Author: tbooth-guest Date: 2015-08-14 14:44:34 +0000 (Fri, 14 Aug 2015) New Revision: 19936
Added: trunk/packages/libsis-jhdf5-java/trunk/debian/patches/rename_jni_library.patch Removed: trunk/packages/libsis-jhdf5-java/trunk/debian/i_hate_java.perl trunk/packages/libsis-jhdf5-java/trunk/debian/patches/fix_link_error.patch trunk/packages/libsis-jhdf5-java/trunk/debian/patches/sort_exceptions.patch Modified: trunk/packages/libsis-jhdf5-java/trunk/debian/README.source trunk/packages/libsis-jhdf5-java/trunk/debian/changelog trunk/packages/libsis-jhdf5-java/trunk/debian/control trunk/packages/libsis-jhdf5-java/trunk/debian/copyright trunk/packages/libsis-jhdf5-java/trunk/debian/patches/fix_dodgy_cast.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/rules trunk/packages/libsis-jhdf5-java/trunk/debian/test/ReadWriteTest.java trunk/packages/libsis-jhdf5-java/trunk/debian/watch Log: This is much better. Now building from the full source. This should work, apart from running the upstream tests which I think involves using the gradle test runner. Modified: trunk/packages/libsis-jhdf5-java/trunk/debian/README.source =================================================================== --- trunk/packages/libsis-jhdf5-java/trunk/debian/README.source 2015-08-13 09:34:09 UTC (rev 19935) +++ trunk/packages/libsis-jhdf5-java/trunk/debian/README.source 2015-08-14 14:44:34 UTC (rev 19936) @@ -11,28 +11,24 @@ 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 +The 'source' distribution' linked on the web page only have the Java source. +The real source you need is in SVN: +svn co http://svncisd.ethz.ch/repos/cisd/jhdf5/trunk/ + 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 +http://svncisd.ethz.ch/repos/cisd/base/trunk/ +See the libsis-base-java package for this. 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 +simply leave out just now. I delete it from jsrc/ before compiling and +also leave out the h5ar.sh script which invokes it. Once 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... @@ -51,9 +47,7 @@ to compile the latest FastQC: libsis-base-java (should be simple) -libsis-jhdf5-java (depends on libsis-base-java + existing libjhdf5-jni) +libsis-jhdf5-java (depends on libsis-base-java + libhdf5, but ignores + existing libjhdf5-jni package) -- 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". Modified: trunk/packages/libsis-jhdf5-java/trunk/debian/changelog =================================================================== --- trunk/packages/libsis-jhdf5-java/trunk/debian/changelog 2015-08-13 09:34:09 UTC (rev 19935) +++ trunk/packages/libsis-jhdf5-java/trunk/debian/changelog 2015-08-14 14:44:34 UTC (rev 19936) @@ -1,6 +1,3 @@ -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 Modified: trunk/packages/libsis-jhdf5-java/trunk/debian/control =================================================================== --- trunk/packages/libsis-jhdf5-java/trunk/debian/control 2015-08-13 09:34:09 UTC (rev 19935) +++ trunk/packages/libsis-jhdf5-java/trunk/debian/control 2015-08-14 14:44:34 UTC (rev 19936) @@ -6,7 +6,8 @@ libcommons-lang-java, libcommons-io-java, libsis-base-java, - libjhdf5-jni ( >> 2.9-3 ) + libhdf5-dev (>= 1.8.13), + openjdk-7-jdk Standards-Version: 3.9.5 Package: libsis-base-java Modified: trunk/packages/libsis-jhdf5-java/trunk/debian/copyright =================================================================== --- trunk/packages/libsis-jhdf5-java/trunk/debian/copyright 2015-08-13 09:34:09 UTC (rev 19935) +++ trunk/packages/libsis-jhdf5-java/trunk/debian/copyright 2015-08-14 14:44:34 UTC (rev 19936) @@ -1,7 +1,7 @@ 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 +Source: http://svncisd.ethz.ch/repos/cisd/jhdf5/tags/release/ Files: ch/* Copyright: Copyright (C) Copyright 2007-2015 ETH Zuerich, CISD Deleted: trunk/packages/libsis-jhdf5-java/trunk/debian/i_hate_java.perl =================================================================== --- trunk/packages/libsis-jhdf5-java/trunk/debian/i_hate_java.perl 2015-08-13 09:34:09 UTC (rev 19935) +++ trunk/packages/libsis-jhdf5-java/trunk/debian/i_hate_java.perl 2015-08-14 14:44:34 UTC (rev 19936) @@ -1,31 +0,0 @@ -#!/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 $_; - } -} Modified: trunk/packages/libsis-jhdf5-java/trunk/debian/patches/fix_dodgy_cast.patch =================================================================== --- trunk/packages/libsis-jhdf5-java/trunk/debian/patches/fix_dodgy_cast.patch 2015-08-13 09:34:09 UTC (rev 19935) +++ trunk/packages/libsis-jhdf5-java/trunk/debian/patches/fix_dodgy_cast.patch 2015-08-14 14:44:34 UTC (rev 19936) @@ -1,7 +1,7 @@ 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 +--- a/source/java/ch/systemsx/cisd/hdf5/HDF5CompoundMemberByteifyerEnumArrayFactory.java ++++ b/source/java/ch/systemsx/cisd/hdf5/HDF5CompoundMemberByteifyerEnumArrayFactory.java @@ -438,7 +438,7 @@ { "unchecked", "rawtypes" }) private static Enum<?> getValue(Class<? extends Enum<?>> enumClass, String value) Deleted: trunk/packages/libsis-jhdf5-java/trunk/debian/patches/fix_link_error.patch =================================================================== --- trunk/packages/libsis-jhdf5-java/trunk/debian/patches/fix_link_error.patch 2015-08-13 09:34:09 UTC (rev 19935) +++ trunk/packages/libsis-jhdf5-java/trunk/debian/patches/fix_link_error.patch 2015-08-14 14:44:34 UTC (rev 19936) @@ -1,52 +0,0 @@ ---- 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; - Modified: 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 2015-08-13 09:34:09 UTC (rev 19935) +++ trunk/packages/libsis-jhdf5-java/trunk/debian/patches/remove_ch_rinn_imports.patch 2015-08-14 14:44:34 UTC (rev 19936) @@ -1,6 +1,6 @@ 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 +--- a/source/java/ch/systemsx/cisd/hdf5/BitSetConversionUtils.java +++ b/ch/systemsx/cisd/hdf5/BitSetConversionUtils.java @@ -23,7 +23,6 @@ @@ -18,7 +18,7 @@ static BitSet fromStorageFormGeneric(final long[] serializedWordArray, int start, int length) { final BitSet result = new BitSet(); ---- a/ch/systemsx/cisd/hdf5/HDF5Utils.java +--- a/source/java/ch/systemsx/cisd/hdf5/HDF5Utils.java +++ b/ch/systemsx/cisd/hdf5/HDF5Utils.java @@ -22,7 +22,6 @@ Added: trunk/packages/libsis-jhdf5-java/trunk/debian/patches/rename_jni_library.patch =================================================================== --- trunk/packages/libsis-jhdf5-java/trunk/debian/patches/rename_jni_library.patch (rev 0) +++ trunk/packages/libsis-jhdf5-java/trunk/debian/patches/rename_jni_library.patch 2015-08-14 14:44:34 UTC (rev 19936) @@ -0,0 +1,14 @@ +There is already a libjhdf5.so on the system. This is an incompatible fork. +Since the .so is tightly bound to the Java library there seems no harm in simply +renaming this one; nothing outside this package should want to link to it. +--- a/source/java/ch/systemsx/cisd/hdf5/hdf5lib/H5.java ++++ b/source/java/ch/systemsx/cisd/hdf5/hdf5lib/H5.java +@@ -36,7 +36,7 @@ + + static + { +- if (NativeLibraryUtilities.loadNativeLibrary("jhdf5") == false) ++ if (NativeLibraryUtilities.loadNativeLibrary("sis-jhdf5") == false) + { + throw new UnsupportedOperationException("No suitable HDF5 native library found for this platform."); + } Modified: trunk/packages/libsis-jhdf5-java/trunk/debian/patches/series =================================================================== --- trunk/packages/libsis-jhdf5-java/trunk/debian/patches/series 2015-08-13 09:34:09 UTC (rev 19935) +++ trunk/packages/libsis-jhdf5-java/trunk/debian/patches/series 2015-08-14 14:44:34 UTC (rev 19936) @@ -1,3 +1,3 @@ fix_dodgy_cast.patch remove_ch_rinn_imports.patch -fix_link_error.patch +rename_jni_library.patch Deleted: trunk/packages/libsis-jhdf5-java/trunk/debian/patches/sort_exceptions.patch =================================================================== --- trunk/packages/libsis-jhdf5-java/trunk/debian/patches/sort_exceptions.patch 2015-08-13 09:34:09 UTC (rev 19935) +++ trunk/packages/libsis-jhdf5-java/trunk/debian/patches/sort_exceptions.patch 2015-08-14 14:44:34 UTC (rev 19936) @@ -1,364 +0,0 @@ -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; - - } Modified: trunk/packages/libsis-jhdf5-java/trunk/debian/rules =================================================================== --- trunk/packages/libsis-jhdf5-java/trunk/debian/rules 2015-08-13 09:34:09 UTC (rev 19935) +++ trunk/packages/libsis-jhdf5-java/trunk/debian/rules 2015-08-14 14:44:34 UTC (rev 19936) @@ -9,16 +9,26 @@ dh $@ --with javahelper override_dh_auto_clean: - rm -rf src lib build *.jar + rm -rf jsrc lib build *.jar + rm -rf source/c/*.log + cd debian/test && rm -f *.h5 *.class #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 + # C build + cd source/c && \ + $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -shared -fPIC -Wl,--exclude-libs,ALL \ + -I/usr/lib/jvm/default-java/include/ \ + jhdf5/*.c hdf-java/*.c -o libsis-jhdf5.so -lz -lhdf5 + # Java build - see README.source about the file being removed + mkdir jsrc ; cp -r source/java/ch source/java/ncsa jsrc + rm jsrc/ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java + # This line is still needed on Ubuntu 14.04 + jh_build sis-jhdf5.jar jsrc + +override_dh_auto_test: + # Try our little test snippet. + export CLASSPATH=".:`readlink -f sis-jhdf5.jar`" JNIPATH="`readlink -f source/c`" ; \ + cd debian/test && javac *.java && \ + java -Djava.library.path="$$JNIPATH" ReadWriteTest + Modified: trunk/packages/libsis-jhdf5-java/trunk/debian/test/ReadWriteTest.java =================================================================== --- trunk/packages/libsis-jhdf5-java/trunk/debian/test/ReadWriteTest.java 2015-08-13 09:34:09 UTC (rev 19935) +++ trunk/packages/libsis-jhdf5-java/trunk/debian/test/ReadWriteTest.java 2015-08-14 14:44:34 UTC (rev 19936) @@ -12,8 +12,6 @@ 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++) { Modified: trunk/packages/libsis-jhdf5-java/trunk/debian/watch =================================================================== --- trunk/packages/libsis-jhdf5-java/trunk/debian/watch 2015-08-13 09:34:09 UTC (rev 19935) +++ trunk/packages/libsis-jhdf5-java/trunk/debian/watch 2015-08-14 14:44:34 UTC (rev 19936) @@ -1,6 +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. +# pull it from the SVN via HTTP. -# see: https://wiki-bsse.ethz.ch/display/JHDF5/Download+Page +# see: http://svncisd.ethz.ch/repos/cisd/jhdf5/tags/release/ _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
