Merge pull request #3 from IgorRodchenkov/master

Updated gradle wrapper and fixed Docker build and README.

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.properties

@@ -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

gradlew

@@ -1,5 +1,21 @@
 #!/usr/bin/env sh
 
+#
+# Copyright 2015 the original author or authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
 ##############################################################################
 ##
 ##  Gradle start up script for UN*X
@@ -28,7 +44,7 @@ APP_NAME="Gradle"
 APP_BASE_NAME=`basename "$0"`
 
 # Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS=""
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD="maximum"
@@ -109,8 +125,8 @@ if $darwin; then
     GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
 fi
 
-# For Cygwin, switch paths to Windows format before running java
-if $cygwin ; then
+# For Cygwin or MSYS, switch paths to Windows format before running java
+if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then
     APP_HOME=`cygpath --path --mixed "$APP_HOME"`
     CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
     JAVACMD=`cygpath --unix "$JAVACMD"`
@@ -138,19 +154,19 @@ if $cygwin ; then
         else
             eval `echo args$i`="\"$arg\""
         fi
-        i=$((i+1))
+        i=`expr $i + 1`
     done
     case $i in
-        (0) set -- ;;
-        (1) set -- "$args0" ;;
-        (2) set -- "$args0" "$args1" ;;
-        (3) set -- "$args0" "$args1" "$args2" ;;
-        (4) set -- "$args0" "$args1" "$args2" "$args3" ;;
-        (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
-        (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
-        (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
-        (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
-        (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
+        0) set -- ;;
+        1) set -- "$args0" ;;
+        2) set -- "$args0" "$args1" ;;
+        3) set -- "$args0" "$args1" "$args2" ;;
+        4) set -- "$args0" "$args1" "$args2" "$args3" ;;
+        5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
+        6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
+        7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
+        8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
+        9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
     esac
 fi
 
@@ -159,14 +175,9 @@ save () {
     for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
     echo " "
 }
-APP_ARGS=$(save "$@")
+APP_ARGS=`save "$@"`
 
 # Collect all arguments for the java command, following the shell quoting and substitution rules
 eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
 
-# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
-if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
-  cd "$(dirname "$0")"
-fi
-
 exec "$JAVACMD" "$@"

gradlew.bat

@@ -1,3 +1,19 @@
+@rem
+@rem Copyright 2015 the original author or authors.
+@rem
+@rem Licensed under the Apache License, Version 2.0 (the "License");
+@rem you may not use this file except in compliance with the License.
+@rem You may obtain a copy of the License at
+@rem
+@rem      https://www.apache.org/licenses/LICENSE-2.0
+@rem
+@rem Unless required by applicable law or agreed to in writing, software
+@rem distributed under the License is distributed on an "AS IS" BASIS,
+@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+@rem See the License for the specific language governing permissions and
+@rem limitations under the License.
+@rem
+
 @if "%DEBUG%" == "" @echo off
 @rem ##########################################################################
 @rem
@@ -13,8 +29,11 @@ if "%DIRNAME%" == "" set DIRNAME=.
 set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 
+@rem Resolve any "." and ".." in APP_HOME to make it shorter.
+for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
+
 @rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-set DEFAULT_JVM_OPTS=
+set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
 
 @rem Find java.exe
 if defined JAVA_HOME goto findJavaFromJavaHome

src/main/resources/config/application.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: