Merge pull request #422 from icgc-argo/feature/regionProgram

Feature/regionProgram

src/main/java/org/icgc/argo/program_service/converter/ProgramConverter.java

@@ -52,7 +52,6 @@ public interface ProgramConverter {
   @Mapping(target = "programPrimarySites", ignore = true)
   @Mapping(target = "programInstitutions", ignore = true)
   @Mapping(target = "programCountries", ignore = true)
-  @Mapping(target = "programRegions", ignore = true)
   @Mapping(target = "active", constant = "true")
   @Mapping(target = "legacyShortName", ignore = true)
   @Mapping(target = "dataCenterId", ignore = true)
@@ -66,7 +65,6 @@ public interface ProgramConverter {
   @Mapping(target = "programPrimarySites", ignore = true)
   @Mapping(target = "programInstitutions", ignore = true)
   @Mapping(target = "programCountries", ignore = true)
-  @Mapping(target = "programRegions", ignore = true)
   void updateProgram(ProgramEntity updatingProgram, @MappingTarget ProgramEntity programToUpdate);
 
   @Mapping(target = "clearField", ignore = true)
@@ -147,8 +145,7 @@ default void updateProgramFromEntity(
         .addAllCancerTypes(entity.listCancerTypes())
         .addAllPrimarySites(entity.listPrimarySites())
         .addAllInstitutions(entity.listInstitutions())
-        .addAllCountries(entity.listCountries())
-        .addAllRegions(entity.listRegions());
+        .addAllCountries(entity.listCountries());
   }
 
   @Mapping(target = "mergeFrom", ignore = true)

src/main/java/org/icgc/argo/program_service/model/dto/Program.java

@@ -24,5 +24,4 @@ public class Program {
   private List<String> primary_sites;
   private List<String> institutions;
   private List<String> countries;
-  private List<String> regions;
 }

src/main/java/org/icgc/argo/program_service/model/dto/ProgramDTO.java

@@ -1,32 +1,30 @@
-package org.icgc.argo.program_service.model.dto;
-
-import java.util.Set;
-import lombok.AllArgsConstructor;
-import lombok.Data;
-import lombok.NoArgsConstructor;
-import lombok.ToString;
-
-@Data
-@NoArgsConstructor
-@AllArgsConstructor
-@ToString
-public class ProgramDTO {
-
-  private String shortName;
-
-  private String description;
-
-  private String name;
-
-  private String website;
-
-  private Set<InstitutionDTO> programInstitutions;
-
-  private Set<CountryDTO> programCountries;
-
-  private Set<RegionDTO> processingRegions;
-
-  private Set<CancerDTO> programCancers;
-
-  private Set<PrimarySiteDTO> programPrimarySites;
-}
+package org.icgc.argo.program_service.model.dto;
+
+import java.util.Set;
+import lombok.AllArgsConstructor;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+import lombok.ToString;
+
+@Data
+@NoArgsConstructor
+@AllArgsConstructor
+@ToString
+public class ProgramDTO {
+
+  private String shortName;
+
+  private String description;
+
+  private String name;
+
+  private String website;
+
+  private Set<InstitutionDTO> programInstitutions;
+
+  private Set<CountryDTO> programCountries;
+
+  private Set<CancerDTO> programCancers;
+
+  private Set<PrimarySiteDTO> programPrimarySites;
+}

src/main/java/org/icgc/argo/program_service/model/dto/ProgramsDTO.java

@@ -1,32 +1,30 @@
-package org.icgc.argo.program_service.model.dto;
-
-import java.util.List;
-import lombok.AllArgsConstructor;
-import lombok.Data;
-import lombok.NoArgsConstructor;
-import lombok.ToString;
-
-@Data
-@NoArgsConstructor
-@AllArgsConstructor
-@ToString
-public class ProgramsDTO {
-
-  private String shortName;
-
-  private String description;
-
-  private String name;
-
-  private String website;
-
-  private List<String> institutions;
-
-  private List<String> countries;
-
-  private List<String> regions;
-
-  private List<String> cancerTypes;
-
-  private List<String> primarySites;
-}
+package org.icgc.argo.program_service.model.dto;
+
+import java.util.List;
+import lombok.AllArgsConstructor;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+import lombok.ToString;
+
+@Data
+@NoArgsConstructor
+@AllArgsConstructor
+@ToString
+public class ProgramsDTO {
+
+  private String shortName;
+
+  private String description;
+
+  private String name;
+
+  private String website;
+
+  private List<String> institutions;
+
+  private List<String> countries;
+
+  private List<String> cancerTypes;
+
+  private List<String> primarySites;
+}

src/main/java/org/icgc/argo/program_service/model/dto/builder/ProgramDTOBuilder.java

@@ -1,35 +1,33 @@
-package org.icgc.argo.program_service.model.dto.builder;
-
-import org.icgc.argo.program_service.model.dto.ProgramDTO;
-import org.icgc.argo.program_service.model.entity.ProgramEntity;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.stereotype.Component;
-
-@Component
-public class ProgramDTOBuilder {
-
-  @Autowired CancerDTOBuilder canerDtoBuilder;
-  @Autowired CountryDTOBuilder countryDTOBuilder;
-  @Autowired InstitutionDTOBuilder institutionDTOBuilder;
-  @Autowired PrimarySiteDTOBuilder primarySiteDTOBuilder;
-  @Autowired RegionDTOBuilder regionDTOBuilder;
-
-  public ProgramDTO convertEntityToDTO(ProgramEntity programEntity) {
-    ProgramDTO programDTO = new ProgramDTO();
-    programDTO.setName(programEntity.getName());
-    programDTO.setWebsite(programEntity.getWebsite());
-    programDTO.setShortName(programEntity.getShortName());
-    programDTO.setDescription(programEntity.getDescription());
-    programDTO.setProcessingRegions(
-        regionDTOBuilder.convertEntityToDTO(programEntity.getProgramRegions()));
-    programDTO.setProgramCancers(
-        canerDtoBuilder.convertEntityToDTO(programEntity.getProgramCancers()));
-    programDTO.setProgramCountries(
-        countryDTOBuilder.convertEntityToDTO(programEntity.getProgramCountries()));
-    programDTO.setProgramPrimarySites(
-        primarySiteDTOBuilder.convertEntityToDTO(programEntity.getProgramPrimarySites()));
-    programDTO.setProgramInstitutions(
-        institutionDTOBuilder.convertEntityToDTO(programEntity.getProgramInstitutions()));
-    return programDTO;
-  }
-}
+package org.icgc.argo.program_service.model.dto.builder;
+
+import org.icgc.argo.program_service.model.dto.ProgramDTO;
+import org.icgc.argo.program_service.model.entity.ProgramEntity;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+@Component
+public class ProgramDTOBuilder {
+
+  @Autowired CancerDTOBuilder canerDtoBuilder;
+  @Autowired CountryDTOBuilder countryDTOBuilder;
+  @Autowired InstitutionDTOBuilder institutionDTOBuilder;
+  @Autowired PrimarySiteDTOBuilder primarySiteDTOBuilder;
+  @Autowired RegionDTOBuilder regionDTOBuilder;
+
+  public ProgramDTO convertEntityToDTO(ProgramEntity programEntity) {
+    ProgramDTO programDTO = new ProgramDTO();
+    programDTO.setName(programEntity.getName());
+    programDTO.setWebsite(programEntity.getWebsite());
+    programDTO.setShortName(programEntity.getShortName());
+    programDTO.setDescription(programEntity.getDescription());
+    programDTO.setProgramCancers(
+        canerDtoBuilder.convertEntityToDTO(programEntity.getProgramCancers()));
+    programDTO.setProgramCountries(
+        countryDTOBuilder.convertEntityToDTO(programEntity.getProgramCountries()));
+    programDTO.setProgramPrimarySites(
+        primarySiteDTOBuilder.convertEntityToDTO(programEntity.getProgramPrimarySites()));
+    programDTO.setProgramInstitutions(
+        institutionDTOBuilder.convertEntityToDTO(programEntity.getProgramInstitutions()));
+    return programDTO;
+  }
+}

src/main/java/org/icgc/argo/program_service/model/entity/ProgramEntity.java

@@ -137,16 +137,6 @@ public class ProgramEntity implements NameableEntity<UUID> {
       orphanRemoval = true)
   private Set<ProgramCountry> programCountries = new TreeSet<>();
 
-  @NotNull
-  @ToString.Exclude
-  @EqualsAndHashCode.Exclude
-  @OneToMany(
-      mappedBy = ProgramRegion.Fields.program,
-      cascade = CascadeType.ALL,
-      fetch = FetchType.LAZY,
-      orphanRemoval = true)
-  private Set<ProgramRegion> programRegions = new TreeSet<>();
-
   @ToString.Exclude
   @EqualsAndHashCode.Exclude
   @OneToMany(
@@ -180,8 +170,4 @@ public List<String> listInstitutions() {
   public List<String> listCountries() {
     return mapToList(getProgramCountries(), c -> c.getCountry().getName());
   }
-
-  public List<String> listRegions() {
-    return mapToList(getProgramRegions(), r -> r.getRegion().getName());
-  }
 }

src/main/java/org/icgc/argo/program_service/repositories/query/ProgramSpecificationBuilder.java

@@ -1,68 +1,63 @@
-/*
- * Copyright (c) 2020 The Ontario Institute for Cancer Research. All rights reserved
- *
- * This program and the accompanying materials are made available under the terms of the GNU Affero General Public License v3.0.
- * You should have received a copy of the GNU Affero General Public License along with
- * this program. If not, see <http://www.gnu.org/licenses/>.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
- * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT
- * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
- * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
- * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
- * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
- * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- *
- *
- */
-
-package org.icgc.argo.program_service.repositories.query;
-
-import static javax.persistence.criteria.JoinType.LEFT;
-
-import java.util.UUID;
-import javax.persistence.criteria.Root;
-import lombok.EqualsAndHashCode;
-import lombok.Setter;
-import lombok.experimental.Accessors;
-import org.icgc.argo.program_service.model.entity.ProgramEntity;
-import org.icgc.argo.program_service.model.join.*;
-
-@Setter
-@Accessors(chain = true)
-@EqualsAndHashCode(callSuper = true)
-public class ProgramSpecificationBuilder extends AbstractSpecificationBuilder<ProgramEntity, UUID> {
-
-  private boolean fetchCancers;
-  private boolean fetchPrimarySites;
-  private boolean fetchInstitutions;
-  private boolean fetchCountries;
-  private boolean fetchRegions;
-
-  @Override
-  protected Root<ProgramEntity> setupFetchStrategy(Root<ProgramEntity> root) {
-    if (fetchCancers) {
-      root.fetch(ProgramEntity.Fields.programCancers, LEFT)
-          .fetch(ProgramCancer.Fields.cancer, LEFT);
-    }
-    if (fetchPrimarySites) {
-      root.fetch(ProgramEntity.Fields.programPrimarySites, LEFT)
-          .fetch(ProgramPrimarySite.Fields.primarySite, LEFT);
-    }
-    if (fetchInstitutions) {
-      root.fetch(ProgramEntity.Fields.programInstitutions, LEFT)
-          .fetch(ProgramInstitution.Fields.institution, LEFT);
-    }
-    if (fetchCountries) {
-      root.fetch(ProgramEntity.Fields.programCountries, LEFT)
-          .fetch(ProgramCountry.Fields.country, LEFT);
-    }
-    if (fetchRegions) {
-      root.fetch(ProgramEntity.Fields.programRegions, LEFT)
-          .fetch(ProgramRegion.Fields.region, LEFT);
-    }
-    return root;
-  }
-}
+/*
+ * Copyright (c) 2020 The Ontario Institute for Cancer Research. All rights reserved
+ *
+ * This program and the accompanying materials are made available under the terms of the GNU Affero General Public License v3.0.
+ * You should have received a copy of the GNU Affero General Public License along with
+ * this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT
+ * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+ * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+ * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+ * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
+ * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
+ * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ *
+ */
+
+package org.icgc.argo.program_service.repositories.query;
+
+import static javax.persistence.criteria.JoinType.LEFT;
+
+import java.util.UUID;
+import javax.persistence.criteria.Root;
+import lombok.EqualsAndHashCode;
+import lombok.Setter;
+import lombok.experimental.Accessors;
+import org.icgc.argo.program_service.model.entity.ProgramEntity;
+import org.icgc.argo.program_service.model.join.*;
+
+@Setter
+@Accessors(chain = true)
+@EqualsAndHashCode(callSuper = true)
+public class ProgramSpecificationBuilder extends AbstractSpecificationBuilder<ProgramEntity, UUID> {
+
+  private boolean fetchCancers;
+  private boolean fetchPrimarySites;
+  private boolean fetchInstitutions;
+  private boolean fetchCountries;
+
+  @Override
+  protected Root<ProgramEntity> setupFetchStrategy(Root<ProgramEntity> root) {
+    if (fetchCancers) {
+      root.fetch(ProgramEntity.Fields.programCancers, LEFT)
+          .fetch(ProgramCancer.Fields.cancer, LEFT);
+    }
+    if (fetchPrimarySites) {
+      root.fetch(ProgramEntity.Fields.programPrimarySites, LEFT)
+          .fetch(ProgramPrimarySite.Fields.primarySite, LEFT);
+    }
+    if (fetchInstitutions) {
+      root.fetch(ProgramEntity.Fields.programInstitutions, LEFT)
+          .fetch(ProgramInstitution.Fields.institution, LEFT);
+    }
+    if (fetchCountries) {
+      root.fetch(ProgramEntity.Fields.programCountries, LEFT)
+          .fetch(ProgramCountry.Fields.country, LEFT);
+    }
+    return root;
+  }
+}