdbi(),
        providesVoteDAO());
  }

  @Provides
  VoteService providesVoteService() {
    return new VoteService(
        providesUserDAO(),
        providesDARCollectionDAO(),
        providesDataAccessRequestDAO(),
        providesDatasetDAO(),
        providesElectionDAO(),
        providesEmailService(),
        providesElasticSearchService(),
        providesUseRestrictionConverter(),
        providesVoteDAO(),
        providesVoteServiceDAO());
  }

  @Provides
  DatasetDAO providesDatasetDAO() {
    return datasetDAO;
  }

  @Provides
  DatasetAssociationDAO providesDatasetAssociationDAO() {
    return datasetAssociationDAO;
  }

  @Provides
  DaaServiceDAO providesDaaServiceDAO() {
    return new DaaServiceDAO(
        providesJdbi(),
        providesDaaDAO(),
        providesFileStorageObjectDAO());
  }

  @Provides
  DacServiceDAO providesDacServiceDAO() {
    return new DacServiceDAO(
        providesJdbi());
  }

  @Provides
  DaaDAO providesDaaDAO() {
    return daaDAO;
  }

  @Provides
  DacDAO providesDacDAO() {
    return dacDAO;
  }

  @Provides
  DaaService providesDaaService() {
    return new DaaService(
        providesDaaServiceDAO(),
        providesDaaDAO(),
        providesGCSService(),
        providesEmailService(),
        providesUserService(),
        providesInstitutionDAO(),
        providesDacDAO());
  }

  @Provides
  DacService providesDacService() {
    return new DacService(
        providesDacDAO(),
        providesUserDAO(),
        providesDatasetDAO(),
        providesElectionDAO(),
        providesDataAccessRequestDAO(),
        providesVoteService(),
        providesDaaService(),
        providesDacServiceDAO());
  }

  @Provides
  ElasticSearchService providesElasticSearchService() {
    return new ElasticSearchService(
        ElasticSearchSupport.createRestClient(config.getElasticSearchConfiguration()),
        config.getElasticSearchConfiguration(),
        providesDacDAO(),
        providesDataAccessRequestDAO(),
        providesUserDAO(),
        providesOntologyService(),
        providesInstitutionDAO(),
        providesDatasetDAO(),
        providesStudyDAO()
    );
  }

  @Provides
  UserDAO providesUserDAO() {
    return userDAO;
  }

  @Provides
  UserRoleDAO providesUserRoleDAO() {
    return userRoleDAO;
  }

  @Provides
  MatchService providesMatchService() {
    return new MatchService(
        providesClient(),
        config.getServicesConfiguration(),
        providesMatchDAO(),
        providesDataAccessRequestDAO(),
        providesDatasetDAO(),
        providesUseRestrictionConverter());
  }

  @Provides
  MatchDAO providesMatchDAO() {
    return matchDAO;
  }

  @Provides
  MailMessageDAO providesMailMessageDAO() {
    return mailMessageDAO;
  }

  @Provides
  MetricsService providesMetricsService() {
    return new MetricsService(
        providesDacService(),
        providesDatasetDAO(),
        providesDataAccessRequestDAO(),
        providesDARCollectionDAO(),
        providesMatchDAO(),
        providesElectionDAO()
    );
  }

  @Provides
  UserPropertyDAO providesUserPropertyDAO() {
    return userPropertyDAO;
  }

  @Provides
  InstitutionDAO providesInstitutionDAO() {
    return institutionDAO;
  }

  @Provides
  FileStorageObjectDAO providesFileStorageObjectDAO() {
    return fileStorageObjectDAO;
  }

  @Provides
  LibraryCardDAO providesLibraryCardDAO() {
    return libraryCardDAO;
  }

  @Provides
  AcknowledgementDAO providesAcknowledgementDAO() {
    return acknowledgementDAO;
  }

  @Provides
  InstitutionService providesInstitutionService() {
    return new InstitutionService(providesInstitutionDAO(), providesUserDAO());
  }

  @Provides
  LibraryCardService providesLibraryCardService() {
    return new LibraryCardService(
        providesLibraryCardDAO(),
        providesInstitutionDAO(),
        providesUserDAO());
  }

  @Provides
  AcknowledgementService providesAcknowledgementService() {
    return new AcknowledgementService(
        providesAcknowledgementDAO()
    );
  }

  @Provides
  DatasetRegistrationService providesDatasetRegistrationService() {
    return new DatasetRegistrationService(
        providesDatasetDAO(),
        providesDacDAO(),
        providesDatasetServiceDAO(),
        providesGCSService(),
        providesElasticSearchService(),
        providesStudyDAO(),
        providesEmailService()
    );
  }

  @Provides
  UserServiceDAO providesUserServiceDAO() {
    return new UserServiceDAO(
        providesJdbi(),
        providesUserDAO(),
        providesUserRoleDAO()
    );
  }

  @Provides
  UserService providesUserService() {
    return new UserService(
        providesUserDAO(),
        providesUserPropertyDAO(),
        providesUserRoleDAO(),
        providesVoteDAO(),
        providesDatasetAssociationDAO(),
        providesInstitutionDAO(),
        providesLibraryCardDAO(),
        providesAcknowledgementDAO(),
        providesFileStorageObjectDAO(),
        providesSamDAO(),
        providesUserServiceDAO(),
        providesDaaDAO(),
        providesEmailService());
  }

  @Provides
  ResearcherService providesResearcherService() {
    return new ResearcherService(
        providesUserPropertyDAO(),
        providesUserDAO()
    );
  }

  @Provides
  NihService providesNihService() {
    return new NihService(
        providesResearcherService(),
        providesUserDAO(),
        providesNIHServiceDAO());
  }

  @Provides
  NihServiceDAO providesNIHServiceDAO() {
    return new NihServiceDAO(jdbi);
  }

  @Provides
  SamService providesSamService() {
    return new SamService(providesSamDAO());
  }

  @Provides
  SamDAO providesSamDAO() {
    return new SamDAO(providesHttpClientUtil(), config.getServicesConfiguration());
  }

  @Provides
  OidcAuthorityDAO providesOidcAuthorityDAO() {
    return new OidcAuthorityDAO(providesHttpClientUtil(), config.getOidcConfiguration());
  }

  @Provides
  OidcService providesOidcService() {
    return new OidcService(providesOidcAuthorityDAO(), config.getOidcConfiguration());
  }

  @Provides
  SupportRequestService providesSupportRequestService() {
    return new SupportRequestService(config.getServicesConfiguration(), providesInstitutionDAO(),
        providesUserDAO());
  }
}

1	package org.broadinstitute.consent.http;
2
3	import com.google.inject.AbstractModule;
4	import com.google.inject.Inject;
5	import com.google.inject.Provides;
6	import io.dropwizard.client.JerseyClientBuilder;
7	import io.dropwizard.core.Configuration;
8	import io.dropwizard.core.setup.Environment;
9	import io.dropwizard.jdbi3.JdbiFactory;
10	import jakarta.ws.rs.client.Client;
11	import org.broadinstitute.consent.http.authentication.OAuthAuthenticator;
12	import org.broadinstitute.consent.http.cloudstore.GCSService;
13	import org.broadinstitute.consent.http.configurations.ConsentConfiguration;
14	import org.broadinstitute.consent.http.db.AcknowledgementDAO;
15	import org.broadinstitute.consent.http.db.CounterDAO;
16	import org.broadinstitute.consent.http.db.DAOContainer;
17	import org.broadinstitute.consent.http.db.DaaDAO;
18	import org.broadinstitute.consent.http.db.DacDAO;
19	import org.broadinstitute.consent.http.db.DarCollectionDAO;
20	import org.broadinstitute.consent.http.db.DarCollectionSummaryDAO;
21	import org.broadinstitute.consent.http.db.DataAccessRequestDAO;
22	import org.broadinstitute.consent.http.db.DatasetAssociationDAO;
23	import org.broadinstitute.consent.http.db.DatasetDAO;
24	import org.broadinstitute.consent.http.db.ElectionDAO;
25	import org.broadinstitute.consent.http.db.FileStorageObjectDAO;
26	import org.broadinstitute.consent.http.db.InstitutionDAO;
27	import org.broadinstitute.consent.http.db.LibraryCardDAO;
28	import org.broadinstitute.consent.http.db.MailMessageDAO;
29	import org.broadinstitute.consent.http.db.MatchDAO;
30	import org.broadinstitute.consent.http.db.OidcAuthorityDAO;
31	import org.broadinstitute.consent.http.db.SamDAO;
32	import org.broadinstitute.consent.http.db.StudyDAO;
33	import org.broadinstitute.consent.http.db.UserDAO;
34	import org.broadinstitute.consent.http.db.UserPropertyDAO;
35	import org.broadinstitute.consent.http.db.UserRoleDAO;
36	import org.broadinstitute.consent.http.db.VoteDAO;
37	import org.broadinstitute.consent.http.mail.SendGridAPI;
38	import org.broadinstitute.consent.http.mail.freemarker.FreeMarkerTemplateHelper;
39	import org.broadinstitute.consent.http.service.AcknowledgementService;
40	import org.broadinstitute.consent.http.service.CounterService;
41	import org.broadinstitute.consent.http.service.DaaService;
42	import org.broadinstitute.consent.http.service.DacService;
43	import org.broadinstitute.consent.http.service.DarCollectionService;
44	import org.broadinstitute.consent.http.service.DataAccessRequestService;
45	import org.broadinstitute.consent.http.service.DatasetRegistrationService;
46	import org.broadinstitute.consent.http.service.DatasetService;
47	import org.broadinstitute.consent.http.service.ElasticSearchService;
48	import org.broadinstitute.consent.http.service.ElectionService;
49	import org.broadinstitute.consent.http.service.EmailService;
50	import org.broadinstitute.consent.http.service.FileStorageObjectService;
51	import org.broadinstitute.consent.http.service.InstitutionService;
52	import org.broadinstitute.consent.http.service.LibraryCardService;
53	import org.broadinstitute.consent.http.service.MatchService;
54	import org.broadinstitute.consent.http.service.MetricsService;
55	import org.broadinstitute.consent.http.service.NihService;
56	import org.broadinstitute.consent.http.service.OidcService;
57	import org.broadinstitute.consent.http.service.OntologyService;
58	import org.broadinstitute.consent.http.service.ResearcherService;
59	import org.broadinstitute.consent.http.service.SupportRequestService;
60	import org.broadinstitute.consent.http.service.UseRestrictionConverter;
61	import org.broadinstitute.consent.http.service.UserService;
62	import org.broadinstitute.consent.http.service.VoteService;
63	import org.broadinstitute.consent.http.service.dao.DaaServiceDAO;
64	import org.broadinstitute.consent.http.service.dao.DacServiceDAO;
65	import org.broadinstitute.consent.http.service.dao.DarCollectionServiceDAO;
66	import org.broadinstitute.consent.http.service.dao.DataAccessRequestServiceDAO;
67	import org.broadinstitute.consent.http.service.dao.DatasetServiceDAO;
68	import org.broadinstitute.consent.http.service.dao.NihServiceDAO;
69	import org.broadinstitute.consent.http.service.dao.UserServiceDAO;
70	import org.broadinstitute.consent.http.service.dao.VoteServiceDAO;
71	import org.broadinstitute.consent.http.service.ontology.ElasticSearchSupport;
72	import org.broadinstitute.consent.http.service.sam.SamService;
73	import org.broadinstitute.consent.http.util.HttpClientUtil;
74	import org.broadinstitute.consent.http.util.gson.GsonUtil;
75	import org.jdbi.v3.core.Jdbi;
76	import org.jdbi.v3.gson2.Gson2Config;
77	import org.jdbi.v3.gson2.Gson2Plugin;
78	import org.jdbi.v3.guava.GuavaPlugin;
79	import org.jdbi.v3.sqlobject.SqlObjectPlugin;
80
81	public class ConsentModule extends AbstractModule {
82
83	@Inject
84	private final ConsentConfiguration config;
85	@Inject
86	private final Environment environment;
87
88	private final Client client;
89	private final Jdbi jdbi;
90	private final CounterDAO counterDAO;
91	private final ElectionDAO electionDAO;
92	private final VoteDAO voteDAO;
93	private final StudyDAO studyDAO;
94	private final DatasetDAO datasetDAO;
95	private final DatasetAssociationDAO datasetAssociationDAO;
96	private final DaaDAO daaDAO;
97	private final DacDAO dacDAO;
98	private final UserDAO userDAO;
99	private final UserRoleDAO userRoleDAO;
100	private final MatchDAO matchDAO;
101	private final MailMessageDAO mailMessageDAO;
102	private final UserPropertyDAO userPropertyDAO;
103	private final DataAccessRequestDAO dataAccessRequestDAO;
104	private final DarCollectionDAO darCollectionDAO;
105	private final DarCollectionSummaryDAO darCollectionSummaryDAO;
106	private final InstitutionDAO institutionDAO;
107	private final LibraryCardDAO libraryCardDAO;
108	private final FileStorageObjectDAO fileStorageObjectDAO;
109	private final AcknowledgementDAO acknowledgementDAO;
110
111	public static final String DB_ENV = "postgresql";
112
113	ConsentModule(ConsentConfiguration consentConfiguration, Environment environment) {	1✔
114	this.config = consentConfiguration;	1✔
115	this.environment = environment;	1✔
116	this.client = new JerseyClientBuilder(environment)	1✔
117	.using(config.getJerseyClientConfiguration())	1✔
118	.build(this.getClass().getName());	1✔
119
120	this.jdbi = new JdbiFactory().build(environment, config.getDataSourceFactory(), DB_ENV);	1✔
121	jdbi.installPlugin(new SqlObjectPlugin());	1✔
122	jdbi.installPlugin(new Gson2Plugin());	1✔
123	jdbi.installPlugin(new GuavaPlugin());	1✔
124	jdbi.getConfig().get(Gson2Config.class).setGson(GsonUtil.buildGson());	1✔
125
126	this.counterDAO = this.jdbi.onDemand(CounterDAO.class);	1✔
127	this.electionDAO = this.jdbi.onDemand(ElectionDAO.class);	1✔
128	this.voteDAO = this.jdbi.onDemand(VoteDAO.class);	1✔
129	this.studyDAO = this.jdbi.onDemand(StudyDAO.class);	1✔
130	this.datasetDAO = this.jdbi.onDemand(DatasetDAO.class);	1✔
131	this.datasetAssociationDAO = this.jdbi.onDemand(DatasetAssociationDAO.class);	1✔
132	this.daaDAO = this.jdbi.onDemand(DaaDAO.class);	1✔
133	this.dacDAO = this.jdbi.onDemand(DacDAO.class);	1✔
134	this.userDAO = this.jdbi.onDemand(UserDAO.class);	1✔
135	this.userRoleDAO = this.jdbi.onDemand(UserRoleDAO.class);	1✔
136	this.matchDAO = this.jdbi.onDemand(MatchDAO.class);	1✔
137	this.mailMessageDAO = this.jdbi.onDemand(MailMessageDAO.class);	1✔
138	this.userPropertyDAO = this.jdbi.onDemand(UserPropertyDAO.class);	1✔
139	this.dataAccessRequestDAO = this.jdbi.onDemand(DataAccessRequestDAO.class);	1✔
140	this.darCollectionDAO = this.jdbi.onDemand(DarCollectionDAO.class);	1✔
141	this.darCollectionSummaryDAO = this.jdbi.onDemand(DarCollectionSummaryDAO.class);	1✔
142	this.institutionDAO = this.jdbi.onDemand((InstitutionDAO.class));	1✔
143	this.libraryCardDAO = this.jdbi.onDemand((LibraryCardDAO.class));	1✔
144	this.fileStorageObjectDAO = this.jdbi.onDemand((FileStorageObjectDAO.class));	1✔
145	this.acknowledgementDAO = this.jdbi.onDemand((AcknowledgementDAO.class));	1✔
146	}	1✔
147
148	@Override
149	protected void configure() {
150	bind(Configuration.class).toInstance(config);	1✔
151	bind(Environment.class).toInstance(environment);	1✔
152	}	1✔
153
154	@Provides
155	public DAOContainer providesDAOContainer() {
156	DAOContainer container = new DAOContainer();	1✔
157	container.setCounterDAO(providesCounterDAO());	1✔
158	container.setDacDAO(providesDacDAO());	1✔
159	container.setDataAccessRequestDAO(providesDataAccessRequestDAO());	1✔
160	container.setDarCollectionDAO(providesDARCollectionDAO());	1✔
161	container.setDarCollectionSummaryDAO(providesDarCollectionSummaryDAO());	1✔
162	container.setDatasetAssociationDAO(providesDatasetAssociationDAO());	1✔
163	container.setDatasetDAO(providesDatasetDAO());	1✔
164	container.setElectionDAO(providesElectionDAO());	1✔
165	container.setMailMessageDAO(providesMailMessageDAO());	1✔
166	container.setMatchDAO(providesMatchDAO());	1✔
167	container.setUserPropertyDAO(providesUserPropertyDAO());	1✔
168	container.setUserDAO(providesUserDAO());	1✔
169	container.setUserRoleDAO(providesUserRoleDAO());	1✔
170	container.setVoteDAO(providesVoteDAO());	1✔
171	container.setStudyDAO(providesStudyDAO());	1✔
172	container.setInstitutionDAO(providesInstitutionDAO());	1✔
173	container.setFileStorageObjectDAO(providesFileStorageObjectDAO());	1✔
174	container.setAcknowledgementDAO(providesAcknowledgementDAO());	1✔
175	return container;	1✔
176	}
177
178	@Provides
179	Client providesClient() {
180	return client;	1✔
181	}
182
183	@Provides
184	HttpClientUtil providesHttpClientUtil() {
185	return new HttpClientUtil(config.getServicesConfiguration());	1✔
186	}
187
188	@Provides
189	Jdbi providesJdbi() {
190	return jdbi;	1✔
191	}
192
193	@Provides
194	UseRestrictionConverter providesUseRestrictionConverter() {
195	return new UseRestrictionConverter(providesClient(), config.getServicesConfiguration());	1✔
196	}
197
198	@Provides
199	OntologyService providesOntologyService() {
200	return new OntologyService(providesClient(), config.getServicesConfiguration());	1✔
201	}
202
203	@Provides
204	OAuthAuthenticator providesOAuthAuthenticator() {
205	return new OAuthAuthenticator(providesSamService());	1✔
206	}
207
208	@Provides
209	DarCollectionService providesDarCollectionService() {
210	return new DarCollectionService(	1✔
211	providesDARCollectionDAO(),	1✔
212	providesDarCollectionServiceDAO(),	1✔
213	providesDatasetDAO(),	1✔
214	providesElectionDAO(),	1✔
215	providesDataAccessRequestDAO(),	1✔
216	providesEmailService(),	1✔
217	providesVoteDAO(),	1✔
218	providesMatchDAO(),	1✔
219	providesDarCollectionSummaryDAO()	1✔
220	);
221	}
222
223	@Provides
224	FileStorageObjectService providesFileStorageObjectService() {
225	return new FileStorageObjectService(	×
226	providesFileStorageObjectDAO(),	×
227	providesGCSService()	×
228	);
229	}
230
231	@Provides
232	GCSService providesGCSService() {
233	return new GCSService(config.getCloudStoreConfiguration());	1✔
234	}
235
236	@Provides
237	CounterDAO providesCounterDAO() {
238	return counterDAO;	1✔
239	}
240
241	@Provides
242	CounterService providesCounterService() {
243	return new CounterService(providesCounterDAO());	1✔
244	}
245
246	@Provides
247	DataAccessRequestService providesDataAccessRequestService() {
248	return new DataAccessRequestService(	1✔
249	providesCounterService(),	1✔
250	providesDAOContainer(),	1✔
251	providesDacService(),	1✔
252	providesDataAccessRequestServiceDAO(),	1✔
253	providesUseRestrictionConverter()	1✔
254	);
255	}
256
257	@Provides
258	DatasetServiceDAO providesDatasetServiceDAO() {
259	return new DatasetServiceDAO(	1✔
260	jdbi,
261	providesDatasetDAO(),	1✔
262	providesStudyDAO());	1✔
263	}
264
265	@Provides
266	DatasetService providesDatasetService() {
267	return new DatasetService(	1✔
268	providesDatasetDAO(),	1✔
269	providesDaaDAO(),	1✔
270	providesDacDAO(),	1✔
271	providesEmailService(),	1✔
272	providesOntologyService(),	1✔
273	providesStudyDAO(),	1✔
274	providesDatasetServiceDAO(),	1✔
275	providesUserDAO());	1✔
276	}
277
278	@Provides
279	ElectionService providesElectionService() {
280	return new ElectionService(	1✔
281	providesElectionDAO()	1✔
282	);
283	}
284
285	@Provides
286	FreeMarkerTemplateHelper providesFreeMarkerTemplateHelper() {
287	return new FreeMarkerTemplateHelper(config.getFreeMarkerConfiguration());	1✔
288	}
289
290	@Provides
291	EmailService providesEmailService() {
292	return new EmailService(	1✔
293	providesDARCollectionDAO(),	1✔
294	providesVoteDAO(),	1✔
295	providesElectionDAO(),	1✔
296	providesUserDAO(),	1✔
297	providesMailMessageDAO(),	1✔
298	providesDatasetDAO(),	1✔
299	providesDacDAO(),	1✔
300	providesSendGridAPI(),	1✔
301	providesFreeMarkerTemplateHelper(),	1✔
302	config.getServicesConfiguration().getLocalURL()	1✔
303	);
304	}
305
306	@Provides
307	SendGridAPI providesSendGridAPI() {
308	return new SendGridAPI(	1✔
309	config.getMailConfiguration(),	1✔
310	providesUserDAO());	1✔
311	}
312
313	@Provides
314	DataAccessRequestDAO providesDataAccessRequestDAO() {
315	return dataAccessRequestDAO;	1✔
316	}
317
318	@Provides
319	DarCollectionDAO providesDARCollectionDAO() {
320	return darCollectionDAO;	1✔
321	}
322
323	@Provides
324	DarCollectionSummaryDAO providesDarCollectionSummaryDAO() {
325	return darCollectionSummaryDAO;	1✔
326	}
327
328	@Provides
329	DarCollectionServiceDAO providesDarCollectionServiceDAO() {
330	return new DarCollectionServiceDAO(	1✔
331	providesDatasetDAO(),	1✔
332	providesElectionDAO(),	1✔
333	providesJdbi(),	1✔
334	providesUserDAO());	1✔
335	}
336
337	@Provides
338	DataAccessRequestServiceDAO providesDataAccessRequestServiceDAO() {
339	return new DataAccessRequestServiceDAO(	1✔
340	providesDataAccessRequestDAO(),	1✔
341	providesJdbi(),	1✔
342	providesDARCollectionDAO()	1✔
343	);
344	}
345
346	@Provides
347	ElectionDAO providesElectionDAO() {
348	return electionDAO;	1✔
349	}
350
351	@Provides
352	VoteDAO providesVoteDAO() {
353	return voteDAO;	1✔
354	}
355
356	@Provides
357	StudyDAO providesStudyDAO() {
358	return studyDAO;	1✔
359	}
360
361	@Provides
362	VoteServiceDAO providesVoteServiceDAO() {
363	return new VoteServiceDAO(	1✔
364	providesJdbi(),	1✔
365	providesVoteDAO());	1✔
366	}
367
368	@Provides
369	VoteService providesVoteService() {
370	return new VoteService(	1✔
371	providesUserDAO(),	1✔
372	providesDARCollectionDAO(),	1✔
373	providesDataAccessRequestDAO(),	1✔
374	providesDatasetDAO(),	1✔
375	providesElectionDAO(),	1✔
376	providesEmailService(),	1✔
377	providesElasticSearchService(),	1✔
378	providesUseRestrictionConverter(),	1✔
379	providesVoteDAO(),	1✔
380	providesVoteServiceDAO());	1✔
381	}
382
383	@Provides
384	DatasetDAO providesDatasetDAO() {
385	return datasetDAO;	1✔
386	}
387
388	@Provides
389	DatasetAssociationDAO providesDatasetAssociationDAO() {
390	return datasetAssociationDAO;	1✔
391	}
392
393	@Provides
394	DaaServiceDAO providesDaaServiceDAO() {
395	return new DaaServiceDAO(	1✔
396	providesJdbi(),	1✔
397	providesDaaDAO(),	1✔
398	providesFileStorageObjectDAO());	1✔
399	}
400
401	@Provides
402	DacServiceDAO providesDacServiceDAO() {
403	return new DacServiceDAO(	1✔
404	providesJdbi());	1✔
405	}
406
407	@Provides
408	DaaDAO providesDaaDAO() {
409	return daaDAO;	1✔
410	}
411
412	@Provides
413	DacDAO providesDacDAO() {
414	return dacDAO;	1✔
415	}
416
417	@Provides
418	DaaService providesDaaService() {
419	return new DaaService(	1✔
420	providesDaaServiceDAO(),	1✔
421	providesDaaDAO(),	1✔
422	providesGCSService(),	1✔
423	providesEmailService(),	1✔
424	providesUserService(),	1✔
425	providesInstitutionDAO(),	1✔
426	providesDacDAO());	1✔
427	}
428
429	@Provides
430	DacService providesDacService() {
431	return new DacService(	1✔
432	providesDacDAO(),	1✔
433	providesUserDAO(),	1✔
434	providesDatasetDAO(),	1✔
435	providesElectionDAO(),	1✔
436	providesDataAccessRequestDAO(),	1✔
437	providesVoteService(),	1✔
438	providesDaaService(),	1✔
439	providesDacServiceDAO());	1✔
440	}
441
442	@Provides
443	ElasticSearchService providesElasticSearchService() {
444	return new ElasticSearchService(	1✔
445	ElasticSearchSupport.createRestClient(config.getElasticSearchConfiguration()),	1✔
446	config.getElasticSearchConfiguration(),	1✔
447	providesDacDAO(),	1✔
448	providesDataAccessRequestDAO(),	1✔
449	providesUserDAO(),	1✔
450	providesOntologyService(),	1✔
451	providesInstitutionDAO(),	1✔
452	providesDatasetDAO(),	1✔
453	providesStudyDAO()	1✔
454	);
455	}
456
457	@Provides
458	UserDAO providesUserDAO() {
459	return userDAO;	1✔
460	}
461
462	@Provides
463	UserRoleDAO providesUserRoleDAO() {
464	return userRoleDAO;	1✔
465	}
466
467	@Provides
468	MatchService providesMatchService() {
469	return new MatchService(	1✔
470	providesClient(),	1✔
471	config.getServicesConfiguration(),	1✔
472	providesMatchDAO(),	1✔
473	providesDataAccessRequestDAO(),	1✔
474	providesDatasetDAO(),	1✔
475	providesUseRestrictionConverter());	1✔
476	}
477
478	@Provides
479	MatchDAO providesMatchDAO() {
480	return matchDAO;	1✔
481	}
482
483	@Provides
484	MailMessageDAO providesMailMessageDAO() {
485	return mailMessageDAO;	1✔
486	}
487
488	@Provides
489	MetricsService providesMetricsService() {
490	return new MetricsService(	1✔
491	providesDacService(),	1✔
492	providesDatasetDAO(),	1✔
493	providesDataAccessRequestDAO(),	1✔
494	providesDARCollectionDAO(),	1✔
495	providesMatchDAO(),	1✔
496	providesElectionDAO()	1✔
497	);
498	}
499
500	@Provides
501	UserPropertyDAO providesUserPropertyDAO() {
502	return userPropertyDAO;	1✔
503	}
504
505	@Provides
506	InstitutionDAO providesInstitutionDAO() {
507	return institutionDAO;	1✔
508	}
509
510	@Provides
511	FileStorageObjectDAO providesFileStorageObjectDAO() {
512	return fileStorageObjectDAO;	1✔
513	}
514
515	@Provides
516	LibraryCardDAO providesLibraryCardDAO() {
517	return libraryCardDAO;	1✔
518	}
519
520	@Provides
521	AcknowledgementDAO providesAcknowledgementDAO() {
522	return acknowledgementDAO;	1✔
523	}
524
525	@Provides
526	InstitutionService providesInstitutionService() {
527	return new InstitutionService(providesInstitutionDAO(), providesUserDAO());	1✔
528	}
529
530	@Provides
531	LibraryCardService providesLibraryCardService() {
532	return new LibraryCardService(	1✔
533	providesLibraryCardDAO(),	1✔
534	providesInstitutionDAO(),	1✔
535	providesUserDAO());	1✔
536	}
537
538	@Provides
539	AcknowledgementService providesAcknowledgementService() {
540	return new AcknowledgementService(	1✔
541	providesAcknowledgementDAO()	1✔
542	);
543	}
544
545	@Provides
546	DatasetRegistrationService providesDatasetRegistrationService() {
547	return new DatasetRegistrationService(	1✔
548	providesDatasetDAO(),	1✔
549	providesDacDAO(),	1✔
550	providesDatasetServiceDAO(),	1✔
551	providesGCSService(),	1✔
552	providesElasticSearchService(),	1✔
553	providesStudyDAO(),	1✔
554	providesEmailService()	1✔
555	);
556	}
557
558	@Provides
559	UserServiceDAO providesUserServiceDAO() {
560	return new UserServiceDAO(	1✔
561	providesJdbi(),	1✔
562	providesUserDAO(),	1✔
563	providesUserRoleDAO()	1✔
564	);
565	}
566
567	@Provides
568	UserService providesUserService() {
569	return new UserService(	1✔
570	providesUserDAO(),	1✔
571	providesUserPropertyDAO(),	1✔
572	providesUserRoleDAO(),	1✔
573	providesVoteDAO(),	1✔
574	providesDatasetAssociationDAO(),	1✔
575	providesInstitutionDAO(),	1✔
576	providesLibraryCardDAO(),	1✔
577	providesAcknowledgementDAO(),	1✔
578	providesFileStorageObjectDAO(),	1✔
579	providesSamDAO(),	1✔
580	providesUserServiceDAO(),	1✔
581	providesDaaDAO(),	1✔
582	providesEmailService());	1✔
583	}
584
585	@Provides
586	ResearcherService providesResearcherService() {
587	return new ResearcherService(	1✔
588	providesUserPropertyDAO(),	1✔
589	providesUserDAO()	1✔
590	);
591	}
592
593	@Provides
594	NihService providesNihService() {
595	return new NihService(	1✔
596	providesResearcherService(),	1✔
597	providesUserDAO(),	1✔
598	providesNIHServiceDAO());	1✔
599	}
600
601	@Provides
602	NihServiceDAO providesNIHServiceDAO() {
603	return new NihServiceDAO(jdbi);	1✔
604	}
605
606	@Provides
607	SamService providesSamService() {
608	return new SamService(providesSamDAO());	1✔
609	}
610
611	@Provides
612	SamDAO providesSamDAO() {
613	return new SamDAO(providesHttpClientUtil(), config.getServicesConfiguration());	1✔
614	}
615
616	@Provides
617	OidcAuthorityDAO providesOidcAuthorityDAO() {
618	return new OidcAuthorityDAO(providesHttpClientUtil(), config.getOidcConfiguration());	1✔
619	}
620
621	@Provides
622	OidcService providesOidcService() {
623	return new OidcService(providesOidcAuthorityDAO(), config.getOidcConfiguration());	1✔
624	}
625
626	@Provides
627	SupportRequestService providesSupportRequestService() {
UNCOV 628	return new SupportRequestService(config.getServicesConfiguration(), providesInstitutionDAO(),	×
UNCOV 629	providesUserDAO());	×
630	}
631	}

DataBiosphere / consent / #5275

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