Ensure that output files are specified in a writeable location

-PT 69579780

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java

@@ -34,8 +34,11 @@ import org.broadinstitute.gatk.engine.io.stubs.Stub;
 import org.broadinstitute.gatk.engine.walkers.Walker;
 import org.broadinstitute.gatk.utils.classloader.JVMUtils;
 import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.io.IOUtils;
 import org.broadinstitute.gatk.utils.sam.SAMFileReaderBuilder;
 
+import java.io.File;
 import java.io.OutputStream;
 import java.lang.reflect.Field;
 import java.util.HashMap;
@@ -114,7 +117,8 @@ public abstract class OutputTracker {
      */
     public <T> void addOutput(Stub<T> stub, Storage<T> storage) {
         stub.register(this);
-        outputs.put(stub,storage);        
+        outputs.put(stub,storage);
+        validateOutputPath(stub);
     }
 
     /**
@@ -148,6 +152,19 @@ public abstract class OutputTracker {
         return (T)storage;
     }
 
+    /**
+     * Ensures that the File associated with this stub (if any) is in a writable location
+     * @param stub
+     */
+    protected <T> void validateOutputPath(final Stub<T> stub) {
+        if (stub.getOutputFile() != null && !(IOUtils.isSpecialFile(stub.getOutputFile()))) {
+            final File parentDir = stub.getOutputFile().getAbsoluteFile().getParentFile();
+            if (! (parentDir.canWrite() && parentDir.canExecute()))
+                throw new UserException.CouldNotCreateOutputFile(stub.getOutputFile(),
+                        "either the containing directory doesn't exist or it isn't writable");
+        }
+    }
+
     /**
      * Install an OutputStreamStub into the given fieldName of the given walker.
      * @param walker Walker into which to inject the field name.

public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/io/OutputTrackerUnitTest.java

@@ -0,0 +1,84 @@
+/*
+* Copyright (c) 2012 The Broad Institute
+*
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+*
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+*
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.engine.io;
+
+import org.broadinstitute.gatk.engine.io.stubs.OutputStreamStub;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.io.File;
+
+public class OutputTrackerUnitTest extends BaseTest {
+
+    private final OutputTracker tracker = new DirectOutputTracker();
+    private File unwriteableDir = null;
+    private File untraversableDir = null;
+
+    @BeforeClass
+    public void createDirectories() {
+        unwriteableDir = new File("unwriteable");
+        unwriteableDir.deleteOnExit();
+        unwriteableDir.mkdir();
+        unwriteableDir.setWritable(false);
+
+        untraversableDir = new File("untraversable");
+        untraversableDir.deleteOnExit();
+        untraversableDir.mkdir();
+        untraversableDir.setExecutable(false);
+    }
+
+    @DataProvider(name = "BadOutputPaths")
+    public Object[][] makeBadOutputPaths() {
+        return new Object[][] {new String[] {"thisDirectoryDoesNotExist/stub.txt"},
+                new String[] {"/thisDirectoryDoesNotExist/dummy.txt"},
+                new String[] {unwriteableDir.getAbsolutePath()+"/dummy.txt"},
+                new String[] {untraversableDir.getAbsolutePath()+"/dummy.txt"}};
+    }
+
+    @DataProvider(name = "GoodOutputPaths")
+    public Object[][] makeGoodOutputPaths() {
+        return new Object[][] {new String[] {publicTestDir+"stub.txt"},
+                new String[] {"dummy.txt"}};
+    }
+
+    @Test(dataProvider = "BadOutputPaths", expectedExceptions = UserException.CouldNotCreateOutputFile.class)
+    public void testInvalidOutputPath(final String path) {
+        tracker.validateOutputPath(new OutputStreamStub(new File(path)));
+    }
+
+    @Test(dataProvider = "GoodOutputPaths")
+    public void testValidOutputPath(final String path) {
+        tracker.validateOutputPath(new OutputStreamStub(new File(path)));
+    }
+
+    @Test
+    public void testOutputPathWithNullFile() {
+        tracker.validateOutputPath(new OutputStreamStub(System.out));
+    }
+}