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Thanks to Platform Computing tech support, found the magical environment variable BSUB_QUIET. 

Minor refactoring to add more of the CLibrary including setenv().

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4819 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2010-12-10 21:27:12 +00:00
parent 5b46a900b3
commit 895cb39f41
5 changed files with 193 additions and 57 deletions
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179
java/src/org/broadinstitute/sting/jna/clibrary/LibC.java 100644
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@ -0,0 +1,179 @@
/*
* Copyright (c) 2010, 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.sting.jna.clibrary;
import com.sun.jna.*;
/**
* Sparse port of the Standard C Library libc -lc.
*/
@SuppressWarnings("unused")
public class LibC {
static {
Native.register("c");
}
/** Operation not permitted */
public static final int EPERM = 1;
/** No such file or directory */
public static final int ENOENT = 2;
/** No such process */
public static final int ESRCH = 3;
/** Interrupted system call */
public static final int EINTR = 4;
/** I/O error */
public static final int EIO = 5;
/** No such device or address */
public static final int ENXIO = 6;
/** Argument list too long */
public static final int E2BIG = 7;
/** Exec format error */
public static final int ENOEXEC = 8;
/** Bad file number */
public static final int EBADF = 9;
/** No child processes */
public static final int ECHILD = 10;
/** Try again */
public static final int EAGAIN = 11;
/** Out of memory */
public static final int ENOMEM = 12;
/** Permission denied */
public static final int EACCES = 13;
/** Bad address */
public static final int EFAULT = 14;
/** Block device required */
public static final int ENOTBLK = 15;
/** Device or resource busy */
public static final int EBUSY = 16;
/** File exists */
public static final int EEXIST = 17;
/** Cross-device link */
public static final int EXDEV = 18;
/** No such device */
public static final int ENODEV = 19;
/** Not a directory */
public static final int ENOTDIR = 20;
/** Is a directory */
public static final int EISDIR = 21;
/** Invalid argument */
public static final int EINVAL = 22;
/** File table overflow */
public static final int ENFILE = 23;
/** Too many open files */
public static final int EMFILE = 24;
/** Not a typewriter */
public static final int ENOTTY = 25;
/** Text file busy */
public static final int ETXTBSY = 26;
/** File too large */
public static final int EFBIG = 27;
/** No space left on device */
public static final int ENOSPC = 28;
/** Illegal seek */
public static final int ESPIPE = 29;
/** Read-only file system */
public static final int EROFS = 30;
/** Too many links */
public static final int EMLINK = 31;
/** Broken pipe */
public static final int EPIPE = 32;
/** Math argument out of domain of func */
public static final int EDOM = 33;
/** Math result not representable */
public static final int ERANGE = 34;
/**
* Inserts or resets the environment variable name in the current environment list. If the variable name does not exist
* in the list, it is inserted with the given value. If the variable does exist, the argument overwrite is tested; if overwrite is zero, the
* variable is not reset, otherwise it is reset to the given value.
* @param name the environment variable name
* @param value the given value
* @param overwrite if overwrite is zero, the variable is not reset, otherwise it is reset to the given value
* @return the value 0 if successful; otherwise the value -1 is returned and the global variable errno is set to indicate the error.
* @throws LastErrorException [ENOMEM] The function failed because it was unable to allocate memory for the environment.
*/
public static native int setenv(String name, String value, int overwrite) throws LastErrorException;
/**
* Obtains the current value of the environment variable, name.
* @param name the environment variable name
* @return the value of the environment variable as a NUL-terminated string. If the variable name is not in the current environment, NULL is returned.
*/
public static native String getenv(String name);
/**
* The unsetenv() function deletes all instances of the variable name pointed to by name from the list. Note that only the variable name
* (e.g., "NAME") should be given; "NAME=value" will not work.
* @param name the environment variable name
* @return the value 0 if successful; otherwise the value -1 is returned and the global variable errno is set to indicate the error.
* @throws LastErrorException The function failed.
*/
public static native int unsetenv(String name) throws LastErrorException;
public static class timeval extends Structure {
public static class ByReference extends timeval implements Structure.ByReference {
}
public static class ByValue extends timeval implements Structure.ByValue {
}
public NativeLong tv_sec;
public NativeLong tv_usec;
}
}

45
java/src/org/broadinstitute/sting/jna/clibrary/Time.java
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@ -1,45 +0,0 @@
/*
* Copyright (c) 2010, 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.sting.jna.clibrary;
import com.sun.jna.NativeLong;
import com.sun.jna.Structure;
/**
* Sparse JNA port of time.h
*/
@SuppressWarnings("unused")
public class Time {
public static class timeval extends Structure {
public static class ByReference extends timeval implements Structure.ByReference {
}
public static class ByValue extends timeval implements Structure.ByValue {
}
public NativeLong tv_sec;
public NativeLong tv_usec;
}
}

4
java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBat.java
View File

@ -27,6 +27,7 @@ package org.broadinstitute.sting.jna.lsf.v7_0_6;
import com.sun.jna.*;
import com.sun.jna.ptr.*;
import org.broadinstitute.sting.jna.clibrary.JNAUtils;
import org.broadinstitute.sting.jna.clibrary.LibC;
/**
* JNA wrappers for LSF's lsbatch.h and -lbat
@ -59,6 +60,9 @@ public class LibBat {
NativeLibrary.addSearchPath("bat", lsfLibDir);
}
NativeLibrary.getInstance("lsf");
// via Platform LSF Configuration Reference, by default quiet the BSUB output.
if ("Y".equals(System.getProperty("BSUB_QUIET", "Y")))
LibC.setenv("BSUB_QUIET", "Y", 1);
Native.register("bat");
}

2
java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibLsf.java
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@ -29,7 +29,7 @@ import com.sun.jna.ptr.FloatByReference;
import com.sun.jna.ptr.IntByReference;
import com.sun.jna.ptr.PointerByReference;
import org.broadinstitute.sting.jna.clibrary.JNAUtils;
import org.broadinstitute.sting.jna.clibrary.Time.*;
import org.broadinstitute.sting.jna.clibrary.LibC.*;
/**
* JNA wrappers for LSF's lsf.h and -llsf

20
java/test/org/broadinstitute/sting/jna/clibrary/JNAUtilsUnitTest.java → java/test/org/broadinstitute/sting/jna/clibrary/LibCUnitTest.java
View File

@ -24,22 +24,20 @@
package org.broadinstitute.sting.jna.clibrary;
import com.sun.jna.Library;
import com.sun.jna.Native;
import org.broadinstitute.sting.BaseTest;
import org.testng.Assert;
import org.testng.annotations.Test;
public class JNAUtilsUnitTest extends BaseTest {
public interface CLib extends Library {
public CLib INSTANCE = (CLib) Native.loadLibrary("c", CLib.class);
public int atol(String str);
}
public class LibCUnitTest extends BaseTest {
@Test
public void testCLibJna() {
int result = CLib.INSTANCE.atol("10");
Assert.assertEquals(result, 10);
public void testEnvironment() {
String testProperty = "test_property";
String testValue = "value";
Assert.assertEquals(LibC.getenv(testProperty), null);
Assert.assertEquals(LibC.setenv(testProperty, testValue, 1), 0);
Assert.assertEquals(LibC.getenv(testProperty), testValue);
Assert.assertEquals(LibC.unsetenv(testProperty), 0);
Assert.assertEquals(LibC.getenv(testProperty), null);
}
}