[med-svn] [ncbi-vdb] branch debian/jessie-backports updated (dd29988 -> 1242b6b)
Andreas Tille
tille at debian.org
Wed Jun 7 19:29:59 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch debian/jessie-backports
in repository ncbi-vdb.
from dd29988 s/default-jdk-headless/openjdk-8-jdk-headless/ since there is no default-jdk-headless in Jessie
adds b366c12 Use wildcard instead of $(CPU) in install to fix FTBFS on i386
adds 78461da New upstream version 2.8.0+dfsg
adds a589d96 Merge tag 'upstream/2.8.0+dfsg'
adds addf477 New upstream version
adds 6fadcd4 Adapt patches
adds de99f24 New Build-Depends: libmbedtls-dev
adds 7e17207 No Makefile dependencies from content of libmbedtls-dev
adds 23fdb54 README was renamed
adds b2d69fa Upload to unstable
adds 53c9411 Make sure libraries are properly linked with libmbed
adds 21f3cda debhelper 10
adds c4e0d08 d/watch: version=4
adds cc8e497 More overrides needed
adds 65a9516 Adjust dependencies from other development packages
adds ea6b76a New upstream version 2.8.1
adds 1ee3605 Merge tag 'upstream/2.8.1'
adds bcf9fd2 New upstream version
adds 879c0ec New upstream version 2.8.1+dfsg
adds fdd6a91 Merge tag 'upstream/2.8.1+dfsg'
adds c9a9ef2 Refresh patches
adds 6ff32b4 Install libs/kfg/certs.kfg as /etc/ncbi/certs.kfg
adds 3e4c0ce Install libs/kfg/*.kfg into /usr/lib/ncbi-vdb/kfg
adds 629b61d Upload to unstable
adds e5395d2 Apply patch by Graham Inggs
adds b36a1ec Upload to unstable
new d24b3a6 Merge branch 'master' into debian/jessie-backports
new 89e71ed Rebuild for jessie-backports
new a9e40ca Make sure jni.h will be really found
new 799b5ef Burte-force libkapp building with -fPIC
new 1242b6b Typo
The 5 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitignore | 1 +
CHANGES | 60 -
CHANGES.md | 26 +
README | 55 -
README.md | 25 +-
build/Makefile.gcc | 4 +-
build/Makefile.install | 28 +-
build/Makefile.vers | 2 +-
build/ld.linux.exe_cmd.sh | 1 +
debian/changelog | 43 +
debian/compat | 2 +-
debian/control | 16 +-
debian/docs | 2 +-
debian/libncbi-vdb2.install | 1 +
debian/patches/find_hdf5_serial.patch | 2 +-
debian/patches/find_ngs-sdk.patch | 4 +-
debian/patches/jessie_kapp_fPIC.patch | 11 +
debian/patches/series | 2 +
debian/patches/skip_failing_test.patch | 43 +-
debian/patches/spelling.patch | 2 +-
debian/patches/use_debian_packaged_libmbedx.patch | 71 +
debian/patches/use_debian_packaged_zlib.patch | 2 +-
debian/rules | 42 +-
debian/watch | 2 +-
interfaces/insdc/sra.vschema | 7 +-
interfaces/kdb/rowset-impl.h | 141 ++
interfaces/kdb/rowset.h | 186 +++
interfaces/kfc/defs.h | 14 +
interfaces/kfc/rc.h | 25 +-
interfaces/kfc/xc.h | 6 +
interfaces/kfg/kfg-priv.h | 14 +-
interfaces/kfg/properties.h | 6 +
interfaces/kfg/repository.h | 8 +-
interfaces/klib/debug.h | 2 +-
interfaces/klib/pack.h | 2 +-
interfaces/klib/rc.h | 28 +-
interfaces/klib/sra-release-version.h | 5 +-
interfaces/klib/status.h | 2 +-
interfaces/klib/text.h | 6 +
interfaces/kns/endpoint.h | 1 +
libs/kns/sysmgr.h => interfaces/kns/http-priv.h | 32 +-
interfaces/kns/http.h | 35 +-
interfaces/kns/kns-mgr-priv.h | 46 +
interfaces/kns/manager.h | 2 +-
interfaces/kns/socket.h | 25 +-
interfaces/kns/{manager.h => tls.h} | 69 +-
interfaces/kproc/timeout.h | 10 +-
interfaces/ktst/unit_test_suite.hpp | 6 +-
interfaces/ncbi/ncbi.vschema | 2 +-
interfaces/vdb/manager.h | 12 +-
interfaces/vdb/vdb.vschema | 2 +-
interfaces/vfs/manager-priv.h | 9 +
interfaces/vfs/resolver.h | 60 +-
libs/align/al_iterator.c | 8 +-
libs/align/align-access.c | 10 +-
libs/align/bam.c | 67 +-
libs/align/reader-refseq.c | 6 +-
libs/align/reader-wgs.c | 4 +-
libs/align/reference.c | 18 +-
libs/align/refseq-mgr.c | 4 +-
libs/align/writer-alignment.c | 22 +-
libs/align/writer-ref.c | 8 +-
libs/align/writer-reference.c | 18 +-
libs/align/writer-refseq.c | 2 +-
libs/align/writer-sequence.c | 12 +-
libs/ascp/unix/connect.c | 2 +-
libs/axf/align-local_ref_id.c | 2 +-
libs/axf/align-local_ref_start.c | 2 +-
libs/axf/align-ref-name.c | 2 +-
libs/axf/align-ref-pos.c | 4 +-
libs/axf/align-ref-seq-id.c | 2 +-
libs/axf/align-restore-read.c | 2 +-
libs/axf/cigar.c | 28 +-
libs/axf/get_mate_align_ids.c | 2 +-
libs/axf/make-cmp-read_desc.c | 2 +-
libs/axf/project_read_from_sequence.c | 4 +-
libs/axf/raw-restore-qual.c | 2 +-
libs/axf/raw-restore-read.c | 2 +-
libs/axf/ref-preserve_qual.c | 2 +-
libs/axf/ref-restore-read.c | 2 +-
libs/axf/ref-tbl-sub-select.c | 8 +-
libs/axf/refseq-stats.c | 2 +-
libs/axf/seq-construct-read.c | 4 +-
libs/axf/seq-restore-linkage-group.c | 4 +-
libs/axf/seq-restore-read.c | 14 +-
libs/blast/blast-mgr.c | 2 +-
libs/blast/reference.c | 40 +-
libs/blast/run-set.h | 3 +-
libs/hdf5/hdf5dir.c | 2 +-
libs/kapp/args-conv.c | 2 +-
libs/kapp/args.c | 14 +-
libs/kapp/loader-file.c | 12 +-
libs/kapp/log-xml.c | 2 +-
libs/kapp/queue-file.c | 4 +-
libs/kapp/tokenizer.c | 2 +-
libs/kdb/Makefile | 2 +
libs/kdb/column-cc.c | 2 +-
libs/kdb/kdb.c | 2 +-
libs/kdb/libkdb.vers.h | 2 +-
libs/kdb/meta.c | 12 +-
libs/kdb/ptrieval-v1.c | 2 +-
libs/kdb/ptrieval-v2.c | 2 +-
libs/kdb/rowset-it.c_old | 385 +++++
libs/kdb/rowset-priv.h_old | 116 ++
libs/kdb/rowset-simple.c | 434 ++++++
libs/kdb/rowset.c | 494 +++++++
libs/kdb/rowset.c_old | 1513 ++++++++++++++++++++
libs/kdb/table.c | 3 +
libs/kdb/trieidx-v1.c | 2 +-
libs/kdb/trieidx-v2.c | 4 +-
libs/kdb/wkdb.c | 2 +-
libs/kdb/wmeta.c | 26 +-
libs/kdb/wtable.c | 3 +
libs/kdb/wtrieidx-v1.c | 10 +-
libs/kdb/wtrieidx-v2.c | 8 +-
libs/kfc/refcount.c | 1 +
libs/kfc/tstate.c | 2 +-
libs/kfc/unix/sysrsrc.c | 2 +-
libs/kfc/vtbl.c | 9 +-
libs/kfg/Makefile | 24 +-
libs/kfg/certs.kfg | 31 +
libs/kfg/config-aws.c | 34 +-
libs/kfg/config.c | 289 ++--
libs/kfg/default.kfg | 10 +-
libs/kfg/properties.c | 47 +
libs/kfg/repository.c | 14 +-
libs/kfs/arc.c | 22 +-
libs/kfs/buffile-write.c | 6 +-
libs/kfs/buffile.c | 4 +-
libs/kfs/cacheteefile.c | 2 +-
libs/kfs/crc32.c | 8 +-
libs/kfs/extendable-ramfile.c | 4 +-
libs/kfs/ffext.c | 6 +-
libs/kfs/ffkey.c | 4 +-
libs/kfs/ffmagic.c | 12 +-
libs/kfs/fileformat.c | 6 +-
libs/kfs/md5.c | 18 +-
libs/kfs/pmem.c | 4 +-
libs/kfs/quickmount.c | 12 +-
libs/kfs/ramfile.c | 6 +-
libs/kfs/sra.c | 2 +-
libs/kfs/tar.c | 50 +-
libs/kfs/tocdir.c | 4 +-
libs/kfs/tocentry.c | 18 +-
libs/kfs/tocfile.c | 2 +-
libs/kfs/unix/sysdir.c | 12 +-
libs/klib/SHA-32bit.c | 10 +-
libs/klib/SHA-64bit.c | 10 +-
libs/klib/btree.c | 45 +-
libs/klib/data-buffer.c | 10 +-
libs/klib/judy/JudyHS.c | 4 +-
libs/klib/judy/JudyInsArray.c | 2 +-
libs/klib/maybeswap.h | 4 +-
libs/klib/md5.c | 6 +-
libs/klib/pack.c | 2 +-
libs/klib/printf.c | 16 +-
libs/klib/ptrie.c | 2 +-
libs/klib/rc-idx-tbl.c | 2 +
libs/klib/rc-tbl.c | 2 +
libs/klib/release-vers.h | 12 +-
libs/klib/report-klib.c | 10 +-
libs/klib/sra-release-version.c | 6 +
libs/klib/status-rc-strings.c | 1 +
libs/klib/status.c | 7 +-
libs/klib/text.c | 41 +-
libs/klib/trie.c | 2 +-
libs/klib/unpack.c | 6 +-
libs/klib/vector.c | 2 +-
libs/klib/vlen-encode.c | 2 +-
libs/klib/writer.c | 9 +-
libs/kns/Makefile | 3 +-
libs/kns/buffered-stream.c | 4 +-
libs/kns/endpoint.c | 2 +-
libs/kns/http-client.c | 664 +++++++--
libs/kns/http-file.c | 7 +-
libs/kns/http-priv.h | 40 +-
libs/kns/http.c | 47 +-
libs/kns/kns_manager-ext.c | 2 +-
libs/kns/linux/sysendpoint.c | 2 +-
libs/kns/manager.c | 631 ++++++--
libs/kns/mgr-priv.h | 15 +-
libs/kns/stream-priv.h | 12 +
libs/kns/sysmgr.h | 2 +-
interfaces/kproc/timeout.h => libs/kns/tls-priv.h | 52 +-
libs/kns/tls.c | 1087 ++++++++++++++
libs/kns/unix/syssock.c | 915 +++++++-----
libs/kns/url-fetcher-curl.c | 6 +-
libs/kproc/procmgr.c | 101 +-
libs/kproc/unix/systimeout.c | 42 +
libs/krypto/cipher-byte.c | 16 +-
libs/krypto/cipher-vec.c | 4 +-
libs/krypto/encfile.c | 6 +-
libs/krypto/encfilev2.c | 11 +-
libs/krypto/key.c | 2 +-
libs/krypto/reencfile.c | 6 +-
libs/krypto/unix/sysrng.c | 2 +-
libs/krypto/wgaencrypt.c | 8 +-
libs/kxml/xtoc.c | 8 +-
libs/loader/common-writer.c | 28 +-
libs/loader/reference-writer.c | 2 +-
libs/loader/sequence-writer.c | 18 +-
libs/ncbi-vdb/Makefile | 3 +
libs/ncbi-vdb/libncbi-vdb.vers | 2 +-
libs/ngs-jni/jni_String.c | 6 +-
libs/ngs/BAM_Alignment.c | 66 +-
libs/ngs/BAM_ReadCollection.c | 18 +-
libs/ngs/CSRA1_Alignment.c | 21 +
libs/ngs/CSRA1_Read.c | 123 +-
libs/ngs/CSRA1_Reference.c | 322 +++--
libs/ngs/CSRA1_ReferenceWindow.c | 253 ++--
libs/ngs/EBI_ReferenceSequence.c | 44 +-
libs/ngs/Makefile | 1 +
libs/ngs/NGS_Alignment.c | 29 +-
libs/ngs/NGS_Alignment.h | 5 +-
libs/ngs/NGS_Cursor.c | 38 +-
libs/ngs/NGS_Cursor.h | 44 +-
libs/ngs/NGS_FragmentBlob.c | 84 +-
libs/ngs/NGS_ReadCollection.c | 6 +-
libs/ngs/NGS_Statistics.c | 1 +
libs/ngs/NGS_String.c | 2 +-
libs/ngs/SRA_Read.c | 271 ++--
libs/ngs/SRA_Read.h | 60 +-
libs/ngs/SRA_ReferenceSequence.c | 46 +-
libs/ngs/SRA_Statistics.c | 51 +-
libs/ngs/VByteBlob.c | 117 ++
libs/{kns/sysmgr.h => ngs/VByteBlob.h} | 16 +-
libs/search/nucstrstr.c | 6 +-
libs/search/sw-search.c | 18 +-
libs/sra/reader-abi.c | 2 +-
libs/sra/reader-cmn.c | 4 +-
libs/sra/reader-fastq.c | 4 +-
libs/sra/reader-illumina.c | 2 +-
libs/sra/reader-sff.c | 16 +-
libs/sra/sracache.c | 10 +-
libs/sra/sramgr-cmn.c | 2 +-
libs/sraxf/extract-name_fmt.c | 2 +-
libs/sraxf/extract-spot_name.c | 2 +-
libs/sraxf/format-spot-name.c | 8 +-
libs/sraxf/fpcodec.c | 8 +-
libs/sraxf/index_lookup.c | 6 +-
libs/sraxf/qual4_decode.c | 4 +-
libs/sraxf/qual4_encode.c | 4 +-
libs/sraxf/read-seg-from-readn.c | 4 +-
libs/sraxf/stats.c | 8 +-
libs/sraxf/tokenize-spot_name-generic-fastq.c | 1 -
libs/sraxf/v0-decompress-init.c | 512 +++----
libs/sraxf/v0-decompress.c | 8 +-
libs/svdb/svdb.c | 6 +-
libs/tui/bsd/systui.c | 2 +-
libs/tui/linux/systui.c | 2 +-
libs/vdb/blob-headers.c | 4 +-
libs/vdb/blob.c | 16 +-
libs/vdb/cursor-cmn.c | 4 +-
libs/vdb/database-cmn.c | 4 +-
libs/vdb/database-depend.c | 2 +-
libs/vdb/dbmgr-cmn.c | 26 +
libs/vdb/environment-read.c | 6 +-
libs/vdb/gen-cast.pl | 2 +-
libs/vdb/index_insert.c | 4 +-
libs/vdb/index_lookup.c | 4 +-
libs/vdb/libvdb.vers.h | 2 +-
libs/vdb/merge.c | 4 +-
libs/vdb/meta-attr-write.c | 2 +-
libs/vdb/meta-write.c | 2 +-
libs/vdb/page-map.c | 30 +-
libs/vdb/parameter-read.c | 4 +-
libs/vdb/phys-cmn.c | 4 +-
libs/vdb/prod-cmn.c | 181 ++-
libs/vdb/prod-expr.c | 2 +-
libs/vdb/schema-dump.c | 4 +-
libs/vdb/schema-func.c | 3 +-
libs/vdb/schema-prod.c | 3 +-
libs/vdb/schema-tbl.c | 2 +-
libs/vdb/table-cmn.c | 2 +-
{test/vxf => libs/vdb/test}/Makefile | 41 +-
libs/vdb/test/test-prod-cmn.c | 10 +
libs/vdb/wcolumn.c | 6 +-
libs/vdb/wdatabase.c | 2 +-
libs/vdb/wphys.c | 4 +-
libs/vfs/manager.c | 225 ++-
libs/vfs/path-priv.h | 1 +
libs/vfs/path.c | 15 +-
libs/vfs/resolver-priv.h | 3 +
libs/vfs/resolver.c | 345 ++++-
libs/vxf/bit_or.c | 2 +-
libs/vxf/cut.c | 2 +-
libs/vxf/diff.c | 2 +-
libs/vxf/entrez.c | 2 +-
libs/vxf/extract_token.c | 2 +-
libs/vxf/fzip.c | 2 +-
libs/vxf/integral_0.c | 7 +-
libs/vxf/irzip.c | 4 +-
libs/vxf/iunzip.c | 24 +-
libs/vxf/izip.c | 28 +-
libs/vxf/rldecode.c | 2 +-
libs/vxf/rlencode.c | 8 +-
libs/vxf/simple-sub-select.c | 4 +-
libs/vxf/sprintf.c | 4 +-
libs/vxf/strtonum.c | 2 +-
libs/vxf/sum.c | 2 +-
libs/vxf/trim.c | 6 +-
libs/wgsxf/build_scaffold.c | 4 +-
libs/xfs/doc.c | 8 +-
libs/xfs/path.c | 18 +-
libs/xfs/unix/operations.c | 9 +-
libs/xfs/xencws.c | 2 +-
libs/xfs/xgap.c | 4 +-
libs/xfs/xgapk.c | 2 +-
libs/xfs/xhttp.c | 16 +-
libs/xfs/zehr.c | 2 +-
setup/konfigure.perl | 9 +-
test/{vxf => align}/Makefile | 40 +-
test/align/indextest.cpp | 113 ++
test/cc/asm-test.cpp | 15 +
test/cipher/test.sh | 5 +-
test/kapp/kapp-test.cpp | 4 +-
test/kdb/Makefile | 23 +-
test/kdb/kdbtest.cpp | 11 +-
test/kdb/remote_open_test.cpp | 4 +-
test/kdb/rowsettest.cpp | 819 +++++++++++
test/kfc/kfc.c | 0
test/kfg/flat-sra-kfg.cpp | 58 +-
test/kfg/kfgtest.cpp | 4 +-
test/kfs/Makefile | 2 +-
test/kfs/cacheteetest.cpp | 13 +-
test/klib/test-klib.cpp | 6 +-
test/kns/Makefile | 50 +
test/kns/TestProxy.hpp | 227 +++
test/kns/http-client.c | 17 +
test/kns/http_dropconnection_test.cpp | 4 +-
test/kns/httptest.cpp | 13 +-
test/kns/knstest.cpp | 47 +-
test/kns/test-proxy-with-env.cpp | 112 ++
test/kns/test-proxy.cpp | 263 ++++
test/kns/test-proxy.h | 7 +
test/kns/test-proxy/2-path-no-env/config | 1 +
test/kns/test-proxy/2-path-no-env/expected | 2 +
test/kns/test-proxy/2-path-no-port-no-env/config | 1 +
test/kns/test-proxy/2-path-no-port-no-env/expected | 2 +
.../MULTIPLE_PROXIES/all.MULTIPLE_PROXIES/config | 1 +
.../all.MULTIPLE_PROXIES/environment | 4 +
.../MULTIPLE_PROXIES/all.MULTIPLE_PROXIES/expected | 10 +
.../disabled.MULTIPLE_PROXIES/config | 2 +
.../disabled.MULTIPLE_PROXIES/environment | 4 +
.../disabled.MULTIPLE_PROXIES/expected | 0
.../enabled.MULTIPLE_PROXIES/config | 2 +
.../enabled.MULTIPLE_PROXIES/environment | 4 +
.../enabled.MULTIPLE_PROXIES/expected | 10 +
.../env-kfg.MULTIPLE_PROXIES/config | 2 +
.../env-kfg.MULTIPLE_PROXIES/environment | 4 +
.../env-kfg.MULTIPLE_PROXIES/expected | 10 +
.../env-only.MULTIPLE_PROXIES/config | 2 +
.../env-only.MULTIPLE_PROXIES/environment | 4 +
.../env-only.MULTIPLE_PROXIES/expected | 8 +
.../ignore.MULTIPLE_PROXIES/config | 2 +
.../ignore.MULTIPLE_PROXIES/environment | 4 +
.../ignore.MULTIPLE_PROXIES/expected | 0
.../kfg-env.MULTIPLE_PROXIES/config | 2 +
.../kfg-env.MULTIPLE_PROXIES/environment | 4 +
.../kfg-env.MULTIPLE_PROXIES/expected | 10 +
.../proxy-not-only.MULTIPLE_PROXIES/config | 2 +
.../proxy-not-only.MULTIPLE_PROXIES/environment | 4 +
.../proxy-not-only.MULTIPLE_PROXIES/expected | 10 +
.../proxy-only.MILTIPLE_PROXIES/config | 2 +
.../proxy-only.MILTIPLE_PROXIES/environment | 4 +
.../proxy-only.MILTIPLE_PROXIES/expected | 10 +
test/kns/test-proxy/all/config | 1 +
test/kns/test-proxy/all/environment | 4 +
test/kns/test-proxy/all/expected | 5 +
test/kns/test-proxy/comma-error/environment | 1 +
.../kns/test-proxy/comma-error/expected | 0
test/kns/test-proxy/disabled/config | 2 +
test/kns/test-proxy/disabled/environment | 4 +
.../kns/test-proxy/disabled/expected | 0
test/kns/test-proxy/enabled/config | 2 +
test/kns/test-proxy/enabled/environment | 4 +
test/kns/test-proxy/enabled/expected | 5 +
test/kns/test-proxy/env-kfg/config | 2 +
test/kns/test-proxy/env-kfg/environment | 4 +
test/kns/test-proxy/env-kfg/expected | 5 +
test/kns/test-proxy/env-only/config | 2 +
test/kns/test-proxy/env-only/environment | 4 +
test/kns/test-proxy/env-only/expected | 4 +
test/kns/test-proxy/error/config | 1 +
test/kns/test-proxy/error/environment | 1 +
.../kns/test-proxy/error/expected | 0
test/kns/test-proxy/http_proxy/environment | 1 +
test/kns/test-proxy/http_proxy/expected | 1 +
test/kns/test-proxy/ignore/config | 2 +
test/kns/test-proxy/ignore/environment | 4 +
.../kns/test-proxy/ignore/expected | 0
test/kns/test-proxy/kfg-env/config | 2 +
test/kns/test-proxy/kfg-env/environment | 4 +
test/kns/test-proxy/kfg-env/expected | 5 +
test/kns/test-proxy/kfg-only/config | 2 +
test/kns/test-proxy/kfg-only/environment | 4 +
test/kns/test-proxy/kfg-only/expected | 1 +
test/kns/test-proxy/no-env/config | 1 +
test/kns/test-proxy/no-env/expected | 1 +
test/kns/test-proxy/no-port-no-env/config | 1 +
test/kns/test-proxy/no-port-no-env/expected | 1 +
test/kns/test-proxy/proxy-not-only/config | 2 +
test/kns/test-proxy/proxy-not-only/environment | 4 +
test/kns/test-proxy/proxy-not-only/expected | 5 +
test/kns/test-proxy/proxy-only/config | 2 +
test/kns/test-proxy/proxy-only/environment | 4 +
test/kns/test-proxy/proxy-only/expected | 5 +
test/kproc/kproctest.cpp | 111 ++
test/krypto/test-aes-ciphers.c | 2 +-
test/krypto/test-cmn.cpp | 4 +-
test/krypto/test-modes.c | 2 +-
test/loader/sequence-writer.c | 18 +-
test/ngs-c++/CSRA1test.cpp | 281 ++--
test/ngs-c++/Makefile | 28 +-
test/ngs-c++/SRAtest.cpp | 120 +-
test/ngs-java/ngs_test_CSRA1.java | 103 ++
test/ngs/ngstest.cpp | 125 +-
test/ngs/ngstest_csra1.cpp | 121 +-
test/ngs/ngstest_csra1_refwin.cpp | 429 +++---
test/ngs/ngstest_reference.cpp | 31 +-
test/ngs/ngstest_sra.cpp | 36 +-
test/only-remote-repository.kfg | 2 +-
test/search/agrep-main.c | 2 +-
test/search/search-vdb.cpp | 2 +-
test/vdb/.gitignore | 1 +
test/vdb/Makefile | 25 +-
test/vdb/kfg/empty/empty.kfg | 4 +-
test/vdb/test-VDB-3060.cpp | 33 +-
test/vdb/test-VDB-3061.cpp | 250 ++++
test/vdb/test-wvdb.cpp | 205 ++-
test/vfs/Makefile | 11 +
.../redirect-rejected-names-cgi-http-to-https.cpp | 213 +++
.../incomplete.kfg | 1 +
test/vxf/Makefile | 25 +-
test/vxf/VDB-2915.cpp | 508 +++++++
test/vxf/local_config/local.kfg | 2 +
vdb3/src/kfc/memory.cpp | 2 +-
437 files changed, 13754 insertions(+), 3657 deletions(-)
delete mode 100644 CHANGES
delete mode 100644 README
create mode 100644 build/ld.linux.exe_cmd.sh
create mode 100644 debian/libncbi-vdb2.install
create mode 100644 debian/patches/jessie_kapp_fPIC.patch
create mode 100644 debian/patches/use_debian_packaged_libmbedx.patch
create mode 100644 interfaces/kdb/rowset-impl.h
create mode 100644 interfaces/kdb/rowset.h
copy libs/kns/sysmgr.h => interfaces/kns/http-priv.h (68%)
copy interfaces/kns/{manager.h => tls.h} (54%)
create mode 100644 libs/kdb/rowset-it.c_old
create mode 100644 libs/kdb/rowset-priv.h_old
create mode 100644 libs/kdb/rowset-simple.c
create mode 100644 libs/kdb/rowset.c
create mode 100644 libs/kdb/rowset.c_old
create mode 100644 libs/kfg/certs.kfg
copy interfaces/kproc/timeout.h => libs/kns/tls-priv.h (63%)
create mode 100644 libs/kns/tls.c
create mode 100644 libs/ngs/VByteBlob.c
copy libs/{kns/sysmgr.h => ngs/VByteBlob.h} (76%)
copy {test/vxf => libs/vdb/test}/Makefile (76%)
create mode 100644 libs/vdb/test/test-prod-cmn.c
copy test/{vxf => align}/Makefile (82%)
create mode 100644 test/align/indextest.cpp
create mode 100644 test/kdb/rowsettest.cpp
mode change 100755 => 100644 test/kfc/kfc.c
create mode 100644 test/kns/TestProxy.hpp
create mode 100644 test/kns/http-client.c
create mode 100644 test/kns/test-proxy-with-env.cpp
create mode 100644 test/kns/test-proxy.cpp
create mode 100644 test/kns/test-proxy.h
create mode 100644 test/kns/test-proxy/2-path-no-env/config
create mode 100644 test/kns/test-proxy/2-path-no-env/expected
create mode 100644 test/kns/test-proxy/2-path-no-port-no-env/config
create mode 100644 test/kns/test-proxy/2-path-no-port-no-env/expected
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/all.MULTIPLE_PROXIES/config
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/all.MULTIPLE_PROXIES/environment
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/all.MULTIPLE_PROXIES/expected
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/disabled.MULTIPLE_PROXIES/config
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/disabled.MULTIPLE_PROXIES/environment
copy interfaces/.gitignore => test/kns/test-proxy/MULTIPLE_PROXIES/disabled.MULTIPLE_PROXIES/expected (100%)
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/enabled.MULTIPLE_PROXIES/config
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/enabled.MULTIPLE_PROXIES/environment
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/enabled.MULTIPLE_PROXIES/expected
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/env-kfg.MULTIPLE_PROXIES/config
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/env-kfg.MULTIPLE_PROXIES/environment
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/env-kfg.MULTIPLE_PROXIES/expected
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/env-only.MULTIPLE_PROXIES/config
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/env-only.MULTIPLE_PROXIES/environment
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/env-only.MULTIPLE_PROXIES/expected
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/ignore.MULTIPLE_PROXIES/config
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/ignore.MULTIPLE_PROXIES/environment
copy interfaces/.gitignore => test/kns/test-proxy/MULTIPLE_PROXIES/ignore.MULTIPLE_PROXIES/expected (100%)
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/kfg-env.MULTIPLE_PROXIES/config
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/kfg-env.MULTIPLE_PROXIES/environment
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/kfg-env.MULTIPLE_PROXIES/expected
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/proxy-not-only.MULTIPLE_PROXIES/config
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/proxy-not-only.MULTIPLE_PROXIES/environment
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/proxy-not-only.MULTIPLE_PROXIES/expected
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/proxy-only.MILTIPLE_PROXIES/config
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/proxy-only.MILTIPLE_PROXIES/environment
create mode 100644 test/kns/test-proxy/MULTIPLE_PROXIES/proxy-only.MILTIPLE_PROXIES/expected
create mode 100644 test/kns/test-proxy/all/config
create mode 100644 test/kns/test-proxy/all/environment
create mode 100644 test/kns/test-proxy/all/expected
create mode 100644 test/kns/test-proxy/comma-error/environment
copy interfaces/.gitignore => test/kns/test-proxy/comma-error/expected (100%)
create mode 100644 test/kns/test-proxy/disabled/config
create mode 100644 test/kns/test-proxy/disabled/environment
copy interfaces/.gitignore => test/kns/test-proxy/disabled/expected (100%)
create mode 100644 test/kns/test-proxy/enabled/config
create mode 100644 test/kns/test-proxy/enabled/environment
create mode 100644 test/kns/test-proxy/enabled/expected
create mode 100644 test/kns/test-proxy/env-kfg/config
create mode 100644 test/kns/test-proxy/env-kfg/environment
create mode 100644 test/kns/test-proxy/env-kfg/expected
create mode 100644 test/kns/test-proxy/env-only/config
create mode 100644 test/kns/test-proxy/env-only/environment
create mode 100644 test/kns/test-proxy/env-only/expected
create mode 100644 test/kns/test-proxy/error/config
create mode 100644 test/kns/test-proxy/error/environment
copy interfaces/.gitignore => test/kns/test-proxy/error/expected (100%)
create mode 100644 test/kns/test-proxy/http_proxy/environment
create mode 100644 test/kns/test-proxy/http_proxy/expected
create mode 100644 test/kns/test-proxy/ignore/config
create mode 100644 test/kns/test-proxy/ignore/environment
copy interfaces/.gitignore => test/kns/test-proxy/ignore/expected (100%)
create mode 100644 test/kns/test-proxy/kfg-env/config
create mode 100644 test/kns/test-proxy/kfg-env/environment
create mode 100644 test/kns/test-proxy/kfg-env/expected
create mode 100644 test/kns/test-proxy/kfg-only/config
create mode 100644 test/kns/test-proxy/kfg-only/environment
create mode 100644 test/kns/test-proxy/kfg-only/expected
create mode 100644 test/kns/test-proxy/no-env/config
create mode 100644 test/kns/test-proxy/no-env/expected
create mode 100644 test/kns/test-proxy/no-port-no-env/config
create mode 100644 test/kns/test-proxy/no-port-no-env/expected
create mode 100644 test/kns/test-proxy/proxy-not-only/config
create mode 100644 test/kns/test-proxy/proxy-not-only/environment
create mode 100644 test/kns/test-proxy/proxy-not-only/expected
create mode 100644 test/kns/test-proxy/proxy-only/config
create mode 100644 test/kns/test-proxy/proxy-only/environment
create mode 100644 test/kns/test-proxy/proxy-only/expected
create mode 100644 test/vdb/.gitignore
create mode 100644 test/vdb/test-VDB-3061.cpp
create mode 100644 test/vfs/redirect-rejected-names-cgi-http-to-https.cpp
create mode 100644 test/vfs/redirect-rejected-names-cgi-http-to-https/incomplete.kfg
create mode 100644 test/vxf/VDB-2915.cpp
create mode 100644 test/vxf/local_config/local.kfg
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