Merge pull request #75 from draeger-lab/config/docker-hub

Changing Travis, Gradle and Docker config to use Docker Hub images where possible

.travis.yml

@@ -1,6 +1,8 @@
 dist: bionic
 language: java
 sudo: required
+env:
+- COMPOSE_FILE=docker-compose.devel.yml 
 jdk:
 - openjdk11
 services:
@@ -14,9 +16,10 @@ before_install:
 - git clone https://github.com/SBRG/bigg_models_data
 install:
 # use current build artifact instead of published version
-- printf "FROM openjdk:11-slim\n\nCOPY ModelPolisher.jar /\nCOPY models /models\nCMD \"/bin/sh\"" > docker/java_docker/Dockerfile
-- gradle lightJar && mv target/*.jar docker/java_docker/ModelPolisher.jar && cp -r bigg_models_data/models docker/java_docker
-- docker-compose up --build -d
+- printf "FROM openjdk:11-slim\n\nCOPY ModelPolisher-2.0.1.jar /\nCOPY models /models\nCMD \"/bin/sh\"" > docker/java_docker/Dockerfile
+- cp -r bigg_models_data/models docker/java_docker
+- gradle devel
+- docker-compose up -d
 - docker ps -a
 before_script:
 # wait for both databases to accept connections
@@ -25,9 +28,9 @@ before_script:
 - while ! pg_isready -h 0.0.0.0 -p 1013 > /dev/null; do sleep 1; done
 - echo "Databases are up"
 script:
-- travis_wait docker-compose run java sh -c "java -jar /ModelPolisher.jar --input=/models/ecoli_core_model.xml --output=/models/out/ecoli_core_model.xml --annotate-with-bigg=true --add-adb-annotations=true --output-combine=true && ls -lish models/out"
-- travis_wait docker-compose run java sh -c "java -jar /ModelPolisher.jar --input=/models/yeast_7.00.xml --output=/models/out/yeast_7.00.xml --annotate-with-bigg=true --add-adb-annotations=true --output-combine=true && ls -lish models/out"
-- travis_wait docker-compose run java sh -c "java -jar /ModelPolisher.jar --input=/models/RECON1.xml --output=/models/out/RECON1.xml --annotate-with-bigg=true --add-adb-annotations=true --output-combine=true && ls -lish models/out"
+- travis_wait docker-compose run java sh -c "java -jar /ModelPolisher-2.0.1.jar --input=/models/ecoli_core_model.xml --output=/models/out/ecoli_core_model.xml --annotate-with-bigg=true --add-adb-annotations=true --output-combine=true && ls -lish models/out"
+- travis_wait docker-compose run java sh -c "java -jar /ModelPolisher-2.0.1.jar --input=/models/yeast_7.00.xml --output=/models/out/yeast_7.00.xml --annotate-with-bigg=true --add-adb-annotations=true --output-combine=true && ls -lish models/out"
+- travis_wait docker-compose run java sh -c "java -jar /ModelPolisher-2.0.1.jar --input=/models/RECON1.xml --output=/models/out/RECON1.xml --annotate-with-bigg=true --add-adb-annotations=true --output-combine=true && ls -lish models/out"
 after_script:
 - docker-compose down
 git:

README.md

@@ -3,7 +3,7 @@
 
 <img align="right" src="doc/img/ModelPolisherIcon256.png" width="64"/>
 
-*Authors:* [Andreas Dräger](https://github.com/draeger/), [Thomas J. Zajac](https://github.com/mephenor/), [Matthias König](https://github.com/matthiaskoenig)
+*Authors:* [Andreas Dräger](https://github.com/draeger/), [Thomas J. Zajac](https://github.com/mephenor/), [Matthias König](https://github.com/matthiaskoenig), [Kaustubh Trivedi](https://github.com/codekaust)
 
 [![Build Status](https://travis-ci.org/draeger-lab/ModelPolisher.svg?branch=master?style=plastic)](https://travis-ci.org/draeger-lab/ModelPolisher)
 [![Stable version](https://img.shields.io/badge/Stable_version-2.0-brightgreen.svg?style=plastic)](https://github.com/draeger-lab/ModelPolisher/releases/)
@@ -41,7 +41,8 @@ ModelPolisher uses `gradle` to build. Make sure you have `gradle (version >= 5.0
 
 First clone this github project and go to directory `<path>/ModelPolisher/`. Then, ModelPolisher can be built using Gradle. Gradle runs task `lightJar` by default which produces `jar` file, with dependencies, for ModelPolisher in `<path>/ModelPolisher/target/` directory. So, in order to build ModelPolisher run any of following command under `ModelPolisher/` directory:
 
-`gradle lightJar` or `gradle`
+`gradle lightJar` or `gradle`  
+Additionally `gradle devel` is provided to easily run a non-release version with [Docker](#non-release).
 
 NOTE: `lightJar` requires `postgresql` database(s) to be set-up to run ModelPolisher.
 
@@ -95,6 +96,13 @@ docker rmi modelpolisher_java:latest modelpolisher_adb:latest modelpolisher_bigg
 docker volume prune
 ```
 
+#### <a name="non-release">Using a non-release jar with Docker</a>
+
+Building using `gradle devel` builds a container with the local ModelPolisher jar.  
+This container can be used analogously to the release version, though either `-f docker-compose.devel.yml` needs to be 
+passed to each invocation of `docker-compose` or the `COMPOSE_FILE` environment variable  needs to be set so it points 
+to `docker-compose.devel.yml`, e.g. using `export COMPOSE_FILE=docker-compose.devel.yml` for sh or bash. 
+
 ## <a name="using-jar"></a>Using ModelPolisher jar
 For polishing models, you essentially need to run ModelPolisher using `jar` produced from [build instructions](#build-instructions).
 

build.gradle

@@ -2,11 +2,11 @@ apply plugin: "java"
 
 defaultTasks "clean", "lightJar"
 // Java versions for compilation and output
-sourceCompatibility = "1.8"
-targetCompatibility = "1.8"
+sourceCompatibility = "1.11"
+targetCompatibility = "1.11"
 archivesBaseName = "ModelPolisher"
 
-version = "2.0"
+version = "2.0.1"
 
 sourceSets {
     main.java.srcDirs = ["src/main/java"]
@@ -27,18 +27,18 @@ repositories {
 }
 
 dependencies {
-    compile 'javax.xml.bind:jaxb-api:2.3.1'
-    compile 'javax.activation:activation:1.1'
-    compile 'org.glassfish.jaxb:jaxb-runtime:2.3.1'
+    compile "javax.xml.bind:jaxb-api:2.3.1"
+    compile "javax.activation:activation:1.1"
+    compile "org.glassfish.jaxb:jaxb-runtime:2.3.1"
     compile "org.sbml.jsbml:jsbml:1.4"
     compile "de.zbit:SysBio:1390"
     compile "org.xerial:sqlite-jdbc:3.21.0"
     compile "org.postgresql:postgresql:42.2.2"
     compile "org.biojava:biojava-ontology:5.0.0"
     compile 'us.hebi.matlab.mat:mfl-core:0.5.3'
-    compile "com.fasterxml.jackson.core:jackson-core:2.9.9"
-    compile "com.fasterxml.jackson.core:jackson-databind:2.9.9.2"
-    compile group: 'net.sf.jtidy', name: 'jtidy', version: 'r938'
+    compile "com.fasterxml.jackson.core:jackson-core:2.9.10"
+    compile "com.fasterxml.jackson.core:jackson-databind:2.9.10"
+    compile "net.sf.jtidy:jtidy:r938"
     compile "de.uni-rostock.sbi:CombineArchive:1.4.0"
     testCompile "org.junit.jupiter:junit-jupiter-engine:5.1.0"
 }
@@ -73,6 +73,16 @@ task lightJar(type: Jar) {
     with jar
 }
 
+//build docker container
+task devel(type: Exec){
+    commandLine "sh", "-c", "cp target/ModelPolisher-" + project.version + ".jar docker/java_docker && " +
+            "export COMPOSE_FILE=docker-compose.devel.yml && " +
+            "docker-compose pull && " +
+            "docker-compose build && " +
+            "rm docker/java_docker/ModelPolisher-" + project.version + ".jar"
+    dependsOn lightJar
+}
+
 // zip lib folder for release
 task zipLibs(type: Zip) {
     from "lib"
@@ -107,6 +117,8 @@ clean.doFirst {
 // bump jar version in ModelPolisher.sh
 if (project.file("./src/scripts/ModelPolisher.sh").exists()) {
     task bumpVersionMP() {
+        replaceVersion("docker/java_docker/Dockerfile")
+        replaceVersion(".travis.yml")
         replaceVersion("./src/scripts/ModelPolisher.sh")
     }
     processResources.dependsOn bumpVersionMP

docker-compose.devel.yml

@@ -0,0 +1,24 @@
+# ------------------------------------------------
+# docker-compose for ModelPolisher development
+# run gradle devel first and then docker-compose -f docker-compose.devel.yml run ... or export COMPOSE_FILE and run normally 
+# ------------------------------------------------
+version: '3'
+services:
+  biggdb:
+    image: mephenor/bigg_docker:1.5
+    container_name: modelpolisher_biggdb
+    ports:
+      - 1310:5432
+  adb:
+    image: mephenor/adb_docker:0.1.1
+    container_name: modelpolisher_adb
+    ports:
+      - 1013:5432
+  java:
+    build: ./docker/java_docker
+    container_name: modelpolisher_java    
+    depends_on:
+      - biggdb
+      - adb
+    stdin_open: true
+    tty: true

docker-compose.yml

@@ -1,23 +1,24 @@
 # ------------------------------------------------
-# docker-compose for ModelPolisher
+# docker-compose for ModelPolisher release version
+# update docker hub images for new releases and change image accordingly
 # ------------------------------------------------
 version: '3'
 services:
   biggdb:
+    image: mephenor/bigg_docker:1.5
     container_name: modelpolisher_biggdb
-    build: ./docker/bigg_docker
     ports:
       - 1310:5432
   adb:
+    image: mephenor/adb_docker:0.1.1
     container_name: modelpolisher_adb
-    build: ./docker/adb_docker
     ports:
       - 1013:5432
   java:
+    image: mephenor/modelpolisher:2.0
     depends_on:
       - biggdb
       - adb
     container_name: modelpolisher_java
-    build: ./docker/java_docker
     stdin_open: true
     tty: true

docker/adb_docker/Dockerfile

@@ -3,12 +3,13 @@ MAINTAINER [email protected]
 
 RUN adduser --disabled-password --gecos '' adb
 
-RUN apt-get update &&\
-    apt-get install wget -y &&\
+RUN apt-get update && \
+    apt-get install curl -y && \
     # Create directory '/adb_dump/' and download adb-v0.1.1 dump as 'adb-v0.1.1.dump'
-    wget -P /adb_dump/ https://modelpolisher.s3.ap-south-1.amazonaws.com/adb-v0.1.1.dump &&\
+    mkdir /adb_dump && \
+    curl -Lo /adb_dump/adb-v0.1.1.dump https://www.dropbox.com/s/qjiey8y88gt4h0l/adb-v0.1.1.dump?dl=0 && \
     rm -rf /var/lib/apt/lists/*
 
 COPY ./scripts/restore_adb.sh /docker-entrypoint-initdb.d/restore_adb.sh
 
-EXPOSE 5432
+EXPOSE 5432

docker/bigg_docker/Dockerfile

@@ -1,10 +1,11 @@
 FROM postgres:9.6.2
 MAINTAINER [email protected]
 
-RUN apt-get update &&\
-    apt-get install wget -y &&\
+RUN apt-get update && \
+    apt-get install curl -y && \
     # Create directory '/bigg_database_dump/' and download bigg_database dump as 'database.dump'
-    wget -P /bigg_database_dump/ https://modelpolisher.s3.ap-south-1.amazonaws.com/bigg_database.dump &&\
+    mkdir /bigg_database_dump && \
+    curl -Lo /bigg_database_dump/database.dump https://www.dropbox.com/s/mem1oa7f258xctf/bigg_database-v1.5.dump?dl=0 && \
     rm -rf /var/lib/apt/lists/*
 
 COPY ./scripts/restore_biggdb.sh /docker-entrypoint-initdb.d/restore_biggdb.sh

docker/java_docker/Dockerfile

@@ -1,9 +1,5 @@
 FROM openjdk:11-slim
 MAINTAINER [email protected]
 
-RUN apt-get update &&\
-apt-get install -y wget &&\
-wget https://modelpolisher.s3.ap-south-1.amazonaws.com/ModelPolisher-2.0.jar &&\
-rm -rf /var/lib/apt/lists/*
-
+COPY ModelPolisher-2.0.1.jar /
 CMD "/bin/sh"

src/main/java/edu/ucsd/sbrg/bigg/ModelPolisher.java

@@ -244,7 +244,9 @@ private void batchProcess(File input, File output, SBProperties args) throws IOE
       processFile(input, output, args);
     } else {
       if (!output.isDirectory()) {
-        throw new IOException(format(mpMessageBundle.getString("WRITE_DIR_TO_FILE_ERROR"), input.getAbsolutePath(), output.getAbsolutePath()));
+          // input == dir && output != dir -> should only happen if already inside a directory and trying to recurse, which is not supported
+          logger.warning(format(mpMessageBundle.getString("WRITE_DIR_TO_FILE_ERROR"), input.getAbsolutePath(), output.getAbsolutePath()));
+          return;
       }
       File[] files = input.listFiles();
       if (files == null) {

src/main/resources/edu/ucsd/sbrg/polisher/Messages.xml

@@ -164,7 +164,7 @@
     <entry key="VAL_ERROR">No SBML validation possible, process terminated with errors.</entry>
     <entry key="VERSION_NR_MISSING">There is no version number provided for this model</entry>
     <entry key="WRITE_COMBINE_ARCHIVE">Writing COMBINE Archive {0}</entry>
-    <entry key="WRITE_DIR_TO_FILE_ERROR">Cannot write inputs from directory {0} to a output file {1}.</entry>
+    <entry key="WRITE_DIR_TO_FILE_ERROR">Cannot write inputs from directory {0} to a output file {1}. Skipping directory.</entry>
     <entry key="WRITE_FILE_INFO">Writing output file {0}</entry>
     <entry key="WRITE_RDF_FILE_INFO">Writing output RDF glossary file {0}</entry>
     <entry key="WRITE_TO_FILE_ERROR">Cannot write to file {0}.</entry>

src/main/resources/edu/ucsd/sbrg/polisher/Messages_de.xml

@@ -164,7 +164,7 @@
     <entry key="VAL_ERROR">Keine SBML Validierung möglich. Prozess mit Fehlern beendet.</entry>
     <entry key="VERSION_NR_MISSING">Die Versionsnummer für das Model fehlt</entry>
     <entry key="WRITE_COMBINE_ARCHIVE">Schreibe COMBINE Archiv {0}</entry>
-    <entry key="WRITE_DIR_TO_FILE_ERROR">Die Eingabedaten aus dem Verzeichnis {0} können nicht in die Ausgabedatei {1} geschrieben werden.</entry>
+    <entry key="WRITE_DIR_TO_FILE_ERROR">Die Eingabedaten aus dem Verzeichnis {0} können nicht in die Ausgabedatei {1} geschrieben werden. Überspringe das Verzeichnis.</entry>
     <entry key="WRITE_FILE_INFO">Schreibe Datei {0}</entry>
     <entry key="WRITE_RDF_FILE_INFO">Schreibe RDF glossary Datei {0}</entry>
     <entry key="WRITE_TO_FILE_ERROR">Kann Datei {0} nicht schreiben.</entry>

src/scripts/ModelPolisher.sh

@@ -12,6 +12,6 @@ DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
 cd ${DIR}/..
 
 ## Launch the program".travis.yml"
-java -jar -Xms8G -Xmx8G -Xss128M -Duser.language=en target/ModelPolisher-2.0.jar $@
+java -jar -Xms8G -Xmx8G -Xss128M -Duser.language=en target/ModelPolisher-2.0.1.jar $@
 
 exit 0