Pull in latest from upstream.

pom.xml

@@ -22,6 +22,11 @@
 	</properties>
 
 	<dependencies>
+		<dependency>
+		    <groupId>org.flywaydb</groupId>
+		    <artifactId>flyway-core</artifactId>
+		    <version>7.7.3</version>
+		</dependency>
 		<dependency>
 			<groupId>org.postgresql</groupId>
 			<artifactId>postgresql</artifactId>

src/main/java/io/swagger/model/germ/PedigreeSearchRequest.java

@@ -654,20 +654,8 @@ public Integer getTotalParameterCount() {
 			count += this.germplasmNames.size();
 		if (this.germplasmPUIs != null)
 			count += this.germplasmPUIs.size();
-		if (this.includeFullTree != null)
-			count += 1;
-		if (this.includeParents != null)
-			count += 1;
-		if (this.includeProgeny != null)
-			count += 1;
-		if (this.includeSiblings != null)
-			count += 1;
 		if (this.instituteCodes != null)
 			count += this.instituteCodes.size();
-		if (this.pedigreeDepth != null)
-			count += 1;
-		if (this.progenyDepth != null)
-			count += 1;
 		if (this.programDbIds != null)
 			count += this.programDbIds.size();
 		if (this.programNames != null)

src/main/java/org/brapi/test/BrAPITestServer/BrapiTestServerConfig.java

@@ -53,5 +53,4 @@ public void addFormatters(FormatterRegistry registry) {
 		    }
 		};
 	}
-
 }

src/main/java/org/brapi/test/BrAPITestServer/auth/oldTokens/TokenController.java

@@ -0,0 +1,59 @@
+package org.brapi.test.BrAPITestServer.auth.oldTokens;
+
+import io.swagger.model.core.ServerInfoResponse;
+import io.swagger.annotations.ApiOperation;
+import io.swagger.annotations.ApiResponse;
+import io.swagger.annotations.ApiResponses;
+import io.swagger.annotations.Authorization;
+import org.brapi.test.BrAPITestServer.controller.core.BrAPIController;
+import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.stereotype.Controller;
+import org.springframework.web.bind.annotation.CrossOrigin;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+import javax.servlet.http.HttpServletRequest;
+
+@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
+@Controller
+public class TokenController extends BrAPIController {
+
+	private static final Logger log = LoggerFactory.getLogger(TokenController.class);
+
+	private final HttpServletRequest request;
+
+	@org.springframework.beans.factory.annotation.Autowired
+	public TokenController(HttpServletRequest request) {
+		this.request = request;
+	}
+
+	@ApiOperation(value = "Get the list of implemented Calls", nickname = "tokenPost", response = ServerInfoResponse.class, authorizations = {
+			@Authorization(value = "AuthorizationToken") }, tags = { "Server Info", })
+	@ApiResponses(value = { @ApiResponse(code = 200, message = "OK", response = ServerInfoResponse.class),
+			@ApiResponse(code = 400, message = "Bad Request", response = String.class),
+			@ApiResponse(code = 401, message = "Unauthorized", response = String.class),
+			@ApiResponse(code = 403, message = "Forbidden", response = String.class) })
+	@RequestMapping(value = "/token", produces = { "application/json" }, method = RequestMethod.POST)
+	@CrossOrigin
+	public ResponseEntity<TokenResponse> tokenPost(@RequestBody TokenRequest body)
+			throws BrAPIServerException {
+
+		log.debug("Request: " + request.getRequestURI());
+		validateSecurityContext(request, "ROLE_ANONYMOUS", "ROLE_USER");
+		validateAcceptHeader(request);
+
+		return new ResponseEntity<TokenResponse>(new TokenResponse(), HttpStatus.OK);
+	}
+
+	private class TokenResponse{
+		@JsonProperty("access_token")
+		private final String accessToken = "YYYY";
+	}
+}

src/main/java/org/brapi/test/BrAPITestServer/auth/oldTokens/TokenRequest.java

@@ -0,0 +1,33 @@
+package org.brapi.test.BrAPITestServer.auth.oldTokens;
+
+import java.util.Optional;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+public class TokenRequest {
+	@JsonProperty("username")
+	private Optional<String> username = null;
+
+	@JsonProperty("password")
+	private Optional<String> password = null;
+
+	public TokenRequest() {
+		// TODO Auto-generated constructor stub
+	}
+
+	public Optional<String> getUsername() {
+		return username;
+	}
+
+	public void setUsername(Optional<String> username) {
+		this.username = username;
+	}
+
+	public Optional<String> getPassword() {
+		return password;
+	}
+
+	public void setPassword(Optional<String> password) {
+		this.password = password;
+	}
+}

src/main/java/org/brapi/test/BrAPITestServer/model/entity/core/StudyEntity.java

@@ -308,5 +308,7 @@ public void setTrial(TrialEntity trial) {
 		this.trial = trial;
 		if (trial.getProgram() != null)
 			setProgram(trial.getProgram());
+		if (trial.getCrop() != null)
+			setCrop(trial.getCrop());
 	}
 }

src/main/java/org/brapi/test/BrAPITestServer/model/entity/pheno/ObservationUnitEntity.java

@@ -75,6 +75,8 @@ public void setTrial(TrialEntity trial) {
 		this.trial = trial;
 		if (trial.getProgram() != null)
 			setProgram(trial.getProgram());
+		if (trial.getCrop() != null)
+			setCrop(trial.getCrop());
 	}
 	public StudyEntity getStudy() {
 		return study;
@@ -83,6 +85,8 @@ public void setStudy(StudyEntity study) {
 		this.study = study;
 		if (study.getTrial() != null)
 			setTrial(study.getTrial());
+		if (study.getCrop() != null)
+			setCrop(study.getCrop());
 	}
 	public GermplasmEntity getGermplasm() {
 		return germplasm;

src/main/java/org/brapi/test/BrAPITestServer/service/core/StudyService.java

@@ -295,8 +295,6 @@ private void updateEntity(StudyEntity entity, StudyNewRequest body) throws BrAPI
 		if (body.getTrialDbId() != null) {
 			TrialEntity trial = trialService.getTrialEntity(body.getTrialDbId());
 			entity.setTrial(trial);
-			entity.setProgram(trial.getProgram());
-			entity.setCrop(trial.getCrop());
 		} else if (body.getCommonCropName() != null) {
 			CropEntity crop = cropService.getCropEntity(body.getCommonCropName());
 			entity.setCrop(crop);
@@ -374,11 +372,13 @@ private Study convertFromEntity(StudyEntity entity) {
 					study.setCommonCropName(entity.getTrial().getProgram().getCrop().getCropName());
 				}
 			}
-		} else if (entity.getProgram() != null) {
+		} 
+		if (entity.getProgram() != null) {
 			if (entity.getProgram().getCrop() != null) {
 				study.setCommonCropName(entity.getProgram().getCrop().getCropName());
 			}
-		} else if (entity.getCrop() != null) {
+		} 
+		if (entity.getCrop() != null) {
 			study.setCommonCropName(entity.getCrop().getCropName());
 		}
 

src/main/java/org/brapi/test/BrAPITestServer/service/core/TrialService.java

@@ -195,7 +195,8 @@ private Trial convertFromEntity(TrialEntity entity) {
 			if (entity.getProgram().getCrop() != null) {
 				trial.setCommonCropName(entity.getProgram().getCrop().getCropName());
 			}
-		} else if (entity.getCrop() != null) {
+		}
+		if (entity.getCrop() != null) {
 			trial.setCommonCropName(entity.getCrop().getCropName());
 		}
 

src/main/java/org/brapi/test/BrAPITestServer/service/pheno/ObservationUnitService.java

@@ -416,14 +416,16 @@ private ObservationUnit convertFromEntity(ObservationUnitEntity entity) {
 					unit.setProgramName(entity.getStudy().getTrial().getProgram().getName());
 				}
 			}
-		} else if (entity.getTrial() != null) {
+		} 
+		if (entity.getTrial() != null) {
 			unit.setTrialDbId(entity.getTrial().getId());
 			unit.setTrialName(entity.getTrial().getTrialName());
 			if (entity.getTrial().getProgram() != null) {
 				unit.setProgramDbId(entity.getTrial().getProgram().getId());
 				unit.setProgramName(entity.getTrial().getProgram().getName());
 			}
-		} else if (entity.getProgram() != null) {
+		} 
+		if (entity.getProgram() != null) {
 			unit.setProgramDbId(entity.getProgram().getId());
 			unit.setProgramName(entity.getProgram().getName());
 		}