Updated gradle wrapper and fixed Docker build and README.

Author: IgorRodchenkov

Dockerfile

@@ -1,5 +1,9 @@
-FROM openjdk:8-jdk-alpine
+FROM openjdk:13-jdk-alpine
 VOLUME /tmp
-ARG JAR_FILE
+ARG JAR_FILE="build/libs/sifgraph-server*.jar"
+ARG DATA_FILE="data.txt.gz"
+ENV DATA_URL="file:${DATA_FILE}"
 COPY ${JAR_FILE} app.jar
-ENTRYPOINT ["java","-Djava.security.egd=file:/dev/./urandom","-jar","/app.jar"]
+COPY ${DATA_FILE} .
+ENTRYPOINT ["java","-Xmx16g","-Djava.security.egd=file:/dev/./urandom","-jar","/app.jar", "--sifgraph.data=${DATA_URL}"]
+EXPOSE 8080

README.md

@@ -10,7 +10,12 @@ on the Pathway Commons' [Extended SIF](http://www.pathwaycommons.org/pc2/formats
 Clone the repository.
 
 See `src/main/resources/config/application.properties` comments; 
-download the extended SIF data file and update the properties accordingly 
+download a Pathway Commons Extended SIF data archive and save it as data.txt.gz in this project directory, e.g.:
+
+```commandline
+wget -O data.txt.gz "https://www.pathwaycommons.org/archives/PC2/v12/PathwayComons12.All.hgnc.txt.gz"
+```
+
 (alternatively, set `--sifgraph.data=...`, etc., options at 
 the end of the `java -jar` command (see below), or set `SIFGRAPH_DATA` system variable.)
 
@@ -23,22 +28,55 @@ Build:
 Run:
 
 ```commandline
-java -jar build/libs/sifgraph-server-0.3.0.jar -Xmx4g --sifgraph.data="file:/path/to/graph.txt.gz" --server.port=8080
+java -Xmx8g -jar build/libs/sifgraph-server*.jar
 ```
 
 Note: override the default list of SIF patterns using `--sifgraph.relationships=...` if needed (depends on the data).
 
-If you want to run __different instances__ of the graph server, e.g., for different species, then simply 
-copy src/main/resources/config/application.properties to the work/current directory, 
+If you want to run __different instances__ of the graph server, e.g., for different species, then  
+copy src/main/resources/config/application.properties to the work directory, 
 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
+java -Xmx8g -jar build/libs/sifgraph-server*.jar --spring.config.name=my
 ```
 
+or
+
+```commandline
+java -Xmx8g  -jar build/libs/sifgraph-server*.jar --sifgraph.data="file:<other.file>" --server.port=<otherPort>
+```
+
+
 RESTful API (Swagger docs):
 
 Once the app is built and running, 
 the auto-generated documentation is available at 
 `http://localhost:8080/sifgraph/`
+
+
+## Docker
+You can also build and run the docker image as follows   
+(`<PORT>` - actual port number where the server will run; data file download step above is also required). 
+
+```commandline
+./gradlew build
+docker build . -t pathwaycommons/sifgraph-server 
+docker run -it --rm --name sifgraph-server -p <PORT>:8080 pathwaycommons/sifgraph-server 
+```
+
+Optionally, (a member of 'pathwaycommons' group) can now push the latest Docker image there:
+
+```commandline
+docker login
+docker push pathwaycommons/sifgraph-server
+```  
+
+So, other users could skip building from sources and simply run the app:
+```commandline
+docker pull
+docker run -p <PORT>:8080 -t pathwaycommons/sifgraph-server
+```
+
+(you can `Ctrl-c` and quit the console; the container is still there running; check with `docker ps`)

build.gradle

@@ -1,6 +1,6 @@
 buildscript {
     ext {
-        springBootVersion = '2.1.0.RELEASE'
+        springBootVersion = '2.2.6.RELEASE'
     }
     repositories {
         maven {
@@ -9,15 +9,13 @@ buildscript {
     }
     dependencies {
         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'
-apply plugin: 'com.palantir.docker'
 
 repositories {
     mavenCentral()
@@ -47,15 +45,5 @@ dependencies {
 
 sourceCompatibility = 1.8
 group = 'pathwaycommons'
-version =  '0.3.0'
+version =  '0.3.1'
 
-docker {
-    dependsOn build
-    name "${project.group}/${bootJar.baseName}"
-    files bootJar.archivePath
-    buildArgs(['JAR_FILE': "${bootJar.archiveName}"])
-}
-
-task wrapper(type: Wrapper) {
-    gradleVersion = '4.8.1'
-}

gradle/wrapper/gradle-wrapper.jar

@@ -1,6 +1,5 @@
-#Mon Nov 19 13:21:17 EST 2018
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-6.3-all.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.8.1-all.zip

gradle/wrapper/gradle-wrapper.properties

@@ -6,9 +6,9 @@ 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"
+#"https://www.pathwaycommons.org/downloads/PathwayCommons*.All.hgnc.txt.gz"
 # manually download and use the local file
-sifgraph.data=file:/home/igor/Downloads/PathwayCommons10.All.hgnc.txt.gz
+sifgraph.data=file:data.txt.gz
 
 # comma-separated list of org.pathwaycommons.sif.util.EdgeAnnotationType names used in the text data file;
 # note: which column names are out there depends on actual input file (it can be customized too); default are: