Feature/dependency upgrades (#326)

Dump low risk dependencies

* maven plugins
* aws, commons, guava, jopt, gson, etc.

Also gives new test environment a work out

Author: denis-yuen

.travis.yml

@@ -11,17 +11,19 @@ cache:
 services:
   - docker
 
-# encryption used for documentation key
+# encryption used for documentation key, pull containers before since Docker Hub can timeout and it should not break a long build
 before_install:
-- docker pull seqware/seqware_test_environment:1.2
-- openssl aes-256-cbc -K $encrypted_b1a0a7dd1d17_key -iv $encrypted_b1a0a7dd1d17_iv -in seqware_jenkins.id_rsa.enc -out seqware_jenkins.id_rsa -d
+- sudo rm /etc/mavenrc
+- echo "MAVEN_OPTS='-Xmx4g -XX:MaxPermSize=1024m'" > ~/.mavenrc
+- docker pull quay.io/seqware/seqware_test_environment:1.3
+#- docker pull seqware/documentation_builder:1.3
+#- openssl aes-256-cbc -K $encrypted_b1a0a7dd1d17_key -iv $encrypted_b1a0a7dd1d17_iv -in seqware_jenkins.id_rsa.enc -out seqware_jenkins.id_rsa -d
 
 script: 
-- docker run -h master -ti --rm -v $HOME/.m2:/home/seqware/.m2 -v $TRAVIS_BUILD_DIR:/home/seqware/gitroot/seqware seqware/seqware_test_environment:1.2 /test-start.sh "cd /home/seqware && sudo chown -R seqware:seqware . && cd /home/seqware/gitroot/seqware && cp .travis/settings ~/.seqware  && export MAVEN_OPTS=\"-Xmx2048m -XX:MaxPermSize=1024m\" && mvn -B clean install -DskipITs=false &&  cp seqware-pipeline/target/seqware ~/bin &&  mvn -B clean install -pl seqware-ext-testing -DskipITs=false -P 'extITs,embeddedTomcat'"
+- docker run -h master -ti --rm -v $HOME/.m2:/home/seqware/.m2 -v $TRAVIS_BUILD_DIR:/home/seqware/gitroot/seqware quay.io/seqware/seqware_test_environment:1.3 /test-start.sh "cd /home/seqware && sudo chown -R seqware:seqware . && cd /home/seqware/gitroot/seqware && cp .travis/settings ~/.seqware  && export MAVEN_OPTS=\"-Xmx4096m -XX:MaxPermSize=1024m\" && mvn -B clean install -DskipITs=false &&  cp seqware-pipeline/target/seqware ~/bin &&  mvn -B clean install -pl seqware-ext-testing -DskipITs=false -P 'extITs,embeddedTomcat'"
 
-after_success:
-- docker pull seqware/documentation_builder:1.2
-- docker run -v $TRAVIS_BUILD_DIR/seqware_jenkins.id_rsa:/root/.ssh/private_key.pem seqware/documentation_builder:1.2 sh -c 'chown -R root $TRAVIS_BUILD_DIR &&  chown root /root/.ssh/private_key.pem && chmod -R 600 /root/.ssh/private_key.pem && eval `ssh-agent -s` && ssh-add /root/.ssh/private_key.pem && locale && export LC_ALL="en_US.UTF-8" && export LANG="en_US.UTF-8" && locale && mvn site-deploy'
+#after_success:
+#- docker run -v $HOME/.m2:/root/.m2 -v $TRAVIS_BUILD_DIR/seqware_jenkins.id_rsa:/root/.ssh/private_key.pem seqware/documentation_builder:1.3 sh -c 'chown -R root . &&  chown root /root/.ssh/private_key.pem && chmod -R 600 /root/.ssh/private_key.pem && eval `ssh-agent -s` && ssh-add /root/.ssh/private_key.pem && locale && export LC_ALL="en_US.UTF-8" && export LANG="en_US.UTF-8" && locale && export MAVEN_OPTS=\"-Xmx4096m -XX:MaxPermSize=1024m\" && mvn site-deploy'
 
 # sudo required for docker based testing
 sudo: required 

pom.xml

@@ -129,6 +129,14 @@
 
     <build>
         <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-checkstyle-plugin</artifactId>
+                <configuration>
+                    <!-- generated code -->
+                    <skip>true</skip>
+                </configuration>
+            </plugin>
             <plugin>
                 <groupId>org.glassfish.embedded</groupId>
                 <artifactId>maven-embedded-glassfish-plugin</artifactId>
@@ -140,7 +148,7 @@
                     <dbVendorName>postgresql</dbVendorName>
                     <libraries>${project.build.directory}/lib/postgresql-${postgresql.version}.jar</libraries>
                     <autoDelete>true</autoDelete>
-                    <goalPrefix>embedded-glassfish</goalPrefix>
+                    <!-- <goalPrefix>embedded-glassfish</goalPrefix> -->
                 </configuration>
             </plugin>
             <plugin>
@@ -168,7 +176,6 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
-                <version>2.3.2</version>
                 <configuration>
                     <source>1.7</source>
                     <target>1.7</target>
@@ -268,7 +275,7 @@
                 </executions>
 
                 <configuration>
-                    <argLine>${argLine} -Xms512m -Xmx512m</argLine>
+                    <!-- <argLine>${argLine} -Xms512m -Xmx512m</argLine> -->
                     <forkMode>pertest</forkMode>
                 </configuration>
             </plugin>

seqware-admin-webservice/pom.xml

@@ -33,13 +33,13 @@
             <plugins>
                 <plugin>
                     <artifactId>maven-archetype-plugin</artifactId>
-                    <version>2.2</version>
+                    <version>2.4</version>
                 </plugin>
 
                 <plugin>
                     <groupId>org.apache.maven.plugins</groupId>
                     <artifactId>maven-resources-plugin</artifactId>
-                    <version>2.6</version>
+                    <version>2.7</version>
                     <configuration>
                         <includeEmptyDirs>true</includeEmptyDirs>
                     </configuration>

seqware-archetypes/seqware-archetype-decider/pom.xml

@@ -33,13 +33,13 @@
             <plugins>
                 <plugin>
                     <artifactId>maven-archetype-plugin</artifactId>
-                    <version>2.2</version>
+                    <version>2.4</version>
                 </plugin>
 
                 <plugin>
                     <groupId>org.apache.maven.plugins</groupId>
                     <artifactId>maven-resources-plugin</artifactId>
-                    <version>2.6</version>
+                    <version>2.7</version>
                     <configuration>
                         <includeEmptyDirs>true</includeEmptyDirs>
                     </configuration>

seqware-archetypes/seqware-archetype-java-workflow/pom.xml

@@ -28,7 +28,7 @@
             <plugins>
                 <plugin>
                     <artifactId>maven-archetype-plugin</artifactId>
-                    <version>2.2</version>
+                    <version>2.4</version>
                 </plugin>
             </plugins>
         </pluginManagement>

seqware-archetypes/seqware-archetype-module/pom.xml

@@ -20,18 +20,9 @@
 
     <build>
         <plugins>
-
-            <plugin>
-                <groupId>org.jacoco</groupId>
-                <artifactId>jacoco-maven-plugin</artifactId>
-                <configuration>
-                    <skip>true</skip>
-                </configuration>
-            </plugin>
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>exec-maven-plugin</artifactId>
-                <version>1.2.1</version>
                 <executions>
                     <execution>
                         <id>generate_markdown</id>

seqware-distribution/pom.xml

@@ -0,0 +1 @@
+../findbugs-exclude.xml

seqware-ext-admin-testing/findbugs-exclude.xml

@@ -116,7 +116,7 @@
                             <port>38080</port>
                             <dbVendorName>postgresql</dbVendorName>
                             <libraries>${project.parent.basedir}/seqware-admin-webservice/target/lib/postgresql-${postgresql.version}.jar</libraries>
-                            <goalPrefix>embedded-glassfish</goalPrefix>
+                            <!-- <goalPrefix>embedded-glassfish</goalPrefix> -->
                         </configuration>
                         <executions>
                             <execution>

seqware-ext-admin-testing/pom.xml

@@ -17,11 +17,6 @@
 package net.sourceforge.seqware.pipeline.plugins;
 
 import com.google.common.io.Files;
-import java.io.File;
-import java.io.IOException;
-import java.util.Map;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 import joptsimple.OptionParser;
 import joptsimple.OptionSet;
 import net.sourceforge.seqware.common.util.Log;
@@ -31,7 +26,12 @@
 import org.apache.commons.exec.ExecuteException;
 import org.apache.commons.exec.PumpStreamHandler;
 import org.apache.commons.io.output.ByteArrayOutputStream;
-import org.junit.Assert;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 /**
  * 
@@ -180,8 +180,9 @@ public static String runArbitraryCommand(String line, int expectedReturnValue, F
         exec.setExitValue(expectedReturnValue);
         try {
             int exitValue = exec.execute(commandline, environment);
-            Assert.assertTrue("exit value for full jar with no params should be " + expectedReturnValue + " was " + exitValue,
-                    exitValue == expectedReturnValue);
+            if (exitValue != expectedReturnValue){
+                throw new RuntimeException("exit value for full jar with no params should be " + expectedReturnValue + " was " + exitValue);
+            }
             String output = outputStream.toString();
             return output;
         } catch (ExecuteException e) {

seqware-ext-admin-testing/src/main/java/net/sourceforge/seqware/pipeline/plugins/ITUtility.java

@@ -149,7 +149,6 @@
         <dependency>
             <groupId>com.github.stefanbirkner</groupId>
             <artifactId>system-rules</artifactId>
-            <version>1.8.0</version>
         </dependency>
     </dependencies>
 
@@ -245,6 +244,7 @@
                     <plugin>
                         <groupId>org.apache.tomcat.maven</groupId>
                         <artifactId>tomcat7-maven-plugin</artifactId>
+                        <version>2.2</version>
                         <configuration>
                             <useNaming>true</useNaming>
                             <contextFile>../seqware-webservice/target/seqware-webservice-${project.version}/META-INF/context.xml</contextFile>

seqware-ext-testing/pom.xml

@@ -17,15 +17,17 @@
 package net.sourceforge.seqware.pipeline.plugins;
 
 import com.google.common.io.Files;
-import java.io.File;
-import java.io.IOException;
-import java.util.Random;
 import net.sourceforge.seqware.common.module.ReturnValue;
 import net.sourceforge.seqware.common.util.Log;
 import org.apache.commons.io.FileUtils;
 import org.junit.BeforeClass;
 import org.junit.Test;
 
+import java.io.File;
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.util.Random;
+
 /**
  * These tests support command-line tools found in the SeqWare User Tutorial, in this case, GenericMetadataSaver
  * 
@@ -53,7 +55,7 @@ public String saveGenericMetadataFileForSample(String sampleAccession, boolean c
         // create a random new file and check that the file we want to save metadata about exists
         File inputFile = File.createTempFile("input", "out");
         final String content = "This is a funky funky test file";
-        FileUtils.write(inputFile, content);
+        FileUtils.write(inputFile, content, StandardCharsets.UTF_8);
 
         Random generator = new Random();
         String random = String.valueOf(generator.nextInt());

seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/plugins/GenericMetadataSaverET.java

@@ -17,17 +17,19 @@
 package net.sourceforge.seqware.pipeline.plugins;
 
 import com.google.common.io.Files;
-import java.io.File;
-import java.io.IOException;
-import java.util.List;
-import java.util.UUID;
 import net.sourceforge.seqware.common.module.ReturnValue;
 import net.sourceforge.seqware.common.util.Log;
 import org.apache.commons.io.FileUtils;
 import org.junit.Assert;
 import org.junit.BeforeClass;
 import org.junit.Test;
 
+import java.io.File;
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.util.List;
+import java.util.UUID;
+
 /**
  * These tests support command-line tools found in the SeqWare User Tutorial, in this case, WorkflowRunReporter
  *
@@ -51,7 +53,7 @@ public void runWorkflowRunReporter() throws IOException {
         Log.info(listOutput);
         File retrievedFile = new File(createTempDir, testOutFile.getName());
         Assert.assertTrue("output file does not exist", retrievedFile.exists());
-        List<String> readLines = FileUtils.readLines(testOutFile);
+        List<String> readLines = FileUtils.readLines(testOutFile, StandardCharsets.UTF_8);
         Assert.assertTrue("incorrect number of lines", readLines.size() == 2);
         long checksumCRC32 = FileUtils.checksumCRC32(testOutFile);
         Assert.assertTrue("incorrect output checksum" + checksumCRC32, checksumCRC32 == 255117433L);
@@ -85,11 +87,11 @@ public void runFirstDate() throws IOException {
         Log.info(listOutput);
         File retrievedFile = new File(createTempDir, testOutFile.getName());
         Assert.assertTrue("output file does not exist", retrievedFile.exists());
-        List<String> readLines = FileUtils.readLines(testOutFile);
+        List<String> readLines = FileUtils.readLines(testOutFile,StandardCharsets.UTF_8);
         Assert.assertTrue("incorrect number of lines ", readLines.size() == 7);
         long checksumCRC32 = FileUtils.checksumCRC32(testOutFile);
         // former is for Java 7, latter is for Java 8, Looks like we didn't solve the sorting problem
-        Assert.assertTrue("incorrect output checksum " + checksumCRC32 + " " + FileUtils.readFileToString(retrievedFile),
+        Assert.assertTrue("incorrect output checksum " + checksumCRC32 + " " + FileUtils.readFileToString(retrievedFile,StandardCharsets.UTF_8),
                 checksumCRC32 == 3873030870L || checksumCRC32 == 2196935470L || checksumCRC32 == 3273287955L);
     }
 
@@ -104,11 +106,11 @@ public void runBothDates() throws IOException {
         Log.info(listOutput);
         File retrievedFile = new File(createTempDir, testOutFile.getName());
         Assert.assertTrue("output file does not exist", retrievedFile.exists());
-        List<String> readLines = FileUtils.readLines(testOutFile);
+        List<String> readLines = FileUtils.readLines(testOutFile,StandardCharsets.UTF_8);
         Assert.assertTrue("incorrect number of lines ", readLines.size() == 4);
         long checksumCRC32 = FileUtils.checksumCRC32(testOutFile);
         // former is for Java 7, latter is for Java 8, Looks like we didn't solve the sorting problem
-        Assert.assertTrue("incorrect output checksum " + checksumCRC32 + " " + FileUtils.readFileToString(retrievedFile),
+        Assert.assertTrue("incorrect output checksum " + checksumCRC32 + " " + FileUtils.readFileToString(retrievedFile,StandardCharsets.UTF_8),
                 checksumCRC32 == 562223107L || checksumCRC32 == 4072825873L);
     }
 

seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/plugins/WorkflowRunReporterET.java

@@ -16,10 +16,6 @@
  */
 package net.sourceforge.seqware.pipeline.tutorial;
 
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
 import net.sourceforge.seqware.common.util.Log;
 import net.sourceforge.seqware.pipeline.plugins.ITUtility;
 import net.sourceforge.seqware.pipeline.plugins.PluginRunnerET;
@@ -29,6 +25,12 @@
 import org.junit.BeforeClass;
 import org.junit.Test;
 
+import java.io.File;
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * Build and install a bundle, used by both the User tutorial and the Developer tutorial
  *
@@ -94,7 +96,7 @@ public static File findTargetBundleDir(File projectDir) {
     @Test
     public void testModifyingTheWorkflow() throws IOException {
         Log.info("Editing java client at " + JavaClient.getAbsolutePath());
-        List<String> readLines = FileUtils.readLines(JavaClient);
+        List<String> readLines = FileUtils.readLines(JavaClient, StandardCharsets.UTF_8);
         // edit lines to match tutorial changes
         boolean linesAdded = false;
         for (int i = 0; i < readLines.size(); i++) {

seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/tutorial/DeveloperPhase1.java

@@ -17,9 +17,6 @@
 package net.sourceforge.seqware.pipeline.tutorial;
 
 import com.google.common.io.Files;
-import java.io.File;
-import java.io.IOException;
-import java.util.Collection;
 import net.sourceforge.seqware.common.module.ReturnValue;
 import net.sourceforge.seqware.pipeline.plugins.ITUtility;
 import net.sourceforge.seqware.pipeline.plugins.PluginRunnerET;
@@ -29,6 +26,11 @@
 import org.junit.Assert;
 import org.junit.Test;
 
+import java.io.File;
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.util.Collection;
+
 /**
  * Tests downloading results in the tutorial
  * 
@@ -95,7 +97,7 @@ private String monitorAndReturnWorkflowRun() throws IOException {
         // check that we have at least one run in the output
         boolean runFound = false;
         String workflowRunSWID = null;
-        for (String line : FileUtils.readLines(foundFile)) {
+        for (String line : FileUtils.readLines(foundFile, StandardCharsets.UTF_8)) {
             if (line.contains("seqwarearchetypejavaworkflow")) {
                 runFound = true;
                 String[] parts = line.split("\t");

seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/tutorial/UserPhase6.java

@@ -123,7 +123,6 @@
         <dependency>
             <groupId>org.mockito</groupId>
             <artifactId>mockito-core</artifactId>
-            <version>1.10.5</version>
             <scope>test</scope>
             <exclusions>
                 <exclusion>
@@ -135,13 +134,13 @@
         <dependency>
             <groupId>org.powermock</groupId>
             <artifactId>powermock-module-junit4</artifactId>
-            <version>1.5.6</version>
+            <version>${powermock.version}</version>
             <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>org.powermock</groupId>
             <artifactId>powermock-api-mockito</artifactId>
-            <version>1.5.6</version>
+            <version>${powermock.version}</version>
             <scope>test</scope>
         </dependency>
         <dependency>
@@ -342,7 +341,7 @@
             <artifactId>powermock-core</artifactId>
             <groupId>org.powermock</groupId>
             <type>jar</type>
-            <version>1.5.6</version>
+            <version>${powermock.version}</version>
             <scope>test</scope>
             <exclusions>
                 <exclusion>