Changes related to "Modify Create Program endpoint to require Data Center id"

src/main/java/org/icgc/argo/program_service/controller/DataCenterController.java

@@ -33,7 +33,6 @@ public ResponseEntity<List<DataCenterDTO>> listDataCenters(
   }
 
   @GetMapping(value = "/{datacenter_short_name}/programs")
-
   public ResponseEntity<ProgramsResponseDTO> listDataCenterPrograms(
       @Parameter(hidden = true) @RequestHeader(value = "Authorization", required = true)
           final String authorization,

src/main/java/org/icgc/argo/program_service/controller/ProgramController.java

@@ -43,7 +43,8 @@ public ResponseEntity<CreateProgramResponseDTO> createProgram(
         grpc2JsonConverter.fromJson(
             grpc2JsonConverter.getJsonFromObject(createProgramRequestDTO),
             CreateProgramRequest.class);
-    CreateProgramResponse response = serviceFacade.createProgram(request);
+    CreateProgramResponse response =
+        serviceFacade.createProgram(request, createProgramRequestDTO.getDataCenterId());
     return new ResponseEntity(
         grpc2JsonConverter.prepareCreateProgramResponse(response), HttpStatus.CREATED);
   }

src/main/java/org/icgc/argo/program_service/exception/ExceptionHandlers.java

@@ -7,10 +7,7 @@
 import javax.servlet.http.HttpServletRequest;
 import lombok.extern.slf4j.Slf4j;
 import lombok.val;
-import org.icgc.argo.program_service.model.exceptions.BadRequestException;
-import org.icgc.argo.program_service.model.exceptions.ForbiddenException;
-import org.icgc.argo.program_service.model.exceptions.NotFoundException;
-import org.icgc.argo.program_service.model.exceptions.UnauthorizedException;
+import org.icgc.argo.program_service.model.exceptions.*;
 import org.springframework.http.HttpHeaders;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.ControllerAdvice;
@@ -79,4 +76,19 @@ public ResponseEntity<Object> handleBadRequestException(
         new HttpHeaders(),
         BAD_REQUEST);
   }
+
+  @ExceptionHandler(RecordNotFoundException.class)
+  public ResponseEntity<Object> handleRecordNotFoundException(
+          HttpServletRequest req, RecordNotFoundException ex) {
+    val message = ex.getMessage();
+    log.error(message);
+    return new ResponseEntity<Object>(
+            Map.of(
+                    "message", ex.getMessage(),
+                    "timestamp", new Date(),
+                    "path", req.getServletPath(),
+                    "error", BAD_REQUEST.getReasonPhrase()),
+            new HttpHeaders(),
+            BAD_REQUEST);
+  }
 }

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

@@ -1,6 +1,7 @@
 package org.icgc.argo.program_service.model.dto;
 
 import java.util.List;
+import java.util.UUID;
 import lombok.AllArgsConstructor;
 import lombok.Builder;
 import lombok.Data;
@@ -13,5 +14,6 @@
 public class CreateProgramRequestDTO {
 
   private Program program;
+  private UUID dataCenterId;
   List<UserDTO> admins;
 }

src/main/java/org/icgc/argo/program_service/model/exceptions/BadRequestException.java

@@ -1,31 +1,38 @@
 /*
- * Copyright (c) 2023. The Ontario Institute for Cancer Research. All rights reserved.
+ * Copyright (c) 2023 The Ontario Institute for Cancer Research. All rights reserved
  *
- *  Licensed under the Apache License, Version 2.0 (the "License");
- *  you may not use this file except in compliance with the License.
- *  You may obtain a copy of the License at
+ * 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/>.
  *
- *      http://www.apache.org/licenses/LICENSE-2.0
+ * 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.
  *
- *  Unless required by applicable law or agreed to in writing, software
- *  distributed under the License is distributed on an "AS IS" BASIS,
- *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- *  See the License for the specific language governing permissions and
- *  limitations under the License.
  *
  */
 
 package org.icgc.argo.program_service.model.exceptions;
 
-import static org.springframework.http.HttpStatus.BAD_REQUEST;
-
 import lombok.NonNull;
-import org.springframework.web.bind.annotation.ResponseStatus;
 
-@ResponseStatus(BAD_REQUEST)
 public class BadRequestException extends RuntimeException {
 
   public BadRequestException(@NonNull String message) {
     super(message);
   }
+
+
+  public static void checkNotFound(
+      boolean expression, @NonNull String message, @NonNull Object... args) {
+    if (!expression) {
+      throw new BadRequestException(String.format(message, args));
+    }
+  }
 }

src/main/java/org/icgc/argo/program_service/model/exceptions/ForbiddenException.java

@@ -1,17 +1,20 @@
 /*
- * Copyright (c) 2019. The Ontario Institute for Cancer Research. All rights reserved.
+ * Copyright (c) 2023 The Ontario Institute for Cancer Research. All rights reserved
  *
- *  Licensed under the Apache License, Version 2.0 (the "License");
- *  you may not use this file except in compliance with the License.
- *  You may obtain a copy of the License at
+ * 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/>.
  *
- *      http://www.apache.org/licenses/LICENSE-2.0
+ * 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.
  *
- *  Unless required by applicable law or agreed to in writing, software
- *  distributed under the License is distributed on an "AS IS" BASIS,
- *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- *  See the License for the specific language governing permissions and
- *  limitations under the License.
  *
  */
 

src/main/java/org/icgc/argo/program_service/model/exceptions/ProgramRuntimeException.java

@@ -0,0 +1,38 @@
+/*
+ * Copyright (c) 2023 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.model.exceptions;
+
+import lombok.NonNull;
+
+public class ProgramRuntimeException extends RuntimeException {
+
+  public ProgramRuntimeException(@NonNull String message) {
+    super(message);
+  }
+
+
+  public static void checkNotFound(
+      boolean expression, @NonNull String message, @NonNull Object... args) {
+    if (!expression) {
+      throw new ProgramRuntimeException(String.format(message, args));
+    }
+  }
+}

src/main/java/org/icgc/argo/program_service/model/exceptions/RecordNotFoundException.java

@@ -0,0 +1,37 @@
+/*
+ * 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.model.exceptions;
+
+import lombok.NonNull;
+
+public class RecordNotFoundException extends RuntimeException {
+
+  public RecordNotFoundException(@NonNull String message) {
+    super(message);
+  }
+
+  public static void checkNotFound(
+      boolean expression, @NonNull String message, @NonNull Object... args) {
+    if (!expression) {
+      throw new RecordNotFoundException(String.format(message, args));
+    }
+  }
+}

src/main/java/org/icgc/argo/program_service/model/exceptions/UnauthorizedException.java

@@ -1,17 +1,20 @@
 /*
- * Copyright (c) 2019. The Ontario Institute for Cancer Research. All rights reserved.
+ * Copyright (c) 2023 The Ontario Institute for Cancer Research. All rights reserved
  *
- *  Licensed under the Apache License, Version 2.0 (the "License");
- *  you may not use this file except in compliance with the License.
- *  You may obtain a copy of the License at
+ * 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/>.
  *
- *      http://www.apache.org/licenses/LICENSE-2.0
+ * 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.
  *
- *  Unless required by applicable law or agreed to in writing, software
- *  distributed under the License is distributed on an "AS IS" BASIS,
- *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- *  See the License for the specific language governing permissions and
- *  limitations under the License.
  *
  */
 

src/main/java/org/icgc/argo/program_service/security/JWTAuthorizationFilter.java

@@ -1,17 +1,21 @@
 /*
- * Copyright (c) 2017. The Ontario Institute for Cancer Research. All rights reserved.
+ * Copyright (c) 2023 The Ontario Institute for Cancer Research. All rights reserved
  *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
+ * 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.
  *
- *     http://www.apache.org/licenses/LICENSE-2.0
  *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
  */
 
 package org.icgc.argo.program_service.security;

src/main/java/org/icgc/argo/program_service/services/ProgramService.java

@@ -36,17 +36,23 @@
 import java.util.List;
 import java.util.Optional;
 import java.util.Set;
+import java.util.UUID;
 import java.util.function.Consumer;
 import java.util.function.Predicate;
 import javax.validation.ValidatorFactory;
+
+import io.netty.util.internal.StringUtil;
 import lombok.NonNull;
 import lombok.extern.slf4j.Slf4j;
 import lombok.val;
+import org.apache.commons.lang.StringUtils;
 import org.icgc.argo.program_service.converter.DataCenterConverter;
 import org.icgc.argo.program_service.converter.ProgramConverter;
 import org.icgc.argo.program_service.model.dto.DataCenterRequestDTO;
 import org.icgc.argo.program_service.model.entity.*;
+import org.icgc.argo.program_service.model.exceptions.BadRequestException;
 import org.icgc.argo.program_service.model.exceptions.NotFoundException;
+import org.icgc.argo.program_service.model.exceptions.RecordNotFoundException;
 import org.icgc.argo.program_service.model.join.*;
 import org.icgc.argo.program_service.proto.Program;
 import org.icgc.argo.program_service.repositories.*;
@@ -159,16 +165,63 @@ public ProgramEntity getProgram(@NonNull String name, boolean allowInactive) {
   }
 
   public ProgramEntity createWithSideEffect(
-      @NonNull Program program, Consumer<ProgramEntity> consumer) {
+          @NonNull Program program, Consumer<ProgramEntity> consumer) {
     val programEntity = createProgram(program);
     consumer.accept(programEntity);
     return programEntity;
   }
 
+  public ProgramEntity createWithSideEffect(
+          @NonNull Program program, Consumer<ProgramEntity> consumer, UUID dataCenterId) {
+    val programEntity = createProgram(program, dataCenterId);
+    consumer.accept(programEntity);
+    return programEntity;
+  }
   public ProgramEntity createProgram(@NonNull Program program)
+          throws DataIntegrityViolationException {
+    val programEntity = programConverter.programToProgramEntity(program);
+
+    val now = LocalDateTime.now(ZoneId.of("UTC"));
+    programEntity.setCreatedAt(now);
+    programEntity.setUpdatedAt(now);
+
+    val p = programRepository.save(programEntity);
+    val cancers = cancerRepository.findAllByNameIn(program.getCancerTypesList());
+    val primarySites = primarySiteRepository.findAllByNameIn(program.getPrimarySitesList());
+    val countries = countryRepository.findAllByNameIn(program.getCountriesList());
+    List<InstitutionEntity> institutions =
+            institutionRepository.findAllByNameIn(program.getInstitutionsList());
+    if (institutions.size() != program.getInstitutionsList().size()) {
+      institutions = filterAndAddInstitutions(program.getInstitutionsList());
+    }
+
+    List<ProgramCancer> programCancers = mapToList(cancers, x -> createProgramCancer(p, x).get());
+    List<ProgramPrimarySite> programPrimarySites =
+            mapToList(primarySites, x -> createProgramPrimarySite(p, x).get());
+    List<ProgramInstitution> programInstitutions =
+            mapToList(institutions, x -> createProgramInstitution(p, x).get());
+    List<ProgramCountry> programCountries =
+            mapToList(countries, x -> createProgramCountry(p, x).get());
+
+    programCancerRepository.saveAll(programCancers);
+    programPrimarySiteRepository.saveAll(programPrimarySites);
+    programInstitutionRepository.saveAll(programInstitutions);
+    programCountryRepository.saveAll(programCountries);
+
+    return programEntity;
+  }
+  public ProgramEntity createProgram(@NonNull Program program, UUID dataCenterId)
       throws DataIntegrityViolationException {
     val programEntity = programConverter.programToProgramEntity(program);
 
+    if (dataCenterId == null) {
+      throw new BadRequestException("DataCenterId cannot be null or empty");
+    }
+    val dataCenterEntity = dataCenterRepository.findById(dataCenterId);
+    if (dataCenterEntity.isEmpty()) {
+      throw new RecordNotFoundException("DataCenterId '" + dataCenterId + "' not found");
+    }
+    programEntity.setDataCenterId(dataCenterId);
     val now = LocalDateTime.now(ZoneId.of("UTC"));
     programEntity.setCreatedAt(now);
     programEntity.setUpdatedAt(now);