first commit

code/backend/.classpath

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+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

code/backend/.project

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+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>HAf-backend</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+	</natures>
+</projectDescription>

code/backend/.settings/org.eclipse.core.resources.prefs

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+eclipse.preferences.version=1
+encoding//src/main/java=UTF-8
+encoding//src/test/java=UTF-8
+encoding/<project>=UTF-8

code/backend/.settings/org.eclipse.jdt.core.prefs

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+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
+org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=ignore
+org.eclipse.jdt.core.compiler.release=disabled
+org.eclipse.jdt.core.compiler.source=1.8

code/backend/.settings/org.eclipse.m2e.core.prefs

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+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1

code/backend/pom.xml

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+<project xmlns="http://maven.apache.org/POM/4.0.0"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+
+	<groupId>edu.ubi.sc</groupId>
+	<artifactId>HAf-backend</artifactId>
+	<version>0.0.1-SNAPSHOT</version>
+	<packaging>jar</packaging>
+
+	<name>HAf-backend</name>
+	<url>http://maven.apache.org</url>
+
+
+	<properties>
+		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+		<undertow.version>2.0.28.Final</undertow.version>
+		<maven.compiler.source>1.8</maven.compiler.source>
+		<maven.compiler.target>1.8</maven.compiler.target>
+	</properties>
+
+	<dependencies>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<version>3.8.1</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>io.undertow</groupId>
+			<artifactId>undertow-core</artifactId>
+			<version>${undertow.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>io.undertow</groupId>
+			<artifactId>undertow-servlet</artifactId>
+			<version>${undertow.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>io.undertow</groupId>
+			<artifactId>undertow-websockets-jsr</artifactId>
+			<version>${undertow.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>com.google.code.gson</groupId>
+			<artifactId>gson</artifactId>
+			<version>2.8.6</version>
+		</dependency>
+		<dependency>
+		    <groupId>org.apache.jena</groupId>
+		    <artifactId>apache-jena-libs</artifactId>
+		    <type>pom</type>
+		    <version>3.13.1</version>
+  		</dependency>
+
+	</dependencies>
+
+	<build>
+		<plugins>
+			<plugin>
+				<artifactId>maven-assembly-plugin</artifactId>
+				<executions>
+					<execution>
+						<phase>package</phase>
+						<goals>
+							<goal>single</goal>
+						</goals>
+					</execution>
+				</executions>
+				<configuration>
+					<archive>
+						<manifest>
+							<addClasspath>true</addClasspath>
+							<mainClass>edu.ubi.sc.haf.App</mainClass>
+						</manifest>
+					</archive>
+					<descriptorRefs>
+						<descriptorRef>jar-with-dependencies</descriptorRef>
+					</descriptorRefs>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>
+
+</project>

code/backend/src/main/java/edu/ubi/sc/haf/App.java

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+package edu.ubi.sc.haf;
+
+import io.undertow.Undertow;
+import io.undertow.server.handlers.BlockingHandler;
+
+
+public class App 
+{
+    public static void main( String[] args )
+    {
+        int serverPort = 8080;
+        if (args.length > 0 && !"".equals(args[0].trim())) {
+        	try {
+        	serverPort = Integer.parseInt(args[0].trim());
+        	} catch (NumberFormatException nfe) {
+        		System.err.println("Failed to parse port <" + args[0].trim() + ">. A numeric argument is required.");
+        		System.exit(1);
+        	}
+        }
+        System.err.println( "Starting up on port " + serverPort );
+        Undertow server = Undertow.builder()
+                .addHttpListener(serverPort, "localhost")
+                .setHandler(new BlockingHandler(new ServiceRequests())).build();
+        server.start();
+
+        System.err.println("Server listening on 127.0.0.1:" + serverPort);
+    }
+}

code/backend/src/main/java/edu/ubi/sc/haf/BackendInput.java

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+package edu.ubi.sc.haf;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import edu.ubi.sc.haf.core.RangeFilter;
+
+public class BackendInput {
+	public static String EFFICACY_STR = "efficacy";
+
+	public static String SAFETY_STR = "safety";
+
+	public static String DURATION_STR = "duration";
+
+	public static String NUM_PATIENTS_STR = "numPatients";
+
+	public static String AVG_AGE_STR = "avgAge";
+
+	public static String PUBLICATION_YEAR_STR = "publicationYear";
+
+	public String disease;
+
+	public String drug1;
+
+	public String drug2;
+
+	public HashMap<String, RangeFilter> filters; // duration,numPatients,avgAge
+
+	public HashMap<String,Double> weights;
+
+	public List<ClinicalTrial> evidence;
+
+	public boolean filtersModified;
+}
+

code/backend/src/main/java/edu/ubi/sc/haf/BackendInputMachineReading.java

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+package edu.ubi.sc.haf;
+
+import java.util.List;
+import java.util.HashMap;
+
+public class BackendInputMachineReading {
+	public String model1;
+
+	public String model2;
+
+	public List<String> included_datasets; // for checkboxes; names: squad, dream, race, race_m, race_h
+
+	public HashMap<String,Double> weights; // key names: accuracy, f1_score, exact_match
+}

code/backend/src/main/java/edu/ubi/sc/haf/BackendOutput.java

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+package edu.ubi.sc.haf;
+import java.util.List;
+import java.util.Map;
+
+public class BackendOutput {
+	public Map<String, Object> verbalization;
+
+	public List<ClinicalTrial> evidence;
+}

code/backend/src/main/java/edu/ubi/sc/haf/BackendOutputMachineReading.java

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+package edu.ubi.sc.haf;
+
+import java.util.Map;
+
+public class BackendOutputMachineReading {
+	public Map<String, Object> verbalization;
+
+	public ExperimentalEvidence	evidenceModel1;
+
+	public ExperimentalEvidence	evidenceModel2;
+}

code/backend/src/main/java/edu/ubi/sc/haf/ClinicalTrial.java

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+package edu.ubi.sc.haf;
+
+public class ClinicalTrial {
+	public String id;
+
+	public String link;
+
+	public String title;
+
+	public String authors;
+
+	public boolean include;
+
+	public String exclusionReason;
+
+	public double year;
+
+	public double duration;
+
+	public double numParticipants;
+
+	public double avgAge;
+
+	public String sponsors;
+
+	public String conflictOfInterest;
+
+	public String affiliation;
+
+	public String reasonOfBias;
+
+	public String abstractFullText;
+
+	public String studyDesign;
+
+	public String arm1Description;
+
+	public String arm2Description;
+}