Merge pull request #36 from biopet/fix-BIOPET-610

compiling ssp-template files with scalate

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.ToolCommandFunction
 import nl.lumc.sasc.biopet.utils.summary.Summary
 import nl.lumc.sasc.biopet.utils.{ IoUtils, Logging, ToolCommand }
 import org.broadinstitute.gatk.utils.commandline.Input
-import org.fusesource.scalate.{ TemplateEngine, TemplateSource }
+import org.fusesource.scalate.TemplateEngine
 
 import scala.collection.mutable
 import scala.language.postfixOps
@@ -236,9 +236,7 @@ object ReportBuilder {
 
   /** Single template render engine, this will have a cache for all compile templates */
   protected val engine = new TemplateEngine()
-
-  /** Cache of temp file for templates from the classpath / jar */
-  private[report] var templateCache: Map[String, File] = Map()
+  engine.allowReload = false
 
   /** This will give the total number of pages including all nested pages */
   def countPages(page: ReportPage): Int = {
@@ -254,15 +252,6 @@ object ReportBuilder {
   def renderTemplate(location: String, args: Map[String, Any] = Map()): String = {
     Logging.logger.info("Rendering: " + location)
 
-    val templateFile: File = templateCache.get(location) match {
-      case Some(template) => template
-      case _ =>
-        val tempFile = File.createTempFile("ssp-template", new File(location).getName)
-        tempFile.deleteOnExit()
-        IoUtils.copyStreamToFile(getClass.getResourceAsStream(location), tempFile)
-        templateCache += location -> tempFile
-        tempFile
-    }
-    engine.layout(TemplateSource.fromFile(templateFile), args)
+    engine.layout(location, args)
   }
 }
\ No newline at end of file

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/ReportBuilderTest.scala

@@ -79,11 +79,8 @@ class ReportBuilderTest extends TestNGSuite with Matchers {
 
   @Test
   def testRenderTemplate: Unit = {
-    ReportBuilder.templateCache = Map()
-    ReportBuilder.templateCache shouldBe empty
     ReportBuilder.renderTemplate("/template.ssp", Map("arg" -> "test")) shouldBe "test"
-    ReportBuilder.templateCache.size shouldBe 1
     ReportBuilder.renderTemplate("/template.ssp", Map("arg" -> "bla")) shouldBe "bla"
-    ReportBuilder.templateCache.size shouldBe 1
   }
+
 }

pom.xml

@@ -127,6 +127,22 @@
                 </executions>
                 <!-- ... (see other usage or goals for details) ... -->
             </plugin>
+            <plugin>
+                <groupId>org.scalatra.scalate</groupId>
+                <artifactId>maven-scalate-plugin_2.10</artifactId>
+                <version>1.7.0</version>
+                <executions>
+                    <execution>
+                        <phase>compile</phase>
+                        <goals>
+                            <goal>precompile</goal>
+                        </goals>
+                        <configuration>
+                            <contextClass>org.fusesource.scalate.DefaultRenderContext</contextClass>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
@@ -280,4 +296,12 @@
             </plugin>
         </plugins>
     </reporting>
+
+    <dependencies>
+        <dependency>
+            <groupId>org.scalatra.scalate</groupId>
+            <artifactId>scalate-core_2.10</artifactId>
+            <version>1.7.0</version>
+        </dependency>
+    </dependencies>
 </project>