#5745

Committed 25 Apr 2025 02:58PM UTC coverage: 79.365% (+0.3%) from 79.087%

Build # #5745

Build Type

push

Committed by

Commit Message

[DT-1167]Make Progress Reports Submittable (#2496)

Co-authored-by: rjohanek <rjohanek@broadinstitute.org>

Run Details

93 of 93 new or added lines in 2 files covered. (100.0%)

5 existing lines in 2 files now uncovered.

10346 of 13036 relevant lines covered (79.36%)

0.79 hits per line

Source File
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69.83

/src/main/java/org/broadinstitute/consent/http/models/DataAccessRequestData.java

package org.broadinstitute.consent.http.models;

import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.annotation.JsonInclude.Include;
import com.google.gson.Gson;
import com.google.gson.annotations.SerializedName;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import java.util.Objects;
import java.util.stream.Collectors;
import java.util.stream.Stream;

@JsonInclude(Include.NON_NULL)
public class DataAccessRequestData {

  /**
   * These properties are deprecated and should no longer be used. In many cases, they represent
   * user properties, consent related properties, deprecated properties, or duplicate existing DAR
   * fields. See <a href="https://broadworkbench.atlassian.net/browse/DUOS-728">DUOS-728</a> for
   * more info.
   */
  public static final List<String> DEPRECATED_PROPS = Arrays
      .asList("referenceId", "investigator",
          "institution", "department", "address1", "address2", "city", "zipcode", "zipCode",
          "state", "country", "researcher", "userId", "isThePi", "havePi",
          "profileName", "pubmedId", "scientificUrl", "eraExpiration", "academicEmail",
          "eraAuthorized", "nihUsername", "linkedIn", "orcid", "researcherGate", "datasetDetail",
          "datasets", "datasetId", "validRestriction", "restriction", "translatedUseRestriction",
          "createDate", "sortDate", "additionalEmail", "checkNotifications", "partialDarCode");

  @Deprecated
  private String referenceId;
  private String projectTitle;
  private Boolean checkNihDataOnly;
  private String rus;
  @SerializedName(value = "nonTechRus", alternate = "non_tech_rus")
  private String nonTechRus;
  private Boolean diseases;
  private Boolean methods;
  private Boolean controls;
  private Boolean population;
  private Boolean other;
  private String otherText;
  private List<OntologyEntry> ontologies;
  private Boolean forProfit;
  @SerializedName(value = "oneGender", alternate = "onegender")
  private Boolean oneGender;
  private String gender;
  private Boolean pediatric;
  @SerializedName(value = "illegalBehavior", alternate = "illegalbehave")
  private Boolean illegalBehavior;
  private Boolean addiction;
  @SerializedName(value = "sexualDiseases", alternate = "sexualdiseases")
  private Boolean sexualDiseases;
  @SerializedName(value = "stigmatizedDiseases", alternate = "stigmatizediseases")
  private Boolean stigmatizedDiseases;
  @SerializedName(value = "vulnerablePopulation", alternate = "vulnerablepop")
  private Boolean vulnerablePopulation;
  @SerializedName(value = "populationMigration", alternate = "popmigration")
  private Boolean populationMigration;
  @SerializedName(value = "psychiatricTraits", alternate = "psychtraits")
  private Boolean psychiatricTraits;
  @SerializedName(value = "notHealth", alternate = "nothealth")
  private Boolean notHealth;
  private Boolean hmb;
  private String status;
  private Boolean poa;
  private List<DatasetEntry> datasets;
  @SerializedName(value = "darCode", alternate = "dar_code")
  private String darCode;
  private Object restriction;
  @SerializedName(value = "validRestriction", alternate = "valid_restriction")
  private Boolean validRestriction;
  @Deprecated
  private Long createDate;
  @Deprecated
  private Long sortDate;
  @Deprecated
  @SerializedName(value = "datasetIds", alternate = {"datasetId", "datasetid"})
  private List<Integer> datasetIds;

  // Progress Report/Closeout Fields
  private String progressReportSummary;
  private String intellectualPropertySummary;
  private List<Publication> publications;
  private List<Presentation> presentations;
  private DataManagementIncident dmi;
  private String researchPlans;
  private CloseoutSupplement closeoutSupplement;

  private Boolean anvilUse;
  private Boolean cloudUse;
  private Boolean localUse;
  private String cloudProvider;
  private String cloudProviderType;
  private String cloudProviderDescription;
  private Boolean geneticStudiesOnly;
  private Boolean irb;
  private String irbDocumentLocation;
  private String irbDocumentName;
  private String irbProtocolExpiration;
  private String itDirector;
  private String itDirectorEmail;
  private String signingOfficial;
  private String signingOfficialEmail;
  private Boolean publication;
  private Boolean collaboration;
  private String collaborationLetterLocation;
  private String collaborationLetterName;
  private Boolean forensicActivities;
  private Boolean sharingDistribution;
  private List<Collaborator> labCollaborators;
  private List<Collaborator> internalCollaborators;
  private List<Collaborator> externalCollaborators;
  private Boolean dsAcknowledgement;
  private Boolean gsoAcknowledgement;
  private Boolean pubAcknowledgement;
  private String piName;
  private String piEmail;

  @Override
  public String toString() {
    return new Gson().toJson(this);
  }

  public static DataAccessRequestData fromString(String jsonString) {
    DataAccessRequestData data = new Gson().fromJson(jsonString, DataAccessRequestData.class);
    validateOntologyEntries(data);
    return data;
  }

  public String getReferenceId() {
    return referenceId;
  }

  public void setReferenceId(String referenceId) {
    this.referenceId = referenceId;
  }

  public String getProjectTitle() {
    return projectTitle;
  }

  public void setProjectTitle(String projectTitle) {
    this.projectTitle = projectTitle;
  }

  public Boolean getCheckNihDataOnly() {
    return checkNihDataOnly;
  }

  public void setCheckNihDataOnly(Boolean checkNihDataOnly) {
    this.checkNihDataOnly = checkNihDataOnly;
  }

  public String getRus() {
    return rus;
  }

  public void setRus(String rus) {
    this.rus = rus;
  }

  public String getNonTechRus() {
    return nonTechRus;
  }

  public void setNonTechRus(String nonTechRus) {
    this.nonTechRus = nonTechRus;
  }

  public Boolean getDiseases() {
    return diseases;
  }

  public void setDiseases(Boolean diseases) {
    this.diseases = diseases;
  }

  public Boolean getMethods() {
    return methods;
  }

  public void setMethods(Boolean methods) {
    this.methods = methods;
  }

  public Boolean getControls() {
    return controls;
  }

  public void setControls(Boolean controls) {
    this.controls = controls;
  }

  public Boolean getPopulation() {
    return population;
  }

  public void setPopulation(Boolean population) {
    this.population = population;
  }

  public Boolean getOther() {
    return other;
  }

  public void setOther(Boolean other) {
    this.other = other;
  }

  public String getOtherText() {
    return otherText;
  }

  public void setOtherText(String otherText) {
    this.otherText = otherText;
  }

  public List<OntologyEntry> getOntologies() {
    if (Objects.isNull(ontologies)) {
      return Collections.emptyList();
    }
    return ontologies;
  }

  public void setOntologies(List<OntologyEntry> ontologies) {
    this.ontologies = ontologies;
  }

  public Boolean getForProfit() {
    return forProfit;
  }

  public void setForProfit(Boolean forProfit) {
    this.forProfit = forProfit;
  }

  public Boolean getOneGender() {
    return oneGender;
  }

  public void setOneGender(Boolean oneGender) {
    this.oneGender = oneGender;
  }

  public String getGender() {
    return gender;
  }

  public void setGender(String gender) {
    this.gender = gender;
  }

  public Boolean getPediatric() {
    return pediatric;
  }

  public void setPediatric(Boolean pediatric) {
    this.pediatric = pediatric;
  }

  public Boolean getIllegalBehavior() {
    return illegalBehavior;
  }

  public void setIllegalBehavior(Boolean illegalBehavior) {
    this.illegalBehavior = illegalBehavior;
  }

  public Boolean getAddiction() {
    return addiction;
  }

  public void setAddiction(Boolean addiction) {
    this.addiction = addiction;
  }

  public Boolean getSexualDiseases() {
    return sexualDiseases;
  }

  public void setSexualDiseases(Boolean sexualDiseases) {
    this.sexualDiseases = sexualDiseases;
  }

  public Boolean getStigmatizedDiseases() {
    return stigmatizedDiseases;
  }

  public void setStigmatizedDiseases(Boolean stigmatizedDiseases) {
    this.stigmatizedDiseases = stigmatizedDiseases;
  }

  public Boolean getVulnerablePopulation() {
    return vulnerablePopulation;
  }

  public void setVulnerablePopulation(Boolean vulnerablePopulation) {
    this.vulnerablePopulation = vulnerablePopulation;
  }

  public Boolean getPopulationMigration() {
    return populationMigration;
  }

  public void setPopulationMigration(Boolean populationMigration) {
    this.populationMigration = populationMigration;
  }

  public Boolean getPsychiatricTraits() {
    return psychiatricTraits;
  }

  public void setPsychiatricTraits(Boolean psychiatricTraits) {
    this.psychiatricTraits = psychiatricTraits;
  }

  public Boolean getNotHealth() {
    return notHealth;
  }

  public void setNotHealth(Boolean notHealth) {
    this.notHealth = notHealth;
  }

  public Boolean getHmb() {
    return hmb;
  }

  public void setHmb(Boolean hmb) {
    this.hmb = hmb;
  }

  public List<DatasetEntry> getDatasets() {
    if (Objects.isNull(datasets)) {
      return Collections.emptyList();
    }
    return datasets;
  }

  public void setDatasets(List<DatasetEntry> datasets) {
    this.datasets = datasets;
  }

  @Deprecated
  public String getDarCode() {
    return darCode;
  }

  @Deprecated
  public void setDarCode(String darCode) {
    this.darCode = darCode;
  }

  public Object getRestriction() {
    return restriction;
  }

  public void setRestriction(Object restriction) {
    this.restriction = restriction;
  }

  public Boolean getValidRestriction() {
    return validRestriction;
  }

  public void setValidRestriction(Boolean validRestriction) {
    this.validRestriction = validRestriction;
  }

  public Long getCreateDate() {
    return createDate;
  }

  public void setCreateDate(Long createDate) {
    this.createDate = createDate;
  }

  public Long getSortDate() {
    return sortDate;
  }

  public void setSortDate(Long sortDate) {
    this.sortDate = sortDate;
  }

  /**
   * Used for the initial population of datasets a DAR is associated to. Intended to be used solely
   * for simpler construction from the UI.
   *
   * @return List of dataset ids associated to the DAR.
   */
  public List<Integer> getDatasetIds() {
    if (Objects.isNull(datasetIds)) {
      return Collections.emptyList();
    }
    return datasetIds;
  }

  public String getStatus() {
    return status;
  }

  public void setStatus(String status) {
    this.status = status;
  }

  public Boolean getPoa() {
    return poa;
  }

  public void setPoa(Boolean poa) {
    this.poa = poa;
  }

  public Boolean getCloudUse() {
    return cloudUse;
  }

  public void setCloudUse(Boolean cloudUse) {
    this.cloudUse = cloudUse;
  }

  public Boolean getAnvilUse() {
    return anvilUse;
  }

  public void setAnvilUse(Boolean anvilUse) {
    this.anvilUse = anvilUse;
  }

  public String getCloudProvider() {
    return cloudProvider;
  }

  public void setCloudProvider(String cloudProvider) {
    this.cloudProvider = cloudProvider;
  }

  public String getCloudProviderType() {
    return cloudProviderType;
  }

  public void setCloudProviderType(String cloudProviderType) {
    this.cloudProviderType = cloudProviderType;
  }

  public Boolean getGeneticStudiesOnly() {
    return geneticStudiesOnly;
  }

  public void setGeneticStudiesOnly(Boolean geneticStudiesOnly) {
    this.geneticStudiesOnly = geneticStudiesOnly;
  }

  public Boolean getIrb() {
    return irb;
  }

  public void setIrb(Boolean irb) {
    this.irb = irb;
  }

  public String getIrbDocumentLocation() {
    return irbDocumentLocation;
  }

  public void setIrbDocumentLocation(String irbDocumentLocation) {
    this.irbDocumentLocation = irbDocumentLocation;
  }

  public String getIrbDocumentName() {
    return irbDocumentName;
  }

  public void setIrbDocumentName(String irbDocumentName) {
    this.irbDocumentName = irbDocumentName;
  }

  public String getIrbProtocolExpiration() {
    return irbProtocolExpiration;
  }

  public void setIrbProtocolExpiration(String irbProtocolExpiration) {
    this.irbProtocolExpiration = irbProtocolExpiration;
  }

  public Boolean getPublication() {
    return publication;
  }

  public void setPublication(Boolean publication) {
    this.publication = publication;
  }

  public Boolean getCollaboration() {
    return collaboration;
  }

  public void setCollaboration(Boolean collaboration) {
    this.collaboration = collaboration;
  }

  public String getCollaborationLetterLocation() {
    return collaborationLetterLocation;
  }

  public void setCollaborationLetterLocation(String collaborationLetterLocation) {
    this.collaborationLetterLocation = collaborationLetterLocation;
  }

  public String getCollaborationLetterName() {
    return collaborationLetterName;
  }

  public void setCollaborationLetterName(String collaborationLetterName) {
    this.collaborationLetterName = collaborationLetterName;
  }

  public Boolean getForensicActivities() {
    return forensicActivities;
  }

  public void setForensicActivities(Boolean forensicActivities) {
    this.forensicActivities = forensicActivities;
  }

  public Boolean getSharingDistribution() {
    return sharingDistribution;
  }

  public void setSharingDistribution(Boolean sharingDistribution) {
    this.sharingDistribution = sharingDistribution;
  }

  public List<Collaborator> getLabCollaborators() {
    if (Objects.isNull(labCollaborators)) {
      return Collections.emptyList();
    }
    return labCollaborators;
  }

  public void setLabCollaborators(
      List<Collaborator> labCollaborators) {
    this.labCollaborators = labCollaborators;
  }

  public List<Collaborator> getInternalCollaborators() {
    if (Objects.isNull(internalCollaborators)) {
      return Collections.emptyList();
    }
    return internalCollaborators;
  }

  public void setInternalCollaborators(
      List<Collaborator> internalCollaborators) {
    this.internalCollaborators = internalCollaborators;
  }

  public List<Collaborator> getLabAndInternalCollaborators() {
    return Stream.of(getInternalCollaborators(), getLabCollaborators())
        .flatMap(List::stream)
        .toList();
  }

  public List<Collaborator> getExternalCollaborators() {
    if (Objects.isNull(externalCollaborators)) {
      return Collections.emptyList();
    }
    return externalCollaborators;
  }

  public void setExternalCollaborators(
      List<Collaborator> externalCollaborators) {
    this.externalCollaborators = externalCollaborators;
  }

  public Boolean getLocalUse() {
    return localUse;
  }

  public void setLocalUse(Boolean localUse) {
    this.localUse = localUse;
  }

  public String getCloudProviderDescription() {
    return cloudProviderDescription;
  }

  public void setCloudProviderDescription(String cloudProviderDescription) {
    this.cloudProviderDescription = cloudProviderDescription;
  }

  public String getItDirector() {
    return itDirector;
  }

  public void setItDirector(String itDirector) {
    this.itDirector = itDirector;
  }

  public String getItDirectorEmail() {
    return itDirectorEmail;
  }

  public void setItDirectorEmail(String itDirectorEmail) {
    this.itDirectorEmail = itDirectorEmail;
  }

  public String getSigningOfficial() {
    return signingOfficial;
  }

  public void setSigningOfficial(String signingOfficial) {
    this.signingOfficial = signingOfficial;
  }

  public String getSigningOfficialEmail() {
    return signingOfficialEmail;
  }

  public void setSigningOfficialEmail(String signingOfficialEmail) {
    this.signingOfficialEmail = signingOfficialEmail;
  }

  public void setDSAcknowledgement(Boolean dsAcknowledgement) {
    this.dsAcknowledgement = dsAcknowledgement;
  }

  public Boolean getDSAcknowledgement() {
    return dsAcknowledgement;
  }

  public void setGSOAcknowledgement(Boolean gsoAcknowledgement) {
    this.gsoAcknowledgement = gsoAcknowledgement;
  }

  public Boolean getGSOAcknowledgement() {
    return gsoAcknowledgement;
  }

  public void setPubAcknowledgement(Boolean pubAcknowledgement) {
    this.pubAcknowledgement = pubAcknowledgement;
  }

  public Boolean getPubAcknowledgement() {
    return pubAcknowledgement;
  }

  public String getPiName() {
    return piName;
  }

  public void setPiName(String piName) {
    this.piName = piName;
  }

  public String getPiEmail() {
    return piEmail;
  }

  public void setPiEmail(String piEmail) {
    this.piEmail = piEmail;
  }

  // Validate all ontology entries
  private static void validateOntologyEntries(DataAccessRequestData data) {
    if (Objects.nonNull(data)
        && !data.getOntologies().isEmpty()) {
      List<OntologyEntry> filteredEntries =
          data.getOntologies().stream()
              .filter(Objects::nonNull)
              .filter(e -> Objects.nonNull(e.getId()))
              .filter(e -> Objects.nonNull(e.getLabel()))
              .collect(Collectors.toList());
      if (filteredEntries.isEmpty()) {
        data.setOntologies(Collections.emptyList());
      } else {
        data.setOntologies(filteredEntries);
      }
    }
  }

  public String getProgressReportSummary() {
    return progressReportSummary;
  }

  public void setProgressReportSummary(String progressReportSummary) {
    this.progressReportSummary = progressReportSummary;
  }

  public String getIntellectualPropertySummary() {
    return intellectualPropertySummary;
  }

  public void setIntellectualPropertySummary(String intellectualPropertySummary) {
    this.intellectualPropertySummary = intellectualPropertySummary;
  }

  public List<Publication> getPublications() {
    return publications;
  }

  public void setPublications(
      List<Publication> publications) {
    this.publications = publications;
  }

  public List<Presentation> getPresentations() {
    return presentations;
  }

  public void setPresentations(
      List<Presentation> presentations) {
    this.presentations = presentations;
  }

  public DataManagementIncident getDmi() {
    return dmi;
  }

  public void setDmi(DataManagementIncident dmi) {
    this.dmi = dmi;
  }

  public String getResearchPlans() {
    return researchPlans;
  }

  public void setResearchPlans(String researchPlans) {
    this.researchPlans = researchPlans;
  }

  public CloseoutSupplement getCloseoutSupplement() {
    return closeoutSupplement;
  }

  public void setCloseoutSupplement(
      CloseoutSupplement closeoutSupplement) {
    this.closeoutSupplement = closeoutSupplement;
  }
}

1	package org.broadinstitute.consent.http.models;
2
3	import com.fasterxml.jackson.annotation.JsonInclude;
4	import com.fasterxml.jackson.annotation.JsonInclude.Include;
5	import com.google.gson.Gson;
6	import com.google.gson.annotations.SerializedName;
7	import java.util.Arrays;
8	import java.util.Collections;
9	import java.util.List;
10	import java.util.Objects;
11	import java.util.stream.Collectors;
12	import java.util.stream.Stream;
13
14	@JsonInclude(Include.NON_NULL)
15	public class DataAccessRequestData {	1✔
16
17	/**
18	* These properties are deprecated and should no longer be used. In many cases, they represent
19	* user properties, consent related properties, deprecated properties, or duplicate existing DAR
20	* fields. See <a href="https://broadworkbench.atlassian.net/browse/DUOS-728">DUOS-728</a> for
21	* more info.
22	*/
23	public static final List<String> DEPRECATED_PROPS = Arrays	1✔
24	.asList("referenceId", "investigator",	1✔
25	"institution", "department", "address1", "address2", "city", "zipcode", "zipCode",
26	"state", "country", "researcher", "userId", "isThePi", "havePi",
27	"profileName", "pubmedId", "scientificUrl", "eraExpiration", "academicEmail",
28	"eraAuthorized", "nihUsername", "linkedIn", "orcid", "researcherGate", "datasetDetail",
29	"datasets", "datasetId", "validRestriction", "restriction", "translatedUseRestriction",
30	"createDate", "sortDate", "additionalEmail", "checkNotifications", "partialDarCode");
31
32	@Deprecated
33	private String referenceId;
34	private String projectTitle;
35	private Boolean checkNihDataOnly;
36	private String rus;
37	@SerializedName(value = "nonTechRus", alternate = "non_tech_rus")
38	private String nonTechRus;
39	private Boolean diseases;
40	private Boolean methods;
41	private Boolean controls;
42	private Boolean population;
43	private Boolean other;
44	private String otherText;
45	private List<OntologyEntry> ontologies;
46	private Boolean forProfit;
47	@SerializedName(value = "oneGender", alternate = "onegender")
48	private Boolean oneGender;
49	private String gender;
50	private Boolean pediatric;
51	@SerializedName(value = "illegalBehavior", alternate = "illegalbehave")
52	private Boolean illegalBehavior;
53	private Boolean addiction;
54	@SerializedName(value = "sexualDiseases", alternate = "sexualdiseases")
55	private Boolean sexualDiseases;
56	@SerializedName(value = "stigmatizedDiseases", alternate = "stigmatizediseases")
57	private Boolean stigmatizedDiseases;
58	@SerializedName(value = "vulnerablePopulation", alternate = "vulnerablepop")
59	private Boolean vulnerablePopulation;
60	@SerializedName(value = "populationMigration", alternate = "popmigration")
61	private Boolean populationMigration;
62	@SerializedName(value = "psychiatricTraits", alternate = "psychtraits")
63	private Boolean psychiatricTraits;
64	@SerializedName(value = "notHealth", alternate = "nothealth")
65	private Boolean notHealth;
66	private Boolean hmb;
67	private String status;
68	private Boolean poa;
69	private List<DatasetEntry> datasets;
70	@SerializedName(value = "darCode", alternate = "dar_code")
71	private String darCode;
72	private Object restriction;
73	@SerializedName(value = "validRestriction", alternate = "valid_restriction")
74	private Boolean validRestriction;
75	@Deprecated
76	private Long createDate;
77	@Deprecated
78	private Long sortDate;
79	@Deprecated
80	@SerializedName(value = "datasetIds", alternate = {"datasetId", "datasetid"})
81	private List<Integer> datasetIds;
82
83	// Progress Report/Closeout Fields
84	private String progressReportSummary;
85	private String intellectualPropertySummary;
86	private List<Publication> publications;
87	private List<Presentation> presentations;
88	private DataManagementIncident dmi;
89	private String researchPlans;
90	private CloseoutSupplement closeoutSupplement;
91
92	private Boolean anvilUse;
93	private Boolean cloudUse;
94	private Boolean localUse;
95	private String cloudProvider;
96	private String cloudProviderType;
97	private String cloudProviderDescription;
98	private Boolean geneticStudiesOnly;
99	private Boolean irb;
100	private String irbDocumentLocation;
101	private String irbDocumentName;
102	private String irbProtocolExpiration;
103	private String itDirector;
104	private String itDirectorEmail;
105	private String signingOfficial;
106	private String signingOfficialEmail;
107	private Boolean publication;
108	private Boolean collaboration;
109	private String collaborationLetterLocation;
110	private String collaborationLetterName;
111	private Boolean forensicActivities;
112	private Boolean sharingDistribution;
113	private List<Collaborator> labCollaborators;
114	private List<Collaborator> internalCollaborators;
115	private List<Collaborator> externalCollaborators;
116	private Boolean dsAcknowledgement;
117	private Boolean gsoAcknowledgement;
118	private Boolean pubAcknowledgement;
119	private String piName;
120	private String piEmail;
121
122	@Override
123	public String toString() {
124	return new Gson().toJson(this);	1✔
125	}
126
127	public static DataAccessRequestData fromString(String jsonString) {
128	DataAccessRequestData data = new Gson().fromJson(jsonString, DataAccessRequestData.class);	1✔
129	validateOntologyEntries(data);	1✔
130	return data;	1✔
131	}
132
133	public String getReferenceId() {
134	return referenceId;	1✔
135	}
136
137	public void setReferenceId(String referenceId) {
138	this.referenceId = referenceId;	1✔
139	}	1✔
140
141	public String getProjectTitle() {
142	return projectTitle;	1✔
143	}
144
145	public void setProjectTitle(String projectTitle) {
146	this.projectTitle = projectTitle;	1✔
147	}	1✔
148
149	public Boolean getCheckNihDataOnly() {
150	return checkNihDataOnly;	×
151	}
152
153	public void setCheckNihDataOnly(Boolean checkNihDataOnly) {
154	this.checkNihDataOnly = checkNihDataOnly;	×
155	}	×
156
157	public String getRus() {
158	return rus;	1✔
159	}
160
161	public void setRus(String rus) {
162	this.rus = rus;	1✔
163	}	1✔
164
165	public String getNonTechRus() {
166	return nonTechRus;	1✔
167	}
168
169	public void setNonTechRus(String nonTechRus) {
170	this.nonTechRus = nonTechRus;	1✔
171	}	1✔
172
173	public Boolean getDiseases() {
174	return diseases;	×
175	}
176
177	public void setDiseases(Boolean diseases) {
178	this.diseases = diseases;	1✔
179	}	1✔
180
181	public Boolean getMethods() {
182	return methods;	1✔
183	}
184
185	public void setMethods(Boolean methods) {
186	this.methods = methods;	1✔
187	}	1✔
188
189	public Boolean getControls() {
190	return controls;	1✔
191	}
192
193	public void setControls(Boolean controls) {
194	this.controls = controls;	1✔
195	}	1✔
196
197	public Boolean getPopulation() {
198	return population;	1✔
199	}
200
201	public void setPopulation(Boolean population) {
202	this.population = population;	1✔
203	}	1✔
204
205	public Boolean getOther() {
206	return other;	1✔
207	}
208
209	public void setOther(Boolean other) {
210	this.other = other;	1✔
211	}	1✔
212
213	public String getOtherText() {
214	return otherText;	1✔
215	}
216
217	public void setOtherText(String otherText) {
218	this.otherText = otherText;	1✔
219	}	1✔
220
221	public List<OntologyEntry> getOntologies() {
222	if (Objects.isNull(ontologies)) {	1✔
223	return Collections.emptyList();	1✔
224	}
225	return ontologies;	1✔
226	}
227
228	public void setOntologies(List<OntologyEntry> ontologies) {
229	this.ontologies = ontologies;	1✔
230	}	1✔
231
232	public Boolean getForProfit() {
233	return forProfit;	1✔
234	}
235
236	public void setForProfit(Boolean forProfit) {
237	this.forProfit = forProfit;	1✔
238	}	1✔
239
240	public Boolean getOneGender() {
241	return oneGender;	×
242	}
243
244	public void setOneGender(Boolean oneGender) {
245	this.oneGender = oneGender;	1✔
246	}	1✔
247
248	public String getGender() {
249	return gender;	1✔
250	}
251
252	public void setGender(String gender) {
253	this.gender = gender;	1✔
254	}	1✔
255
256	public Boolean getPediatric() {
257	return pediatric;	1✔
258	}
259
260	public void setPediatric(Boolean pediatric) {
261	this.pediatric = pediatric;	1✔
262	}	1✔
263
264	public Boolean getIllegalBehavior() {
265	return illegalBehavior;	1✔
266	}
267
268	public void setIllegalBehavior(Boolean illegalBehavior) {
269	this.illegalBehavior = illegalBehavior;	1✔
270	}	1✔
271
272	public Boolean getAddiction() {
273	return addiction;	1✔
274	}
275
276	public void setAddiction(Boolean addiction) {
277	this.addiction = addiction;	1✔
278	}	1✔
279
280	public Boolean getSexualDiseases() {
281	return sexualDiseases;	1✔
282	}
283
284	public void setSexualDiseases(Boolean sexualDiseases) {
285	this.sexualDiseases = sexualDiseases;	1✔
286	}	1✔
287
288	public Boolean getStigmatizedDiseases() {
289	return stigmatizedDiseases;	1✔
290	}
291
292	public void setStigmatizedDiseases(Boolean stigmatizedDiseases) {
293	this.stigmatizedDiseases = stigmatizedDiseases;	1✔
294	}	1✔
295
296	public Boolean getVulnerablePopulation() {
297	return vulnerablePopulation;	1✔
298	}
299
300	public void setVulnerablePopulation(Boolean vulnerablePopulation) {
301	this.vulnerablePopulation = vulnerablePopulation;	1✔
302	}	1✔
303
304	public Boolean getPopulationMigration() {
305	return populationMigration;	1✔
306	}
307
308	public void setPopulationMigration(Boolean populationMigration) {
309	this.populationMigration = populationMigration;	1✔
310	}	1✔
311
312	public Boolean getPsychiatricTraits() {
313	return psychiatricTraits;	1✔
314	}
315
316	public void setPsychiatricTraits(Boolean psychiatricTraits) {
317	this.psychiatricTraits = psychiatricTraits;	1✔
318	}	1✔
319
320	public Boolean getNotHealth() {
321	return notHealth;	1✔
322	}
323
324	public void setNotHealth(Boolean notHealth) {
325	this.notHealth = notHealth;	1✔
326	}	1✔
327
328	public Boolean getHmb() {
329	return hmb;	1✔
330	}
331
332	public void setHmb(Boolean hmb) {
333	this.hmb = hmb;	1✔
334	}	1✔
335
336	public List<DatasetEntry> getDatasets() {
337	if (Objects.isNull(datasets)) {	×
338	return Collections.emptyList();	×
339	}
340	return datasets;	×
341	}
342
343	public void setDatasets(List<DatasetEntry> datasets) {
344	this.datasets = datasets;	1✔
345	}	1✔
346
347	@Deprecated
348	public String getDarCode() {
349	return darCode;	×
350	}
351
352	@Deprecated
353	public void setDarCode(String darCode) {
354	this.darCode = darCode;	1✔
355	}	1✔
356
357	public Object getRestriction() {
358	return restriction;	1✔
359	}
360
361	public void setRestriction(Object restriction) {
362	this.restriction = restriction;	×
363	}	×
364
365	public Boolean getValidRestriction() {
366	return validRestriction;	1✔
367	}
368
369	public void setValidRestriction(Boolean validRestriction) {
370	this.validRestriction = validRestriction;	1✔
371	}	1✔
372
373	public Long getCreateDate() {
UNCOV 374	return createDate;	×
375	}
376
377	public void setCreateDate(Long createDate) {
378	this.createDate = createDate;	1✔
379	}	1✔
380
381	public Long getSortDate() {
UNCOV 382	return sortDate;	×
383	}
384
385	public void setSortDate(Long sortDate) {
UNCOV 386	this.sortDate = sortDate;	×
UNCOV 387	}	×
388
389	/**
390	* Used for the initial population of datasets a DAR is associated to. Intended to be used solely
391	* for simpler construction from the UI.
392	*
393	* @return List of dataset ids associated to the DAR.
394	*/
395	public List<Integer> getDatasetIds() {
396	if (Objects.isNull(datasetIds)) {	1✔
397	return Collections.emptyList();	1✔
398	}
399	return datasetIds;	1✔
400	}
401
402	public String getStatus() {
403	return status;	1✔
404	}
405
406	public void setStatus(String status) {
407	this.status = status;	1✔
408	}	1✔
409
410	public Boolean getPoa() {
411	return poa;	1✔
412	}
413
414	public void setPoa(Boolean poa) {
415	this.poa = poa;	1✔
416	}	1✔
417
418	public Boolean getCloudUse() {
419	return cloudUse;	×
420	}
421
422	public void setCloudUse(Boolean cloudUse) {
423	this.cloudUse = cloudUse;	1✔
424	}	1✔
425
426	public Boolean getAnvilUse() {
427	return anvilUse;	×
428	}
429
430	public void setAnvilUse(Boolean anvilUse) {
431	this.anvilUse = anvilUse;	1✔
432	}	1✔
433
434	public String getCloudProvider() {
435	return cloudProvider;	×
436	}
437
438	public void setCloudProvider(String cloudProvider) {
439	this.cloudProvider = cloudProvider;	1✔
440	}	1✔
441
442	public String getCloudProviderType() {
443	return cloudProviderType;	×
444	}
445
446	public void setCloudProviderType(String cloudProviderType) {
447	this.cloudProviderType = cloudProviderType;	×
448	}	×
449
450	public Boolean getGeneticStudiesOnly() {
451	return geneticStudiesOnly;	×
452	}
453
454	public void setGeneticStudiesOnly(Boolean geneticStudiesOnly) {
455	this.geneticStudiesOnly = geneticStudiesOnly;	×
456	}	×
457
458	public Boolean getIrb() {
459	return irb;	×
460	}
461
462	public void setIrb(Boolean irb) {
463	this.irb = irb;	×
464	}	×
465
466	public String getIrbDocumentLocation() {
467	return irbDocumentLocation;	1✔
468	}
469
470	public void setIrbDocumentLocation(String irbDocumentLocation) {
471	this.irbDocumentLocation = irbDocumentLocation;	1✔
472	}	1✔
473
474	public String getIrbDocumentName() {
475	return irbDocumentName;	1✔
476	}
477
478	public void setIrbDocumentName(String irbDocumentName) {
479	this.irbDocumentName = irbDocumentName;	1✔
480	}	1✔
481
482	public String getIrbProtocolExpiration() {
483	return irbProtocolExpiration;	×
484	}
485
486	public void setIrbProtocolExpiration(String irbProtocolExpiration) {
487	this.irbProtocolExpiration = irbProtocolExpiration;	×
488	}	×
489
490	public Boolean getPublication() {
491	return publication;	×
492	}
493
494	public void setPublication(Boolean publication) {
495	this.publication = publication;	×
496	}	×
497
498	public Boolean getCollaboration() {
499	return collaboration;	×
500	}
501
502	public void setCollaboration(Boolean collaboration) {
503	this.collaboration = collaboration;	×
504	}	×
505
506	public String getCollaborationLetterLocation() {
507	return collaborationLetterLocation;	1✔
508	}
509
510	public void setCollaborationLetterLocation(String collaborationLetterLocation) {
511	this.collaborationLetterLocation = collaborationLetterLocation;	1✔
512	}	1✔
513
514	public String getCollaborationLetterName() {
515	return collaborationLetterName;	1✔
516	}
517
518	public void setCollaborationLetterName(String collaborationLetterName) {
519	this.collaborationLetterName = collaborationLetterName;	1✔
520	}	1✔
521
522	public Boolean getForensicActivities() {
523	return forensicActivities;	×
524	}
525
526	public void setForensicActivities(Boolean forensicActivities) {
527	this.forensicActivities = forensicActivities;	×
528	}	×
529
530	public Boolean getSharingDistribution() {
531	return sharingDistribution;	×
532	}
533
534	public void setSharingDistribution(Boolean sharingDistribution) {
535	this.sharingDistribution = sharingDistribution;	×
536	}	×
537
538	public List<Collaborator> getLabCollaborators() {
539	if (Objects.isNull(labCollaborators)) {	1✔
540	return Collections.emptyList();	1✔
541	}
542	return labCollaborators;	1✔
543	}
544
545	public void setLabCollaborators(
546	List<Collaborator> labCollaborators) {
547	this.labCollaborators = labCollaborators;	1✔
548	}	1✔
549
550	public List<Collaborator> getInternalCollaborators() {
551	if (Objects.isNull(internalCollaborators)) {	1✔
552	return Collections.emptyList();	1✔
553	}
554	return internalCollaborators;	1✔
555	}
556
557	public void setInternalCollaborators(
558	List<Collaborator> internalCollaborators) {
559	this.internalCollaborators = internalCollaborators;	1✔
560	}	1✔
561
562	public List<Collaborator> getLabAndInternalCollaborators() {
563	return Stream.of(getInternalCollaborators(), getLabCollaborators())	1✔
564	.flatMap(List::stream)	1✔
565	.toList();	1✔
566	}
567
568	public List<Collaborator> getExternalCollaborators() {
569	if (Objects.isNull(externalCollaborators)) {	1✔
570	return Collections.emptyList();	1✔
571	}
572	return externalCollaborators;	1✔
573	}
574
575	public void setExternalCollaborators(
576	List<Collaborator> externalCollaborators) {
577	this.externalCollaborators = externalCollaborators;	1✔
578	}	1✔
579
580	public Boolean getLocalUse() {
581	return localUse;	×
582	}
583
584	public void setLocalUse(Boolean localUse) {
585	this.localUse = localUse;	×
586	}	×
587
588	public String getCloudProviderDescription() {
589	return cloudProviderDescription;	×
590	}
591
592	public void setCloudProviderDescription(String cloudProviderDescription) {
593	this.cloudProviderDescription = cloudProviderDescription;	1✔
594	}	1✔
595
596	public String getItDirector() {
597	return itDirector;	×
598	}
599
600	public void setItDirector(String itDirector) {
601	this.itDirector = itDirector;	×
602	}	×
603
604	public String getItDirectorEmail() {
605	return itDirectorEmail;	1✔
606	}
607
608	public void setItDirectorEmail(String itDirectorEmail) {
609	this.itDirectorEmail = itDirectorEmail;	1✔
610	}	1✔
611
612	public String getSigningOfficial() {
613	return signingOfficial;	×
614	}
615
616	public void setSigningOfficial(String signingOfficial) {
617	this.signingOfficial = signingOfficial;	×
618	}	×
619
620	public String getSigningOfficialEmail() {
621	return signingOfficialEmail;	1✔
622	}
623
624	public void setSigningOfficialEmail(String signingOfficialEmail) {
625	this.signingOfficialEmail = signingOfficialEmail;	1✔
626	}	1✔
627
628	public void setDSAcknowledgement(Boolean dsAcknowledgement) {
629	this.dsAcknowledgement = dsAcknowledgement;	×
630	}	×
631
632	public Boolean getDSAcknowledgement() {
633	return dsAcknowledgement;	×
634	}
635
636	public void setGSOAcknowledgement(Boolean gsoAcknowledgement) {
637	this.gsoAcknowledgement = gsoAcknowledgement;	×
638	}	×
639
640	public Boolean getGSOAcknowledgement() {
641	return gsoAcknowledgement;	×
642	}
643
644	public void setPubAcknowledgement(Boolean pubAcknowledgement) {
645	this.pubAcknowledgement = pubAcknowledgement;	×
646	}	×
647
648	public Boolean getPubAcknowledgement() {
649	return pubAcknowledgement;	×
650	}
651
652	public String getPiName() {
653	return piName;	×
654	}
655
656	public void setPiName(String piName) {
657	this.piName = piName;	×
658	}	×
659
660	public String getPiEmail() {
661	return piEmail;	1✔
662	}
663
664	public void setPiEmail(String piEmail) {
665	this.piEmail = piEmail;	1✔
666	}	1✔
667
668	// Validate all ontology entries
669	private static void validateOntologyEntries(DataAccessRequestData data) {
670	if (Objects.nonNull(data)	1✔
671	&& !data.getOntologies().isEmpty()) {	1✔
672	List<OntologyEntry> filteredEntries =	×
673	data.getOntologies().stream()	×
674	.filter(Objects::nonNull)	×
675	.filter(e -> Objects.nonNull(e.getId()))	×
676	.filter(e -> Objects.nonNull(e.getLabel()))	×
677	.collect(Collectors.toList());	×
678	if (filteredEntries.isEmpty()) {	×
679	data.setOntologies(Collections.emptyList());	×
680	} else {
681	data.setOntologies(filteredEntries);	×
682	}
683	}
684	}	1✔
685
686	public String getProgressReportSummary() {
687	return progressReportSummary;	1✔
688	}
689
690	public void setProgressReportSummary(String progressReportSummary) {
691	this.progressReportSummary = progressReportSummary;	1✔
692	}	1✔
693
694	public String getIntellectualPropertySummary() {
695	return intellectualPropertySummary;	1✔
696	}
697
698	public void setIntellectualPropertySummary(String intellectualPropertySummary) {
699	this.intellectualPropertySummary = intellectualPropertySummary;	1✔
700	}	1✔
701
702	public List<Publication> getPublications() {
703	return publications;	1✔
704	}
705
706	public void setPublications(
707	List<Publication> publications) {
708	this.publications = publications;	1✔
709	}	1✔
710
711	public List<Presentation> getPresentations() {
712	return presentations;	1✔
713	}
714
715	public void setPresentations(
716	List<Presentation> presentations) {
717	this.presentations = presentations;	1✔
718	}	1✔
719
720	public DataManagementIncident getDmi() {
721	return dmi;	1✔
722	}
723
724	public void setDmi(DataManagementIncident dmi) {
725	this.dmi = dmi;	1✔
726	}	1✔
727
728	public String getResearchPlans() {
729	return researchPlans;	1✔
730	}
731
732	public void setResearchPlans(String researchPlans) {
733	this.researchPlans = researchPlans;	1✔
734	}	1✔
735
736	public CloseoutSupplement getCloseoutSupplement() {
737	return closeoutSupplement;	1✔
738	}
739
740	public void setCloseoutSupplement(
741	CloseoutSupplement closeoutSupplement) {
742	this.closeoutSupplement = closeoutSupplement;	1✔
743	}	1✔
744	}

DataBiosphere / consent / #5745

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