Merge branch 'feature-license' into 'develop'

Feature license

Issue: #47
Added license to the project. Bash script to check and reformat if needed.

Also fix for #90 and #91

See merge request !59

license_header.sh

+#!/bin/bash
+#
+# Copyright (c) 2014 Leiden University Medical Center - Sequencing Analysis Support Core <sasc@lumc.nl>
+# @author Peter van 't Hof <p.j.van_t_hof@lumc.nl>
+#
+
+DIR=`readlink -f \`dirname $0\``
+MODE=check
+
+if [ $1 ] ; then
+    MODE=$1
+fi
+
+mvn -f $DIR/public/pom.xml license:$MODE -Dlicense.header=$DIR/public/LICENSE
+
+mvn -f $DIR/protected/pom.xml license:$MODE -Dlicense.header=$DIR/protected/LICENSE
\ No newline at end of file

protected/LICENSE

+biopet-gatk-extensions/src/main/resources/nl/lumc/sasc/biopet/License.txt
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/resources/nl/lumc/sasc/biopet/License.txt

+** This part of Biopet can only be used inside the LUMC **
+

protected/biopet-protected-package/pom.xml

@@ -15,7 +15,12 @@
     
     <inceptionYear>2014</inceptionYear>
     <name>BiopetProtectedPackage</name>
-    
+
+    <properties>
+        <sting.shade.phase>package</sting.shade.phase>
+        <app.main.class>nl.lumc.sasc.biopet.core.BiopetExecutableProtected</app.main.class>
+    </properties>
+
     <dependencies>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
@@ -56,6 +61,12 @@
                         </transformer>
                     </transformers>
                     <filters>
+                        <filter>
+                            <artifact>nl.lumc.sasc:BiopetFramework</artifact>
+                            <excludes>
+                                <exclude>nl/lumc/sasc/biopet/License.txt</exclude>
+                            </excludes>
+                        </filter>
                     </filters>
                 </configuration>
                 <executions>

public/LICENSE

+biopet-framework/src/main/resources/nl/lumc/sasc/biopet/License.txt
\ No newline at end of file

public/biopet-framework/src/main/resources/log4j.properties

@@ -3,6 +3,7 @@ log4j.rootLogger=INFO, A1
 
 # A1 is set to be a ConsoleAppender.
 log4j.appender.A1=org.apache.log4j.ConsoleAppender
+log4j.appender.A1.Target=System.err
 
 # A1 uses PatternLayout.
 log4j.appender.A1.layout=org.apache.log4j.PatternLayout

public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/License.txt

-This file is part of ${project.name}.
-
-${project.name} is built on top of GATK Queue for building bioinformatic 
+Biopet is built on top of GATK Queue for building bioinformatic 
 pipelines. It is mainly intended to support LUMC SHARK cluster which is running 
 SGE. But other types of HPC that are supported by GATK Queue (such as PBS) 
 should also be able to execute Biopet tools and pipelines.
 
-Copyright ${project.inceptionYear} ${owner}
+Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
 
-Contact us at: ${email}
+Contact us at: sasc@lumc.nl
 
 A dual licensing mode is applied. The source code within this project that are 
 not part of GATK Queue is freely available for non-commercial use under an AGPL 
 license; For commercial users or users who do not want to follow the AGPL 
 license, please contact us to obtain a separate license.
 
-${project.name} is free software: you can redistribute it and/or modify
+Biopet is free software: you can redistribute it and/or modify
 it under the terms of the GNU Affero General Public License as published by
 the Free Software Foundation, either version 3 of the License, or
 (at your option) any later version.
 
-${project.name} is distributed in the hope that it will be useful,
+Biopet is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 GNU Affero General Public License for more details.
 
 You should have received a copy of the GNU Affero General Public License
-along with ${project.name}. If not, see <http://www.gnu.org/licenses/>.
\ No newline at end of file
+along with Biopet. If not, see <http://www.gnu.org/licenses/>.
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala

 package nl.lumc.sasc.biopet.core
 
+import java.io.{ PrintWriter, StringWriter }
 import java.util.Properties
+import nl.lumc.sasc.biopet.core.BiopetExecutable._
 import org.apache.log4j.Logger
+import scala.io.Source
 
 trait BiopetExecutable extends Logging {
 
@@ -18,6 +21,7 @@ trait BiopetExecutable extends Logging {
    * @param args the command line arguments
    */
   def main(args: Array[String]): Unit = {
+    checkDirtyBuild(logger)
 
     def toBulletedList(m: List[MainCommand], kind: String = "", bullet: String = "-") =
       "Available %s(s):\n  ".format(kind) + bullet + " " + m.map(x => x.commandName).sorted.mkString("\n  " + bullet + " ")
@@ -37,6 +41,7 @@ trait BiopetExecutable extends Logging {
         |
         |Subcommands:
         |  - version
+        |  - license
         |
         |Questions or comments? Email sasc@lumc.nl or check out the project page at https://git.lumc.nl/biopet/biopet.git
       """.stripMargin.format(modules.keys.mkString(","), getVersion, usage)
@@ -56,31 +61,48 @@ trait BiopetExecutable extends Logging {
         System.err.println(s"ERROR: command '$name' does not exist in module '$module'\n" + usage(module))
         System.exit(1)
       }
-      return command.get
+      command.get
     }
 
     args match {
       case Array("version") => {
         println("version: " + getVersion)
       }
+      case Array("license") => {
+        println(getLicense)
+      }
       case Array(module, name, passArgs @ _*) => {
-        getCommand(module, name).main(passArgs.toArray)
+        try {
+          getCommand(module, name).main(passArgs.toArray)
+        } catch {
+          case e: Exception => {
+            val sWriter = new StringWriter()
+            val pWriter = new PrintWriter(sWriter)
+            e.printStackTrace(pWriter)
+            pWriter.close()
+            val trace = (sWriter.toString.split("\n"))
+
+            if (!logger.isDebugEnabled) {
+              logger.error(trace.head)
+              logger.error("For more info please run with -l debug")
+            } else {
+              trace.foreach(logger.debug(_))
+            }
+            sys.exit(1)
+          }
+        }
       }
       case Array(module) => {
         System.err.println(usage(module))
-        System.exit(1)
+        sys.exit(1)
       }
       case _ => {
         System.err.println(usage())
-        System.exit(1)
+        sys.exit(1)
       }
     }
   }
 
-  def getVersion = BiopetExecutable.getVersion
-
-  def getCommitHash = BiopetExecutable.getCommitHash
-
   def checkDirtyBuild(logger: Logger) {
     val prop = new Properties()
     prop.load(getClass.getClassLoader.getResourceAsStream("git.properties"))
@@ -92,7 +114,6 @@ trait BiopetExecutable extends Logging {
       logger.warn("**********************************************************")
     }
   }
-  checkDirtyBuild(logger)
 }
 
 object BiopetExecutable {
@@ -105,4 +126,9 @@ object BiopetExecutable {
     prop.load(getClass.getClassLoader.getResourceAsStream("git.properties"))
     prop.getProperty("git.commit.id.abbrev")
   }
+
+  def getLicense: String = {
+    val stream = getClass.getClassLoader.getResourceAsStream("nl/lumc/sasc/biopet/License.txt")
+    Source.fromInputStream(stream).getLines().mkString("\n", "\n", "\n")
+  }
 }
\ No newline at end of file

public/biopet-public-package/pom.xml

@@ -22,7 +22,6 @@
         <app.main.class>nl.lumc.sasc.biopet.core.BiopetExecutablePublic</app.main.class>
     </properties>
 
-    
     <dependencies>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>

public/pom.xml

@@ -144,6 +144,25 @@
                     </gitDescribe>
                 </configuration>
             </plugin>
-        </plugins>
+          <plugin>
+              <groupId>com.mycila</groupId>
+              <artifactId>license-maven-plugin</artifactId>
+              <version>2.6</version>
+              <configuration>
+                  <excludes>
+                      <exclude>**/*git*</exclude>
+                      <exclude>**/License*</exclude>
+                      <exclude>**/*.bam</exclude>
+                      <exclude>**/*.bai</exclude>
+                      <exclude>**/*.gtf</exclude>
+                      <exclude>**/*.fq</exclude>
+                      <exclude>**/*.sam</exclude>
+                      <exclude>**/*.bed</exclude>
+                      <exclude>**/*.refFlat</exclude>
+                      <exclude>**/*.R</exclude>
+                  </excludes>
+              </configuration>
+          </plugin>
+      </plugins>
     </build>
 </project>
\ No newline at end of file

templates/public_license.txt

+This file is part of Biopet
+
+Biopet is built on top of GATK Queue for building bioinformatic 
+pipelines. It is mainly intended to support LUMC SHARK cluster which is running 
+SGE. But other types of HPC that are supported by GATK Queue (such as PBS) 
+should also be able to execute Biopet tools and pipelines.
+
+Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+
+Contact us at: sasc@lumc.nl
+
+A dual licensing mode is applied. The source code within this project that are 
+not part of GATK Queue is freely available for non-commercial use under an AGPL 
+license; For commercial users or users who do not want to follow the AGPL 
+license, please contact us to obtain a separate license.
+
+Biopet is free software: you can redistribute it and/or modify
+it under the terms of the GNU Affero General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+Biopet is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU Affero General Public License for more details.
+
+You should have received a copy of the GNU Affero General Public License
+along with Biopet. If not, see <http://www.gnu.org/licenses/>.