Add Spring AI for OQL Assistant

.gitignore

@@ -74,6 +74,7 @@ portal/src/main/webapp/WEB-INF/logback.xml
 firehose-importer/reference_data/gene_info
 portal.properties
 src/main/resources/application.properties
+microservices/assistant/src/main/resources/application.properties
 importer.properties
 log4j.properties
 build.properties

microservices/assistant/Dockerfile

@@ -0,0 +1,19 @@
+FROM maven:3-eclipse-temurin-17 as build
+
+WORKDIR /assistant
+
+COPY pom.xml .
+
+RUN mvn dependency:go-offline --fail-never
+
+COPY src ./src
+
+RUN mvn install package -DskipTests
+
+FROM eclipse-temurin:17-jre-jammy
+
+WORKDIR /assistant
+
+COPY --from=build /assistant/target/assistant.jar .
+
+ENTRYPOINT ["java","-jar","assistant.jar"]

microservices/assistant/pom.xml

@@ -0,0 +1,257 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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>org.cbioportal.assistant</groupId>
+    <artifactId>assistant</artifactId>
+    <version>1.0.0-SNAPSHOT</version>
+    <packaging>jar</packaging>
+
+    <name>gene-assistant</name>
+    <description>Gene Assistant Microservice</description>
+
+    <properties>
+        <java.version>17</java.version>
+        <maven.compiler.source>${java.version}</maven.compiler.source>
+        <maven.compiler.target>${java.version}</maven.compiler.target>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <spring-boot.version>3.2.5</spring-boot.version>
+        <jib-maven-plugin.version>3.4.2</jib-maven-plugin.version>
+        <spotless.version>2.43.0</spotless.version>
+        <jacoco.version>0.8.12</jacoco.version>
+        <maven-failsafe-plugin.version>3.2.5</maven-failsafe-plugin.version>
+        <maven-surefire-plugin.version>3.2.5</maven-surefire-plugin.version>
+        <build-helper-maven-plugin.version>3.6.0</build-helper-maven-plugin.version>
+        <test.server.port>8080</test.server.port>
+    </properties>
+
+    <dependencyManagement>
+        <dependencies>
+            <dependency>
+                <groupId>org.springframework.boot</groupId>
+                <artifactId>spring-boot-dependencies</artifactId>
+                <version>${spring-boot.version}</version>
+                <type>pom</type>
+                <scope>import</scope>
+            </dependency>
+        </dependencies>
+    </dependencyManagement>
+
+    <dependencies>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-actuator</artifactId>
+        </dependency>
+        <dependency>
+          <groupId>org.springframework.ai</groupId>
+          <artifactId>spring-ai-starter-model-azure-openai</artifactId>
+          <version>1.0.3</version>
+        </dependency>
+        <dependency>
+          <groupId>org.springframework.ai</groupId>
+          <artifactId>spring-ai-azure-openai</artifactId>
+          <version>1.0.3</version>
+        </dependency>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-data-jpa</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-thymeleaf</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-web</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-devtools</artifactId>
+            <scope>runtime</scope>
+            <optional>true</optional>
+        </dependency>
+        <dependency>
+            <groupId>com.h2database</groupId>
+            <artifactId>h2</artifactId>
+            <scope>runtime</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.projectlombok</groupId>
+            <artifactId>lombok</artifactId>
+            <optional>true</optional>
+        </dependency>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-test</artifactId>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+
+    <build>
+        <finalName>${project.artifactId}</finalName>
+        <plugins>
+            <plugin>
+                <groupId>org.springframework.boot</groupId>
+                <artifactId>spring-boot-maven-plugin</artifactId>
+                <version>${spring-boot.version}</version>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>repackage</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>3.13.0</version>
+                <configuration>
+                    <source>${java.version}</source>
+                    <target>${java.version}</target>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <version>${maven-surefire-plugin.version}</version>
+                <configuration>
+                    <runOrder>random</runOrder>
+                    <rerunFailingTestsCount>1</rerunFailingTestsCount>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.jacoco</groupId>
+                <artifactId>jacoco-maven-plugin</artifactId>
+                <version>${jacoco.version}</version>
+                <executions>
+                    <execution>
+                        <id>default-prepare-agent</id>
+                        <goals>
+                            <goal>prepare-agent</goal>
+                        </goals>
+                    </execution>
+                    <execution>
+                        <id>default-report</id>
+                        <phase>test</phase>
+                        <goals>
+                            <goal>report</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-failsafe-plugin</artifactId>
+                <version>${maven-failsafe-plugin.version}</version>
+                <configuration>
+                    <classesDirectory>${project.build.outputDirectory}</classesDirectory>
+                </configuration>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>integration-test</goal>
+                            <goal>verify</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>com.diffplug.spotless</groupId>
+                <artifactId>spotless-maven-plugin</artifactId>
+                <version>${spotless.version}</version>
+                <configuration>
+                    <java>
+                        <googleJavaFormat>
+                            <version>1.25.2</version>
+                            <style>AOSP</style>
+                        </googleJavaFormat>
+                    </java>
+                </configuration>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>check</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>build-helper-maven-plugin</artifactId>
+                <version>${build-helper-maven-plugin.version}</version>
+                <executions>
+                    <execution>
+                        <id>reserve-network-port</id>
+                        <goals>
+                            <goal>reserve-network-port</goal>
+                        </goals>
+                        <phase>process-resources</phase>
+                        <configuration>
+                            <portNames>
+                                <portName>test.server.port</portName>
+                            </portNames>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+
+    <profiles>
+        <profile>
+            <id>jib</id>
+            <activation>
+                <activeByDefault>false</activeByDefault>
+            </activation>
+            <build>
+                <plugins>
+                    <plugin>
+                        <groupId>com.google.cloud.tools</groupId>
+                        <artifactId>jib-maven-plugin</artifactId>
+                        <version>${jib-maven-plugin.version}</version>
+                        <configuration>
+                            <from>
+                                <image>eclipse-temurin:17-jre-jammy</image>
+                            </from>
+                            <to>
+                                <image>ghcr.io/cbioportal/gene-assistant:${project.version}</image>
+                            </to>
+                            <container>
+                                <ports>
+                                    <port>8080</port>
+                                </ports>
+                            </container>
+                        </configuration>
+                        <executions>
+                            <execution>
+                                <goals>
+                                    <goal>build</goal>
+                                </goals>
+                                <phase>package</phase>
+                            </execution>
+                        </executions>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
+    </profiles>
+
+    <repositories>
+        <repository>
+            <id>central</id>
+            <url>https://repo.maven.apache.org/maven2</url>
+        </repository>
+    </repositories>
+
+    <distributionManagement>
+        <repository>
+            <id>github</id>
+            <name>GitHub Packages</name>
+            <url>https://maven.pkg.github.com/cbioportal/cbioportal</url>
+        </repository>
+    </distributionManagement>
+
+</project>

microservices/assistant/src/main/java/org/cbioportal/assistant/Application.java

@@ -0,0 +1,44 @@
+package org.cbioportal.assistant;
+
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.media.Schema;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import org.springframework.ai.chat.model.ChatResponse;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.SpringApplication;
+import org.springframework.boot.autoconfigure.SpringBootApplication;
+import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.PostMapping;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RestController;
+
+@SpringBootApplication
+@RestController
+@ConditionalOnProperty(name = "spring.ai.enabled", havingValue = "true")
+public class Application {
+
+    public static void main(String[] args) {
+        SpringApplication.run(Application.class, args);
+    }
+
+    private final AssistantService assistantService;
+
+    @Autowired
+    public Application(AssistantService assistantService) {
+        this.assistantService = assistantService;
+    }
+
+    @Operation(description = "Send query to AI model for gene assistance")
+    @ApiResponse(
+            responseCode = "200",
+            description = "OK",
+            content = @Content(schema = @Schema(implementation = ChatResponse.class)))
+    @PostMapping(value = "/", produces = MediaType.APPLICATION_JSON_VALUE)
+    public ResponseEntity<String> fetchGeneAssistantResponse(@RequestBody String message) {
+        ChatResponse chatResponse = assistantService.generateResponse(message);
+        return ResponseEntity.ok(chatResponse.getResult().getOutput().getText().toString());
+    }
+}

microservices/assistant/src/main/java/org/cbioportal/assistant/AssistantService.java

@@ -0,0 +1,47 @@
+package org.cbioportal.assistant;
+
+import java.io.IOException;
+import java.io.UncheckedIOException;
+import java.nio.charset.StandardCharsets;
+import java.util.List;
+import org.springframework.ai.chat.messages.Message;
+import org.springframework.ai.chat.messages.SystemMessage;
+import org.springframework.ai.chat.messages.UserMessage;
+import org.springframework.ai.chat.model.ChatModel;
+import org.springframework.ai.chat.model.ChatResponse;
+import org.springframework.ai.chat.prompt.Prompt;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.core.io.ClassPathResource;
+import org.springframework.core.io.Resource;
+import org.springframework.stereotype.Service;
+
+@Service
+public class AssistantService {
+
+    private static final String OQL_CONTEXT_FILE = "oql-context.st";
+    private final ChatModel chatModel;
+
+    @Autowired
+    public AssistantService(ChatModel chatModel) {
+        this.chatModel = chatModel;
+    }
+
+    public ChatResponse generateResponse(String message) {
+        try {
+            Resource oqlContextResource = new ClassPathResource(OQL_CONTEXT_FILE);
+            String oqlContext =
+                    new String(
+                            oqlContextResource.getInputStream().readAllBytes(),
+                            StandardCharsets.UTF_8);
+            Message systemMessage = new SystemMessage(oqlContext);
+            Message userMessage = new UserMessage(message);
+
+            Prompt prompt = new Prompt(List.of(systemMessage, userMessage));
+            ChatResponse response = this.chatModel.call(prompt);
+            return response;
+
+        } catch (IOException e) {
+            throw new UncheckedIOException("Failed to read oql context prompt resource", e);
+        }
+    }
+}

microservices/assistant/src/main/resources/application.properties.EXAMPLE

@@ -0,0 +1,8 @@
+server.port=8090
+
+# Spring AI Properties 1.0.3, see https://docs.spring.io/spring-ai/reference/api/chatmodel.html for other configurable models
+spring.ai.enabled=true
+spring.ai.azure.openai.api-key=
+spring.ai.azure.openai.endpoint=
+spring.ai.azure.openai.chat.options.deployment-name=
+spring.ai.model.chat=