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Example 1 with SequencingObjectRepository

use of ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequencingObjectRepository in project irida by phac-nml.

the class ProjectServiceImplTest method setUp.

@Before
public void setUp() {
    validator = mock(Validator.class);
    projectRepository = mock(ProjectRepository.class);
    sampleRepository = mock(SampleRepository.class);
    userRepository = mock(UserRepository.class);
    pujRepository = mock(ProjectUserJoinRepository.class);
    psjRepository = mock(ProjectSampleJoinRepository.class);
    relatedProjectRepository = mock(RelatedProjectRepository.class);
    referenceFileRepository = mock(ReferenceFileRepository.class);
    prfjRepository = mock(ProjectReferenceFileJoinRepository.class);
    ugpjRepository = mock(UserGroupProjectJoinRepository.class);
    sequencingObjectRepository = mock(SequencingObjectRepository.class);
    projectService = new ProjectServiceImpl(projectRepository, sampleRepository, userRepository, pujRepository, psjRepository, relatedProjectRepository, referenceFileRepository, prfjRepository, ugpjRepository, ssoRepository, pasRepository, sequencingObjectRepository, validator);
}
Also used : SampleRepository(ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepository) RelatedProjectRepository(ca.corefacility.bioinformatics.irida.repositories.joins.project.RelatedProjectRepository) ProjectRepository(ca.corefacility.bioinformatics.irida.repositories.ProjectRepository) UserRepository(ca.corefacility.bioinformatics.irida.repositories.user.UserRepository) RelatedProjectRepository(ca.corefacility.bioinformatics.irida.repositories.joins.project.RelatedProjectRepository) ProjectSampleJoinRepository(ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectSampleJoinRepository) SequencingObjectRepository(ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequencingObjectRepository) UserGroupProjectJoinRepository(ca.corefacility.bioinformatics.irida.repositories.joins.project.UserGroupProjectJoinRepository) ProjectUserJoinRepository(ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectUserJoinRepository) ReferenceFileRepository(ca.corefacility.bioinformatics.irida.repositories.referencefile.ReferenceFileRepository) Validator(javax.validation.Validator) ProjectReferenceFileJoinRepository(ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectReferenceFileJoinRepository) ProjectServiceImpl(ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl) Before(org.junit.Before)

Example 2 with SequencingObjectRepository

use of ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequencingObjectRepository in project irida by phac-nml.

the class SampleServiceImplTest method setUp.

@Before
public void setUp() {
    sampleRepository = mock(SampleRepository.class);
    psjRepository = mock(ProjectSampleJoinRepository.class);
    analysisRepository = mock(AnalysisRepository.class);
    ssoRepository = mock(SampleSequencingObjectJoinRepository.class);
    qcEntryRepository = mock(QCEntryRepository.class);
    sequencingObjectRepository = mock(SequencingObjectRepository.class);
    sampleGenomeAssemblyJoinRepository = mock(SampleGenomeAssemblyJoinRepository.class);
    ValidatorFactory factory = Validation.buildDefaultValidatorFactory();
    validator = factory.getValidator();
    sampleService = new SampleServiceImpl(sampleRepository, psjRepository, analysisRepository, ssoRepository, qcEntryRepository, sequencingObjectRepository, sampleGenomeAssemblyJoinRepository, userRepository, validator);
}
Also used : SampleRepository(ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepository) QCEntryRepository(ca.corefacility.bioinformatics.irida.repositories.sample.QCEntryRepository) ValidatorFactory(javax.validation.ValidatorFactory) SampleGenomeAssemblyJoinRepository(ca.corefacility.bioinformatics.irida.repositories.joins.sample.SampleGenomeAssemblyJoinRepository) ProjectSampleJoinRepository(ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectSampleJoinRepository) SampleServiceImpl(ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl) SequencingObjectRepository(ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequencingObjectRepository) AnalysisRepository(ca.corefacility.bioinformatics.irida.repositories.analysis.AnalysisRepository) SampleSequencingObjectJoinRepository(ca.corefacility.bioinformatics.irida.repositories.joins.sample.SampleSequencingObjectJoinRepository) Before(org.junit.Before)

Example 3 with SequencingObjectRepository

use of ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequencingObjectRepository in project irida by phac-nml.

the class ReadSequencingObjectPermissionTest method setUp.

@Before
public void setUp() {
    userRepository = mock(UserRepository.class);
    ssoRepository = mock(SampleSequencingObjectJoinRepository.class);
    sequencingObjectRepository = mock(SequencingObjectRepository.class);
    psjRepository = mock(ProjectSampleJoinRepository.class);
    sampleRepository = mock(SampleRepository.class);
    readProjectPermission = mock(ReadProjectPermission.class);
    samplePermission = new ReadSamplePermission(sampleRepository, psjRepository, readProjectPermission);
    permission = new ReadSequencingObjectPermission(sequencingObjectRepository, samplePermission, ssoRepository);
}
Also used : SampleRepository(ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepository) ReadSequencingObjectPermission(ca.corefacility.bioinformatics.irida.security.permissions.files.ReadSequencingObjectPermission) ReadProjectPermission(ca.corefacility.bioinformatics.irida.security.permissions.project.ReadProjectPermission) UserRepository(ca.corefacility.bioinformatics.irida.repositories.user.UserRepository) ProjectSampleJoinRepository(ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectSampleJoinRepository) SequencingObjectRepository(ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequencingObjectRepository) SampleSequencingObjectJoinRepository(ca.corefacility.bioinformatics.irida.repositories.joins.sample.SampleSequencingObjectJoinRepository) ReadSamplePermission(ca.corefacility.bioinformatics.irida.security.permissions.sample.ReadSamplePermission) Before(org.junit.Before)

Aggregations

ProjectSampleJoinRepository (ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectSampleJoinRepository)3 SampleRepository (ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepository)3 SequencingObjectRepository (ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequencingObjectRepository)3 Before (org.junit.Before)3 SampleSequencingObjectJoinRepository (ca.corefacility.bioinformatics.irida.repositories.joins.sample.SampleSequencingObjectJoinRepository)2 UserRepository (ca.corefacility.bioinformatics.irida.repositories.user.UserRepository)2 ProjectRepository (ca.corefacility.bioinformatics.irida.repositories.ProjectRepository)1 AnalysisRepository (ca.corefacility.bioinformatics.irida.repositories.analysis.AnalysisRepository)1 ProjectReferenceFileJoinRepository (ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectReferenceFileJoinRepository)1 ProjectUserJoinRepository (ca.corefacility.bioinformatics.irida.repositories.joins.project.ProjectUserJoinRepository)1 RelatedProjectRepository (ca.corefacility.bioinformatics.irida.repositories.joins.project.RelatedProjectRepository)1 UserGroupProjectJoinRepository (ca.corefacility.bioinformatics.irida.repositories.joins.project.UserGroupProjectJoinRepository)1 SampleGenomeAssemblyJoinRepository (ca.corefacility.bioinformatics.irida.repositories.joins.sample.SampleGenomeAssemblyJoinRepository)1 ReferenceFileRepository (ca.corefacility.bioinformatics.irida.repositories.referencefile.ReferenceFileRepository)1 QCEntryRepository (ca.corefacility.bioinformatics.irida.repositories.sample.QCEntryRepository)1 ReadSequencingObjectPermission (ca.corefacility.bioinformatics.irida.security.permissions.files.ReadSequencingObjectPermission)1 ReadProjectPermission (ca.corefacility.bioinformatics.irida.security.permissions.project.ReadProjectPermission)1 ReadSamplePermission (ca.corefacility.bioinformatics.irida.security.permissions.sample.ReadSamplePermission)1 ProjectServiceImpl (ca.corefacility.bioinformatics.irida.service.impl.ProjectServiceImpl)1 SampleServiceImpl (ca.corefacility.bioinformatics.irida.service.impl.sample.SampleServiceImpl)1