Author: tbooth-guest
Date: 2015-08-13 09:24:15 +0000 (Thu, 13 Aug 2015)
New Revision: 19933
Added:
trunk/packages/libsis-jhdf5-java/trunk/debian/README.source
trunk/packages/libsis-jhdf5-java/trunk/debian/changelog
trunk/packages/libsis-jhdf5-java/trunk/debian/compat
trunk/packages/libsis-jhdf5-java/trunk/debian/control
trunk/packages/libsis-jhdf5-java/trunk/debian/copyright
trunk/packages/libsis-jhdf5-java/trunk/debian/i_hate_java.perl
trunk/packages/libsis-jhdf5-java/trunk/debian/jlibs
trunk/packages/libsis-jhdf5-java/trunk/debian/manifest
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/fix_dodgy_cast.patch
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/fix_link_error.patch
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/remove_ch_rinn_imports.patch
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/series
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/sort_exceptions.patch
trunk/packages/libsis-jhdf5-java/trunk/debian/rules
trunk/packages/libsis-jhdf5-java/trunk/debian/source/
trunk/packages/libsis-jhdf5-java/trunk/debian/source/format
trunk/packages/libsis-jhdf5-java/trunk/debian/test/
trunk/packages/libsis-jhdf5-java/trunk/debian/test/ReadWriteTest.java
trunk/packages/libsis-jhdf5-java/trunk/debian/watch
Log:
This is very broken because of missing source.
If the patches look wrong it's because they are wrong.
The file under debian/test is, however, functional and useful for testing.
Added: trunk/packages/libsis-jhdf5-java/trunk/debian/README.source
===================================================================
--- trunk/packages/libsis-jhdf5-java/trunk/debian/README.source
(rev 0)
+++ trunk/packages/libsis-jhdf5-java/trunk/debian/README.source 2015-08-13
09:24:15 UTC (rev 19933)
@@ -0,0 +1,59 @@
+We have 2 Free Java libraries for HDF5:
+
+1) The "NCSA" lib distributed by hdfgroup.org with classes in namespace
+ncsa.hdf.hdf5lib, packaged on Debian as libjhdf5-java.
+
+2) The "CISD" aka. "SIS" lib distributed by ethz.ch with classes in the
+namespace ch.systemsx, not currently packaged on Debian.
+
+The SIS library forks some Java code from the ncsa.hdf namespace, and
+also needs to link against the NCSA native library (via JNI) at runtime.
+
+So, trying to package sis-jhdf5:
+
+wget
+'https://wiki-bsse.ethz.ch/download/attachments/26609237/sis-jhdf5-14.12.1-r33502.zip?version=1&modificationDate=1424599261225&api=v2'
+# The source is in a zip within the zip...
+unzip sis-*
+mkdir sis-jhdf5-14.12.1
+cd !$
+unzip ../sis-jhdf5/src/sis-jhdf5-src.zip
+
+For compilation to succeed, we also need sis-base, not to be confused
+with the entirely separate project at sis.apache.org!
+
+wget
+http://bs-svn01.ethz.ch/repos/cisd/libraries/trunk/sis-base/sis-base-src.zip
+
+The code also depends on their own args4j library, but only for the CLI
+under ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java which we can
+simply leave out just now. I delete it from src/ before compiling and
+also leave out the h5ar.sh script which invokes it. If args4j is packaged
+this can be reinstated and the h5ar command can be added to /usr/bin
+( http://bs-svn01.ethz.ch/repos/cisd/libraries/trunk/cisd-args4j/ )
+
+
+So - can we exclude the ncsa.hdf.hdf5lib.* classes from sis-jhdf5 and
+compile it against the existing classes in /usr/share/java/jhdf5.jar?
+My conclusion is not, because...
+
+The version of ncsa/hdf/hdf5lib/exceptions/HDF5Exception.java supplied
+with the sis-jhdf5 code subclasses RuntimeException but the version in
+libhdf5-java does not. The result is that the code here does not need
+to declare the exceptions being thrown, and thus simply ignores them
+all. One can go through and add all "throws" declarations (there are a
+_lot_ of them!!), but then any client code using the library will also
+break unless it is likewise patched or the code is modified to handle
+the exceptions internally. I think we'd best just admit defeat here and
+use the code supplied with sis-jhdf5.
+
+So, I'm going to try rolling two new packages, and see if that allows me
+to compile the latest FastQC:
+
+libsis-base-java (should be simple)
+libsis-jhdf5-java (depends on libsis-base-java + existing libjhdf5-jni)
+
+-- Tim Booth on 12th Aug 2015
+
+A further note - the dependency on libjhdf5-jni (>> 2.9-3) is there because
+2.9-3 on Trusty is buggy and fails "ldd -r /usr/lib/jni/libjhdf5.so".
Added: trunk/packages/libsis-jhdf5-java/trunk/debian/changelog
===================================================================
--- trunk/packages/libsis-jhdf5-java/trunk/debian/changelog
(rev 0)
+++ trunk/packages/libsis-jhdf5-java/trunk/debian/changelog 2015-08-13
09:24:15 UTC (rev 19933)
@@ -0,0 +1,8 @@
+This build is totally broken. If you attempt to make it work without reading
+the README.source you are wasting your time.
+
+libsis-jhdf5-java (14.12.1-0biolinux1) trusty; urgency=medium
+
+ * Build for Trusty
+
+ -- Tim Booth <[email protected]> Wed, 12 Aug 2015 12:15:17 +0100
Added: trunk/packages/libsis-jhdf5-java/trunk/debian/compat
===================================================================
--- trunk/packages/libsis-jhdf5-java/trunk/debian/compat
(rev 0)
+++ trunk/packages/libsis-jhdf5-java/trunk/debian/compat 2015-08-13
09:24:15 UTC (rev 19933)
@@ -0,0 +1 @@
+9
Added: trunk/packages/libsis-jhdf5-java/trunk/debian/control
===================================================================
--- trunk/packages/libsis-jhdf5-java/trunk/debian/control
(rev 0)
+++ trunk/packages/libsis-jhdf5-java/trunk/debian/control 2015-08-13
09:24:15 UTC (rev 19933)
@@ -0,0 +1,19 @@
+Source: libsis-jhdf5-java
+Section: java
+Priority: extra
+Maintainer: Tim Booth <[email protected]>
+Build-Depends: debhelper (>= 9), default-jdk, javahelper,
+ libcommons-lang-java,
+ libcommons-io-java,
+ libsis-base-java,
+ libjhdf5-jni ( >> 2.9-3 )
+Standards-Version: 3.9.5
+
+Package: libsis-base-java
+Architecture: all
+Depends: ${misc:Depends}, ${java:Depends}, libjhdf5-jni
+Description: easy-to-use HDF library for Java
+ JHDF5 is a Java binding to the HDF Group library for HDF5 focusing on
+ ease-of-use, which was developed by CISD and is now maintained by ETH SIS.
+ The library uses HDF5 1.8 from the HDF Group and files created with
+ JHDF5 are fully compatible with HDF5 1.6/1.8 (as you choose).
Added: trunk/packages/libsis-jhdf5-java/trunk/debian/copyright
===================================================================
--- trunk/packages/libsis-jhdf5-java/trunk/debian/copyright
(rev 0)
+++ trunk/packages/libsis-jhdf5-java/trunk/debian/copyright 2015-08-13
09:24:15 UTC (rev 19933)
@@ -0,0 +1,21 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: JHDF5 (HDF5 for Java)
+Upstream-Contact:
https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=26609113
+Source: https://wiki-bsse.ethz.ch/display/JHDF5/Download+Page
+
+Files: ch/*
+Copyright: Copyright (C) Copyright 2007-2015 ETH Zuerich, CISD
+License: Apache
+ On Debian systems, you can read the full text of the Apache
+ License in ‘/usr/share/common-licenses/Apache-2.0’.
+
+Files: ncsa/*
+Copyright: Copyright (C) The HDF Group.
+ Copyright (C) the Board of Trustees of the University of Illinois
+License: Apache
+ On Debian systems, you can read the full text of the Apache
+ License in ‘/usr/share/common-licenses/Apache-2.0’.
+
+Files: debian/*
+Copyright: © Tim Booth <[email protected]>
+License: Whatever
Added: trunk/packages/libsis-jhdf5-java/trunk/debian/i_hate_java.perl
===================================================================
--- trunk/packages/libsis-jhdf5-java/trunk/debian/i_hate_java.perl
(rev 0)
+++ trunk/packages/libsis-jhdf5-java/trunk/debian/i_hate_java.perl
2015-08-13 09:24:15 UTC (rev 19933)
@@ -0,0 +1,31 @@
+#!/usr/bin/perl
+#debian/i_hate_java.perl - created Wed Aug 12 18:11:25 BST 2015
+
+use strict;
+use warnings;
+
+while (<>)
+{
+ if(/^\s*public static native ([a-z]* .*)/)
+ {
+ until(/;\s*$/) {
+ chomp();
+ s/$/' '.<>/e;
+ }
+ /^(\s*public static) native ([a-z]* (\w+)\((.*)\)(.*));/
+ or die "Failed match on $_";
+
+ my $firstbit = "$1 $2";
+ my $func = "ncsa.hdf.hdf5lib.H5.$3";
+
+ my @args = map { (split())[-1] } split(/,/, $4);
+
+ my $secondbit = "{ return $func(" . join(',',@args) . "); }";
+
+ print "$firstbit $secondbit\n";
+ }
+ else
+ {
+ print $_;
+ }
+}
Property changes on:
trunk/packages/libsis-jhdf5-java/trunk/debian/i_hate_java.perl
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/libsis-jhdf5-java/trunk/debian/jlibs
===================================================================
--- trunk/packages/libsis-jhdf5-java/trunk/debian/jlibs
(rev 0)
+++ trunk/packages/libsis-jhdf5-java/trunk/debian/jlibs 2015-08-13 09:24:15 UTC
(rev 19933)
@@ -0,0 +1 @@
+*.jar
Added: trunk/packages/libsis-jhdf5-java/trunk/debian/manifest
===================================================================
--- trunk/packages/libsis-jhdf5-java/trunk/debian/manifest
(rev 0)
+++ trunk/packages/libsis-jhdf5-java/trunk/debian/manifest 2015-08-13
09:24:15 UTC (rev 19933)
@@ -0,0 +1,2 @@
+usr/share/java/sis-jhdf5.jar:
+ Class-Path: commons-lang.jar commons-io.jar sis-base.jar
Added:
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/fix_dodgy_cast.patch
===================================================================
--- trunk/packages/libsis-jhdf5-java/trunk/debian/patches/fix_dodgy_cast.patch
(rev 0)
+++ trunk/packages/libsis-jhdf5-java/trunk/debian/patches/fix_dodgy_cast.patch
2015-08-13 09:24:15 UTC (rev 19933)
@@ -0,0 +1,13 @@
+This is why I don't program Java any more. Templated classes are nasty,
nasty, nasty.
+
+--- a/ch/systemsx/cisd/hdf5/HDF5CompoundMemberByteifyerEnumArrayFactory.java
++++ b/ch/systemsx/cisd/hdf5/HDF5CompoundMemberByteifyerEnumArrayFactory.java
+@@ -438,7 +438,7 @@
+ { "unchecked", "rawtypes" })
+ private static Enum<?> getValue(Class<? extends Enum<?>> enumClass,
String value)
+ {
+- return Enum.valueOf((Class<Enum>) enumClass, value);
++ return Enum.valueOf((Class) enumClass, value);
+ }
+
+ }
Added:
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/fix_link_error.patch
===================================================================
--- trunk/packages/libsis-jhdf5-java/trunk/debian/patches/fix_link_error.patch
(rev 0)
+++ trunk/packages/libsis-jhdf5-java/trunk/debian/patches/fix_link_error.patch
2015-08-13 09:24:15 UTC (rev 19933)
@@ -0,0 +1,52 @@
+--- a/ch/systemsx/cisd/hdf5/hdf5lib/H5.java
++++ b/ch/systemsx/cisd/hdf5/hdf5lib/H5.java
+@@ -14,9 +14,11 @@
+ import ncsa.hdf.hdf5lib.exceptions.HDF5Exception;
+ import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException;
+ import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException;
++import ncsa.hdf.hdf5lib.H5.*;
+
+ import ch.systemsx.cisd.base.utilities.NativeLibraryUtilities;
+
++
+ /**
+ * The low-level C function wrappers. These functions are <i>not</i>
thread-safe and need to be used
+ * through thread-safe wrappers.
+@@ -159,7 +161,7 @@
+ * @return a non-negative value if successful
+ * @exception HDF5LibraryException - Error from the HDF-5 Library.
+ */
+- private static native int H5dont_atexit() throws HDF5LibraryException;
++ public static native int H5dont_atexit() throws HDF5LibraryException;
+
+ /**
+ * H5get_libversion retrieves the major, minor, and release numbers of
the version of the HDF
+@@ -1946,7 +1948,7 @@
+ // //
+ // ////////////////////////////////////////////////////////////
+
+- private static native int H5Rcreate(byte[] ref, int loc_id, String name,
int ref_type,
++ public static native int H5Rcreate(byte[] ref, int loc_id, String name,
int ref_type,
+ int space_id) throws HDF5LibraryException, NullPointerException,
+ IllegalArgumentException;
+
+--- a/ncsa/hdf/hdf5lib/H5.java
++++ b/ncsa/hdf/hdf5lib/H5.java
+@@ -356,7 +356,7 @@
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ **/
+-private synchronized static native int H5dont_atexit()
++public synchronized static native int H5dont_atexit()
+ throws HDF5LibraryException;
+
+ /**
+@@ -6861,7 +6861,7 @@
+ ////
+ //////////////////////////////////////////////////////////////
+
+-private synchronized static native int H5Rcreate(byte[] ref, int loc_id,
++public synchronized static native int H5Rcreate(byte[] ref, int loc_id,
+ String name, int ref_type, int space_id)
+ throws HDF5LibraryException, NullPointerException,
IllegalArgumentException;
+
Added:
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/remove_ch_rinn_imports.patch
===================================================================
---
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/remove_ch_rinn_imports.patch
(rev 0)
+++
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/remove_ch_rinn_imports.patch
2015-08-13 09:24:15 UTC (rev 19933)
@@ -0,0 +1,38 @@
+I can't find a definition of this decorator, and we hopefully don't need it at
all.
+
+--- a/ch/systemsx/cisd/hdf5/BitSetConversionUtils.java
++++ b/ch/systemsx/cisd/hdf5/BitSetConversionUtils.java
+@@ -23,7 +23,6 @@
+
+ import org.apache.commons.lang.SystemUtils;
+
+-import ch.rinn.restrictions.Private;
+ import ch.systemsx.cisd.base.mdarray.MDLongArray;
+
+ /**
+@@ -122,7 +121,6 @@
+ }
+ }
+
+- @Private
+ static BitSet fromStorageFormGeneric(final long[] serializedWordArray,
int start, int length)
+ {
+ final BitSet result = new BitSet();
+--- a/ch/systemsx/cisd/hdf5/HDF5Utils.java
++++ b/ch/systemsx/cisd/hdf5/HDF5Utils.java
+@@ -22,7 +22,6 @@
+
+ import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException;
+
+-import ch.rinn.restrictions.Private;
+
+ /**
+ * Some utility methods used by {@link HDF5Reader} and {@link HDF5Writer}.
+@@ -43,7 +42,6 @@
+ static final String TYPE_VARIANT_ATTRIBUTE_NAME = "TYPE_VARIANT";
+
+ /** The minimal size of a chunk. */
+- @Private
+ static final int MIN_CHUNK_SIZE = 1;
+
+ /** The minimal size of a data set in order to allow for chunking. */
Added: trunk/packages/libsis-jhdf5-java/trunk/debian/patches/series
===================================================================
--- trunk/packages/libsis-jhdf5-java/trunk/debian/patches/series
(rev 0)
+++ trunk/packages/libsis-jhdf5-java/trunk/debian/patches/series
2015-08-13 09:24:15 UTC (rev 19933)
@@ -0,0 +1,3 @@
+fix_dodgy_cast.patch
+remove_ch_rinn_imports.patch
+fix_link_error.patch
Added:
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/sort_exceptions.patch
===================================================================
--- trunk/packages/libsis-jhdf5-java/trunk/debian/patches/sort_exceptions.patch
(rev 0)
+++ trunk/packages/libsis-jhdf5-java/trunk/debian/patches/sort_exceptions.patch
2015-08-13 09:24:15 UTC (rev 19933)
@@ -0,0 +1,364 @@
+This is my initial attempt to get the code to compile against
/usr/share/java/jhdf5.jar that is
+in /usr/share/java/jhdf5.jar, but I realised the amount of pacthing was
getting silly.
+
+I'm leaving this partial patch in the package for info.
+
+Index: sis-jhdf5-14.12.1/ch/systemsx/cisd/hdf5/HDF5Utils.java
+===================================================================
+--- sis-jhdf5-14.12.1.orig/ch/systemsx/cisd/hdf5/HDF5Utils.java
2015-08-10 17:27:59.874762864 +0100
++++ sis-jhdf5-14.12.1/ch/systemsx/cisd/hdf5/HDF5Utils.java 2015-08-10
17:27:59.866762864 +0100
+@@ -344,7 +344,7 @@
+ *
+ * @throws HDF5JavaException If <var>dimensions</var> do not define a
one-dimensional array.
+ */
+- static int getOneDimensionalArraySize(final int[] dimensions)
++ static int getOneDimensionalArraySize(final int[] dimensions) throws
HDF5JavaException
+ {
+ assert dimensions != null;
+
+@@ -366,7 +366,7 @@
+ * @throws HDF5JavaException If <var>dimensions</var> do not define a
one-dimensional array or
+ * if <code>dimensions[0]</code> overflows the
<code>int</code> type.
+ */
+- static int getOneDimensionalArraySize(final long[] dimensions)
++ static int getOneDimensionalArraySize(final long[] dimensions) throws
HDF5JavaException
+ {
+ assert dimensions != null;
+
+Index: sis-jhdf5-14.12.1/ch/systemsx/cisd/hdf5/HDF5BaseReader.java
+===================================================================
+--- sis-jhdf5-14.12.1.orig/ch/systemsx/cisd/hdf5/HDF5BaseReader.java
2015-08-10 17:27:59.874762864 +0100
++++ sis-jhdf5-14.12.1/ch/systemsx/cisd/hdf5/HDF5BaseReader.java
2015-08-10 17:48:16.774795452 +0100
+@@ -114,7 +114,7 @@
+ final CharacterEncoding encodingForNewDataSets;
+
+ HDF5BaseReader(File hdf5File, boolean performNumericConversions, boolean
autoDereference,
+- FileFormat fileFormat, boolean overwrite, String
preferredHouseKeepingNameSuffix)
++ FileFormat fileFormat, boolean overwrite, String
preferredHouseKeepingNameSuffix) throws HDF5FileNotFoundException
+ {
+ this(hdf5File, performNumericConversions, false, autoDereference,
fileFormat, overwrite,
+ preferredHouseKeepingNameSuffix);
+@@ -122,7 +122,7 @@
+
+ HDF5BaseReader(File hdf5File, boolean performNumericConversions, boolean
useUTF8CharEncoding,
+ boolean autoDereference, FileFormat fileFormat, boolean overwrite,
+- String preferredHouseKeepingNameSuffix)
++ String preferredHouseKeepingNameSuffix) throws
HDF5FileNotFoundException
+ {
+ assert hdf5File != null;
+ assert preferredHouseKeepingNameSuffix != null;
+@@ -176,7 +176,7 @@
+ }
+ }
+
+- int openFile(FileFormat fileFormat, boolean overwrite)
++ int openFile(FileFormat fileFormat, boolean overwrite) throws
HDF5FileNotFoundException
+ {
+ if (hdf5File.exists() == false)
+ {
+@@ -465,7 +465,7 @@
+ * <code>nullWhenOutside == true</code>.
+ */
+ DataSpaceParameters tryGetSpaceParameters(final int dataSetId, final long
offset,
+- final int blockSize, boolean nullWhenOutside, ICleanUpRegistry
registry)
++ final int blockSize, boolean nullWhenOutside, ICleanUpRegistry
registry) throws HDF5JavaException
+ {
+ return tryGetSpaceParameters(dataSetId, 0, offset, blockSize,
nullWhenOutside, registry);
+ }
+@@ -474,7 +474,7 @@
+ * Returns the {@link DataSpaceParameters} for a 1d block of the given
<var>dataSetId</var>.
+ */
+ DataSpaceParameters getSpaceParameters(final int dataSetId, final long
offset,
+- final int blockSize, ICleanUpRegistry registry)
++ final int blockSize, ICleanUpRegistry registry) throws
HDF5JavaException
+ {
+ return tryGetSpaceParameters(dataSetId, 0, offset, blockSize, false,
registry);
+ }
+@@ -483,7 +483,7 @@
+ * Returns the {@link DataSpaceParameters} for a 1d block of the given
<var>dataSetId</var>.
+ */
+ DataSpaceParameters getSpaceParameters(final int dataSetId, final long
memoryOffset,
+- final long offset, final int blockSize, ICleanUpRegistry registry)
++ final long offset, final int blockSize, ICleanUpRegistry
registry) throws HDF5JavaException
+ {
+ return tryGetSpaceParameters(dataSetId, memoryOffset, offset,
blockSize, false, registry);
+ }
+@@ -493,7 +493,7 @@
+ */
+ DataSpaceParameters tryGetSpaceParameters(final int dataSetId, final long
memoryOffset,
+ final long offset, final int blockSize, boolean nullWhenOutside,
+- ICleanUpRegistry registry)
++ ICleanUpRegistry registry) throws HDF5JavaException
+ {
+ final int memorySpaceId;
+ final int dataSpaceId;
+@@ -551,7 +551,7 @@
+ * <var>dataSetId</var>.
+ */
+ DataSpaceParameters getSpaceParameters(final int dataSetId, final long[]
offset,
+- final int[] blockDimensionsOrNull, ICleanUpRegistry registry)
++ final int[] blockDimensionsOrNull, ICleanUpRegistry registry)
throws HDF5JavaException
+ {
+ return tryGetSpaceParameters(dataSetId, offset,
blockDimensionsOrNull, false, registry);
+ }
+@@ -561,7 +561,7 @@
+ * <var>dataSetId</var>.
+ */
+ DataSpaceParameters tryGetSpaceParameters(final int dataSetId, final
long[] offset,
+- final int[] blockDimensionsOrNull, boolean nullWhenOutside,
ICleanUpRegistry registry)
++ final int[] blockDimensionsOrNull, boolean nullWhenOutside,
ICleanUpRegistry registry) throws HDF5JavaException
+ {
+ final int memorySpaceId;
+ final int dataSpaceId;
+@@ -610,7 +610,7 @@
+ * mapped to a block in memory.
+ */
+ DataSpaceParameters getBlockSpaceParameters(final int dataSetId, final
int[] memoryOffset,
+- final int[] memoryDimensions, ICleanUpRegistry registry)
++ final int[] memoryDimensions, ICleanUpRegistry registry) throws
HDF5JavaException
+ {
+ return tryGetBlockSpaceParameters(dataSetId, memoryOffset,
memoryDimensions, false,
+ registry);
+@@ -621,7 +621,7 @@
+ * mapped to a block in memory.
+ */
+ DataSpaceParameters tryGetBlockSpaceParameters(final int dataSetId, final
int[] memoryOffset,
+- final int[] memoryDimensions, final boolean nullWhenOutside,
ICleanUpRegistry registry)
++ final int[] memoryDimensions, final boolean nullWhenOutside,
ICleanUpRegistry registry) throws HDF5JavaException
+ {
+ assert memoryOffset != null;
+ assert memoryDimensions != null;
+@@ -653,7 +653,7 @@
+ */
+ DataSpaceParameters getBlockSpaceParameters(final int dataSetId, final
int[] memoryOffset,
+ final int[] memoryDimensions, final long[] offset, final int[]
blockDimensions,
+- ICleanUpRegistry registry)
++ ICleanUpRegistry registry) throws HDF5JavaException
+ {
+ return tryGetBlockSpaceParameters(dataSetId, memoryOffset,
memoryDimensions, offset,
+ blockDimensions, false, registry);
+@@ -665,7 +665,7 @@
+ */
+ DataSpaceParameters tryGetBlockSpaceParameters(final int dataSetId, final
int[] memoryOffset,
+ final int[] memoryDimensions, final long[] offset, final int[]
blockDimensions,
+- final boolean nullWhenOutside, ICleanUpRegistry registry)
++ final boolean nullWhenOutside, ICleanUpRegistry registry) throws
HDF5JavaException
+ {
+ assert memoryOffset != null;
+ assert memoryDimensions != null;
+@@ -790,7 +790,7 @@
+ * @param dataSetPath The name (including path information) of the data
set to return
+ * information about.
+ */
+- HDF5DataSetInformation getDataSetInformation(final String dataSetPath)
++ HDF5DataSetInformation getDataSetInformation(final String dataSetPath)
throws HDF5JavaException
+ {
+ return getDataSetInformation(dataSetPath,
DataTypeInfoOptions.DEFAULT, true);
+ }
+@@ -806,7 +806,7 @@
+ * @param fillDimensions If <code>true</code>, fill in the dimensions of
the dataset
+ */
+ HDF5DataSetInformation getDataSetInformation(final String dataSetPath,
+- final DataTypeInfoOptions options, final boolean fillDimensions)
++ final DataTypeInfoOptions options, final boolean fillDimensions)
throws HDF5JavaException
+ {
+ assert dataSetPath != null;
+
+@@ -814,7 +814,7 @@
+ new ICallableWithCleanUp<HDF5DataSetInformation>()
+ {
+ @Override
+- public HDF5DataSetInformation call(ICleanUpRegistry
registry)
++ public HDF5DataSetInformation call(ICleanUpRegistry
registry) throws HDF5JavaException
+ {
+ final int dataSetId = h5.openDataSet(fileId,
dataSetPath, registry);
+ final int dataTypeId =
h5.getDataTypeForDataSet(dataSetId, registry);
+@@ -872,7 +872,7 @@
+ * the array rank into one rank. It is a failure condition if the
<var>objectPath</var> does not
+ * exist or does not identify a data set. This method follows symbolic
links.
+ */
+- int getRank(String dataSetPath)
++ int getRank(String dataSetPath) throws HDF5JavaException
+ {
+ final HDF5DataSetInformation info =
+ getDataSetInformation(dataSetPath,
DataTypeInfoOptions.MINIMAL, true);
+@@ -885,7 +885,7 @@
+ * space). It is a failure condition if the <var>objectPath</var> does
not exist or does not
+ * identify a data set. This method follows symbolic links.
+ */
+- long[] getDimensions(String dataSetPath)
++ long[] getDimensions(String dataSetPath) throws HDF5JavaException
+ {
+ assert dataSetPath != null;
+
+@@ -918,7 +918,7 @@
+ return runner.call(informationDeterminationRunnable);
+ }
+
+- HDF5DataTypeVariant tryGetTypeVariant(final String objectPath)
++ HDF5DataTypeVariant tryGetTypeVariant(final String objectPath) throws
HDF5JavaException
+ {
+ assert objectPath != null;
+
+@@ -926,7 +926,7 @@
+ new ICallableWithCleanUp<HDF5DataTypeVariant>()
+ {
+ @Override
+- public HDF5DataTypeVariant call(ICleanUpRegistry
registry)
++ public HDF5DataTypeVariant call(ICleanUpRegistry
registry) throws HDF5JavaException
+ {
+ final int objectId = h5.openObject(fileId,
objectPath, registry);
+ return tryGetTypeVariant(objectId, registry);
+@@ -936,7 +936,7 @@
+ return runner.call(readRunnable);
+ }
+
+- HDF5DataTypeVariant tryGetTypeVariant(final String objectPath, final
String attributeName)
++ HDF5DataTypeVariant tryGetTypeVariant(final String objectPath, final
String attributeName) throws HDF5JavaException
+ {
+ assert objectPath != null;
+
+@@ -944,7 +944,7 @@
+ new ICallableWithCleanUp<HDF5DataTypeVariant>()
+ {
+ @Override
+- public HDF5DataTypeVariant call(ICleanUpRegistry
registry)
++ public HDF5DataTypeVariant call(ICleanUpRegistry
registry) throws HDF5JavaException
+ {
+ final int objectId = h5.openObject(fileId,
objectPath, registry);
+ return tryGetTypeVariant(objectId, attributeName,
registry);
+@@ -955,7 +955,7 @@
+ }
+
+ HDF5EnumerationValueArray getEnumValueArray(final int attributeId, final
String objectPath,
+- final String attributeName, ICleanUpRegistry registry)
++ final String attributeName, ICleanUpRegistry registry) throws
HDF5JavaException
+ {
+ final int storageDataTypeId = h5.getDataTypeForAttribute(attributeId,
registry);
+ final int nativeDataTypeId = h5.getNativeDataType(storageDataTypeId,
registry);
+@@ -1000,7 +1000,7 @@
+ }
+
+ HDF5EnumerationValueMDArray getEnumValueMDArray(final int attributeId,
final String objectPath,
+- final String attributeName, ICleanUpRegistry registry)
++ final String attributeName, ICleanUpRegistry registry) throws
HDF5JavaException
+ {
+ final int storageDataTypeId = h5.getDataTypeForAttribute(attributeId,
registry);
+ final int nativeDataTypeId = h5.getNativeDataType(storageDataTypeId,
registry);
+@@ -1054,7 +1054,7 @@
+ }
+
+ HDF5DataTypeVariant[] tryGetTypeVariantForCompoundMembers(String
dataTypePathOrNull,
+- ICleanUpRegistry registry)
++ ICleanUpRegistry registry) throws HDF5JavaException
+ {
+ if (dataTypePathOrNull == null)
+ {
+@@ -1089,14 +1089,14 @@
+ }
+ }
+
+- HDF5DataTypeVariant tryGetTypeVariant(final int objectId,
ICleanUpRegistry registry)
++ HDF5DataTypeVariant tryGetTypeVariant(final int objectId,
ICleanUpRegistry registry) throws HDF5JavaException
+ {
+ final int typeVariantOrdinal = getAttributeTypeVariant(objectId,
registry);
+ return typeVariantOrdinal < 0 ? null :
HDF5DataTypeVariant.values()[typeVariantOrdinal];
+ }
+
+ HDF5DataTypeVariant tryGetTypeVariant(final int objectId, String
attributeName,
+- ICleanUpRegistry registry)
++ ICleanUpRegistry registry) throws HDF5JavaException
+ {
+ final int typeVariantOrdinal = getAttributeTypeVariant(objectId,
attributeName, registry);
+ return typeVariantOrdinal < 0 ? null :
HDF5DataTypeVariant.values()[typeVariantOrdinal];
+@@ -1109,7 +1109,7 @@
+ * @param objectId The id of the data set object in the file.
+ * @return The ordinal of the type variant or <code>null</code>.
+ */
+- int getAttributeTypeVariant(final int objectId, ICleanUpRegistry registry)
++ int getAttributeTypeVariant(final int objectId, ICleanUpRegistry
registry) throws HDF5JavaException
+ {
+ checkOpen();
+ final String dataTypeVariantAttributeName =
+@@ -1130,7 +1130,7 @@
+ * @param attributeName The name of the attribute to get the type variant
for.
+ * @return The ordinal of the type variant or <code>null</code>.
+ */
+- int getAttributeTypeVariant(final int objectId, String attributeName,
ICleanUpRegistry registry)
++ int getAttributeTypeVariant(final int objectId, String attributeName,
ICleanUpRegistry registry) throws HDF5JavaException
+ {
+ checkOpen();
+ final String typeVariantAttrName =
+@@ -1380,7 +1380,7 @@
+
+ HDF5EnumerationType getEnumTypeForStorageDataType(final String nameOrNull,
+ final int storageDataTypeId, final boolean resolveName, final
String objectPathOrNull,
+- final String attributeNameOrNull, final ICleanUpRegistry registry)
++ final String attributeNameOrNull, final ICleanUpRegistry
registry) throws HDF5JavaException
+ {
+ int classType = h5.getClassType(storageDataTypeId);
+ final boolean isArray = (classType == H5T_ARRAY);
+@@ -1423,7 +1423,7 @@
+ values, this);
+ }
+
+- void checkEnumValues(int dataTypeId, final String[] values, final String
nameOrNull)
++ void checkEnumValues(int dataTypeId, final String[] values, final String
nameOrNull) throws HDF5JavaException
+ {
+ final String[] valuesStored =
h5.getNamesForEnumOrCompoundMembers(dataTypeId);
+ if (valuesStored.length != values.length)
+@@ -1462,13 +1462,13 @@
+ }
+ }
+
+- boolean isScaledEnum(final int objectId, final ICleanUpRegistry registry)
++ boolean isScaledEnum(final int objectId, final ICleanUpRegistry registry)
throws HDF5JavaException
+ {
+ final HDF5DataTypeVariant typeVariantOrNull =
tryGetTypeVariant(objectId, registry);
+ return (HDF5DataTypeVariant.ENUM == typeVariantOrNull);
+ }
+
+- boolean isScaledBitField(final int objectId, final ICleanUpRegistry
registry)
++ boolean isScaledBitField(final int objectId, final ICleanUpRegistry
registry) throws HDF5JavaException
+ {
+ final HDF5DataTypeVariant typeVariantOrNull =
tryGetTypeVariant(objectId, registry);
+ return (HDF5DataTypeVariant.BITFIELD == typeVariantOrNull);
+@@ -1518,7 +1518,7 @@
+ }
+
+ String[] getStringArrayAttribute(final int objectId, final String
objectPath,
+- final String attributeName, final boolean readRaw, final
ICleanUpRegistry registry)
++ final String attributeName, final boolean readRaw, final
ICleanUpRegistry registry) throws HDF5JavaException
+ {
+ final int attributeId = h5.openAttribute(objectId, attributeName,
registry);
+ final int stringArrayDataTypeId =
h5.getDataTypeForAttribute(attributeId, registry);
+@@ -1568,7 +1568,7 @@
+ }
+
+ MDArray<String> getStringMDArrayAttribute(final int objectId, final
String objectPath,
+- final String attributeName, final boolean readRaw, final
ICleanUpRegistry registry)
++ final String attributeName, final boolean readRaw, final
ICleanUpRegistry registry) throws HDF5JavaException
+ {
+ final int attributeId = h5.openAttribute(objectId, attributeName,
registry);
+ final int stringArrayDataTypeId =
h5.getDataTypeForAttribute(attributeId, registry);
+Index:
sis-jhdf5-14.12.1/ch/systemsx/cisd/hdf5/cleanup/ICallableWithCleanUp.java
+===================================================================
+---
sis-jhdf5-14.12.1.orig/ch/systemsx/cisd/hdf5/cleanup/ICallableWithCleanUp.java
2015-02-22 10:46:50.000000000 +0000
++++ sis-jhdf5-14.12.1/ch/systemsx/cisd/hdf5/cleanup/ICallableWithCleanUp.java
2015-08-10 17:42:56.198786867 +0100
+@@ -16,6 +16,8 @@
+
+ package ch.systemsx.cisd.hdf5.cleanup;
+
++import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException;
++
+ /**
+ * A role that calls a method which requires one or more clean-up steps that
need to be run reliably
+ * at the end of the method regardless of whether the method is finished
normally or whether it
+@@ -29,6 +31,6 @@
+ {
+
+ /** Calls the method requiring clean-up. */
+- public T call(ICleanUpRegistry registry);
++ public T call(ICleanUpRegistry registry) throws HDF5JavaException;
+
+ }
Added: trunk/packages/libsis-jhdf5-java/trunk/debian/rules
===================================================================
--- trunk/packages/libsis-jhdf5-java/trunk/debian/rules
(rev 0)
+++ trunk/packages/libsis-jhdf5-java/trunk/debian/rules 2015-08-13 09:24:15 UTC
(rev 19933)
@@ -0,0 +1,24 @@
+#!/usr/bin/make -f
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+export
CLASSPATH=/usr/share/java/commons-lang.jar:/usr/share/java/commons-io.jar:/usr/share/java/sis-base.jar
+
+%:
+ dh $@ --with javahelper
+
+override_dh_auto_clean:
+ rm -rf src lib build *.jar
+ #find test -name '*.class' -delete
+
+override_dh_auto_build:
+ # Avoids jh_build thinking that files in .svn or .pc are things it
+ # needs to compile.
+ mkdir src ; cp -r ch ncsa src
+ # See README.source about this file being removed
+ rm src/ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java
+ # This I cannot adequately explain:
+# perl debian/i_hate_java.perl < ch/systemsx/cisd/hdf5/hdf5lib/H5.java \
+# > src/ch/systemsx/cisd/hdf5/hdf5lib/H5.java
+ jh_build sis-jhdf5.jar src
Property changes on: trunk/packages/libsis-jhdf5-java/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/libsis-jhdf5-java/trunk/debian/source/format
===================================================================
--- trunk/packages/libsis-jhdf5-java/trunk/debian/source/format
(rev 0)
+++ trunk/packages/libsis-jhdf5-java/trunk/debian/source/format 2015-08-13
09:24:15 UTC (rev 19933)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/libsis-jhdf5-java/trunk/debian/test/ReadWriteTest.java
===================================================================
--- trunk/packages/libsis-jhdf5-java/trunk/debian/test/ReadWriteTest.java
(rev 0)
+++ trunk/packages/libsis-jhdf5-java/trunk/debian/test/ReadWriteTest.java
2015-08-13 09:24:15 UTC (rev 19933)
@@ -0,0 +1,50 @@
+/* Test class based on the sample code at
https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=26609113
+ * and amednded for the Deb package by Tim Booth. Running this assures us
thet the JNI library can
+ * be loaded and that the code is at least somewhat functional.
+ * This is too simple to be worth pulling in any kind of test framework.
+ */
+
+import ch.systemsx.cisd.hdf5.HDF5Factory;
+import ch.systemsx.cisd.hdf5.IHDF5SimpleWriter;
+import ch.systemsx.cisd.hdf5.IHDF5SimpleReader;
+
+public class ReadWriteTest {
+
+ public static void main(String[] args) {
+
+ System.loadLibrary("jhdf5");
+
+ //Make an array
+ double[] mydata = new double[1000];
+ for (int nn=0 ; nn < mydata.length ; nn++) {
+ mydata[nn] = Math.cos(nn);
+ }
+
+ //Write it
+ IHDF5SimpleWriter writer = HDF5Factory.open("out.h5");
+ writer.writeDoubleArray("cosines", mydata);
+ writer.close();
+
+ //Read it back
+ IHDF5SimpleReader reader = HDF5Factory.openForReading("out.h5");
+ double[] readdata = reader.readDoubleArray("cosines");
+ reader.close();
+
+ //Inspect it
+ if(readdata.length != mydata.length) {
+ System.out.println("Array length is not 1000 as expected");
+ System.exit(1);
+ }
+
+ for (int nn=0 ; nn < mydata.length ; nn++ ) {
+ if(readdata[nn] != mydata[nn]) {
+ System.out.println("Data mismatch at index " + nn);
+ System.exit(1);
+ }
+ }
+
+ //Happy!
+ System.out.println("OK");
+ //exit(0);
+ }
+}
Added: trunk/packages/libsis-jhdf5-java/trunk/debian/watch
===================================================================
--- trunk/packages/libsis-jhdf5-java/trunk/debian/watch
(rev 0)
+++ trunk/packages/libsis-jhdf5-java/trunk/debian/watch 2015-08-13 09:24:15 UTC
(rev 19933)
@@ -0,0 +1,6 @@
+# The source is packed into a .zip within the binary distribution.
+#
+# TODO - make a get_orig_source script to extract it, or work out how to
+# pull it from the SVN.
+
+# see: https://wiki-bsse.ethz.ch/display/JHDF5/Download+Page
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