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Use GATKPathSpecifier for tmpDir arg. #5832

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Apr 8, 2019
Merged

Use GATKPathSpecifier for tmpDir arg. #5832

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10 changes: 5 additions & 5 deletions src/main/java/org/broadinstitute/hellbender/cmdline/CommandLineProgram.java
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.broadinstitute.barclay.argparser.*;
import org.broadinstitute.hellbender.engine.GATKPathSpecifier;
import org.broadinstitute.hellbender.exceptions.UserException;
import org.broadinstitute.hellbender.utils.LoggingUtils;
import org.broadinstitute.hellbender.utils.Utils;
Expand Down Expand Up @@ -61,7 +62,7 @@ public abstract class CommandLineProgram implements CommandLinePluginProvider {
private static final String DEFAULT_TOOLKIT_SHORT_NAME = "GATK";

@Argument(fullName = StandardArgumentDefinitions.TMP_DIR_NAME, common=true, optional=true, doc = "Temp directory to use.")
public String tmpDir;
public GATKPathSpecifier tmpDir;

@ArgumentCollection(doc="Special Arguments that have meaning to the argument parsing system. " +
"It is unlikely these will ever need to be accessed by the command line program")
Expand Down Expand Up @@ -144,9 +145,8 @@ public final Object runTool(){

public Object instanceMainPostParseArgs() {
// Provide one temp directory if the caller didn't
// TODO - this should use the HTSJDK IOUtil.getDefaultTmpDirPath, which is somehow broken in the current HTSJDK version
if (tmpDir == null || tmpDir.isEmpty()) {
tmpDir = IOUtils.getAbsolutePathWithoutFileProtocol(IOUtils.getPath(System.getProperty("java.io.tmpdir")));
if (tmpDir == null) {
tmpDir = new GATKPathSpecifier(System.getProperty("java.io.tmpdir"));
}

// Build the default headers
Expand All @@ -157,7 +157,7 @@ public Object instanceMainPostParseArgs() {
LoggingUtils.setLoggingLevel(VERBOSITY); // propagate the VERBOSITY level to logging frameworks

// set the temp directory as a java property, checking for existence and read/write access
final Path p = IOUtils.getPath(tmpDir);
final Path p = tmpDir.toPath();
try {
p.getFileSystem().provider().checkAccess(p, AccessMode.READ, AccessMode.WRITE);
System.setProperty("java.io.tmpdir", IOUtils.getAbsolutePathWithoutFileProtocol(p));
Expand Down