Fix content type issue, move genomic processor service to hpds repo

genomic-processor/pom.xml

@@ -0,0 +1,60 @@
+<?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">
+    <parent>
+        <artifactId>pic-sure-hpds</artifactId>
+        <groupId>edu.harvard.hms.dbmi.avillach.hpds</groupId>
+        <version>3.0.0-SNAPSHOT</version>
+    </parent>
+    <modelVersion>4.0.0</modelVersion>
+
+    <artifactId>genomic-processor</artifactId>
+
+    <properties>
+        <maven.compiler.source>18</maven.compiler.source>
+        <maven.compiler.target>18</maven.compiler.target>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    </properties>
+
+
+    <dependencies>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-web</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-test</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.springframework</groupId>
+            <artifactId>spring-webflux</artifactId>
+        </dependency>
+
+        <dependency>
+            <groupId>edu.harvard.hms.dbmi.avillach.hpds</groupId>
+            <artifactId>service</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>edu.harvard.hms.dbmi.avillach.hpds</groupId>
+            <artifactId>etl</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>edu.harvard.hms.dbmi.avillach.hpds</groupId>
+            <artifactId>data</artifactId>
+        </dependency>
+    </dependencies>
+
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.springframework.boot</groupId>
+                <artifactId>spring-boot-maven-plugin</artifactId>
+            </plugin>
+        </plugins>
+    </build>
+
+</project>

genomic-processor/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/GenomicProcessorController.java

@@ -0,0 +1,47 @@
+package edu.harvard.hms.dbmi.avillach.hpds.genomic;
+
+import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.InfoColumnMeta;
+import edu.harvard.hms.dbmi.avillach.hpds.processing.DistributableQuery;
+import edu.harvard.hms.dbmi.avillach.hpds.processing.GenomicProcessor;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PostMapping;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RestController;
+import reactor.core.publisher.Mono;
+
+import java.math.BigInteger;
+import java.util.Collection;
+import java.util.List;
+
+
+@RestController
+public class GenomicProcessorController {
+
+    private GenomicProcessor genomicProcessor;
+
+    @Autowired
+    public GenomicProcessorController(GenomicProcessor genomicProcessor) {
+        this.genomicProcessor = genomicProcessor;
+    }
+
+    @PostMapping("/patients")
+    public Mono<BigInteger> queryForPatientMask(@RequestBody DistributableQuery distributableQuery) throws InterruptedException {
+        return genomicProcessor.getPatientMask(distributableQuery);
+    }
+
+    @PostMapping("/variants")
+    public Mono<Collection<String>> queryForVariants(@RequestBody DistributableQuery distributableQuery) {
+        return genomicProcessor.getVariantList(distributableQuery);
+    }
+
+    @GetMapping("/patients/ids")
+    public List<String> getPatientIds() {
+        return genomicProcessor.getPatientIds();
+    }
+
+    @GetMapping("/info/meta")
+    public List<InfoColumnMeta> getInfoMetadata() {
+        return genomicProcessor.getInfoColumnMeta();
+    }
+}

genomic-processor/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/HpdsGenomicProcessorApplication.java

@@ -0,0 +1,13 @@
+package edu.harvard.hms.dbmi.avillach.hpds.genomic;
+
+import org.springframework.boot.SpringApplication;
+import org.springframework.boot.autoconfigure.SpringBootApplication;
+
+@SpringBootApplication
+public class HpdsGenomicProcessorApplication {
+
+	public static void main(String[] args) {
+		SpringApplication.run(HpdsGenomicProcessorApplication.class, args);
+	}
+
+}

genomic-processor/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/ServletInitializer.java

@@ -0,0 +1,13 @@
+package edu.harvard.hms.dbmi.avillach.hpds.genomic;
+
+import org.springframework.boot.builder.SpringApplicationBuilder;
+import org.springframework.boot.web.servlet.support.SpringBootServletInitializer;
+
+public class ServletInitializer extends SpringBootServletInitializer {
+
+	@Override
+	protected SpringApplicationBuilder configure(SpringApplicationBuilder application) {
+		return application.sources(HpdsGenomicProcessorApplication.class);
+	}
+
+}

genomic-processor/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/config/ApplicationConfig.java

@@ -0,0 +1,21 @@
+package edu.harvard.hms.dbmi.avillach.hpds.genomic.config;
+
+import edu.harvard.hms.dbmi.avillach.hpds.processing.GenomicProcessor;
+import edu.harvard.hms.dbmi.avillach.hpds.processing.GenomicProcessorNodeImpl;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.boot.autoconfigure.SpringBootApplication;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.PropertySource;
+
+@SpringBootApplication
+@PropertySource("classpath:application.properties")
+public class ApplicationConfig {
+
+    @Value( "${hpds.genomicDataDirectory}" )
+    private String genomicDataDirectory;
+
+    @Bean
+    public GenomicProcessor genomicProcessor() {
+        return new GenomicProcessorNodeImpl(genomicDataDirectory);
+    }
+}

genomic-processor/src/main/resources/application.properties

@@ -0,0 +1,2 @@
+hpds.genomicDataDirectory = /opt/local/hpds/orchestration/1040/20/all/
+server.port=8090

genomic-processor/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/HpdsGenomicProcessorApplicationTests.java

@@ -0,0 +1,13 @@
+package edu.harvard.hms.dbmi.avillach.hpds.genomic;
+
+import org.junit.jupiter.api.Test;
+import org.springframework.boot.test.context.SpringBootTest;
+
+@SpringBootTest
+class HpdsGenomicProcessorApplicationTests {
+
+	@Test
+	void contextLoads() {
+	}
+
+}

pom.xml

@@ -23,6 +23,7 @@
 		<module>processing</module>
 		<module>war</module>
 		<module>client-api</module>
+		<module>genomic-processor</module>
 	</modules>
 	<properties>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>

service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureService.java

@@ -280,7 +280,7 @@ private ResponseEntity _querySync(QueryRequest resultRequest) throws IOException
 
 		case INFO_COLUMN_LISTING:
 			List<InfoColumnMeta> infoColumnMeta = abstractProcessor.getInfoStoreMeta();
-			return ResponseEntity.ok(infoColumnMeta);
+			return ResponseEntity.ok().contentType(MediaType.APPLICATION_JSON).body(infoColumnMeta);
 
 		case DATAFRAME:
 		case SECRET_ADMIN_DATAFRAME: