Merge pull request #28 from Breeding-Insight/release/0.9

Merging release v0.9

Author: mlm483

.github/pull.yml

@@ -0,0 +1,11 @@
+version: "1"
+rules:
+  - base: develop
+    upstream: plantbreeding:brapi-server-v2
+    mergeMethod: merge
+    assignees:
+      - nickpalladino
+      - mlm483
+      - dmeidlin
+      - davedrp
+label: "upstream-merge"

README.md

@@ -34,9 +34,11 @@ Use [/calls](https://test-server.brapi.org/brapi/v1/call) (V1) or [/serverinfo](
 
 ## DataBase
 
-The database is created automatically at run time thanks to Java Spring Data and Hibernate. All dummy data is loaded from the SQL files in the `/resources/sql` directory. Additional SQL files may be added, but they must be explicitly listed in the `application.properties` file to be loaded automatically.
+The database is created automatically at run time by [flyway](https://documentation.red-gate.com/flyway).
+SQL-based migrations under `src/main/resources/db/migration` or `src/main/resources/db/sql`, and Java-based migrations under `src/main/java/org/brapi/test/BrAPITestServer/db/migration` will be run.
+The `src/main/resources/db/migration` directory is for schema changes, while `src/main/resources/db/sql` is for seed data. Modify `spring.flyway.locations` in `application.properties` to change what flyway runs.
 
-When running in Docker, you can edit or add dummy data by adding the volume `-v /<Local_Path_To_SQL>/:/home/brapi/sql` to your docker command. 
+When running in Docker, you can edit or add seed data by adding the volume `-v /<Local_Path_To_SQL>/:/home/brapi/sql` to your docker command. 
 
 Below is a UML diagram of the whole database schema:
 

pom.xml

@@ -22,10 +22,15 @@
 	</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>
-			<version>42.4.3</version>
+			<version>42.7.2</version>
 		</dependency>
 		<dependency>
 			<groupId>jakarta.validation</groupId>

src/main/java/io/swagger/model/BrAPIDataModel.java

@@ -1,36 +1,25 @@
 package io.swagger.model;
 
-import java.util.HashMap;
-import java.util.Map;
-
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 public abstract class BrAPIDataModel {
 
 	@JsonProperty("additionalInfo")
-	protected Map<String, Object> additionalInfo = null;
+	protected Object additionalInfo = null;
 
 	@JsonProperty("externalReferences")
 	protected ExternalReferences externalReferences = null;
 
-	final public BrAPIDataModel additionalInfo(Map<String, Object> additionalInfo) {
+	final public BrAPIDataModel additionalInfo(Object additionalInfo) {
 		this.additionalInfo = additionalInfo;
 		return this;
 	}
 
-	final public BrAPIDataModel putAdditionalInfoItem(String key, String additionalInfoItem) {
-		if (this.additionalInfo == null) {
-			this.additionalInfo = new HashMap<String, Object>();
-		}
-		this.additionalInfo.put(key, additionalInfoItem);
-		return this;
-	}
-
-	final public Map<String, Object> getAdditionalInfo() {
+	final public Object getAdditionalInfo() {
 		return additionalInfo;
 	}
 
-	final public void setAdditionalInfo(Map<String, Object> additionalInfo) {
+	final public void setAdditionalInfo(Object additionalInfo) {
 		this.additionalInfo = additionalInfo;
 	}
 

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

@@ -5,8 +5,6 @@
 import io.swagger.annotations.ApiModelProperty;
 import io.swagger.model.ExternalReferences;
 
-import java.util.HashMap;
-import java.util.Map;
 import java.time.OffsetDateTime;
 import org.springframework.validation.annotation.Validated;
 import jakarta.validation.Valid;
@@ -19,7 +17,7 @@
 public class ListBaseFields implements ListBaseFieldsInterface  {
   @JsonProperty("additionalInfo")
   @Valid
-  private Map<String, Object> additionalInfo = null;
+  private Object additionalInfo = null;
 
   @JsonProperty("dateCreated")
   private OffsetDateTime dateCreated = null;
@@ -51,30 +49,23 @@ public class ListBaseFields implements ListBaseFieldsInterface  {
   @JsonProperty("listType")
   private ListTypes listType = null;
 
-  public ListBaseFields additionalInfo(Map<String, Object> additionalInfo) {
+  public ListBaseFields additionalInfo(Object additionalInfo) {
     this.additionalInfo = additionalInfo;
     return this;
   }
 
-  public ListBaseFields putAdditionalInfoItem(String key, String additionalInfoItem) {
-    if (this.additionalInfo == null) {
-      this.additionalInfo = new HashMap<String, Object>();
-    }
-    this.additionalInfo.put(key, additionalInfoItem);
-    return this;
-  }
-
   /**
    * Additional arbitrary info
+   *
    * @return additionalInfo
-  **/
+   **/
   @ApiModelProperty(example = "{}", value = "Additional arbitrary info")
 
-    public Map<String, Object> getAdditionalInfo() {
+    public Object getAdditionalInfo() {
     return additionalInfo;
   }
 
-  public void setAdditionalInfo(Map<String, Object> additionalInfo) {
+  public void setAdditionalInfo(Object additionalInfo) {
     this.additionalInfo = additionalInfo;
   }
 

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

@@ -1,19 +1,16 @@
 package io.swagger.model.core;
 
-import java.util.Map;
 import java.time.OffsetDateTime;
 
 import io.swagger.model.ExternalReferences;
 
 public interface ListBaseFieldsInterface {
 
-	public ListBaseFieldsInterface additionalInfo(Map<String, Object> additionalInfo);
+	public ListBaseFieldsInterface additionalInfo(Object additionalInfo);
 
-	public ListBaseFieldsInterface putAdditionalInfoItem(String key, String additionalInfoItem);
+	public Object getAdditionalInfo();
 
-	public Map<String, Object> getAdditionalInfo();
-
-	public void setAdditionalInfo(Map<String, Object> additionalInfo);
+	public void setAdditionalInfo(Object additionalInfo);
 
 	public ListBaseFieldsInterface dateCreated(OffsetDateTime dateCreated);
 

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

@@ -7,8 +7,6 @@
 import io.swagger.annotations.ApiModelProperty;
 import io.swagger.model.ExternalReferences;
 
-import java.util.HashMap;
-import java.util.Map;
 import org.springframework.validation.annotation.Validated;
 import jakarta.validation.Valid;
 
@@ -20,7 +18,7 @@
 public class PersonNewRequest   {
   @JsonProperty("additionalInfo")
   @Valid
-  private Map<String, Object> additionalInfo = null;
+  private Object additionalInfo = null;
 
   @JsonProperty("description")
   private String description = null;
@@ -49,30 +47,22 @@ public class PersonNewRequest   {
   @JsonProperty("userID")
   private String userID = null;
 
-  public PersonNewRequest additionalInfo(Map<String, Object> additionalInfo) {
+  public PersonNewRequest additionalInfo(Object additionalInfo) {
     this.additionalInfo = additionalInfo;
     return this;
   }
 
-  public PersonNewRequest putAdditionalInfoItem(String key, String additionalInfoItem) {
-    if (this.additionalInfo == null) {
-      this.additionalInfo = new HashMap<String, Object>();
-    }
-    this.additionalInfo.put(key, additionalInfoItem);
-    return this;
-  }
-
   /**
    * Additional arbitrary info
    * @return additionalInfo
   **/
   @ApiModelProperty(value = "Additional arbitrary info")
 
-    public Map<String, Object> getAdditionalInfo() {
+    public Object getAdditionalInfo() {
     return additionalInfo;
   }
 
-  public void setAdditionalInfo(Map<String, Object> additionalInfo) {
+  public void setAdditionalInfo(Object additionalInfo) {
     this.additionalInfo = additionalInfo;
   }
 

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

@@ -8,9 +8,7 @@
 import io.swagger.model.ExternalReferences;
 
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 import java.time.LocalDate;
 import org.springframework.validation.annotation.Validated;
 import jakarta.validation.Valid;
@@ -26,7 +24,7 @@ public class TrialNewRequest   {
 
   @JsonProperty("additionalInfo")
   @Valid
-  private Map<String, Object> additionalInfo = null;
+  private Object additionalInfo = null;
 
   @JsonProperty("commonCropName")
   private String commonCropName = null;
@@ -89,30 +87,22 @@ public void setActive(Boolean active) {
     this.active = active;
   }
 
-  public TrialNewRequest additionalInfo(Map<String, Object> additionalInfo) {
+  public TrialNewRequest additionalInfo(Object additionalInfo) {
     this.additionalInfo = additionalInfo;
     return this;
   }
 
-  public TrialNewRequest putAdditionalInfoItem(String key, String additionalInfoItem) {
-    if (this.additionalInfo == null) {
-      this.additionalInfo = new HashMap<String, Object>();
-    }
-    this.additionalInfo.put(key, additionalInfoItem);
-    return this;
-  }
-
   /**
    * Additional arbitrary info
    * @return additionalInfo
   **/
   @ApiModelProperty(value = "Additional arbitrary info")
 
-    public Map<String, Object> getAdditionalInfo() {
+    public Object getAdditionalInfo() {
     return additionalInfo;
   }
 
-  public void setAdditionalInfo(Map<String, Object> additionalInfo) {
+  public void setAdditionalInfo(Object additionalInfo) {
     this.additionalInfo = additionalInfo;
   }
 

src/main/java/io/swagger/model/geno/Call.java

@@ -4,13 +4,11 @@
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 
 public class Call {
 	@JsonProperty("additionalInfo")
-	private Map<String, Object> additionalInfo = null;
+	private Object additionalInfo = null;
 
 	@JsonProperty("callSetDbId")
 	private String callSetDbId = null;
@@ -79,24 +77,16 @@ public Call addGenotypeMetadataItem(CallGenotypeMetadata genotypeMetadata) {
 		return this;
 	}
 
-	public Call additionalInfo(Map<String, Object> additionalInfo) {
+	public Call additionalInfo(Object additionalInfo) {
 		this.additionalInfo = additionalInfo;
 		return this;
 	}
 
-	public Call putAdditionalInfoItem(String key, String additionalInfoItem) {
-		if (this.additionalInfo == null) {
-			this.additionalInfo = new HashMap<String, Object>();
-		}
-		this.additionalInfo.put(key, additionalInfoItem);
-		return this;
-	}
-
-	public Map<String, Object> getAdditionalInfo() {
+	public Object getAdditionalInfo() {
 		return additionalInfo;
 	}
 
-	public void setAdditionalInfo(Map<String, Object> additionalInfo) {
+	public void setAdditionalInfo(Object additionalInfo) {
 		this.additionalInfo = additionalInfo;
 	}
 

src/main/java/io/swagger/model/geno/GenomeMap.java

@@ -5,8 +5,6 @@
 
 
 import io.swagger.annotations.ApiModelProperty;
-import java.util.HashMap;
-import java.util.Map;
 import java.time.OffsetDateTime;
 import org.springframework.validation.annotation.Validated;
 import jakarta.validation.Valid;
@@ -20,7 +18,7 @@
 public class GenomeMap   {
   @JsonProperty("additionalInfo")
   @Valid
-  private Map<String, Object> additionalInfo = null;
+  private Object additionalInfo = null;
 
   @JsonProperty("comments")
   private String comments = null;
@@ -58,30 +56,22 @@ public class GenomeMap   {
   @JsonProperty("unit")
   private String unit = null;
 
-  public GenomeMap additionalInfo(Map<String, Object> additionalInfo) {
+  public GenomeMap additionalInfo(Object additionalInfo) {
     this.additionalInfo = additionalInfo;
     return this;
   }
 
-  public GenomeMap putAdditionalInfoItem(String key, String additionalInfoItem) {
-    if (this.additionalInfo == null) {
-      this.additionalInfo = new HashMap<String, Object>();
-    }
-    this.additionalInfo.put(key, additionalInfoItem);
-    return this;
-  }
-
   /**
    * Additional arbitrary info
    * @return additionalInfo
   **/
   @ApiModelProperty(value = "Additional arbitrary info")
 
-    public Map<String, Object> getAdditionalInfo() {
+    public Object getAdditionalInfo() {
     return additionalInfo;
   }
 
-  public void setAdditionalInfo(Map<String, Object> additionalInfo) {
+  public void setAdditionalInfo(Object additionalInfo) {
     this.additionalInfo = additionalInfo;
   }