DT-2302: WIP: Convert Draft Study/Dataset to Study with Datasets

src/main/java/org/broadinstitute/consent/http/models/draft/AccessManagement.java

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+package org.broadinstitute.consent.http.models.draft;
+
+public enum AccessManagement {
+  OPEN("open"),
+  CONTROLLED("controlled"),
+  EXTERNAL("external");
+  private final String value;
+
+  AccessManagement(String value) {
+    this.value = value;
+  }
+
+  @Override
+  public String toString() {
+    return this.value;
+  }
+
+  public String value() {
+    return this.value;
+  }
+
+}

src/main/java/org/broadinstitute/consent/http/models/draft/AlternativeDataSharingPlanAccessManagement.java

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+package org.broadinstitute.consent.http.models.draft;
+
+public enum AlternativeDataSharingPlanAccessManagement {
+  CONTROLLED_ACCESS("Controlled Access"),
+  OPEN_ACCESS("Open Access"),
+  EXTERNAL_ACCESS("External Access");
+  private final String value;
+
+  AlternativeDataSharingPlanAccessManagement(String value) {
+    this.value = value;
+  }
+
+  @Override
+  public String toString() {
+    return this.value;
+  }
+
+  public String value() {
+    return this.value;
+  }
+
+}

src/main/java/org/broadinstitute/consent/http/models/draft/AlternativeDataSharingPlanDataSubmitted.java

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+package org.broadinstitute.consent.http.models.draft;
+
+public enum AlternativeDataSharingPlanDataSubmitted {
+
+  WITHIN_3_MONTHS_OF_THE_LAST_DATA_GENERATED_OR_LAST_CLINICAL_VISIT(
+      "Within 3 months of the last data generated or last clinical visit"),
+  BY_BATCHES_OVER_STUDY_TIMELINE_E_G_BASED_ON_CLINICAL_TRIAL_ENROLLMENT_BENCHMARKS(
+      "By batches over Study Timeline (e.g. based on clinical trial enrollment benchmarks)");
+  private final String value;
+
+  AlternativeDataSharingPlanDataSubmitted(String value) {
+    this.value = value;
+  }
+
+  @Override
+  public String toString() {
+    return this.value;
+  }
+
+  public String value() {
+    return this.value;
+  }
+
+}

src/main/java/org/broadinstitute/consent/http/models/draft/AlternativeDataSharingPlanReason.java

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+package org.broadinstitute.consent.http.models.draft;
+
+public enum AlternativeDataSharingPlanReason {
+
+  LEGAL_RESTRICTIONS("Legal Restrictions"),
+  INFORMED_CONSENT_PROCESSES_ARE_INADEQUATE_TO_SUPPORT_DATA_FOR_SHARING_FOR_THE_FOLLOWING_REASONS(
+      "Informed consent processes are inadequate to support data for sharing for the following reasons:"),
+  THE_CONSENT_FORMS_ARE_UNAVAILABLE_OR_NON_EXISTENT_FOR_SAMPLES_COLLECTED_AFTER_JANUARY_25_2015(
+      "The consent forms are unavailable or non-existent for samples collected after January 25, 2015"),
+  THE_CONSENT_PROCESS_DID_NOT_SPECIFICALLY_ADDRESS_FUTURE_USE_OR_BROAD_DATA_SHARING_FOR_SAMPLES_COLLECTED_AFTER_JANUARY_25_2015(
+      "The consent process did not specifically address future use or broad data sharing for samples collected after January 25, 2015"),
+  THE_CONSENT_PROCESS_INADEQUATELY_ADDRESSES_RISKS_RELATED_TO_FUTURE_USE_OR_BROAD_DATA_SHARING_FOR_SAMPLES_COLLECTED_AFTER_JANUARY_25_2015(
+      "The consent process inadequately addresses risks related to future use or broad data sharing for samples collected after January 25, 2015"),
+  THE_CONSENT_PROCESS_SPECIFICALLY_PRECLUDES_FUTURE_USE_OR_BROAD_DATA_SHARING_INCLUDING_A_STATEMENT_THAT_USE_OF_DATA_WILL_BE_LIMITED_TO_THE_ORIGINAL_RESEARCHERS(
+      "The consent process specifically precludes future use or broad data sharing (including a statement that use of data will be limited to the original researchers)"),
+  OTHER_INFORMED_CONSENT_LIMITATIONS_OR_CONCERNS("Other informed consent limitations or concerns"),
+  OTHER("Other");
+  private final String value;
+  AlternativeDataSharingPlanReason(String value) {
+    this.value = value;
+  }
+
+  @Override
+  public String toString() {
+    return this.value;
+  }
+
+  public String value() {
+    return this.value;
+  }
+}

src/main/java/org/broadinstitute/consent/http/models/draft/ConsentGroup.java

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+package org.broadinstitute.consent.http.models.draft;
+
+import java.net.URI;
+import java.util.List;
+
+public record ConsentGroup(
+    Integer datasetId,
+    String datasetIdentifier,
+    String consentGroupName,
+    AccessManagement accessManagement,
+    Boolean generalResearchUse,
+    Boolean hmb,
+    List<String> diseaseSpecificUse,
+    Boolean poa,
+    String otherPrimary,
+    Boolean nmds,
+    Boolean gso,
+    Boolean pub,
+    Boolean col,
+    Boolean irb,
+    String gs,
+    Boolean mor,
+    String morDate,
+    Boolean npu,
+    String otherSecondary,
+    Integer dataAccessCommitteeId,
+    DataLocation dataLocation,
+    URI url,
+    Integer numberOfParticipants,
+    List<FileTypeObject> fileTypes
+) {}

src/main/java/org/broadinstitute/consent/http/models/draft/DataLocation.java

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+package org.broadinstitute.consent.http.models.draft;
+
+public enum DataLocation {
+
+  AN_VIL_WORKSPACE("AnVIL Workspace"),
+  TERRA_WORKSPACE("Terra Workspace"),
+  TDR_LOCATION("TDR Location"),
+  NOT_DETERMINED("Not Determined");
+  private final String value;
+
+  DataLocation(String value) {
+    this.value = value;
+  }
+
+  @Override
+  public String toString() {
+    return this.value;
+  }
+
+  public String value() {
+    return this.value;
+  }
+
+}

src/main/java/org/broadinstitute/consent/http/models/draft/FileType.java

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+package org.broadinstitute.consent.http.models.draft;
+
+public enum FileType {
+
+  ARRAYS("Arrays"),
+  GENOME("Genome"),
+  EXOME("Exome"),
+  SURVEY("Survey"),
+  PHENOTYPE("Phenotype");
+  private final String value;
+
+  FileType(String value) {
+    this.value = value;
+  }
+
+  @Override
+  public String toString() {
+    return this.value;
+  }
+
+  public String value() {
+    return this.value;
+  }
+
+}

src/main/java/org/broadinstitute/consent/http/models/draft/FileTypeObject.java

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+package org.broadinstitute.consent.http.models.draft;
+
+public record FileTypeObject(
+    FileType fileType,
+    String functionalEquivalence
+) {}

src/main/java/org/broadinstitute/consent/http/models/draft/LegacyRegistration.java

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+package org.broadinstitute.consent.http.models.draft;
+
+import java.util.List;
+
+public record LegacyRegistration(
+    Integer studyId,
+    String studyName,
+    String studyDescription,
+    List<String> dataTypes,
+    Boolean publicVisibility,
+    String piName,
+    String phenotypeIndication,
+    StudyType studyType,
+    String species,
+    Integer dataSubmitterUserId,
+    List<String> dataCustodianEmail,
+    NihAnvilUse nihAnvilUse,
+    Boolean submittingToAnvil,
+    String dbGaPPhsID,
+    String dbGaPStudyRegistrationName,
+    String embargoReleaseDate,
+    String sequencingCenter,
+    Integer piInstitution,
+    String nihGrantContractNumber,
+    List<NihICsSupportingStudy> nihICsSupportingStudy,
+    String nihProgramOfficerName,
+    NihInstitutionCenterSubmission nihInstitutionCenterSubmission,
+    String nihGenomicProgramAdministratorName,
+    Boolean multiCenterStudy,
+    List<String> collaboratingSites,
+    Boolean controlledAccessRequiredForGenomicSummaryResultsGSR,
+    String controlledAccessRequiredForGenomicSummaryResultsGSRRequiredExplanation,
+    Boolean alternativeDataSharingPlan,
+    List<AlternativeDataSharingPlanReason> alternativeDataSharingPlanReasons,
+    String alternativeDataSharingPlanExplanation,
+    String alternativeDataSharingPlanFileName,
+    AlternativeDataSharingPlanDataSubmitted alternativeDataSharingPlanDataSubmitted,
+    Boolean alternativeDataSharingPlanDataReleased,
+    String alternativeDataSharingPlanTargetDeliveryDate,
+    String alternativeDataSharingPlanTargetPublicReleaseDate,
+    AlternativeDataSharingPlanAccessManagement alternativeDataSharingPlanAccessManagement,
+    List<ConsentGroup> consentGroups
+) {}

src/main/java/org/broadinstitute/consent/http/models/draft/NihAnvilUse.java

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+package org.broadinstitute.consent.http.models.draft;
+
+public enum NihAnvilUse {
+
+  I_AM_NHGRI_FUNDED_AND_I_HAVE_A_DB_GA_P_PHS_ID_ALREADY(
+      "I am NHGRI funded and I have a dbGaP PHS ID already"),
+  I_AM_NHGRI_FUNDED_AND_I_DO_NOT_HAVE_A_DB_GA_P_PHS_ID(
+      "I am NHGRI funded and I do not have a dbGaP PHS ID"),
+  I_AM_NOT_NHGRI_FUNDED_BUT_I_AM_SEEKING_TO_SUBMIT_DATA_TO_AN_VIL(
+      "I am not NHGRI funded but I am seeking to submit data to AnVIL"),
+  I_AM_NOT_NHGRI_FUNDED_AND_DO_NOT_PLAN_TO_STORE_DATA_IN_AN_VIL(
+      "I am not NHGRI funded and do not plan to store data in AnVIL");
+  private final String value;
+
+  @Override
+  public String toString() {
+    return this.value;
+  }
+
+  NihAnvilUse(String value) {
+    this.value = value;
+  }
+
+}

src/main/java/org/broadinstitute/consent/http/models/draft/NihICsSupportingStudy.java

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+package org.broadinstitute.consent.http.models.draft;
+
+public enum NihICsSupportingStudy {
+
+  NCI("NCI"),
+  NEI("NEI"),
+  NHLBI("NHLBI"),
+  NHGRI("NHGRI"),
+  NIA("NIA"),
+  NIAAA("NIAAA"),
+  NIAID("NIAID"),
+  NIAMS("NIAMS"),
+  NIBIB("NIBIB"),
+  NICHD("NICHD"),
+  NIDCD("NIDCD"),
+  NIDCR("NIDCR"),
+  NIDDK("NIDDK"),
+  NIDA("NIDA"),
+  NIEHS("NIEHS"),
+  NIGMS("NIGMS"),
+  NIMH("NIMH"),
+  NIMHD("NIMHD"),
+  NINDS("NINDS"),
+  NINR("NINR"),
+  NLM("NLM"),
+  CC("CC"),
+  CIT("CIT"),
+  CSR("CSR"),
+  FIC("FIC"),
+  NCATS("NCATS"),
+  NCCIH("NCCIH");
+  private final String value;
+
+  NihICsSupportingStudy(String value) {
+    this.value = value;
+  }
+
+  @Override
+  public String toString() {
+    return this.value;
+  }
+
+  public String value() {
+    return this.value;
+  }
+
+}

src/main/java/org/broadinstitute/consent/http/models/draft/NihInstitutionCenterSubmission.java

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+package org.broadinstitute.consent.http.models.draft;
+
+public enum NihInstitutionCenterSubmission {
+
+  NCI("NCI"),
+  NEI("NEI"),
+  NHLBI("NHLBI"),
+  NHGRI("NHGRI"),
+  NIA("NIA"),
+  NIAAA("NIAAA"),
+  NIAID("NIAID"),
+  NIAMS("NIAMS"),
+  NIBIB("NIBIB"),
+  NICHD("NICHD"),
+  NIDCD("NIDCD"),
+  NIDCR("NIDCR"),
+  NIDDK("NIDDK"),
+  NIDA("NIDA"),
+  NIEHS("NIEHS"),
+  NIGMS("NIGMS"),
+  NIMH("NIMH"),
+  NIMHD("NIMHD"),
+  NINDS("NINDS"),
+  NINR("NINR"),
+  NLM("NLM"),
+  CC("CC"),
+  CIT("CIT"),
+  CSR("CSR"),
+  FIC("FIC"),
+  NCATS("NCATS"),
+  NCCIH("NCCIH");
+  private final String value;
+  NihInstitutionCenterSubmission(String value) {
+    this.value = value;
+  }
+
+  @Override
+  public String toString() {
+    return this.value;
+  }
+
+  public String value() {
+    return this.value;
+  }
+
+}