[med-svn] [ncbi-vdb] branch upstream updated (5c0fa48 -> 78461da)
Andreas Tille
tille at debian.org
Fri Nov 4 08:31:08 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository ncbi-vdb.
from 5c0fa48 Imported Upstream version 2.7.0+dfsg
new 78461da New upstream version 2.8.0+dfsg
The 1 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 | 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/{adapt.h => tls.h} | 67 +-
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 +-
libs/{kdb/idstats-priv.h => kns/tls-priv.h} | 54 +-
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 ++
.../cc/vc++/stdint.h => libs/ngs/VByteBlob.h | 25 +-
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/cc => libs/vdb/test}/Makefile | 31 +-
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/{kproc => align}/Makefile | 25 +-
test/{ngs-c++/NGStest.cpp => align/indextest.cpp} | 70 +-
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 +
.../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-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, 12317 insertions(+), 2663 deletions(-)
delete mode 100644 CHANGES
delete mode 100644 README
create mode 100644 build/ld.linux.exe_cmd.sh
create mode 100644 interfaces/kdb/rowset-impl.h
create mode 100644 interfaces/kdb/rowset.h
copy interfaces/kns/{adapt.h => tls.h} (58%)
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 libs/{kdb/idstats-priv.h => kns/tls-priv.h} (64%)
create mode 100644 libs/kns/tls.c
create mode 100644 libs/ngs/VByteBlob.c
copy interfaces/cc/vc++/stdint.h => libs/ngs/VByteBlob.h (76%)
copy {test/cc => libs/vdb/test}/Makefile (78%)
create mode 100644 libs/vdb/test/test-prod-cmn.c
copy test/{kproc => align}/Makefile (84%)
copy test/{ngs-c++/NGStest.cpp => align/indextest.cpp} (51%)
create mode 100644 test/kdb/rowsettest.cpp
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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