Updated Spring version; maped root to swagger endpoint; fixed code st…

…yle.

Dockerfile

@@ -0,0 +1,5 @@
+FROM openjdk:8-jdk-alpine
+VOLUME /tmp
+ARG JAR_FILE
+COPY ${JAR_FILE} app.jar
+ENTRYPOINT ["java","-Djava.security.egd=file:/dev/./urandom","-jar","/app.jar"]

README.md

@@ -16,14 +16,14 @@ the end of the `java -jar` command (see below), or set `SIFGRAPH_DATA` system va
 
 Build:
 
-```
+```commandline
 ./gradlew build
 ```
 
 Run:
 
-```
-java -jar build/libs/sifgraph-server.jar --sifgraph.data="file:path/to/graph.txt.gz" --server.port=8080
+```commandline
+java -jar build/libs/sifgraph-server-0.3.0.jar -Xmx4g --sifgraph.data="file:/path/to/graph.txt.gz" --server.port=8080
 ```
 
 Note: override the default list of SIF patterns using `--sifgraph.relationships=...` if needed (depends on the data).
@@ -33,12 +33,12 @@ copy src/main/resources/config/application.properties to the work/current direct
 rename (e.g., my.properties), modify (e.g., set another `server.port`, `sifgraph.relationships` 
 and `sifgraph.data` file), and run as:
 
-```
+```commandline
 java -jar build/libs/sifgraph-server.jar --spring.config.name=my
 ```
 
 RESTful API (Swagger docs):
 
 Once the app is built and running, 
 the auto-generated documentation is available at 
-`http://localhost:8080/sifgraph/swagger-ui.html`
+`http://localhost:8080/sifgraph/`

build.gradle

@@ -1,57 +1,61 @@
 buildscript {
+    ext {
+        springBootVersion = '2.1.0.RELEASE'
+    }
     repositories {
-        mavenCentral()
+        maven {
+            url "https://plugins.gradle.org/m2/"
+        }
     }
     dependencies {
-        classpath("org.springframework.boot:spring-boot-gradle-plugin:2.0.2.RELEASE")
+        classpath "org.springframework.boot:spring-boot-gradle-plugin:${springBootVersion}"
+        classpath "gradle.plugin.com.palantir.gradle.docker:gradle-docker:0.20.1"
     }
 }
 
 apply plugin: 'java'
 apply plugin: 'idea'
 apply plugin: 'org.springframework.boot'
 apply plugin: 'io.spring.dependency-management'
-
-jar {
-    baseName = 'sifgraph-server'
-    version =  '0.2.0'
-}
+apply plugin: 'com.palantir.docker'
 
 repositories {
     mavenCentral()
-
     maven {
         url "https://oss.sonatype.org/content/groups/public/"
     }
 }
 
-sourceCompatibility = 1.8
-targetCompatibility = 1.8
-
 dependencies {
-    compile("org.springframework.boot:spring-boot-starter-web")
-    // tag::actuator[]
-    compile("org.springframework.boot:spring-boot-starter-actuator")
-    // end::actuator[]
-    // tag::tests[]
-    testCompile("org.springframework.boot:spring-boot-starter-test")
-    // end::tests[]
-
-    compile("pathwaycommons.sif:sifgraph:1.0.0-SNAPSHOT")
-
-    compileOnly("org.springframework.boot:spring-boot-devtools")
-
-    //can use the following instead 'compileOnly' since gradle 4.6:
-    annotationProcessor "org.springframework.boot:spring-boot-configuration-processor"
-
-    //Swagger and UI
-    compile "io.springfox:springfox-swagger2:2.7.0"
-    compile "io.springfox:springfox-swagger-ui:2.7.0"
+    implementation 'pathwaycommons.sif:sifgraph:1.0.0-SNAPSHOT'
+
+    implementation 'org.springframework.boot:spring-boot-starter-actuator'
+    implementation 'org.springframework.boot:spring-boot-starter-web'
+    implementation "org.springframework.boot:spring-boot-configuration-processor"
+    implementation 'io.springfox:springfox-swagger2:2.7.0'
+    implementation 'io.springfox:springfox-swagger-ui:2.7.0'
+
+    runtimeOnly 'org.springframework.boot:spring-boot-devtools'
+    testImplementation 'org.springframework.boot:spring-boot-starter-test'
+
+    //java 9+ does not have Jax B Dependents
+    implementation 'javax.xml.bind:jaxb-api:2.3.0'
+    implementation 'com.sun.xml.bind:jaxb-core:2.3.0'
+    implementation 'com.sun.xml.bind:jaxb-impl:2.3.0'
+    implementation 'javax.activation:activation:1.1.1'
+}
 
-    //enable JSR-303
-//    compile "io.springfox:springfox-bean-validators:2.7.0"
+sourceCompatibility = 1.8
+group = 'pathwaycommons'
+version =  '0.3.0'
+
+docker {
+    dependsOn build
+    name "${project.group}/${bootJar.baseName}"
+    files bootJar.archivePath
+    buildArgs(['JAR_FILE': "${bootJar.archiveName}"])
 }
 
 task wrapper(type: Wrapper) {
-    gradleVersion = '4.7'
+    gradleVersion = '4.8.1'
 }

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
-#Fri May 11 20:06:17 EDT 2018
+#Mon Nov 19 13:21:17 EST 2018
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.7-all.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-4.8.1-all.zip

settings.gradle

@@ -0,0 +1 @@
+rootProject.name = 'sifgraph-server'

src/main/java/org/pathwaycommons/sif/server/Application.java

@@ -4,17 +4,24 @@
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 import org.springframework.boot.context.properties.EnableConfigurationProperties;
 import org.springframework.context.ApplicationContext;
+import org.springframework.web.servlet.config.annotation.ViewControllerRegistry;
+import org.springframework.web.servlet.config.annotation.WebMvcConfigurer;
 
 import java.io.IOException;
 
 @SpringBootApplication
 @EnableConfigurationProperties(SifgraphProperties.class)
-public class Application {
+public class Application implements WebMvcConfigurer {
 
     public static void main(String[] args) throws IOException {
         ApplicationContext ctx = SpringApplication.run(Application.class, args);
         ((Controller)ctx.getBean("controller")).init();
     }
 
+    @Override
+    public void addViewControllers(ViewControllerRegistry registry) {
+        registry.addRedirectViewController("/", "/swagger-ui.html");
+    }
+
 }
 

src/main/java/org/pathwaycommons/sif/server/Controller.java

@@ -46,7 +46,7 @@ public Controller(SifgraphProperties properties) {
   }
 
   @PostConstruct
-  void init() throws IOException {
+  protected void init() throws IOException {
     final EdgeAnnotationType[] annotationTypes = props.getAnnotations();
     sifWriter = new org.pathwaycommons.sif.io.Writer(false, annotationTypes);
     InputStream is = new GZIPInputStream(resourceLoader.getResource(props.getData()).getInputStream());
@@ -69,21 +69,17 @@ public String nhood(
     @ApiParam("Set of gene identifiers (HGNC Symbol) - 'seeds' for the graph traversal algorithm.")
     @RequestParam(required = true) String[] source,
     @ApiParam("Filter by binary relationship (SIF edge) type(s)")
-    @RequestParam(required = false) RelationTypeEnum[] pattern
-  ) {
+    @RequestParam(required = false) RelationTypeEnum[] pattern) throws IOException
+  {
     Set<String> sources = new HashSet();
     for (String s : source)
       sources.add(s);
 
-    pattern = (pattern != null && pattern.length > 0) ? pattern : DEFAULT_RELS;
-    try {
-      Set<Object> result = QueryExecutor.searchNeighborhood(graph,
-        new RelationTypeSelector(pattern), sources, direction, limit);
+    Set<Object> result = QueryExecutor.searchNeighborhood(graph,
+      new RelationTypeSelector((pattern!=null && pattern.length>0)?pattern:DEFAULT_RELS),
+      sources, direction, limit);
 
-      return write(result);
-    } catch (Exception e) {
-      throw new RuntimeException("/neighborhood failed: " + e);
-    }
+    return write(result);
   }
 
   @RequestMapping(path = "/pathsbetween")
@@ -100,21 +96,17 @@ public String pathsbetween(
     @ApiParam("A set of gene identifiers.")
     @RequestParam(required = true) String[] source,
     @ApiParam("Filter by binary relationship (SIF edge) type(s)")
-    @RequestParam(required = false) RelationTypeEnum[] pattern
-  ) {
+    @RequestParam(required = false) RelationTypeEnum[] pattern) throws IOException
+  {
     Set<String> sources = new HashSet();
     for (String s : source)
       sources.add(s);
 
-    try {
-      Set<Object> result = QueryExecutor.searchPathsBetween(graph,
-        new RelationTypeSelector((pattern != null && pattern.length > 0) ? pattern : DEFAULT_RELS),
-        sources, directed, limit);
+    Set<Object> result = QueryExecutor.searchPathsBetween(graph,
+      new RelationTypeSelector((pattern!=null && pattern.length>0)?pattern:DEFAULT_RELS),
+      sources, directed, limit);
 
-      return write(result);
-    } catch (Exception e) {
-      throw new RuntimeException("/pathsbetween failed: " + e);
-    }
+    return write(result);
   }
 
   @RequestMapping(path = "/commonstream")
@@ -131,20 +123,16 @@ public String commonstream(
     @ApiParam("A set of gene identifiers.")
     @RequestParam(required = true) String[] source,
     @ApiParam("Filter by binary relationship (SIF edge) type(s)")
-    @RequestParam(required = false) RelationTypeEnum[] pattern
-  ) {
+    @RequestParam(required = false) RelationTypeEnum[] pattern) throws IOException
+  {
     Set<String> sources = new HashSet();
     for (String s : source) sources.add(s);
 
-    try {
-      Set<Object> result = QueryExecutor.searchCommonStream(graph,
-        new RelationTypeSelector((pattern != null && pattern.length > 0) ? pattern : DEFAULT_RELS),
-        sources, direction, limit);
+    Set<Object> result = QueryExecutor.searchCommonStream(graph,
+      new RelationTypeSelector((pattern!=null && pattern.length>0)?pattern:DEFAULT_RELS),
+      sources, direction, limit);
 
-      return write(result);
-    } catch (Exception e) {
-      throw new RuntimeException("/commonstream failed: " + e);
-    }
+    return write(result);
   }
 
   @RequestMapping(path = "/pathsfromto")
@@ -161,23 +149,19 @@ public String pathsfromto(
     @ApiParam("A target set of gene identifiers.")
     @RequestParam(required = true) String[] target,
     @ApiParam("Filter by binary relationship (SIF edge) type(s)")
-    @RequestParam(required = false) RelationTypeEnum[] pattern
-  ) {
+    @RequestParam(required = false) RelationTypeEnum[] pattern) throws IOException
+  {
     Set<String> sources = new HashSet();
     for (String s : source) sources.add(s);
 
     Set<String> targets = new HashSet();
     for (String s : target) targets.add(s);
 
-    try {
-      Set<Object> result = QueryExecutor.searchPathsFromTo(graph,
-        new RelationTypeSelector((pattern != null && pattern.length > 0) ? pattern : DEFAULT_RELS),
-        sources, targets, limit);
+    Set<Object> result = QueryExecutor.searchPathsFromTo(graph,
+      new RelationTypeSelector((pattern!=null && pattern.length>0) ? pattern:DEFAULT_RELS),
+      sources, targets, limit);
 
-      return write(result);
-    } catch (Exception e) {
-      throw new RuntimeException("/pathsfromto failed: " + e);
-    }
+    return write(result);
   }
 
   private String write(Set<Object> result) throws IOException {

src/main/resources/config/application.properties

@@ -1,6 +1,9 @@
 server.port=8080
 server.servlet.context-path = /sifgraph
 #server.error.whitelabel.enabled = false
+# * - enables all actuator endpoints
+management.endpoints.web.exposure.include=health,info
+#management.endpoints.web.exposure.exclude=
 
 # data location (Pathway Commons Extended SIF format)
 #"http://www.pathwaycommons.org/archives/PC2/v10/PathwayCommons10.All.hgnc.txt.gz"