- Add field to federated query

- Add field to federated query
- Add it in agg search resource
- Also add some documentation about code formatting

README.md

@@ -11,6 +11,7 @@ This is the git repository for version 2+ of the PIC-SURE API.
 * Java 11
 * Before contributing code, please set up our git hook:
   `cp code-formatting/pre-commit.sh .git/hooks/pre-commit`
+    * To skip formatting on a block of code, wrap in `spotless:off`, `spotless:on` comments
 
 ## Build
 The build consists of the following top level maven modules:

pic-sure-resources/pic-sure-passthrough-resource/src/main/resources/META-INF/persistence.xml

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<persistence version="2.1"
+             xmlns="http://xmlns.jcp.org/xml/ns/persistence" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+             xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/persistence http://xmlns.jcp.org/xml/ns/persistence/persistence_2_1.xsd">
+    <persistence-unit name="picsure">
+    </persistence-unit>
+</persistence>

pic-sure-resources/pic-sure-passthrough-resource/src/main/resources/webapp/META-INF/context.xml

@@ -1,3 +1,3 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE xml>
-<Context/>
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE xml>
+<Context/>

pic-sure-resources/pic-sure-passthrough-resource/src/main/resources/webapp/WEB-INF/beans.xml

@@ -1,6 +1,6 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://xmlns.jcp.org/xml/ns/javaee"
-       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-       xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee http://xmlns.jcp.org/xml/ns/javaee/beans_1_1.xsd"
-       bean-discovery-mode="all">
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://xmlns.jcp.org/xml/ns/javaee"
+       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+       xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee http://xmlns.jcp.org/xml/ns/javaee/beans_1_1.xsd"
+       bean-discovery-mode="all">
 </beans>

pic-sure-resources/pic-sure-passthrough-resource/src/main/resources/webapp/WEB-INF/web.xml

@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="utf-8"?>
+<web-app xmlns="http://xmlns.jcp.org/xml/ns/javaee"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee
+         http://xmlns.jcp.org/xml/ns/javaee/web-app_3_1.xsd"
+         version="3.1">
+    <display-name>JAX-RS Simple Service</display-name>
+    <description>JAX-RS Simple Service</description>
+    <context-param>
+        <param-name>contextConfigLocation</param-name>
+        <param-value>webapp/WEB-INF/beans.xml</param-value>
+    </context-param>
+    <context-param>
+        <param-name>resteasy.scan</param-name>
+        <param-value>true</param-value>
+    </context-param>
+    <listener>
+        <listener-class>org.springframework.web.context.ContextLoaderListener</listener-class>
+    </listener>
+</web-app>

pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/FederatedQueryRequest.java

@@ -6,117 +6,132 @@
 import java.util.Map;
 import java.util.UUID;
 
+// spotless:off
 @Schema(name = "QueryRequest", description = "Object containing credentials map under 'resourceCredentials' and query" +
-		" object under 'query'. The query object expectedResultType can be on of the following " +
-		"\"COUNT\", \"CROSS_COUNT\", \"INFO_COLUMN_LISTING\", \"OBSERVATION_COUNT\", \"OBSERVATION_CROSS_COUNT\", \"DATAFRAME\". ",
-		example = "{\n" +
-				"    \"resourceUUID\": \"<RESOURCE UUID>\",\n" +
-				"    \"query\": {\n" +
-				"        \"categoryFilters\": {\n" +
-				"            \"\\\\demographics\\\\SEX\\\\\": [\n" +
-				"                \"female\",\n" +
-				"                \"male\"\n" +
-				"            ]\n" +
-				"        },\n" +
-				"        \"numericFilters\": {\n" +
-				"            \"\\\\demographics\\\\AGE\\\\\": {\n" +
-				"                \"min\": \"0\",\n" +
-				"                \"max\": \"85\"\n" +
-				"            }\n" +
-				"        },\n" +
-				"        \"requiredFields\": [],\n" +
-				"        \"anyRecordOf\": [\n" +
-				"            \"\\\\demographics\\\\RACE\\\\\"\n" +
-				"        ],\n" +
-				"        \"variantInfoFilters\": [\n" +
-				"            {\n" +
-				"                \"categoryVariantInfoFilters\": {},\n" +
-				"                \"numericVariantInfoFilters\": {}\n" +
-				"            }\n" +
-				"        ],\n" +
-				"        \"expectedResultType\": \"DATAFRAME\",\n" +
-				"        \"fields\": []\n" +
-				"    }\n" +
-				"}")
+	" object under 'query'. The query object expectedResultType can be on of the following " +
+	"\"COUNT\", \"CROSS_COUNT\", \"INFO_COLUMN_LISTING\", \"OBSERVATION_COUNT\", \"OBSERVATION_CROSS_COUNT\", \"DATAFRAME\". ",
+	example = "{\n" +
+		"    \"resourceUUID\": \"<RESOURCE UUID>\",\n" +
+		"    \"query\": {\n" +
+		"        \"categoryFilters\": {\n" +
+		"            \"\\\\demographics\\\\SEX\\\\\": [\n" +
+		"                \"female\",\n" +
+		"                \"male\"\n" +
+		"            ]\n" +
+		"        },\n" +
+		"        \"numericFilters\": {\n" +
+		"            \"\\\\demographics\\\\AGE\\\\\": {\n" +
+		"                \"min\": \"0\",\n" +
+		"                \"max\": \"85\"\n" +
+		"            }\n" +
+		"        },\n" +
+		"        \"requiredFields\": [],\n" +
+		"        \"anyRecordOf\": [\n" +
+		"            \"\\\\demographics\\\\RACE\\\\\"\n" +
+		"        ],\n" +
+		"        \"variantInfoFilters\": [\n" +
+		"            {\n" +
+		"                \"categoryVariantInfoFilters\": {},\n" +
+		"                \"numericVariantInfoFilters\": {}\n" +
+		"            }\n" +
+		"        ],\n" +
+		"        \"expectedResultType\": \"DATAFRAME\",\n" +
+		"        \"fields\": []\n" +
+		"    }\n" +
+		"}")
+
+//spotless:on
 
 /*
- * QueryRequests for vanilla GIC PIC-SURE. Includes details about the source
- * of the request, the requester, and any unifying identifiers for sharing
+ * QueryRequests for vanilla GIC PIC-SURE. Includes details about the source of the request, the requester, and any unifying identifiers for
+ * sharing
  */
 public class FederatedQueryRequest implements QueryRequest {
 
-	@Schema(hidden = true)
-	private Map<String, String> resourceCredentials = new HashMap<>();
-
-	@Schema(hidden = true)
-	private Object query;
-
-	@Schema(hidden = true)
-	private UUID resourceUUID;
-
-	@Schema(hidden = true)
-	private UUID commonAreaUUID;
-
-	@Schema(hidden = true)
-	private String institutionOfOrigin;
-
-	@Override
-	public Map<String, String> getResourceCredentials() {
-		return resourceCredentials;
-	}
-
-	@Override
-	public FederatedQueryRequest setResourceCredentials(Map<String, String> resourceCredentials) {
-		this.resourceCredentials = resourceCredentials;
-		return this;
-	}
-
-	@Override
-	public Object getQuery() {
-		return query;
-	}
-
-	@Override
-	public FederatedQueryRequest setQuery(Object query) {
-		this.query = query;
-		return this;
-	}
-
-	@Override
-	public UUID getResourceUUID() {
-		return resourceUUID;
-	}
-
-	@Override
-	public void setResourceUUID(UUID resourceUUID) {
-		this.resourceUUID = resourceUUID;
-	}
-
-	@Override
-	public FederatedQueryRequest copy() {
-		FederatedQueryRequest request = new FederatedQueryRequest();
-		request.setQuery(getQuery());
-		request.setResourceCredentials(getResourceCredentials());
-		request.setResourceUUID(getResourceUUID());
-		request.setCommonAreaUUID(getCommonAreaUUID());
-		request.setInstitutionOfOrigin(getInstitutionOfOrigin());
-
-		return request;
-	}
-
-	public UUID getCommonAreaUUID() {
-		return commonAreaUUID;
-	}
-
-	public void setCommonAreaUUID(UUID commonAreaUUID) {
-		this.commonAreaUUID = commonAreaUUID;
-	}
-
-	public String getInstitutionOfOrigin() {
-		return institutionOfOrigin;
-	}
-
-	public void setInstitutionOfOrigin(String institutionOfOrigin) {
-		this.institutionOfOrigin = institutionOfOrigin;
-	}
+    @Schema(hidden = true)
+    private Map<String, String> resourceCredentials = new HashMap<>();
+
+    @Schema(hidden = true)
+    private Object query;
+
+    @Schema(hidden = true)
+    private UUID resourceUUID;
+
+    @Schema(hidden = true)
+    private UUID commonAreaUUID;
+
+    @Schema(hidden = true)
+    private String institutionOfOrigin;
+
+    @Schema(hidden = true)
+    private String requesterEmail;
+
+    @Override
+    public Map<String, String> getResourceCredentials() {
+        return resourceCredentials;
+    }
+
+    @Override
+    public FederatedQueryRequest setResourceCredentials(Map<String, String> resourceCredentials) {
+        this.resourceCredentials = resourceCredentials;
+        return this;
+    }
+
+    @Override
+    public Object getQuery() {
+        return query;
+    }
+
+    @Override
+    public FederatedQueryRequest setQuery(Object query) {
+        this.query = query;
+        return this;
+    }
+
+    @Override
+    public UUID getResourceUUID() {
+        return resourceUUID;
+    }
+
+    @Override
+    public void setResourceUUID(UUID resourceUUID) {
+        this.resourceUUID = resourceUUID;
+    }
+
+    @Override
+    public FederatedQueryRequest copy() {
+        FederatedQueryRequest request = new FederatedQueryRequest();
+        request.setQuery(getQuery());
+        request.setResourceCredentials(getResourceCredentials());
+        request.setResourceUUID(getResourceUUID());
+        request.setCommonAreaUUID(getCommonAreaUUID());
+        request.setInstitutionOfOrigin(getInstitutionOfOrigin());
+        request.setRequesterEmail(getRequesterEmail());
+
+        return request;
+    }
+
+    public UUID getCommonAreaUUID() {
+        return commonAreaUUID;
+    }
+
+    public void setCommonAreaUUID(UUID commonAreaUUID) {
+        this.commonAreaUUID = commonAreaUUID;
+    }
+
+    public String getInstitutionOfOrigin() {
+        return institutionOfOrigin;
+    }
+
+    public void setInstitutionOfOrigin(String institutionOfOrigin) {
+        this.institutionOfOrigin = institutionOfOrigin;
+    }
+
+    public String getRequesterEmail() {
+        return requesterEmail;
+    }
+
+    public void setRequesterEmail(String requesterEmail) {
+        this.requesterEmail = requesterEmail;
+    }
 }

pom.xml

@@ -48,6 +48,7 @@
                 <version>4.26</version>
                 <file>code-formatting/eclipse-formatter.xml</file>
               </eclipse>
+              <toggleOffOn />
             </java>
           </configuration>
         </plugin>