hdf5.git - Mirror from: https://github.com/HDFGroup/hdf5.git

Mirror from: https://github.com/HDFGroup/hdf5.git

	Commit message (Expand)	Author	Age	Files	Lines
*	[svn-r780] * empty log message *	Robb Matzke	1998-10-23	1	-0/+0

IR"/slf4j-simple-1.7.5.jar:"$TESTJARFILE"" +CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-1.7.25.jar:"$BLDLIBDIR"/slf4j-simple-1.7.25.jar:"$TESTJARFILE"" TEST=/usr/bin/test if [ ! -x /usr/bin/test ] diff --git a/java/examples/datatypes/Makefile.am b/java/examples/datatypes/Makefile.am index f6e58f1..5e0e971 100644 --- a/java/examples/datatypes/Makefile.am +++ b/java/examples/datatypes/Makefile.am @@ -28,7 +28,7 @@ classes: pkgpath = examples/datatypes hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar -CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.5.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.5.jar:$$CLASSPATH +CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH jarfile = jar$(PACKAGE_TARNAME)datatypes.jar diff --git a/java/examples/groups/JavaGroupExample.sh.in b/java/examples/groups/JavaGroupExample.sh.in index 53c0045..36df02e 100644 --- a/java/examples/groups/JavaGroupExample.sh.in +++ b/java/examples/groups/JavaGroupExample.sh.in @@ -51,8 +51,8 @@ test -d $BLDREFDIR || mkdir -p $BLDREFDIR # Comment '#' without space can be used. # -------------------------------------------------------------------- LIST_LIBRARY_FILES=" -$HDFLIB_HOME/slf4j-api-1.7.5.jar -$HDFLIB_HOME/ext/slf4j-simple-1.7.5.jar +$HDFLIB_HOME/slf4j-api-1.7.25.jar +$HDFLIB_HOME/ext/slf4j-simple-1.7.25.jar $top_builddir/src/.libs/libhdf5.* $top_builddir/java/src/jni/.libs/libhdf5_java.* $top_builddir/java/src/$JARFILE @@ -109,7 +109,7 @@ CLEAN_LIBFILES_AND_BLDLIBDIR() # skip rm if srcdir is same as destdir # this occurs when build/test performed in source dir and # make cp fail - SDIR=`$DIRNAME $HDFLIB_HOME/slf4j-api-1.7.5.jar` + SDIR=`$DIRNAME $HDFLIB_HOME/slf4j-api-1.7.25.jar` INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'` if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then @@ -225,7 +225,7 @@ COPY_LIBFILES_TO_BLDLIBDIR COPY_DATAFILES_TO_BLDDIR COPY_REFFILES_TO_BLDREFDIR -CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-1.7.5.jar:"$BLDLIBDIR"/slf4j-simple-1.7.5.jar:"$TESTJARFILE"" +CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-1.7.25.jar:"$BLDLIBDIR"/slf4j-simple-1.7.25.jar:"$TESTJARFILE"" TEST=/usr/bin/test if [ ! -x /usr/bin/test ] diff --git a/java/examples/groups/Makefile.am b/java/examples/groups/Makefile.am index 4da17f9..09df743 100644 --- a/java/examples/groups/Makefile.am +++ b/java/examples/groups/Makefile.am @@ -28,7 +28,7 @@ classes: pkgpath = examples/groups hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar -CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.5.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.5.jar:$$CLASSPATH +CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH jarfile = jar$(PACKAGE_TARNAME)groups.jar diff --git a/java/examples/intro/JavaIntroExample.sh.in b/java/examples/intro/JavaIntroExample.sh.in index 3c3036a..077146d 100644 --- a/java/examples/intro/JavaIntroExample.sh.in +++ b/java/examples/intro/JavaIntroExample.sh.in @@ -49,8 +49,8 @@ test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR # Comment '#' without space can be used. # -------------------------------------------------------------------- LIST_LIBRARY_FILES=" -$HDFLIB_HOME/slf4j-api-1.7.5.jar -$HDFLIB_HOME/ext/slf4j-simple-1.7.5.jar +$HDFLIB_HOME/slf4j-api-1.7.25.jar +$HDFLIB_HOME/ext/slf4j-simple-1.7.25.jar $top_builddir/src/.libs/libhdf5.* $top_builddir/java/src/jni/.libs/libhdf5_java.* $top_builddir/java/src/$JARFILE @@ -103,7 +103,7 @@ CLEAN_LIBFILES_AND_BLDLIBDIR() # skip rm if srcdir is same as destdir # this occurs when build/test performed in source dir and # make cp fail - SDIR=`$DIRNAME $HDFLIB_HOME/slf4j-api-1.7.5.jar` + SDIR=`$DIRNAME $HDFLIB_HOME/slf4j-api-1.7.25.jar` INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'` if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then @@ -168,7 +168,7 @@ JAVAEXEFLAGS=@H5_JAVAFLAGS@ COPY_LIBFILES_TO_BLDLIBDIR COPY_DATAFILES_TO_BLDDIR -CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-1.7.5.jar:"$BLDLIBDIR"/slf4j-simple-1.7.5.jar:"$TESTJARFILE"" +CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-1.7.25.jar:"$BLDLIBDIR"/slf4j-simple-1.7.25.jar:"$TESTJARFILE"" TEST=/usr/bin/test if [ ! -x /usr/bin/test ] diff --git a/java/examples/intro/Makefile.am b/java/examples/intro/Makefile.am index 0df08cb..33f44c2 100644 --- a/java/examples/intro/Makefile.am +++ b/java/examples/intro/Makefile.am @@ -28,7 +28,7 @@ classes: pkgpath = examples/intro hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar -CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.5.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.5.jar:$$CLASSPATH +CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH jarfile = jar$(PACKAGE_TARNAME)intro.jar diff --git a/java/lib/ext/slf4j-nop-1.7.25.jar b/java/lib/ext/slf4j-nop-1.7.25.jar new file mode 100644 index 0000000..78c7295 Binary files /dev/null and b/java/lib/ext/slf4j-nop-1.7.25.jar differ diff --git a/java/lib/ext/slf4j-nop-1.7.5.jar b/java/lib/ext/slf4j-nop-1.7.5.jar deleted file mode 100644 index e55bdd8..0000000 Binary files a/java/lib/ext/slf4j-nop-1.7.5.jar and /dev/null differ diff --git a/java/lib/ext/slf4j-simple-1.7.25.jar b/java/lib/ext/slf4j-simple-1.7.25.jar new file mode 100644 index 0000000..b29ca12 Binary files /dev/null and b/java/lib/ext/slf4j-simple-1.7.25.jar differ diff --git a/java/lib/ext/slf4j-simple-1.7.5.jar b/java/lib/ext/slf4j-simple-1.7.5.jar deleted file mode 100644 index 9dece31..0000000 Binary files a/java/lib/ext/slf4j-simple-1.7.5.jar and /dev/null differ diff --git a/java/lib/slf4j-api-1.7.25.jar b/java/lib/slf4j-api-1.7.25.jar new file mode 100644 index 0000000..7e62f13 Binary files /dev/null and b/java/lib/slf4j-api-1.7.25.jar differ diff --git a/java/lib/slf4j-api-1.7.5.jar b/java/lib/slf4j-api-1.7.5.jar deleted file mode 100644 index 8766455..0000000 Binary files a/java/lib/slf4j-api-1.7.5.jar and /dev/null differ diff --git a/java/src/Makefile.am b/java/src/Makefile.am index 64eef0c..bd55c39 100644 --- a/java/src/Makefile.am +++ b/java/src/Makefile.am @@ -37,7 +37,7 @@ jarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar hdf5_javadir = $(libdir) pkgpath = hdf/hdf5lib -CLASSPATH_ENV=CLASSPATH=.:$(top_srcdir)/java/lib/slf4j-api-1.7.5.jar:$$CLASSPATH +CLASSPATH_ENV=CLASSPATH=.:$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$$CLASSPATH AM_JAVACFLAGS = $(H5_JAVACFLAGS) -deprecation diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java index f826fbc..4060ca9 100644 --- a/java/src/hdf/hdf5lib/H5.java +++ b/java/src/hdf/hdf5lib/H5.java @@ -1752,14 +1752,8 @@ public class H5 implements java.io.Serializable { (String[]) obj); } else if (is1D && (dataClass.getComponentType() == String.class)) { - log.trace("H5Dread_string type"); - if (H5.H5Tis_variable_str(mem_type_id)) { - status = H5Dread_VLStrings(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (Object[]) obj); - } - else { - status = H5Dread_string(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, - (String[]) obj); - } + log.trace("H5DreadVL type"); + status = H5DreadVL(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (Object[]) obj); } else { // Create a data buffer to hold the data into a Java Array @@ -1979,7 +1973,7 @@ public class H5 implements java.io.Serializable { Class dataClass = obj.getClass(); if (!dataClass.isArray()) { - throw (new HDF5JavaException("H5Dread: data is not an array")); + throw (new HDF5JavaException("H5Dwrite: data is not an array")); } String cname = dataClass.getName(); @@ -2011,14 +2005,8 @@ public class H5 implements java.io.Serializable { (double[]) obj, isCriticalPinning); } else if (is1D && (dataClass.getComponentType() == String.class)) { - log.trace("H5Dwrite_string type"); - if (H5.H5Tis_variable_str(mem_type_id)) { - status = H5Dwrite_VLStrings(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (Object[]) obj); - } - else { - status = H5Dwrite_string(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, - (String[]) obj); - } + log.trace("H5DwriteVL type"); + status = H5DwriteVL(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (Object[]) obj); } else { HDFArray theArray = new HDFArray(obj); @@ -2084,6 +2072,9 @@ public class H5 implements java.io.Serializable { public synchronized static native int H5Dwrite_string(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; + public synchronized static native int H5DwriteVL(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException; + /** * H5Dwrite_VLStrings writes a (partial) variable length String dataset, specified by its identifier dataset_id, from * the application memory buffer buf into the file. diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c index 1d7b823..6d4d8f1 100644 --- a/java/src/jni/h5dImp.c +++ b/java/src/jni/h5dImp.c @@ -56,6 +56,7 @@ extern jobject visit_callback; static herr_t H5DreadVL_asstr (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf); static herr_t H5DreadVL_str (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf); static herr_t H5DreadVL_array (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf); +static herr_t H5DwriteVL_asstr (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf); static herr_t H5DwriteVL_str (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf); static herr_t H5DwriteVL_array (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf); @@ -1194,7 +1195,7 @@ H5DreadVL_asstr /* we will need to read n number of hvl_t structures */ rdata = (hvl_t*)HDcalloc((size_t)n, sizeof(hvl_t)); if (rdata == NULL) { - h5JNIFatalError(env, "H5DreadVL_notstr: failed to allocate buff for read"); + h5JNIFatalError(env, "H5DreadVL_asstr: failed to allocate buff for read"); } /* end if */ else { status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, rdata); @@ -1202,7 +1203,7 @@ H5DreadVL_asstr if (status < 0) { H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata); HDfree(rdata); - h5JNIFatalError(env, "H5DreadVL_notstr: failed to read data"); + h5JNIFatalError(env, "H5DreadVL_asstr: failed to read data"); } /* end if */ else { /* calculate the largest size of all the hvl_t structures read */ @@ -1220,7 +1221,7 @@ H5DreadVL_asstr if (h5str.s == NULL) { H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata); HDfree(rdata); - h5JNIFatalError(env, "H5DreadVL_notstr: failed to allocate buf"); + h5JNIFatalError(env, "H5DreadVL_asstr: failed to allocate buf"); } /* end if */ else { H5T_class_t tclass = H5Tget_class(tid); @@ -1329,6 +1330,104 @@ H5DreadVL_str /* * Class: hdf_hdf5lib_H5 + * Method: H5DwriteVL + * Signature: (JJJJJ[Ljava/lang/String;)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5DwriteVL + (JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id, + jlong file_space_id, jlong xfer_plist_id, jobjectArray buf) +{ + herr_t status = -1; + htri_t isStr = 0; + htri_t isVlenStr = 0; + htri_t isComplex = 0; + + if (buf == NULL) { + h5nullArgument(env, "H5DwriteVL: buf is NULL"); + } /* end if */ + else { + isStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING); + if (H5Tget_class((hid_t)mem_type_id) == H5T_COMPOUND) { + unsigned i; + int nm = H5Tget_nmembers(mem_type_id); + for(i = 0; i 0 || isVlenStr) { + status = H5DwriteVL_asstr(env, (hid_t)dataset_id, (hid_t)mem_type_id, + (hid_t)mem_space_id, (hid_t)file_space_id, + (hid_t)xfer_plist_id, buf); + } + else if (isStr > 0) { + status = H5DwriteVL_str(env, (hid_t)dataset_id, (hid_t)mem_type_id, + (hid_t)mem_space_id, (hid_t)file_space_id, + (hid_t)xfer_plist_id, buf); + } + } /* end else */ + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1VL */ + +herr_t +H5DwriteVL_asstr + (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf) +{ + herr_t status = -1; + hvl_t *wdata; + jsize size; + jint i; + jint n; + + /* Get size of string array */ + n = ENVPTR->GetArrayLength(ENVPAR buf); + wdata = (hvl_t*)HDcalloc((size_t)n, sizeof(hvl_t)); + + if (wdata == NULL) { + h5JNIFatalError(env, "H5DwriteVL_asstr: failed to allocate buff for write"); + } /* end if */ + else { + for (i = 0; i < n; ++i) { + jstring obj = (jstring) ENVPTR->GetObjectArrayElement(ENVPAR (jobjectArray)buf,