Examples with Study uk.ac.ebi.spot.goci.model.Study used on opensource projects

Example 51 with Study

use of uk.ac.ebi.spot.goci.model.Study in project goci by EBISPOT.

the class StudyNoteOperationsService method updateDuplicatedNote.

public void updateDuplicatedNote(StudyNote copiedNote, SecureUser user) {
    String body = copiedNote.getTextNote();
    Curator curator = curatorService.getCuratorIdByEmail(user.getEmail());
    Study sourceStudy = copiedNote.getStudy();
    copiedNote.setTextNote(body.concat("\n").concat("Duplicated to other studies with Pubmed ID ").concat(sourceStudy.getPublicationId().getPubmedId()).concat(" by ").concat(curator.getLastName()));
    studyNoteService.saveStudyNote(copiedNote);
}

Example 52 with Study

use of uk.ac.ebi.spot.goci.model.Study in project goci by EBISPOT.

the class AssociationControllerTest method addMultiSnpsWithNoErrors.

// @Test
// public void addMultiSnpsWithErrors() throws Exception {
// AssociationValidationView associationValidationView =
// new AssociationValidationView("OR", "Value is empty", false);
// List<AssociationValidationView> errors = Collections.singletonList(associationValidationView);
// 
// // Stubbing
// when(studyRepository.findOne(Matchers.anyLong())).thenReturn(STUDY);
// when(currentUserDetailsService.getUserFromRequest(Matchers.any(HttpServletRequest.class))).thenReturn(
// SECURE_USER);
// when(associationOperationsService.checkSnpAssociationFormErrors(Matchers.any(SnpAssociationStandardMultiForm.class),
// Matchers.anyString()))
// .thenReturn(Collections.EMPTY_LIST);
// when(singleSnpMultiSnpAssociationService.createAssociation(Matchers.any(SnpAssociationStandardMultiForm.class)))
// .thenReturn(ASSOCIATION);
// when(associationOperationsService.saveAssociationCreatedFromForm(STUDY, ASSOCIATION, SECURE_USER, "")).thenReturn(
// errors);
// 
// mockMvc.perform(post("/studies/1234/associations/add_multi").param("measurementType", "or"))
// .andExpect(status().isOk())
// .andExpect(model().attribute("form", instanceOf(SnpAssociationStandardMultiForm.class)))
// .andExpect(model().attribute("errors", instanceOf(List.class)))
// .andExpect(model().attribute("errors", hasSize(1)))
// .andExpect(model().attributeExists("study"))
// .andExpect(model().attributeExists("measurementType"))
// .andExpect(view().name("add_multi_snp_association"));
// 
// //verify properties of bound object
// ArgumentCaptor<SnpAssociationStandardMultiForm> formArgumentCaptor =
// ArgumentCaptor.forClass(SnpAssociationStandardMultiForm.class);
// verify(associationOperationsService).checkSnpAssociationFormErrors(formArgumentCaptor.capture(),
// Matchers.anyString());
// verify(singleSnpMultiSnpAssociationService).createAssociation(formArgumentCaptor.capture());
// verify(studyRepository, times(1)).findOne(Matchers.anyLong());
// verify(currentUserDetailsService, times(1)).getUserFromRequest(Matchers.any(HttpServletRequest.class));
// verify(associationOperationsService, times(1)).saveAssociationCreatedFromForm(Matchers.any(Study.class),
// Matchers.any(Association.class),
// Matchers.any(SecureUser.class),
// Matchers.anyString());
// }
@Test
public void addMultiSnpsWithNoErrors() throws Exception {
    AssociationValidationView associationValidationView = new AssociationValidationView("SNP", "SNP identifier rs34tt is not valid", true);
    List<AssociationValidationView> errors = Collections.singletonList(associationValidationView);
    // Stubbing
    when(studyRepository.findOne(Matchers.anyLong())).thenReturn(STUDY);
    when(currentUserDetailsService.getUserFromRequest(Matchers.any(HttpServletRequest.class))).thenReturn(SECURE_USER);
    when(associationOperationsService.checkSnpAssociationFormErrors(Matchers.any(SnpAssociationStandardMultiForm.class), Matchers.anyString())).thenReturn(Collections.EMPTY_LIST);
    when(singleSnpMultiSnpAssociationService.createAssociation(Matchers.any(SnpAssociationStandardMultiForm.class))).thenReturn(ASSOCIATION);
    when(associationOperationsService.saveAssociationCreatedFromForm(STUDY, ASSOCIATION, SECURE_USER, "")).thenReturn(errors);
    mockMvc.perform(post("/studies/1234/associations/add_multi").param("measurementType", "or")).andExpect(status().is3xxRedirection()).andExpect(model().attributeExists("study")).andExpect(model().attributeExists("measurementType")).andExpect(view().name("redirect:/associations/100"));
    // verify properties of bound object
    ArgumentCaptor<SnpAssociationStandardMultiForm> formArgumentCaptor = ArgumentCaptor.forClass(SnpAssociationStandardMultiForm.class);
    verify(associationOperationsService).checkSnpAssociationFormErrors(formArgumentCaptor.capture(), Matchers.anyString());
    verify(singleSnpMultiSnpAssociationService).createAssociation(formArgumentCaptor.capture());
    verify(studyRepository, times(1)).findOne(Matchers.anyLong());
    verify(currentUserDetailsService, times(1)).getUserFromRequest(Matchers.any(HttpServletRequest.class));
    verify(associationOperationsService, times(1)).saveAssociationCreatedFromForm(Matchers.any(Study.class), Matchers.any(Association.class), Matchers.any(SecureUser.class), Matchers.anyString());
}

Example 53 with Study

use of uk.ac.ebi.spot.goci.model.Study in project goci by EBISPOT.

the class AssociationControllerTest method addMultiSnpsWithRowErrors.

@Test
public void addMultiSnpsWithRowErrors() throws Exception {
    AssociationValidationView associationValidationView = new AssociationValidationView("SNP", "Value is empty", false);
    List<AssociationValidationView> errors = Collections.singletonList(associationValidationView);
    // Stubbing
    when(studyRepository.findOne(Matchers.anyLong())).thenReturn(STUDY);
    when(associationOperationsService.checkSnpAssociationFormErrors(Matchers.any(SnpAssociationStandardMultiForm.class), Matchers.anyString())).thenReturn(errors);
    mockMvc.perform(post("/studies/1234/associations/add_multi").param("measurementType", "or")).andExpect(status().isOk()).andExpect(model().attribute("form", instanceOf(SnpAssociationStandardMultiForm.class))).andExpect(model().attribute("errors", instanceOf(List.class))).andExpect(model().attribute("errors", hasSize(1))).andExpect(model().attributeExists("study")).andExpect(model().attributeExists("measurementType")).andExpect(view().name("add_multi_snp_association"));
    // verify properties of bound object
    ArgumentCaptor<SnpAssociationStandardMultiForm> formArgumentCaptor = ArgumentCaptor.forClass(SnpAssociationStandardMultiForm.class);
    verify(associationOperationsService).checkSnpAssociationFormErrors(formArgumentCaptor.capture(), Matchers.anyString());
    verify(studyRepository, times(1)).findOne(Matchers.anyLong());
    verifyZeroInteractions(singleSnpMultiSnpAssociationService);
    verifyZeroInteractions(currentUserDetailsService);
    verify(associationOperationsService, never()).saveAssociationCreatedFromForm(Matchers.any(Study.class), Matchers.any(Association.class), Matchers.any(SecureUser.class), Matchers.anyString());
}

Example 54 with Study

use of uk.ac.ebi.spot.goci.model.Study in project goci by EBISPOT.

the class AssociationControllerTest method addSnpInteractionsWithNoErrors.

// @Test
// public void addSnpInteractionWithErrors() throws Exception {
// AssociationValidationView associationValidationView =
// new AssociationValidationView("OR", "Value is empty", false);
// List<AssociationValidationView> errors = Collections.singletonList(associationValidationView);
// 
// // Stubbing
// when(studyRepository.findOne(Matchers.anyLong())).thenReturn(STUDY);
// when(currentUserDetailsService.getUserFromRequest(Matchers.any(HttpServletRequest.class))).thenReturn(
// SECURE_USER);
// when(associationOperationsService.checkSnpAssociationInteractionFormErrors(Matchers.any(
// SnpAssociationInteractionForm.class), Matchers.anyString()))
// .thenReturn(Collections.EMPTY_LIST);
// when(snpInteractionAssociationService.createAssociation(Matchers.any(SnpAssociationInteractionForm.class)))
// .thenReturn(ASSOCIATION);
// when(associationOperationsService.saveAssociationCreatedFromForm(STUDY, ASSOCIATION, SECURE_USER,"")).thenReturn(
// errors);
// 
// mockMvc.perform(post("/studies/1234/associations/add_interaction").param("measurementType", "or"))
// .andExpect(status().isOk())
// .andExpect(model().attribute("form", instanceOf(SnpAssociationInteractionForm.class)))
// .andExpect(model().attribute("errors", instanceOf(List.class)))
// .andExpect(model().attribute("errors", hasSize(1)))
// .andExpect(model().attributeExists("study"))
// .andExpect(model().attributeExists("measurementType"))
// .andExpect(view().name("add_snp_interaction_association"));
// 
// //verify properties of bound object
// ArgumentCaptor<SnpAssociationInteractionForm> formArgumentCaptor =
// ArgumentCaptor.forClass(SnpAssociationInteractionForm.class);
// verify(associationOperationsService).checkSnpAssociationInteractionFormErrors(formArgumentCaptor.capture(),
// Matchers.anyString());
// verify(snpInteractionAssociationService).createAssociation(formArgumentCaptor.capture());
// verify(studyRepository, times(1)).findOne(Matchers.anyLong());
// verify(currentUserDetailsService, times(1)).getUserFromRequest(Matchers.any(HttpServletRequest.class));
// verify(associationOperationsService, times(1)).saveAssociationCreatedFromForm(Matchers.any(Study.class),
// Matchers.any(Association.class),
// Matchers.any(SecureUser.class),
// Matchers.anyString());
// }
@Test
public void addSnpInteractionsWithNoErrors() throws Exception {
    AssociationValidationView associationValidationView = new AssociationValidationView("SNP", "SNP identifier rs34tt is not valid", true);
    List<AssociationValidationView> errors = Collections.singletonList(associationValidationView);
    // Stubbing
    when(studyRepository.findOne(Matchers.anyLong())).thenReturn(STUDY);
    when(currentUserDetailsService.getUserFromRequest(Matchers.any(HttpServletRequest.class))).thenReturn(SECURE_USER);
    when(associationOperationsService.checkSnpAssociationInteractionFormErrors(Matchers.any(SnpAssociationInteractionForm.class), Matchers.anyString())).thenReturn(Collections.EMPTY_LIST);
    when(snpInteractionAssociationService.createAssociation(Matchers.any(SnpAssociationInteractionForm.class))).thenReturn(ASSOCIATION);
    when(associationOperationsService.saveAssociationCreatedFromForm(STUDY, ASSOCIATION, SECURE_USER, "")).thenReturn(errors);
    mockMvc.perform(post("/studies/1234/associations/add_interaction").param("measurementType", "or")).andExpect(status().is3xxRedirection()).andExpect(model().attributeExists("study")).andExpect(model().attributeExists("measurementType")).andExpect(view().name("redirect:/associations/100"));
    // verify properties of bound object
    ArgumentCaptor<SnpAssociationInteractionForm> formArgumentCaptor = ArgumentCaptor.forClass(SnpAssociationInteractionForm.class);
    verify(associationOperationsService).checkSnpAssociationInteractionFormErrorsForView(formArgumentCaptor.capture(), Matchers.anyString());
    verify(snpInteractionAssociationService).createAssociation(formArgumentCaptor.capture());
    verify(studyRepository, times(1)).findOne(Matchers.anyLong());
    verify(currentUserDetailsService, times(1)).getUserFromRequest(Matchers.any(HttpServletRequest.class));
    verify(associationOperationsService, times(1)).saveAssociationCreatedFromForm(Matchers.any(Study.class), Matchers.any(Association.class), Matchers.any(SecureUser.class), Matchers.anyString());
}

Example 55 with Study

use of uk.ac.ebi.spot.goci.model.Study in project goci by EBISPOT.

the class AncestryController method viewStudySampleDescription.

/* Ancestry/Sample information associated with a study */
// Generate view of ancestry/sample information linked to a study
@RequestMapping(value = "/studies/{studyId}/sampledescription", produces = MediaType.TEXT_HTML_VALUE, method = RequestMethod.GET)
public String viewStudySampleDescription(Model model, @PathVariable Long studyId) {
    // Two types of ancestry information which the view needs to form two different tables
    Collection<Ancestry> initialStudyAncestryDescriptions = new ArrayList<>();
    Collection<Ancestry> replicationStudyAncestryDescriptions = new ArrayList<>();
    String initialType = "initial";
    String replicationType = "replication";
    initialStudyAncestryDescriptions.addAll(ancestryRepository.findByStudyIdAndType(studyId, initialType));
    replicationStudyAncestryDescriptions.addAll(ancestryRepository.findByStudyIdAndType(studyId, replicationType));
    Collection<Ancestry> allAncestry = new ArrayList<>();
    allAncestry.addAll(initialStudyAncestryDescriptions);
    allAncestry.addAll(replicationStudyAncestryDescriptions);
    for (Ancestry ancestry : allAncestry) {
        if (ancestry.getCountryOfRecruitment() == null || ancestry.getCountryOfRecruitment().isEmpty()) {
            String message = "No country of recruitment recorded for at least one ancestry entry!";
            model.addAttribute("noCountryRecruitment", message);
            break;
        }
    }
    // Add all ancestry/sample information for the study to our model
    model.addAttribute("initialStudyAncestryDescriptions", initialStudyAncestryDescriptions);
    model.addAttribute("replicationStudyAncestryDescriptions", replicationStudyAncestryDescriptions);
    // Return an empty ancestry object so curators can add new ancestry/sample information to study
    model.addAttribute("ancestry", new Ancestry());
    // Return an SampleDescription object for each type
    Study study = studyRepository.findOne(studyId);
    if (study.getInitialSampleSize() != null && !study.getInitialSampleSize().isEmpty()) {
        InitialSampleDescription initialSampleDescription = new InitialSampleDescription();
        initialSampleDescription.setInitialSampleDescription(study.getInitialSampleSize());
        model.addAttribute("initialSampleDescription", initialSampleDescription);
    } else {
        model.addAttribute("initialSampleDescription", new InitialSampleDescription());
    }
    if (study.getReplicateSampleSize() != null && !study.getReplicateSampleSize().isEmpty()) {
        ReplicationSampleDescription replicationSampleDescription = new ReplicationSampleDescription();
        replicationSampleDescription.setReplicationSampleDescription(study.getReplicateSampleSize());
        model.addAttribute("replicationSampleDescription", replicationSampleDescription);
    } else {
        model.addAttribute("replicationSampleDescription", new ReplicationSampleDescription());
    }
    // Also passes back study object to view so we can create links back to main study page
    model.addAttribute("study", study);
    return "study_sample_description";
}