[med-svn] [ncbi-vdb] 03/06: Merge tag 'upstream/2.8.0+dfsg'
Andreas Tille
tille at debian.org
Fri Nov 4 08:31:06 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository ncbi-vdb.
commit a589d96457b0546c42d041588bb4c954f0308f4f
Merge: b366c12 78461da
Author: Andreas Tille <tille at debian.org>
Date: Fri Nov 4 08:26:23 2016 +0100
Merge tag 'upstream/2.8.0+dfsg'
Upstream version 2.8.0+dfsg
.gitignore | 1 +
CHANGES | 60 -
CHANGES.md | 20 +
README | 55 -
README.md | 25 +-
build/Makefile.gcc | 4 +-
build/Makefile.install | 28 +-
build/Makefile.vers | 2 +-
build/ld.linux.exe_cmd.sh | 1 +
interfaces/kdb/rowset-impl.h | 141 ++
interfaces/kdb/rowset.h | 186 +++
interfaces/kfc/rc.h | 25 +-
interfaces/kfc/xc.h | 6 +
interfaces/kfg/kfg-priv.h | 6 +
interfaces/kfg/properties.h | 6 +
interfaces/klib/rc.h | 28 +-
interfaces/klib/status.h | 2 +-
interfaces/klib/text.h | 6 +
interfaces/kns/endpoint.h | 1 +
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 | 5 +-
interfaces/vdb/manager.h | 12 +-
interfaces/vdb/vdb.vschema | 2 +-
interfaces/vfs/manager-priv.h | 9 +
interfaces/vfs/resolver.h | 60 +-
libs/align/bam.c | 9 +-
libs/ascp/unix/connect.c | 2 +-
libs/blast/blast-mgr.c | 2 +-
libs/kapp/loader-file.c | 10 +-
libs/kdb/Makefile | 2 +
libs/kdb/libkdb.vers.h | 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/wtable.c | 3 +
libs/kfc/refcount.c | 1 +
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 | 255 ++--
libs/kfg/default.kfg | 10 +-
libs/kfg/properties.c | 47 +
libs/kfg/repository.c | 10 +
libs/kfs/tar.c | 48 +-
libs/klib/rc-idx-tbl.c | 2 +
libs/klib/rc-tbl.c | 2 +
libs/klib/release-vers.h | 2 +-
libs/klib/report-klib.c | 8 +-
libs/klib/status-rc-strings.c | 1 +
libs/klib/status.c | 7 +-
libs/klib/text.c | 35 +
libs/klib/writer.c | 3 +-
libs/kns/Makefile | 3 +-
libs/kns/http-client.c | 526 ++++++-
libs/kns/http-file.c | 5 +-
libs/kns/http-priv.h | 40 +-
libs/kns/http.c | 47 +-
libs/kns/kns_manager-ext.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 | 907 +++++++-----
libs/kproc/procmgr.c | 101 +-
libs/kproc/unix/systimeout.c | 42 +
libs/ncbi-vdb/Makefile | 3 +
libs/ncbi-vdb/libncbi-vdb.vers | 2 +-
libs/ngs-jni/jni_String.c | 4 +-
libs/ngs/BAM_Alignment.c | 66 +-
libs/ngs/CSRA1_Alignment.c | 21 +
libs/ngs/CSRA1_Read.c | 123 +-
libs/ngs/CSRA1_Reference.c | 322 +++--
libs/ngs/CSRA1_ReferenceWindow.c | 251 ++--
libs/ngs/EBI_ReferenceSequence.c | 41 +-
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/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/sra/sramgr-cmn.c | 2 +-
libs/svdb/svdb.c | 2 +-
libs/vdb/database-cmn.c | 4 +-
libs/vdb/database-depend.c | 2 +-
libs/vdb/dbmgr-cmn.c | 26 +
libs/vdb/libvdb.vers.h | 2 +-
libs/vdb/prod-cmn.c | 181 ++-
{test/vxf => libs/vdb/test}/Makefile | 41 +-
libs/vdb/test/test-prod-cmn.c | 10 +
libs/vdb/wdatabase.c | 2 +-
libs/vfs/manager.c | 219 ++-
libs/vfs/path-priv.h | 1 +
libs/vfs/path.c | 15 +-
libs/vfs/resolver-priv.h | 3 +
libs/vfs/resolver.c | 345 ++++-
libs/vxf/entrez.c | 2 +-
libs/vxf/fzip.c | 2 +-
libs/vxf/irzip.c | 4 +-
libs/vxf/izip.c | 2 +-
libs/xfs/path.c | 14 +-
libs/xfs/unix/operations.c | 9 +-
libs/xfs/xgap.c | 4 +-
libs/xfs/xhttp.c | 16 +-
test/{vxf => align}/Makefile | 40 +-
test/align/indextest.cpp | 113 ++
test/cc/asm-test.cpp | 15 +
test/kdb/Makefile | 23 +-
test/kdb/remote_open_test.cpp | 4 +-
test/kdb/rowsettest.cpp | 819 +++++++++++
test/kfg/flat-sra-kfg.cpp | 44 +-
test/kfg/kfgtest.cpp | 4 +-
test/kfs/cacheteetest.cpp | 13 +-
test/kns/Makefile | 50 +
test/kns/TestProxy.hpp | 227 +++
test/kns/http-client.c | 17 +
test/kns/httptest.cpp | 5 +-
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 +
test/kns/test-proxy/comma-error/expected | 0
test/kns/test-proxy/disabled/config | 2 +
test/kns/test-proxy/disabled/environment | 4 +
test/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 +
test/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 +
test/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-modes.c | 2 +-
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/vdb/.gitignore | 1 +
test/vdb/Makefile | 25 +-
test/vdb/test-VDB-3060.cpp | 33 +-
test/vdb/test-VDB-3061.cpp | 249 ++++
test/vdb/test-wvdb.cpp | 205 ++-
test/vfs/Makefile | 11 +
.../redirect-rejected-names-cgi-http-to-https.cpp | 189 +++
.../incomplete.kfg | 1 +
test/vxf/Makefile | 25 +-
test/vxf/VDB-2915.cpp | 508 +++++++
test/vxf/local_config/local.kfg | 2 +
236 files changed, 12378 insertions(+), 2661 deletions(-)
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