genome preparing embedded driver

jdk_8_maven/cs/rest-gui/genome-nexus/.gitignore

@@ -6,7 +6,7 @@ pom.xml.next
 release.properties
 dependency-reduced-pom.xml
 buildNumber.properties
-application.properties
+#application.properties
 *.iml
 .idea/
 *.ipr

jdk_8_maven/cs/rest-gui/genome-nexus/web/pom.xml

@@ -126,6 +126,10 @@
               <goal>build-info</goal>
               <goal>repackage</goal>
             </goals>
+              <configuration>
+                  <finalName>genome-nexus</finalName>
+                  <classifier>sut</classifier>
+              </configuration>
           </execution>
         </executions>
       </plugin>

jdk_8_maven/cs/rest-gui/genome-nexus/web/src/main/resources/application.properties

@@ -0,0 +1,71 @@
+# VEP web API URL with additional parameters. Note that "VARIANT" field will be replaced with
+# the actual variant value before each VEP request.
+vep.url=http://grch37.rest.ensembl.org/vep/human/hgvs/VARIANT?content-type=application/json&xref_refseq=1&ccds=1&canonical=1&domains=1&hgvs=1&numbers=1&protein=1
+
+# 200 is the max page size allowed by the public VEP service, it might be possible to increase this for a private instance
+vep.max_page_size=200
+
+# response timeout arg when sending requests to own VEP
+# should only be turned on when pointing to own VEP
+# 300 seconds is recommended with vep.max_page_size set to 5000
+# gn_vep.timeout.seconds=300
+
+# it is possible to use your own VEP instance by running https://github.com/genome-nexus/genome-nexus-vep
+# This is only the VEP part of the Ensembl REST API.
+# e.g. when running on port 6060:
+# gn_vep.region.url=http://localhost:6060/vep/human/region/VARIANT
+# gn_vep.cache.version=
+# gn_vep.server.version=
+# Note that this overrides vep.url
+# To get the full advantage of running your own VEP, several optimizations are
+# required, please read documentation in
+# https://github.com/genome-nexus/genome-nexus-vep
+
+# the gene external references URL
+genexrefs.url=http://grch37.rest.ensembl.org/xrefs/id/ACCESSION?content-type=application/json
+
+# Mutation Assessor web API URL
+#"VARIANT" will be replaced with actual variant upon each request.
+mutationAssessor.url=http://mutationassessor.org/r3/?cm=var&var=VARIANT&frm=json&fts=input,rgaa,rgvt,msa,pdb,F_impact,F_score,vc_score,vs_score,info,var,gene,uprot,rsprot,gaps,msa_height,chr,rs_pos,rs_res,up_pos,up_res,cnt_cosmic,cnt_snps
+# mutationAssessor url for GRCh38
+# mutationAssessor.url=http://mutationassessor.org/r3/?cm=var&var=hg38,VARIANT&frm=json&fts=input,rgaa,rgvt,msa,pdb,F_impact,F_score,vc_score,vs_score,info,var,gene,uprot,rsprot,gaps,msa_height,chr,rs_pos,rs_res,up_pos,up_res,cnt_cosmic,cnt_snps
+
+# my variant info web API URL
+#"VARIANT" will be replaced with actual variant upon each request.
+myvariantinfo.url=https://myvariant.info/v1/variant/VARIANT
+myvariantinfo.max_page_size=200
+# myvariantinfo url for GRCh38
+# myvariantinfo.url=https://myvariant.info/v1/variant/VARIANT?assembly=hg38
+
+# PDB header web service URL
+pdb.header_service_url=http://files.rcsb.org/header/PDB_ID.pdb
+
+# MongoDB URI in the form of mongodb://<USERNAME>:<PASSWORD>@<HOST>:<PORT>/<DB>
+spring.data.mongodb.uri=mongodb://127.0.0.1:27017/annotator
+
+# Server port number for the embedded tomcat. This property is required only when building
+# a jar file, and ignored when building a war file.
+server.port=38080
+genomenexus.server.version=1.0.2
+
+# For testing use same embeded mongo version as genome-nexus-importer
+# https://github.com/genome-nexus/genome-nexus-importer/blob/master/Dockerfile#L1
+spring.mongodb.embedded.version=3.6.2
+
+# enable compression when running embedded tomcat
+server.compression.enabled=true
+server.compression.min-response-size=2048
+server.compression.mime-types=application/json,application/xml,text/html,text/xml,text/plain,application/javascript,text/css
+
+# increase the header size limitation
+server.max-http-header-size=10000000
+
+# include full git info in /actuator/info endpoint
+management.info.git.mode=full
+
+# oncokb
+oncokb.url=https://www.oncokb.org/api/v1/annotate/mutations/byProteinChange?PROTEINCHANGE
+
+# For testing use same embeded mongo version as genome-nexus-importer
+# https://github.com/genome-nexus/genome-nexus-importer/blob/master/Dockerfile#L1
+spring.mongodb.embedded.version=3.6.2

jdk_8_maven/cs/rest-gui/pom.xml

@@ -15,6 +15,7 @@
     <modules>
         <module>ocvn</module>
         <module>gestaohospital</module>
+        <module>genome-nexus</module>
     </modules>
 
 

jdk_8_maven/em/embedded/rest/genome-nexus/pom.xml

@@ -0,0 +1,51 @@
+<?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>
+
+    <properties>
+        <mongo.version>3.6.2</mongo.version>
+    </properties>
+
+    <artifactId>evomaster-benchmark-em-embedded-rest-genome-nexus</artifactId>
+    <packaging>jar</packaging>
+
+    <parent>
+        <groupId>org.evomaster</groupId>
+        <artifactId>evomaster-benchmark-em-embedded-rest</artifactId>
+        <version>1.5.1-SNAPSHOT</version>
+    </parent>
+
+
+    <dependencies>
+        <dependency>
+            <groupId>org.mongodb</groupId>
+            <artifactId>mongo-java-driver</artifactId>
+            <version>${mongo.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.cbioportal.genome_nexus</groupId>
+            <artifactId>web</artifactId>
+            <version>1.1.49</version>
+        </dependency>
+        <dependency>
+            <groupId>org.testcontainers</groupId>
+            <artifactId>testcontainers</artifactId>
+            <scope>compile</scope>
+        </dependency>
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <scope>compile</scope>
+            <version>4.11</version>
+        </dependency>
+        <dependency>
+            <groupId>org.springframework</groupId>
+            <artifactId>spring-jdbc</artifactId>
+            <version>5.3.9</version>
+        </dependency>
+    </dependencies>
+
+
+</project>

jdk_8_maven/em/embedded/rest/genome-nexus/src/main/java/org/cbioportal/genome_nexus/EmbeddedEvoMasterController.java

@@ -0,0 +1,133 @@
+package org.cbioportal.genome_nexus;
+
+import com.mongodb.MongoClient;
+import org.evomaster.client.java.controller.EmbeddedSutController;
+import org.evomaster.client.java.controller.InstrumentedSutStarter;
+import org.evomaster.client.java.controller.api.dto.AuthenticationDto;
+import org.evomaster.client.java.controller.api.dto.SutInfoDto;
+import org.evomaster.client.java.controller.internal.db.DbSpecification;
+import org.evomaster.client.java.controller.problem.ProblemInfo;
+import org.evomaster.client.java.controller.problem.RestProblem;
+import org.springframework.boot.SpringApplication;
+import org.springframework.context.ConfigurableApplicationContext;
+import org.testcontainers.containers.GenericContainer;
+
+import java.util.List;
+import java.util.Map;
+
+
+/**
+ * Class used to start/stop the SUT. This will be controller by the EvoMaster process
+ */
+public class EmbeddedEvoMasterController extends EmbeddedSutController {
+
+    public static void main(String[] args) {
+
+        int port = 40100;
+        if (args.length > 0) {
+            port = Integer.parseInt(args[0]);
+        }
+
+        EmbeddedEvoMasterController controller = new EmbeddedEvoMasterController(port);
+        InstrumentedSutStarter starter = new InstrumentedSutStarter(controller);
+
+        starter.start();
+    }
+
+
+    private ConfigurableApplicationContext ctx;
+
+    private static final int MONGODB_PORT = 27017;
+
+    private static final String MONGODB_VERSION = "3.6.2";
+
+    private static final String MONGODB_DATABASE_NAME = "genome";
+
+    private static final GenericContainer mongodbContainer = new GenericContainer("mongo:" + MONGODB_VERSION)
+            .withExposedPorts(MONGODB_PORT);
+
+
+    public EmbeddedEvoMasterController() {
+        this(0);
+    }
+
+    public EmbeddedEvoMasterController(int port) {
+        setControllerPort(port);
+    }
+
+
+    @Override
+    public String startSut() {
+
+        mongodbContainer.start();
+
+        ctx = SpringApplication.run(GenomeNexusAnnotation.class,
+                new String[]{"--server.port=0",
+                        "--spring.data.mongodb.uri=mongodb://" + mongodbContainer.getContainerIpAddress() + ":" + mongodbContainer.getMappedPort(MONGODB_PORT) + "/" + MONGODB_DATABASE_NAME,
+                        "--spring.cache.type=NONE"
+                });
+
+        return "http://localhost:" + getSutPort();
+    }
+
+    protected int getSutPort() {
+        return (Integer) ((Map) ctx.getEnvironment()
+                .getPropertySources().get("server.ports").getSource())
+                .get("local.server.port");
+    }
+
+
+    @Override
+    public boolean isSutRunning() {
+        return ctx != null && ctx.isRunning();
+    }
+
+    @Override
+    public void stopSut() {
+        ctx.stop();
+        ctx.close();
+
+        mongodbContainer.stop();
+    }
+
+    @Override
+    public String getPackagePrefixesToCover() {
+        return "org.cbioportal.genome_nexus.";
+    }
+
+    @Override
+    public void resetStateOfSUT() {
+        MongoClient mongoClient = new MongoClient(mongodbContainer.getContainerIpAddress(),
+                mongodbContainer.getMappedPort(MONGODB_PORT));
+
+        mongoClient.getDatabase(MONGODB_DATABASE_NAME).drop();
+    }
+
+
+    @Override
+    public List<DbSpecification> getDbSpecifications() {
+        return null;
+    }
+
+
+    @Override
+    public List<AuthenticationDto> getInfoForAuthentication() {
+        return null;
+    }
+
+
+    @Override
+    public ProblemInfo getProblemInfo() {
+        return new RestProblem(
+                "http://localhost:" + getSutPort() + "/v2/api-docs",
+                null
+        );
+    }
+
+    @Override
+    public SutInfoDto.OutputFormat getPreferredOutputFormat() {
+        return SutInfoDto.OutputFormat.JAVA_JUNIT_4;
+    }
+
+
+}

jdk_8_maven/em/embedded/rest/pom.xml

@@ -24,6 +24,7 @@
         <module>languagetool</module>
         <module>restcountries</module>
         <module>gestaohospital</module>
+        <module>genome-nexus</module>
     </modules>
 
 </project>