Merge pull request #116 from SeqWare/feature/bundle-conf

denis-yuen · denis-yuen · commit 426b4a6e83e3 · 2013-09-19T08:59:49.000-07:00
Feature/bundle conf Former-commit-id: 506a2d6
diff --git a/seqware-common/src/main/java/net/sourceforge/seqware/common/metadata/MetadataWS.java b/seqware-common/src/main/java/net/sourceforge/seqware/common/metadata/MetadataWS.java
@@ -189,17 +189,6 @@ public ReturnValue addWorkflow(String name, String version, String description,
         workflow.setWorkflowType(workflow_type);
         workflow.setWorkflowEngine(workflow_engine);
 
-        Log.info("Posting workflow");
-        try {
-            workflow = ll.addWorkflow(workflow);
-            Log.stdout("WORKFLOW_ACCESSION: " + workflow.getSwAccession());
-            ret.setAttribute("sw_accession", workflow.getSwAccession().toString());
-            ret.setReturnValue(workflow.getWorkflowId());
-        } catch (Exception e) {
-            e.printStackTrace();
-            ret.setExitStatus(ReturnValue.FAILURE);
-            return ret;
-        }
         // open the ini file and parse each item
         // FIXME: this assumes there is one ini file which is generally fine for
         // bundled workflows but we could make this more flexible
@@ -215,7 +204,19 @@ public ReturnValue addWorkflow(String name, String version, String description,
           }
       }
 
-        // foreach workflow param add an entry in the workflow_param table
+      Log.info("Posting workflow");
+      try {
+          workflow = ll.addWorkflow(workflow);
+          Log.stdout("WORKFLOW_ACCESSION: " + workflow.getSwAccession());
+          ret.setAttribute("sw_accession", workflow.getSwAccession().toString());
+          ret.setReturnValue(workflow.getWorkflowId());
+      } catch (Exception e) {
+          e.printStackTrace();
+          ret.setExitStatus(ReturnValue.FAILURE);
+          return ret;
+      }
+
+      // foreach workflow param add an entry in the workflow_param table
         int count = 0;
         for (String key : hm.keySet()) {
             count++;
diff --git a/seqware-common/src/main/java/net/sourceforge/seqware/common/util/maptools/MapTools.java b/seqware-common/src/main/java/net/sourceforge/seqware/common/util/maptools/MapTools.java
@@ -1,5 +1,7 @@
 package net.sourceforge.seqware.common.util.maptools;
 
+import static net.sourceforge.seqware.common.util.Rethrow.rethrow;
+
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileInputStream;
@@ -12,6 +14,7 @@
 import java.util.Iterator;
 import java.util.Map;
 import java.util.Properties;
+
 import net.sourceforge.seqware.common.util.Log;
 
 /**
@@ -89,12 +92,8 @@ public static void ini2RichMap(String iniFile, Map<String, Map<String, String>>
                     hm.put(kv[0], detailsMap);
                 }
             }
-        } catch (FileNotFoundException e) {
-            e.printStackTrace();
-            Log.stderr(e.getMessage());
-        } catch (IOException e) {
-            e.printStackTrace();
-            Log.stderr(e.getMessage());
+        } catch (Exception e) {
+            rethrow(e);
         }
 
     }
diff --git a/seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/cli_tutorial/CLIDeveloperPhase2.java b/seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/cli_tutorial/CLIDeveloperPhase2.java
@@ -30,12 +30,12 @@ public class CLIDeveloperPhase2 extends DeveloperPhase2{
     
     @Override
     protected void testWorkflow() throws IOException {
-        ITUtility.runSeqwareCLI(" bundle test  --dir " + DeveloperPhase1.BundleDir.getAbsolutePath(), ReturnValue.SUCCESS, null);
+        ITUtility.runSeqwareCLI(" bundle test  --dir " + DeveloperPhase1.BuildDir.getAbsolutePath(), ReturnValue.SUCCESS, null);
     }
 
     @Override
     protected void packageBundle(File tempPackageDir) throws IOException {
         ITUtility.runSeqwareCLI(" bundle package --to  " + tempPackageDir.getAbsolutePath() + 
-               " --dir " + DeveloperPhase1.BundleDir.getAbsolutePath() , ReturnValue.SUCCESS, null);
+               " --dir " + DeveloperPhase1.BuildDir.getAbsolutePath() , ReturnValue.SUCCESS, null);
     }
 }
diff --git a/seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/tutorial/DeveloperPhase1.java b/seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/tutorial/DeveloperPhase1.java
@@ -20,12 +20,15 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
+
 import junit.framework.Assert;
 import net.sourceforge.seqware.common.util.Log;
 import net.sourceforge.seqware.pipeline.plugins.ITUtility;
 import net.sourceforge.seqware.pipeline.plugins.PluginRunnerET;
 import net.sourceforge.seqware.pipeline.runner.PluginRunner;
+
 import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.filefilter.WildcardFileFilter;
 import org.junit.BeforeClass;
 import org.junit.Test;
 
@@ -37,6 +40,7 @@ public class DeveloperPhase1 {
     
     public static final String WORKFLOW = "Workflow";
     public static File BundleDir = null;
+    public static File BuildDir = null;
     public static File JavaClient = null;
     
     @BeforeClass
@@ -73,9 +77,20 @@ public static void testListAvailableWorkflowsAndTheirParameters() throws IOExcep
         
         // allocate needed items for future tests
         BundleDir = bundleDir;
+        BuildDir = findTargetBundleDir(bundleDir);
         JavaClient = workflowClientJava;
         
     }
+
+    public static File findTargetBundleDir(File projectDir) {
+      File targetDir = new File(projectDir, "target");
+      for (File f : targetDir.listFiles()){
+        if (f.isDirectory() && f.getName().startsWith("Workflow_Bundle_")){
+          return f;
+        }
+      }
+      throw new RuntimeException("Could not locate target/WorkflowBundle_* directory");
+    }
     
     @Test
     public void testModifyingTheWorkflow() throws IOException{
diff --git a/seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/tutorial/DeveloperPhase2.java b/seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/tutorial/DeveloperPhase2.java
@@ -17,11 +17,14 @@
 package net.sourceforge.seqware.pipeline.tutorial;
 
 import com.google.common.io.Files;
+
 import java.io.File;
 import java.io.IOException;
+
 import net.sourceforge.seqware.common.module.ReturnValue;
 import net.sourceforge.seqware.pipeline.plugins.ITUtility;
 import net.sourceforge.seqware.pipeline.plugins.PluginRunnerET;
+
 import org.apache.commons.io.FileUtils;
 import org.junit.AfterClass;
 import org.junit.Test;
@@ -51,12 +54,12 @@ public static void cleanup() throws IOException{
     }
 
     protected void testWorkflow() throws IOException {
-        ITUtility.runSeqWareJar("-p net.sourceforge.seqware.pipeline.plugins.BundleManager -- -b " + DeveloperPhase1.BundleDir.getAbsolutePath() + 
+        ITUtility.runSeqWareJar("-p net.sourceforge.seqware.pipeline.plugins.BundleManager -- -b " + DeveloperPhase1.BuildDir.getAbsolutePath() + 
                " -t --workflow seqware-archetype-java-workflow --version 1.0-SNAPSHOT", ReturnValue.SUCCESS, null);
     }
 
     protected void packageBundle(File tempPackageDir) throws IOException {
         ITUtility.runSeqWareJar("-p net.sourceforge.seqware.pipeline.plugins.BundleManager -- -b " + tempPackageDir.getAbsolutePath() + 
-               " -p " + DeveloperPhase1.BundleDir.getAbsolutePath() , ReturnValue.SUCCESS, null);
+               " -p " + DeveloperPhase1.BuildDir.getAbsolutePath() , ReturnValue.SUCCESS, null);
     }
 }
diff --git a/seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/bundle/Bundle.java b/seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/bundle/Bundle.java
@@ -130,7 +130,11 @@ public ReturnValue unpackageBundle(File bundle) {
     String bundleName = bundle.getName();
     bundleName = bundleName.replaceAll(".zip", "");
     File outputDir = new File(bundleDir + File.separator + bundleName);
-    FileTools.unzipFile(bundle, outputDir);
+    if (outputDir.exists()){
+      Log.stdout("Expanded bundle directory already exists, skipping unzip.");
+    } else {
+      FileTools.unzipFile(bundle, outputDir);
+    }
     ret.setAttribute("outputDir", outputDir.getAbsolutePath());
     setOutputDir(outputDir.getAbsolutePath());
     FileTools.listFilesRecursive(outputDir, filesArray);
@@ -381,6 +385,18 @@ public ReturnValue validateBundle(File bundle) {
           bi.parseFromFile(file);
         }
         // TODO: add more validation here based on what's pulled out of the metadata bundle
+
+        for (WorkflowInfo wi : bi.getWorkflowInfo()) {
+          // ensure conf file exists
+          String orig = wi.getConfigPath();
+          String abs = orig.replaceAll("\\$\\{workflow_bundle_dir\\}", outputDir);
+          File f = new File(abs);
+          if (!f.exists()){
+            ret.setExitStatus(ReturnValue.FAILURE);
+            ret.setStderr("ERROR: Configuration file does not exist: " + orig);
+          }
+        }
+
       }
     } catch (Exception e) {
       ret.setExitStatus(ReturnValue.FAILURE);
diff --git a/seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/plugins/BundleManager.java b/seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/plugins/BundleManager.java
@@ -138,18 +138,24 @@ public ReturnValue do_run() {
                 println("Bundle Validates!");
             }
         } else if (options.has("bundle") && options.has("test")) {
-            println("Testing Bundle");
-            String bundlePath = (String) options.valueOf("bundle");
-            File bundle = new File(bundlePath);
-            if (options.has("workflow") && options.has("version")) {
-                // then just run the test for a particular workflow and version
-                ret = b.testBundle(bundle, specificMetadataFile, (String) options.valueOf("workflow"), (String) options.valueOf("version"));
-            } else {
-                ret = b.testBundle(bundle, specificMetadataFile);
-            }
-            if (ret.getExitStatus() == ReturnValue.SUCCESS) {
-                println("Bundle Passed Test!");
-            }
+          println("Validating Bundle structure");
+          String bundlePath = (String) options.valueOf("bundle");
+          File bundle = new File(bundlePath);
+          ret = b.validateBundle(bundle);
+          if (ret.getExitStatus() == ReturnValue.SUCCESS) {
+              println("Bundle Validates!");
+              println("Testing Bundle");
+              if (options.has("workflow") && options.has("version")) {
+                  // then just run the test for a particular workflow and version
+                  ret = b.testBundle(bundle, specificMetadataFile, (String) options.valueOf("workflow"), (String) options.valueOf("version"));
+              } else {
+                  ret = b.testBundle(bundle, specificMetadataFile);
+              }
+              if (ret.getExitStatus() == ReturnValue.SUCCESS) {
+                  println("Bundle Passed Test!");
+              }
+          }
+
         } else if (options.has("bundle") && options.has("path-to-package")) {
             println("Packaging Bundle");
             String bundleOutput = (String) options.valueOf("bundle");
diff --git a/seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/runner/PluginRunner.java b/seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/runner/PluginRunner.java
@@ -304,8 +304,12 @@ private void evaluateReturn(Plugin app, String methodName) {
 
     // On failure, update metadb and exit
     if (newReturn.getExitStatus() > ReturnValue.SUCCESS) {
-      Log.stderr("The method '" + methodName + "' exited abnormally so the Runner will terminate here!");
-      Log.stderr("Return value was: " + newReturn.getExitStatus());
+      if (newReturn.getStderr() != null){
+        Log.stderr(newReturn.getStderr());
+      } else {
+        Log.stderr("The method '" + methodName + "' exited abnormally so the Runner will terminate here!");
+        Log.stderr("Return value was: " + newReturn.getExitStatus());
+      }
       System.exit(newReturn.getExitStatus());
     }
 

Original file line number	Diff line number	Diff line change
`@@ -30,12 +30,12 @@ public class CLIDeveloperPhase2 extends DeveloperPhase2{`
`30`	`30`
`31`	`31`	`@Override`
`32`	`32`	`protected void testWorkflow() throws IOException {`
`33`		`- ITUtility.runSeqwareCLI(" bundle test --dir " + DeveloperPhase1.BundleDir.getAbsolutePath(), ReturnValue.SUCCESS, null);`
	`33`	`+ ITUtility.runSeqwareCLI(" bundle test --dir " + DeveloperPhase1.BuildDir.getAbsolutePath(), ReturnValue.SUCCESS, null);`
`34`	`34`	`}`
`35`	`35`
`36`	`36`	`@Override`
`37`	`37`	`protected void packageBundle(File tempPackageDir) throws IOException {`
`38`	`38`	`ITUtility.runSeqwareCLI(" bundle package --to " + tempPackageDir.getAbsolutePath() +`
`39`		`- " --dir " + DeveloperPhase1.BundleDir.getAbsolutePath() , ReturnValue.SUCCESS, null);`
	`39`	`+ " --dir " + DeveloperPhase1.BuildDir.getAbsolutePath() , ReturnValue.SUCCESS, null);`
`40`	`40`	`}`
`41`	`41`	`}`