bug/BI-2817

.github/pull_request_template.md

@@ -0,0 +1,20 @@
+# Description
+**Story:** _Please include a link to the story in Jira_
+
+_Please include a summary of the change that was made._
+
+
+
+# Dependencies
+_Please include any dependencies to other code branches, testing configurations, scripts to be run, etc._
+
+# Testing
+_Please include any details needed for reviewers to test this code_
+
+
+# Checklist:
+
+- [ ] I have performed a self-review of my own code
+- [ ] I have tested my code and ensured it meets the acceptance criteria of the story
+- [ ] I have commented my code, particularly in hard-to-understand areas
+- [ ] I have either updated the source of truth or arranged for update with product owner if needed https://breedinginsight.atlassian.net/wiki/spaces/BI/pages/1559953409/Source+of+Truth

src/main/java/io/swagger/api/pheno/ObservationLevelNamesApi.java

@@ -0,0 +1,68 @@
+package io.swagger.api.pheno;
+
+import io.swagger.annotations.*;
+import io.swagger.model.pheno.*;
+import jakarta.validation.Valid;
+import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerException;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.*;
+
+import java.util.List;
+
+@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2024-05-21T16:32:22.556Z[GMT]")
+@Api(value = "observationlevelnames", description = "the observationlevelnames API")
+public interface ObservationLevelNamesApi {
+    @ApiOperation(value = "Get the Observation Level Names", nickname = "observationlevelnamesGet", notes = "Call to retrieve the list of supported observation level names", response = ObservationLevelListResponse.class, authorizations = {
+            @Authorization(value = "AuthorizationToken") }, tags = { "Observation level names", })
+    @ApiResponses(value = { @ApiResponse(code = 200, message = "OK", response = ObservationLevelListResponse.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 = "/observationlevelnames", produces = { "application/json" }, method = RequestMethod.GET)
+    ResponseEntity<ObservationLevelListResponse> observationlevelnamesGet(
+            @ApiParam(value = "programDbId") @Valid @RequestParam(value = "programDbId", required = false) String programDbId,
+            @ApiParam(value = "all") @Valid @RequestParam(value = "all", required = false) Boolean all,
+            @ApiParam(value = "page") @Valid @RequestParam(value = "page", required = false) Integer page,
+            @ApiParam(value = "pageSize") @Valid @RequestParam(value = "pageSize", required = false) Integer pageSize,
+            @ApiParam(value = "HTTP HEADER - Token used for Authorization   <strong> Bearer {token_string} </strong>") @RequestHeader(value = "Authorization", required = false) String authorization)
+            throws BrAPIServerException;
+
+    @ApiOperation(value = "Create Observation Level Names", nickname = "observationlevelnamesPost", notes = "Call to save a list of observation level names", response = ObservationLevelListResponse.class, authorizations = {
+            @Authorization(value = "AuthorizationToken") }, tags = { "Observation level names", })
+    @ApiResponses(value = { @ApiResponse(code = 200, message = "OK", response = ObservationLevelListResponse.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 = "/observationlevelnames", produces = { "application/json" }, method = RequestMethod.POST)
+    ResponseEntity<ObservationLevelListResponse> observationlevelnamesPost(
+            @ApiParam(value = "") @Valid @RequestBody List<ObservationLevelNewRequest> body,
+            @ApiParam(value = "HTTP HEADER - Token used for Authorization   <strong> Bearer {token_string} </strong>") @RequestHeader(value = "Authorization", required = false) String authorization)
+            throws BrAPIServerException;
+
+    @ApiOperation(value = "Delete Observation Level Names", nickname = "observationlevelnamesGet", notes = "Call to delete a list of observation level names", response = ObservationLevelListResponse.class, authorizations = {
+            @Authorization(value = "AuthorizationToken") }, tags = { "Observation level names", })
+    @ApiResponses(value = { @ApiResponse(code = 200, message = "OK", response = ObservationLevelListResponse.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 = "/observationlevelnames/{observationlevelnameDbId}", produces = { "application/json" }, method = RequestMethod.DELETE)
+    ResponseEntity<ObservationLevelListResponse> observationlevelnamesDelete(
+            @ApiParam(value = "The unique ID of this generic list", required = true) @PathVariable("observationlevelnameDbId") String observationLevelNameDbId,
+            @ApiParam(value = "HTTP HEADER - Token used for Authorization   <strong> Bearer {token_string} </strong>") @RequestHeader(value = "Authorization", required = false) String authorization)
+            throws BrAPIServerException;
+
+    @ApiOperation(value = "Update an existing Observation Level Name", nickname = "observationlevelnamesDbIdPut", notes = "Update an existing Observation Level Name", response = ObservationLevelListResponse.class, authorizations = {
+            @Authorization(value = "AuthorizationToken") }, tags = { "Observation Units", })
+    @ApiResponses(value = { @ApiResponse(code = 200, message = "OK", response = ObservationUnitHierarchyLevel.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 = "/observationlevelnames/{observationlevelnameDbId}", produces = { "application/json" }, consumes = {
+            "application/json" }, method = RequestMethod.PUT)
+    ResponseEntity<ObservationLevelSingleResponse> observationlevelnamesDbIdPut(
+            @ApiParam(value = "The unique ID of the specific Observation Level Name", required = true) @PathVariable("observationlevelnameDbId") String observationlevelnameDbId,
+            @ApiParam(value = "") @Valid @RequestBody ObservationLevelNewRequest body,
+            @ApiParam(value = "HTTP HEADER - Token used for Authorization   <strong> Bearer {token_string} </strong>") @RequestHeader(value = "Authorization", required = false) String authorization)
+            throws BrAPIServerException;
+}
+

src/main/java/io/swagger/model/core/StudyNewRequest.java

@@ -84,6 +84,9 @@ public class StudyNewRequest extends BrAPIDataModel{
 	@JsonProperty("trialDbId")
 	private String trialDbId = null;
 
+	@JsonProperty("programDbId")
+	private String programDbId = null;
+
 	@JsonProperty("trialName")
 	private String trialName = null;
 
@@ -463,6 +466,14 @@ public void setTrialDbId(String trialDbId) {
 		this.trialDbId = trialDbId;
 	}
 
+	public String getProgramDbId() {
+		return programDbId;
+	}
+
+	public void setProgramDbId(String programDbId) {
+		this.programDbId = programDbId;
+	}
+
 	public StudyNewRequest trialName(String trialName) {
 		this.trialName = trialName;
 		return this;

src/main/java/io/swagger/model/pheno/ObservationLevelNewRequest.java

@@ -0,0 +1,13 @@
+package io.swagger.model.pheno;
+
+public class ObservationLevelNewRequest extends ObservationUnitHierarchyLevel {
+    private Boolean global = null;
+
+    public Boolean getGlobal() {
+        return global;
+    }
+
+    public void setGlobal(Boolean value) {
+        this.global = value;
+    }
+}

src/main/java/io/swagger/model/pheno/ObservationLevelSingleResponse.java

@@ -0,0 +1,127 @@
+package io.swagger.model.pheno;
+
+import java.util.Objects;
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+
+import io.swagger.annotations.ApiModelProperty;
+import io.swagger.model.BrAPIResponse;
+import io.swagger.model.Context;
+import io.swagger.model.Metadata;
+
+import io.swagger.model.pheno.ObservationLevelListResponseResult;
+import org.springframework.validation.annotation.Validated;
+import jakarta.validation.Valid;
+
+
+/**
+ * ObservationLevelListResponse
+ */
+@Validated
+@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:32:22.556Z[GMT]")
+public class ObservationLevelSingleResponse implements BrAPIResponse<ObservationUnitHierarchyLevel>  {
+    @JsonProperty("@context")
+    private Context _atContext = null;
+
+    @JsonProperty("metadata")
+    private Metadata metadata = null;
+
+    @JsonProperty("result")
+    private ObservationUnitHierarchyLevel result = null;
+
+    public ObservationLevelSingleResponse _atContext(Context _atContext) {
+        this._atContext = _atContext;
+        return this;
+    }
+
+
+
+    public void set_atContext(Context _atContext) {
+        this._atContext = _atContext;
+    }
+
+    public ObservationLevelSingleResponse metadata(Metadata metadata) {
+        this.metadata = metadata;
+        return this;
+    }
+
+    /**
+     * Get metadata
+     * @return metadata
+     **/
+    @ApiModelProperty(required = true, value = "")
+
+
+    @Valid
+    public Metadata getMetadata() {
+        return metadata;
+    }
+
+    public void setMetadata(Metadata metadata) {
+        this.metadata = metadata;
+    }
+
+    public ObservationLevelSingleResponse result(ObservationUnitHierarchyLevel result) {
+        this.result = result;
+        return this;
+    }
+
+    /**
+     * Get result
+     * @return result
+     **/
+    @ApiModelProperty(required = true, value = "")
+
+
+    @Valid
+    public ObservationUnitHierarchyLevel getResult() {
+        return result;
+    }
+
+    public void setResult(ObservationUnitHierarchyLevel result) {
+        this.result = result;
+    }
+
+
+    @Override
+    public boolean equals(java.lang.Object o) {
+        if (this == o) {
+            return true;
+        }
+        if (o == null || getClass() != o.getClass()) {
+            return false;
+        }
+        ObservationLevelSingleResponse observationLevelSingleResponse = (ObservationLevelSingleResponse) o;
+        return Objects.equals(this._atContext, observationLevelSingleResponse._atContext) &&
+                Objects.equals(this.metadata, observationLevelSingleResponse.metadata) &&
+                Objects.equals(this.result, observationLevelSingleResponse.result);
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(_atContext, metadata, result);
+    }
+
+    @Override
+    public String toString() {
+        StringBuilder sb = new StringBuilder();
+        sb.append("class ObservationLevelListResponse {\n");
+
+        sb.append("    _atContext: ").append(toIndentedString(_atContext)).append("\n");
+        sb.append("    metadata: ").append(toIndentedString(metadata)).append("\n");
+        sb.append("    result: ").append(toIndentedString(result)).append("\n");
+        sb.append("}");
+        return sb.toString();
+    }
+
+    /**
+     * Convert the given object to string with each line indented by 4 spaces
+     * (except the first line).
+     */
+    private String toIndentedString(java.lang.Object o) {
+        if (o == null) {
+            return "null";
+        }
+        return o.toString().replace("\n", "\n    ");
+    }
+}

src/main/java/io/swagger/model/pheno/ObservationTableHeaderRowEnum.java

@@ -15,15 +15,7 @@ public enum ObservationTableHeaderRowEnum {
     GERMPLASMNAME("germplasmName"),
     POSITIONCOORDINATEX("positionCoordinateX"),
     POSITIONCOORDINATEY("positionCoordinateY"),
-    YEAR("year"),
-    FIELD("field"),
-    PLOT("plot"),
-    SUB_PLOT("sub-plot"),
-    PLANT("plant"),
-    POT("pot"),
-    BLOCK("block"),
-    ENTRY("entry"),
-    REP("rep");
+    YEAR("year");
 private String value;
 
     ObservationTableHeaderRowEnum(String value) {

src/main/java/io/swagger/model/pheno/ObservationUnitHierarchyLevel.java

@@ -2,26 +2,42 @@
 
 import java.util.Objects;
 
+import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 public class ObservationUnitHierarchyLevel {
 
+	@JsonProperty("levelNameDbId")
+	private String levelNameDbId = null;
+
 	@JsonProperty("levelName")
-	private ObservationUnitHierarchyLevelEnum levelName = null;
+	private String levelName = null;
 
 	@JsonProperty("levelOrder")
 	private Integer levelOrder = null;
 
-	public ObservationUnitHierarchyLevel levelName(ObservationUnitHierarchyLevelEnum levelName) {
-		this.levelName = levelName;
-		return this;
+	@JsonProperty("programDbId")
+	@JsonInclude(JsonInclude.Include.NON_NULL)
+	private String programDbId = null;
+
+	// NOTE: This property is NOT used for lookups, only responses.
+	@JsonProperty("programName")
+	@JsonInclude(JsonInclude.Include.NON_NULL)
+	private String programName = null;
+
+	public String getLevelNameDbId() {
+		return levelNameDbId;
+	}
+
+	public void setLevelNameDbId(String value) {
+		this.levelNameDbId = value;
 	}
 
-	public ObservationUnitHierarchyLevelEnum getLevelName() {
+	public String getLevelName() {
 		return levelName;
 	}
 
-	public void setLevelName(ObservationUnitHierarchyLevelEnum levelName) {
+	public void setLevelName(String levelName) {
 		this.levelName = levelName;
 	}
 
@@ -38,6 +54,22 @@ public void setLevelOrder(Integer levelOrder) {
 		this.levelOrder = levelOrder;
 	}
 
+	public String getProgramDbId() {
+		return programDbId;
+	}
+
+	public void setProgramDbId(String value) {
+		this.programDbId = value;
+	}
+
+	public String getProgramName() {
+		return programName;
+	}
+
+	public void setProgramName(String value) {
+		this.programName = value;
+	}
+
 	@Override
 	public boolean equals(java.lang.Object o) {
 		if (this == o) {
@@ -47,13 +79,12 @@ public boolean equals(java.lang.Object o) {
 			return false;
 		}
 		ObservationUnitHierarchyLevel observationUnitHierarchyLevel = (ObservationUnitHierarchyLevel) o;
-		return Objects.equals(this.levelName, observationUnitHierarchyLevel.levelName)
-				&& Objects.equals(this.levelOrder, observationUnitHierarchyLevel.levelOrder);
+		return Objects.equals(this.levelNameDbId, observationUnitHierarchyLevel.levelNameDbId);
 	}
 
 	@Override
 	public int hashCode() {
-		return Objects.hash(levelName, levelOrder);
+		return Objects.hash(levelNameDbId);
 	}
 
 	@Override
@@ -63,7 +94,9 @@ public String toString() {
 
 		sb.append("    levelName: ").append(toIndentedString(levelName)).append("\n");
 		sb.append("    levelOrder: ").append(toIndentedString(levelOrder)).append("\n");
-		sb.append("}");
+		sb.append("    levelNameDbId:  ").append(toIndentedString(levelNameDbId)).append("\n");
+		sb.append("    programDbId: ").append(toIndentedString(programDbId)).append("\n");
+		sb.append("    programName:  ").append(toIndentedString(programName)).append("\n");
 		return sb.toString();
 	}
 

src/main/java/io/swagger/model/pheno/ObservationUnitLevel.java

@@ -24,14 +24,14 @@ public boolean equals(Object obj) {
 		if (getClass() != obj.getClass())
 			return false;
 		ObservationUnitLevel other = (ObservationUnitLevel) obj;
-		return Objects.equals(levelCode, other.levelCode);
+		return Objects.equals(getLevelNameDbId(), other.getLevelNameDbId());
 	}
 
 	@Override
 	public int hashCode() {
 		final int prime = 31;
 		int result = super.hashCode();
-		result = prime * result + Objects.hash(levelCode);
+		result = prime * result + Objects.hash(getLevelNameDbId());
 		return result;
 	}
 

src/main/java/org/brapi/test/BrAPITestServer/auth/BrapiTestServerAuthConfig.java → src/main/java/org/brapi/test/BrAPITestServer/config/BrapiTestServerAuthConfig.java

@@ -1,5 +1,6 @@
-package org.brapi.test.BrAPITestServer.auth;
+package org.brapi.test.BrAPITestServer.config;
 
+import org.brapi.test.BrAPITestServer.auth.BrapiTestServerJWTAuthFilter;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;