Merge pull request #248 from AAFC-BICoE/35276_add_metagenomic_workflo…

…w_resource

35276 add metagenomic workflow resource

src/main/java/ca/gc/aafc/seqdb/api/dto/MetagenomicsBatchDto.java

@@ -0,0 +1,45 @@
+package ca.gc.aafc.seqdb.api.dto;
+
+import ca.gc.aafc.dina.dto.ExternalRelationDto;
+import ca.gc.aafc.dina.dto.RelatedEntity;
+import ca.gc.aafc.dina.repository.meta.JsonApiExternalRelation;
+import ca.gc.aafc.seqdb.api.entities.MetagenomicsBatch;
+
+import io.crnk.core.resource.annotations.JsonApiId;
+import io.crnk.core.resource.annotations.JsonApiRelation;
+import io.crnk.core.resource.annotations.JsonApiResource;
+import java.time.OffsetDateTime;
+import java.util.UUID;
+import lombok.AllArgsConstructor;
+import lombok.Builder;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
+@Builder
+@Data
+@NoArgsConstructor
+@AllArgsConstructor
+@JsonApiResource(type = MetagenomicsBatchDto.TYPENAME)
+@RelatedEntity(MetagenomicsBatch.class)
+public class MetagenomicsBatchDto {
+
+  public static final String TYPENAME = "metagenomics-batch";
+
+  @JsonApiId
+  private UUID uuid;
+
+  private String createdBy;
+
+  private OffsetDateTime createdOn;
+  private String group;
+
+  private String name;
+
+  @JsonApiExternalRelation(type = "protocol")
+  @JsonApiRelation
+  private ExternalRelationDto protocol;
+
+  @JsonApiRelation
+  private IndexSetDto indexSet;
+
+}

src/main/java/ca/gc/aafc/seqdb/api/dto/MetagenomicsBatchItemDto.java

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+package ca.gc.aafc.seqdb.api.dto;
+
+import ca.gc.aafc.dina.dto.RelatedEntity;
+import ca.gc.aafc.seqdb.api.dto.pcr.PcrBatchItemDto;
+import ca.gc.aafc.seqdb.api.entities.MetagenomicsBatchItem;
+
+import io.crnk.core.resource.annotations.JsonApiId;
+import io.crnk.core.resource.annotations.JsonApiRelation;
+import io.crnk.core.resource.annotations.JsonApiResource;
+import java.time.OffsetDateTime;
+import java.util.UUID;
+
+import org.javers.core.metamodel.annotation.ShallowReference;
+
+import lombok.AllArgsConstructor;
+import lombok.Builder;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
+@Builder
+@Data
+@NoArgsConstructor
+@AllArgsConstructor
+@JsonApiResource(type = MetagenomicsBatchItemDto.TYPENAME)
+@RelatedEntity(MetagenomicsBatchItem.class)
+public class MetagenomicsBatchItemDto {
+
+  public static final String TYPENAME = "metagenomics-batch-item";
+
+  @JsonApiId
+  private UUID uuid;
+
+  private String createdBy;
+
+  private OffsetDateTime createdOn;
+
+  @JsonApiRelation
+  private MetagenomicsBatchDto metagenomicsBatch;
+
+  @JsonApiRelation
+  private PcrBatchItemDto pcrBatchItem;
+
+  @ShallowReference
+  @JsonApiRelation
+  private MolecularAnalysisRunItemDto molecularAnalysisRunItem;
+
+  @JsonApiRelation
+  private NgsIndexDto indexI5;
+
+  @JsonApiRelation
+  private NgsIndexDto indexI7;
+
+}

src/main/java/ca/gc/aafc/seqdb/api/entities/MetagenomicsBatch.java

@@ -0,0 +1,68 @@
+package ca.gc.aafc.seqdb.api.entities;
+
+import org.hibernate.annotations.Generated;
+import org.hibernate.annotations.GenerationTime;
+import org.hibernate.annotations.NaturalId;
+
+import ca.gc.aafc.dina.entity.DinaEntity;
+import ca.gc.aafc.seqdb.api.entities.libraryprep.IndexSet;
+
+import java.time.OffsetDateTime;
+import java.util.UUID;
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+import javax.validation.constraints.NotBlank;
+import javax.validation.constraints.NotNull;
+import javax.validation.constraints.Size;
+import lombok.AllArgsConstructor;
+import lombok.Builder;
+import lombok.Getter;
+import lombok.NoArgsConstructor;
+import lombok.Setter;
+
+@Getter
+@Entity
+@Builder
+@Setter
+@NoArgsConstructor
+@AllArgsConstructor
+@Table(name = "metagenomics_batch")
+public class MetagenomicsBatch implements DinaEntity {
+
+  @Id
+  @GeneratedValue(strategy = GenerationType.IDENTITY)
+  private Integer id;
+
+  @NotNull
+  @NaturalId
+  private UUID uuid;
+
+  @NotBlank
+  @Column(name = "created_by", updatable = false)
+  private String createdBy;
+
+  @Column(name = "created_on", insertable = false, updatable = false)
+  @Generated(value = GenerationTime.INSERT)
+  private OffsetDateTime createdOn;
+
+  @Column(name = "_group")
+  private String group;
+
+  @NotBlank
+  @Size(max = 100)
+  private String name;
+
+  private UUID protocol;
+
+  @ManyToOne(fetch = FetchType.LAZY)
+  @JoinColumn(name = "index_set_id")
+  private IndexSet indexSet;
+
+}

src/main/java/ca/gc/aafc/seqdb/api/entities/MetagenomicsBatchItem.java

@@ -0,0 +1,84 @@
+package ca.gc.aafc.seqdb.api.entities;
+
+import org.hibernate.annotations.Generated;
+import org.hibernate.annotations.GenerationTime;
+import org.hibernate.annotations.NaturalId;
+
+import ca.gc.aafc.dina.entity.DinaEntity;
+import ca.gc.aafc.seqdb.api.entities.libraryprep.NgsIndex;
+import ca.gc.aafc.seqdb.api.entities.pcr.PcrBatchItem;
+
+import java.time.OffsetDateTime;
+import java.util.UUID;
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+import javax.validation.constraints.NotBlank;
+import javax.validation.constraints.NotNull;
+import lombok.AllArgsConstructor;
+import lombok.Builder;
+import lombok.Getter;
+import lombok.NoArgsConstructor;
+import lombok.Setter;
+
+@Getter
+@Entity
+@Builder
+@Setter
+@NoArgsConstructor
+@AllArgsConstructor
+@Table(name = "metagenomics_batch_item")
+public class MetagenomicsBatchItem implements DinaEntity {
+
+  @Id
+  @GeneratedValue(strategy = GenerationType.IDENTITY)
+  private Integer id;
+
+  @NotNull
+  @NaturalId
+  private UUID uuid;
+
+  @NotBlank
+  @Column(name = "created_by", updatable = false)
+  private String createdBy;
+
+  @Column(name = "created_on", insertable = false, updatable = false)
+  @Generated(value = GenerationTime.INSERT)
+  private OffsetDateTime createdOn;
+
+  // eager since we need it for group-based permission
+  @ManyToOne(fetch = FetchType.EAGER)
+  @JoinColumn(name = "metagenomics_batch_id")
+  private MetagenomicsBatch metagenomicsBatch;
+
+  @ManyToOne(fetch = FetchType.LAZY)
+  @JoinColumn(name = "pcr_batch_item_id")
+  private PcrBatchItem pcrBatchItem;
+
+  @ManyToOne(fetch = FetchType.LAZY)
+  @JoinColumn(name = "molecular_analysis_run_item_id")
+  private MolecularAnalysisRunItem molecularAnalysisRunItem;
+
+  @ManyToOne(fetch = FetchType.LAZY)
+  @JoinColumn(name = "indexi5_id")
+  private NgsIndex indexI5;
+
+  @ManyToOne(fetch = FetchType.LAZY)
+  @JoinColumn(name = "indexi7_id")
+  private NgsIndex indexI7;
+
+  @Override
+  public String getGroup() {
+    if (metagenomicsBatch == null) {
+      return null;
+    }
+    return metagenomicsBatch.getGroup();
+  }
+
+}

src/main/java/ca/gc/aafc/seqdb/api/repository/MetagenomicsBatchItemRepository.java

@@ -0,0 +1,51 @@
+package ca.gc.aafc.seqdb.api.repository;
+
+import org.springframework.boot.info.BuildProperties;
+import org.springframework.stereotype.Repository;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import ca.gc.aafc.dina.mapper.DinaMapper;
+import ca.gc.aafc.dina.repository.DinaRepository;
+import ca.gc.aafc.dina.repository.external.ExternalResourceProvider;
+import ca.gc.aafc.dina.security.DinaAuthenticatedUser;
+import ca.gc.aafc.dina.security.auth.DinaAuthorizationService;
+import ca.gc.aafc.seqdb.api.dto.MetagenomicsBatchItemDto;
+import ca.gc.aafc.seqdb.api.entities.MetagenomicsBatchItem;
+import ca.gc.aafc.seqdb.api.service.MetagenomicsBatchItemService;
+
+import java.util.Optional;
+import lombok.NonNull;
+
+@Repository
+public class MetagenomicsBatchItemRepository extends DinaRepository<MetagenomicsBatchItemDto, MetagenomicsBatchItem> {
+
+  private Optional<DinaAuthenticatedUser> dinaAuthenticatedUser;
+
+  public MetagenomicsBatchItemRepository(
+    @NonNull MetagenomicsBatchItemService dinaService,
+    DinaAuthorizationService groupAuthorizationService,
+    @NonNull BuildProperties props,
+    ExternalResourceProvider externalResourceProvider,
+    Optional<DinaAuthenticatedUser> dinaAuthenticatedUser,
+    ObjectMapper objMapper) {
+    super(
+      dinaService,
+      groupAuthorizationService,
+      Optional.empty(),
+      new DinaMapper<>(MetagenomicsBatchItemDto.class),
+      MetagenomicsBatchItemDto.class,
+      MetagenomicsBatchItem.class,
+      null,
+      externalResourceProvider,
+      props, objMapper);
+    this.dinaAuthenticatedUser = dinaAuthenticatedUser;
+  }
+
+  @Override
+  public <S extends MetagenomicsBatchItemDto> S create(S resource) {
+    dinaAuthenticatedUser.ifPresent(
+      authenticatedUser -> resource.setCreatedBy(authenticatedUser.getUsername()));
+    return super.create(resource);
+  }
+}

src/main/java/ca/gc/aafc/seqdb/api/repository/MetagenomicsBatchRepository.java

@@ -0,0 +1,51 @@
+package ca.gc.aafc.seqdb.api.repository;
+
+import org.springframework.boot.info.BuildProperties;
+import org.springframework.stereotype.Repository;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import ca.gc.aafc.dina.mapper.DinaMapper;
+import ca.gc.aafc.dina.repository.DinaRepository;
+import ca.gc.aafc.dina.repository.external.ExternalResourceProvider;
+import ca.gc.aafc.dina.security.DinaAuthenticatedUser;
+import ca.gc.aafc.dina.security.auth.DinaAuthorizationService;
+import ca.gc.aafc.seqdb.api.dto.MetagenomicsBatchDto;
+import ca.gc.aafc.seqdb.api.entities.MetagenomicsBatch;
+import ca.gc.aafc.seqdb.api.service.MetagenomicsBatchService;
+
+import java.util.Optional;
+import lombok.NonNull;
+
+@Repository
+public class MetagenomicsBatchRepository extends DinaRepository<MetagenomicsBatchDto, MetagenomicsBatch> {
+
+  private Optional<DinaAuthenticatedUser> dinaAuthenticatedUser;
+
+  public MetagenomicsBatchRepository(
+    @NonNull MetagenomicsBatchService dinaService,
+    DinaAuthorizationService groupAuthorizationService,
+    @NonNull BuildProperties props,
+    ExternalResourceProvider externalResourceProvider,
+    Optional<DinaAuthenticatedUser> dinaAuthenticatedUser,
+    ObjectMapper objMapper) {
+    super(
+      dinaService,
+      groupAuthorizationService,
+      Optional.empty(),
+      new DinaMapper<>(MetagenomicsBatchDto.class),
+      MetagenomicsBatchDto.class,
+      MetagenomicsBatch.class,
+      null,
+      externalResourceProvider,
+      props, objMapper);
+    this.dinaAuthenticatedUser = dinaAuthenticatedUser;
+  }
+
+  @Override
+  public <S extends MetagenomicsBatchDto> S create(S resource) {
+    dinaAuthenticatedUser.ifPresent(
+      authenticatedUser -> resource.setCreatedBy(authenticatedUser.getUsername()));
+    return super.create(resource);
+  }
+}

src/main/java/ca/gc/aafc/seqdb/api/service/MetagenomicsBatchItemService.java

@@ -0,0 +1,27 @@
+package ca.gc.aafc.seqdb.api.service;
+
+import lombok.NonNull;
+
+import org.springframework.stereotype.Service;
+import org.springframework.validation.SmartValidator;
+
+import ca.gc.aafc.dina.jpa.BaseDAO;
+import ca.gc.aafc.dina.service.DefaultDinaService;
+import ca.gc.aafc.dina.util.UUIDHelper;
+import ca.gc.aafc.seqdb.api.entities.MetagenomicsBatchItem;
+
+@Service
+public class MetagenomicsBatchItemService extends DefaultDinaService<MetagenomicsBatchItem> {
+
+  public MetagenomicsBatchItemService(
+    @NonNull BaseDAO baseDAO, @NonNull SmartValidator sv) {
+    super(baseDAO, sv);
+  }
+
+  @Override
+  protected void preCreate(MetagenomicsBatchItem entity) {
+    entity.setUuid(UUIDHelper.generateUUIDv7());
+  }
+
+}
+