From 4eb9858461f25d3e1f1e0d0beca21ebda86d6d7b Mon Sep 17 00:00:00 2001 From: Phillip Dexheimer Date: Wed, 28 May 2014 22:44:37 -0400 Subject: [PATCH] Ensure that output files are specified in a writeable location -PT 69579780 --- .../gatk/engine/io/OutputTracker.java | 19 ++++- .../gatk/engine/io/OutputTrackerUnitTest.java | 84 +++++++++++++++++++ 2 files changed, 102 insertions(+), 1 deletion(-) create mode 100644 public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/io/OutputTrackerUnitTest.java diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java index 2a3b0b02d..f32779276 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java +++ b/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 void addOutput(Stub stub, Storage 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 void validateOutputPath(final Stub 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. diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/io/OutputTrackerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/io/OutputTrackerUnitTest.java new file mode 100644 index 000000000..735fce63c --- /dev/null +++ b/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)); + } +}