Merge pull request #18 from Breeding-Insight/release/0.8.1

Release v0.8.1

Author: mlm483

README.md

@@ -4,7 +4,7 @@
 This server implements all BrAPI calls. It is backed by a custom database with dummy data.
 
 * BrAPI V1 Base URL (v1.0, v1.1, v1.2, v1.3): [test-server.brapi.org/brapi/v1/](https://test-server.brapi.org/brapi/v1/)
-* BrAPI V2 Base URL (v2.0): [test-server.brapi.org/brapi/v2/](https://test-server.brapi.org/brapi/v2/)
+* BrAPI V2 Base URL (v2.0, v2.1): [test-server.brapi.org/brapi/v2/](https://test-server.brapi.org/brapi/v2/)
 
 Use [/calls](https://test-server.brapi.org/brapi/v1/call) (V1) or [/serverinfo](https://test-server.brapi.org/brapi/v2/serverinfo) (V2) to check the available endpoints.
 

pom.xml

@@ -25,7 +25,7 @@
 		<dependency>
 			<groupId>org.postgresql</groupId>
 			<artifactId>postgresql</artifactId>
-			<version>42.3.3</version>
+			<version>42.4.3</version>
 		</dependency>
 		<dependency>
 			<groupId>jakarta.validation</groupId>

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

@@ -1,101 +1,77 @@
 package io.swagger.model.core;
 
 import java.util.Objects;
-import com.fasterxml.jackson.annotation.JsonProperty;
 
-import io.swagger.annotations.ApiModel;
-import io.swagger.annotations.ApiModelProperty;
-import org.springframework.validation.annotation.Validated;
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.JsonProperty;
 
-/**
- * The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology
- */
-@ApiModel(description = "The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology")
-@Validated
-@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
-public class StudyExperimentalDesign   {
-  @JsonProperty("PUI")
-  private String PUI = null;
+public class StudyExperimentalDesign {
+	@JsonProperty("PUI")
+	private String PUI = null;
 
-  @JsonProperty("description")
-  private String description = null;
+	@JsonProperty("description")
+	private String description = null;
 
-  public StudyExperimentalDesign PUI(String PUI) {
-    this.PUI = PUI;
-    return this;
-  }
+	public StudyExperimentalDesign PUI(String PUI) {
+		this.PUI = PUI;
+		return this;
+	}
 
-  /**
-   * MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental  design of the study, in the form of an accession number from the Crop Ontology.
-   * @return PUI
-  **/
-  @ApiModelProperty(example = "CO_715:0000145", value = "MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental  design of the study, in the form of an accession number from the Crop Ontology.")
-  
-    public String getPUI() {
-    return PUI;
-  }
+	@JsonIgnore
+	public String getPUI() {
+		return PUI;
+	}
 
-  public void setPUI(String PUI) {
-    this.PUI = PUI;
-  }
+	public void setPUI(String PUI) {
+		this.PUI = PUI;
+	}
 
-  public StudyExperimentalDesign description(String description) {
-    this.description = description;
-    return this;
-  }
+	public StudyExperimentalDesign description(String description) {
+		this.description = description;
+		return this;
+	}
 
-  /**
-   * MIAPPE V1.1 (DM-22) Description of the experimental design - Short description of the experimental design, possibly including statistical design. In specific cases, e.g. legacy datasets or data computed from several studies, the experimental design can be \"unknown\"/\"NA\", \"aggregated/reduced data\", or simply 'none'.
-   * @return description
-  **/
-  @ApiModelProperty(example = "Lines were repeated twice at each location using a complete block design. In order to limit competition effects, each block was organized into four sub-blocks corresponding to earliest groups based on a prior information.", value = "MIAPPE V1.1 (DM-22) Description of the experimental design - Short description of the experimental design, possibly including statistical design. In specific cases, e.g. legacy datasets or data computed from several studies, the experimental design can be \"unknown\"/\"NA\", \"aggregated/reduced data\", or simply 'none'.")
-  
-    public String getDescription() {
-    return description;
-  }
+	public String getDescription() {
+		return description;
+	}
 
-  public void setDescription(String description) {
-    this.description = description;
-  }
+	public void setDescription(String description) {
+		this.description = description;
+	}
 
+	@Override
+	public boolean equals(java.lang.Object o) {
+		if (this == o) {
+			return true;
+		}
+		if (o == null || getClass() != o.getClass()) {
+			return false;
+		}
+		StudyExperimentalDesign studyNewRequestExperimentalDesign = (StudyExperimentalDesign) o;
+		return Objects.equals(this.PUI, studyNewRequestExperimentalDesign.PUI)
+				&& Objects.equals(this.description, studyNewRequestExperimentalDesign.description);
+	}
 
-  @Override
-  public boolean equals(java.lang.Object o) {
-    if (this == o) {
-      return true;
-    }
-    if (o == null || getClass() != o.getClass()) {
-      return false;
-    }
-    StudyExperimentalDesign studyNewRequestExperimentalDesign = (StudyExperimentalDesign) o;
-    return Objects.equals(this.PUI, studyNewRequestExperimentalDesign.PUI) &&
-        Objects.equals(this.description, studyNewRequestExperimentalDesign.description);
-  }
+	@Override
+	public int hashCode() {
+		return Objects.hash(PUI, description);
+	}
 
-  @Override
-  public int hashCode() {
-    return Objects.hash(PUI, description);
-  }
+	@Override
+	public String toString() {
+		StringBuilder sb = new StringBuilder();
+		sb.append("class StudyNewRequestExperimentalDesign {\n");
 
-  @Override
-  public String toString() {
-    StringBuilder sb = new StringBuilder();
-    sb.append("class StudyNewRequestExperimentalDesign {\n");
-    
-    sb.append("    PUI: ").append(toIndentedString(PUI)).append("\n");
-    sb.append("    description: ").append(toIndentedString(description)).append("\n");
-    sb.append("}");
-    return sb.toString();
-  }
+		sb.append("    PUI: ").append(toIndentedString(PUI)).append("\n");
+		sb.append("    description: ").append(toIndentedString(description)).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    ");
-  }
+	private String toIndentedString(java.lang.Object o) {
+		if (o == null) {
+			return "null";
+		}
+		return o.toString().replace("\n", "\n    ");
+	}
 }

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

@@ -1,101 +1,77 @@
 package io.swagger.model.core;
 
 import java.util.Objects;
-import com.fasterxml.jackson.annotation.JsonProperty;
 
-import io.swagger.annotations.ApiModel;
-import io.swagger.annotations.ApiModelProperty;
-import org.springframework.validation.annotation.Validated;
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.JsonProperty;
 
-/**
- * Short description of the facility in which the study was carried out.
- */
-@ApiModel(description = "Short description of the facility in which the study was carried out.")
-@Validated
-@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
-public class StudyGrowthFacility   {
-  @JsonProperty("PUI")
-  private String PUI = null;
+public class StudyGrowthFacility {
+	@JsonProperty("PUI")
+	private String PUI = null;
 
-  @JsonProperty("description")
-  private String description = null;
+	@JsonProperty("description")
+	private String description = null;
 
-  public StudyGrowthFacility PUI(String PUI) {
-    this.PUI = PUI;
-    return this;
-  }
+	public StudyGrowthFacility PUI(String PUI) {
+		this.PUI = PUI;
+		return this;
+	}
 
-  /**
-   * MIAPPE V1.1 (DM-27) Type of growth facility - Type of growth facility in which the study was carried out, in the form of an accession number from the Crop Ontology.
-   * @return PUI
-  **/
-  @ApiModelProperty(example = "CO_715:0000162", value = "MIAPPE V1.1 (DM-27) Type of growth facility - Type of growth facility in which the study was carried out, in the form of an accession number from the Crop Ontology.")
-  
-    public String getPUI() {
-    return PUI;
-  }
+	@JsonIgnore
+	public String getPUI() {
+		return PUI;
+	}
 
-  public void setPUI(String PUI) {
-    this.PUI = PUI;
-  }
+	public void setPUI(String PUI) {
+		this.PUI = PUI;
+	}
 
-  public StudyGrowthFacility description(String description) {
-    this.description = description;
-    return this;
-  }
+	public StudyGrowthFacility description(String description) {
+		this.description = description;
+		return this;
+	}
 
-  /**
-   * MIAPPE V1.1 (DM-26) Description of growth facility - Short description of the facility in which the study was carried out.
-   * @return description
-  **/
-  @ApiModelProperty(example = "field environment condition, greenhouse", value = "MIAPPE V1.1 (DM-26) Description of growth facility - Short description of the facility in which the study was carried out.")
-  
-    public String getDescription() {
-    return description;
-  }
+	public String getDescription() {
+		return description;
+	}
 
-  public void setDescription(String description) {
-    this.description = description;
-  }
+	public void setDescription(String description) {
+		this.description = description;
+	}
 
+	@Override
+	public boolean equals(java.lang.Object o) {
+		if (this == o) {
+			return true;
+		}
+		if (o == null || getClass() != o.getClass()) {
+			return false;
+		}
+		StudyGrowthFacility studyNewRequestGrowthFacility = (StudyGrowthFacility) o;
+		return Objects.equals(this.PUI, studyNewRequestGrowthFacility.PUI)
+				&& Objects.equals(this.description, studyNewRequestGrowthFacility.description);
+	}
 
-  @Override
-  public boolean equals(java.lang.Object o) {
-    if (this == o) {
-      return true;
-    }
-    if (o == null || getClass() != o.getClass()) {
-      return false;
-    }
-    StudyGrowthFacility studyNewRequestGrowthFacility = (StudyGrowthFacility) o;
-    return Objects.equals(this.PUI, studyNewRequestGrowthFacility.PUI) &&
-        Objects.equals(this.description, studyNewRequestGrowthFacility.description);
-  }
+	@Override
+	public int hashCode() {
+		return Objects.hash(PUI, description);
+	}
 
-  @Override
-  public int hashCode() {
-    return Objects.hash(PUI, description);
-  }
+	@Override
+	public String toString() {
+		StringBuilder sb = new StringBuilder();
+		sb.append("class StudyNewRequestGrowthFacility {\n");
 
-  @Override
-  public String toString() {
-    StringBuilder sb = new StringBuilder();
-    sb.append("class StudyNewRequestGrowthFacility {\n");
-    
-    sb.append("    PUI: ").append(toIndentedString(PUI)).append("\n");
-    sb.append("    description: ").append(toIndentedString(description)).append("\n");
-    sb.append("}");
-    return sb.toString();
-  }
+		sb.append("    PUI: ").append(toIndentedString(PUI)).append("\n");
+		sb.append("    description: ").append(toIndentedString(description)).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    ");
-  }
+	private String toIndentedString(java.lang.Object o) {
+		if (o == null) {
+			return "null";
+		}
+		return o.toString().replace("\n", "\n    ");
+	}
 }

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

@@ -37,25 +37,25 @@ public class PedigreeSearchRequest extends SearchRequest {
 	private List<String> germplasmPUIs = null;
 
 	@JsonProperty("includeFullTree")
-	private Boolean includeFullTree = null;
+	private Boolean includeFullTree = false;
 
 	@JsonProperty("includeParents")
-	private Boolean includeParents = null;
+	private Boolean includeParents = true;
 
 	@JsonProperty("includeProgeny")
-	private Boolean includeProgeny = null;
+	private Boolean includeProgeny = true;
 
 	@JsonProperty("includeSiblings")
-	private Boolean includeSiblings = null;
+	private Boolean includeSiblings = false;
 
 	@JsonProperty("instituteCodes")
 	private List<String> instituteCodes = null;
 
 	@JsonProperty("pedigreeDepth")
-	private Integer pedigreeDepth = null;
+	private Integer pedigreeDepth = 1;
 
 	@JsonProperty("progenyDepth")
-	private Integer progenyDepth = null;
+	private Integer progenyDepth = 1;
 
 	@JsonProperty("programDbIds")
 	private List<String> programDbIds = null;