[med-svn] [ncbi-vdb] branch master updated (b36a1ec -> a7912ef)
Andreas Tille
tille at debian.org
Thu Oct 19 21:47:11 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository ncbi-vdb.
from b36a1ec Upload to unstable
adds a68f5ec New upstream version 2.8.2-2+dfsg
adds 4a6d68d Updated version 2.8.2-2+dfsg from 'upstream/2.8.2-2+dfsg'
adds 576a74a New upstream version
adds 4caeb28 cme fix dpkg-control, Standards-Version: 4.1.1
adds d138bb0 More adaptations to Debian packaged libmbedx
adds 76989af Do not parse changelog
adds 5066e45 More adaptations to Debian packaged libmbedx
adds a7912ef Try better hardening
No new revisions were added by this update.
Summary of changes:
.gitignore | 1 +
CHANGES.md | 23 +
build/Makefile.env | 12 +-
build/Makefile.install | 91 +-
build/Makefile.vers | 2 +-
debian/changelog | 11 +
debian/control | 8 +-
debian/patches/mbedtls_ssl_init.patch | 266 ++
debian/patches/series | 1 +
debian/rules | 42 +-
interfaces/align/bam.h | 33 +-
interfaces/insdc/sra.vschema | 4 +-
interfaces/{cc/vc++/va_copy.h => kfg/kart-priv.h} | 18 +-
interfaces/kfg/kart.h | 40 +-
interfaces/kfs/directory.h | 7 +
interfaces/kfs/filetools.h | 12 +-
interfaces/{align/manager.h => kfs/limitfile.h} | 42 +-
interfaces/klib/debug.h | 3 +-
interfaces/klib/namelist.h | 7 +
interfaces/klib/time.h | 16 +
interfaces/kns/endpoint.h | 6 +
interfaces/kns/kns-mgr-priv.h | 1 -
interfaces/kns/stream.h | 7 +
interfaces/ktst/unit_test_suite.hpp | 28 +-
interfaces/sra/generic-fastq.vschema | 9 +
interfaces/tui/tui.hpp | 1 +
interfaces/vfs/path.h | 11 +-
interfaces/vfs/resolver.h | 14 +-
.../{cc/vc++/compiler.h => vfs/services-priv.h} | 53 +-
interfaces/vfs/services.h | 138 +
libs/align/align-access.c | 55 +-
libs/align/bam.c | 610 +--
libs/ascp/ascp.c | 2 +-
libs/blast/blast-mgr.c | 2 +-
libs/blast/reference.c | 5 +-
libs/kdb/libkdb.vers.h | 2 +-
libs/kfg/config.c | 87 +-
libs/kfg/kart.c | 331 +-
libs/kfg/keystore.c | 6 +
libs/kfs/Makefile | 3 +-
libs/kfs/cacheteefile.c | 129 +-
libs/kfs/from_to_namelist.c | 55 +-
libs/kfs/gzip.c | 110 +-
libs/kfs/limitfile.c | 206 ++
libs/kfs/unix/sysdir.c | 24 +
libs/klib/log.c | 28 +-
libs/klib/release-vers.h | 2 +-
libs/klib/time.c | 28 +
libs/klib/unix/systime.c | 66 +-
libs/klib/vector_namelist.c | 59 +
libs/kns/Makefile | 1 +
libs/kns/http-client.c | 113 +-
libs/kns/http-file.c | 54 +-
libs/kns/http-priv.h | 16 +-
libs/kns/http.c | 1 -
libs/kns/linux/sysendpoint.c | 10 +
libs/kns/manager.c | 110 +-
libs/kns/mgr-priv.h | 7 +
libs/kns/stream-from-buffer.c | 192 +
libs/kns/tls.c | 158 +-
libs/kns/unix/syssock.c | 11 +
libs/ktst/testcase.cpp | 2 +-
libs/ktst/testenv.cpp | 15 +
libs/ncbi-vdb/libncbi-vdb.vers | 2 +-
libs/ngs/BAM_ReadCollection.c | 191 +-
libs/ngs/CSRA1_Alignment.c | 2 +-
libs/ngs/CSRA1_Read.c | 101 +-
libs/ngs/CSRA1_ReadCollection.c | 4 +-
libs/ngs/CSRA1_Reference.c | 33 +-
libs/ngs/CSRA1_Reference.h | 7 +-
libs/ngs/CSRA1_ReferenceWindow.c | 185 +-
libs/ngs/Makefile | 6 +-
libs/ngs/NGS_FragmentBlob.c | 26 +-
libs/ngs/NGS_FragmentBlob.h | 6 +
libs/ngs/NGS_FragmentBlobIterator.c | 6 +
libs/ngs/NGS_ReadCollection.c | 8 +-
libs/ngs/NGS_Reference.c | 127 +-
libs/ngs/NGS_Reference.h | 31 +-
libs/ngs/NGS_ReferenceBlob.c | 296 ++
libs/ngs/NGS_ReferenceBlob.h | 100 +
...tBlobIterator.c => NGS_ReferenceBlobIterator.c} | 76 +-
...tBlobIterator.h => NGS_ReferenceBlobIterator.h} | 33 +-
libs/ngs/SRA_DB_ReadCollection.c | 10 +-
libs/ngs/SRA_Read.c | 1 +
libs/ngs/SRA_Read.h | 5 +-
libs/ngs/SRA_ReadCollection.c | 10 +-
libs/ngs/VByteBlob.c | 31 +-
libs/ngs/VByteBlob.h | 4 +-
libs/tui/tui_dlg_helper.c | 128 +-
libs/vdb/cursor-cmn.c | 2 +-
libs/vdb/libvdb.vers.h | 2 +-
libs/vfs/Makefile | 5 +-
libs/vfs/manager.c | 38 +-
libs/vfs/path-priv.h | 79 +
libs/vfs/path.c | 290 +-
libs/vfs/remote-services.c | 3905 ++++++++++++++++++++
libs/vfs/resolver-priv.h | 7 +-
libs/vfs/resolver.c | 315 +-
libs/vfs/services-priv.h | 126 +
libs/vfs/services.c | 280 ++
libs/vfs/srv-response.c | 580 +++
py_vdb/L1-manager.py | 57 +
py_vdb/L10-fastq.py | 81 +
py_vdb/L2-table_read.py | 80 +
py_vdb/L3-table_write.py | 94 +
py_vdb/L4-database_read.py | 58 +
py_vdb/L5-database_write.py | 111 +
py_vdb/L6-meta_read.py | 47 +
py_vdb/L7-table-rnd-write.py | 49 +
py_vdb/L8-import-csv.py | 44 +
py_vdb/L9-index_usage.py | 57 +
py_vdb/custom_fastq.py | 27 +
py_vdb/ref_var.py | 375 ++
py_vdb/tst_config.py | 48 +
py_vdb/vdb.py | 2229 +++++++++++
setup/konfigure.perl | 99 +-
setup/package.prl | 12 +-
test/Makefile | 1 +
test/{align => align-access}/Makefile | 9 +-
test/align-access/align-access.hpp | 182 +
.../report-kns-agent.c => align-access/main.c} | 27 +-
test/align-access/test.cpp | 192 +
test/align-access/test.pl | 132 +
test/install/.gitignore | 2 +
test/install/Makefile | 139 +
test/kdb/kdbtest.cpp | 31 +-
test/kfg/flat-sra-kfg.cpp | 4 +-
test/kfg/keystoretest.cpp | 48 +-
test/kfg/kfgtest.cpp | 3 +-
test/kfs/Makefile | 70 +-
test/kfs/cachetee-out-of-space.cpp | 187 +
test/kfs/cacheteetest.cpp | 4 +-
test/kfs/fuse_proxy.c | 668 ++++
test/kfs/kdf.cpp | 303 ++
test/kfs/run-cachetee-out-of-space-test.sh | 87 +
test/klib/Makefile | 13 +
test/klib/test-log.cpp | 36 +
test/klib/test-time.cpp | 87 +
test/kns/Makefile | 98 +-
test/kns/test-proxy-with-scheme.cpp | 162 +
test/kns/test-proxy.cpp | 16 +
.../env-with-schema-and-port/environment | 1 +
.../expected | 0
test/kns/test-proxy/env-with-schema/environment | 1 +
test/kns/test-proxy/env-with-schema/expected | 1 +
.../kns/test-proxy/kfg-with-schema-and-port/config | 1 +
.../expected | 0
test/kns/test-proxy/kfg-with-schema/config | 1 +
test/kns/test-proxy/kfg-with-schema/expected | 1 +
test/krypto/Makefile | 10 +-
test/ktst/ktsttest.cpp | 52 +
test/ngs-java/ngs_test_CSRA1.java | 292 +-
test/ngs/Makefile | 43 +-
test/ngs/ngs_c_fixture.hpp | 2 +-
test/ngs/ngstest_byteblob.cpp | 314 ++
test/ngs/ngstest_csra1.cpp | 502 ---
test/ngs/ngstest_fragmentblob.cpp | 29 +-
test/ngs/ngstest_reference.cpp | 582 ++-
test/ngs/ngstest_referenceblob.cpp | 773 ++++
test/vdb/Makefile | 22 +-
test/vdb/test-VDB-3060.cpp | 2 +-
test/vdb/test-VDB-3061.cpp | 40 +-
test/vdb/test-VDB-3305.cpp | 161 +
test/vdb/test-vdb.cpp | 90 +-
test/vfs/Makefile | 26 +-
.../redirect-rejected-names-cgi-http-to-https.cpp | 10 +-
test/vfs/resolvertest.cpp | 12 +-
test/vfs/test-caching.cpp | 4 +-
test/vfs/test-names-30.cpp | 503 +++
vdb3/itf/kfc/except.hpp | 36 +-
vdb3/itf/kfc/memmgr.hpp | 9 +-
vdb3/itf/kfc/ptr.hpp | 20 +-
vdb3/itf/kfc/rsrc.hpp | 15 +-
vdb3/itf/kfc/string.hpp | 9 +-
vdb3/src/kfc/Makefile | 16 +-
vdb3/src/kfc/rsrc.cpp | 1 +
vdb3/src/kfc/string.cpp | 80 +-
177 files changed, 18014 insertions(+), 2081 deletions(-)
create mode 100644 debian/patches/mbedtls_ssl_init.patch
copy interfaces/{cc/vc++/va_copy.h => kfg/kart-priv.h} (84%)
copy interfaces/{align/manager.h => kfs/limitfile.h} (68%)
copy interfaces/{cc/vc++/compiler.h => vfs/services-priv.h} (58%)
create mode 100644 interfaces/vfs/services.h
create mode 100644 libs/kfs/limitfile.c
create mode 100644 libs/kns/stream-from-buffer.c
create mode 100644 libs/ngs/NGS_ReferenceBlob.c
create mode 100644 libs/ngs/NGS_ReferenceBlob.h
copy libs/ngs/{NGS_FragmentBlobIterator.c => NGS_ReferenceBlobIterator.c} (63%)
copy libs/ngs/{NGS_FragmentBlobIterator.h => NGS_ReferenceBlobIterator.h} (61%)
create mode 100644 libs/vfs/remote-services.c
create mode 100644 libs/vfs/services-priv.h
create mode 100644 libs/vfs/services.c
create mode 100644 libs/vfs/srv-response.c
create mode 100755 py_vdb/L1-manager.py
create mode 100755 py_vdb/L10-fastq.py
create mode 100755 py_vdb/L2-table_read.py
create mode 100755 py_vdb/L3-table_write.py
create mode 100755 py_vdb/L4-database_read.py
create mode 100755 py_vdb/L5-database_write.py
create mode 100755 py_vdb/L6-meta_read.py
create mode 100755 py_vdb/L7-table-rnd-write.py
create mode 100755 py_vdb/L8-import-csv.py
create mode 100755 py_vdb/L9-index_usage.py
create mode 100755 py_vdb/custom_fastq.py
create mode 100755 py_vdb/ref_var.py
create mode 100755 py_vdb/tst_config.py
create mode 100644 py_vdb/vdb.py
copy test/{align => align-access}/Makefile (93%)
create mode 100644 test/align-access/align-access.hpp
copy test/{kapp/report-kns-agent.c => align-access/main.c} (79%)
create mode 100644 test/align-access/test.cpp
create mode 100644 test/align-access/test.pl
create mode 100644 test/install/.gitignore
create mode 100644 test/install/Makefile
create mode 100644 test/kfs/cachetee-out-of-space.cpp
create mode 100644 test/kfs/fuse_proxy.c
create mode 100644 test/kfs/kdf.cpp
create mode 100755 test/kfs/run-cachetee-out-of-space-test.sh
create mode 100644 test/klib/test-time.cpp
create mode 100644 test/kns/test-proxy-with-scheme.cpp
create mode 100644 test/kns/test-proxy/env-with-schema-and-port/environment
copy test/kns/test-proxy/{http_proxy => env-with-schema-and-port}/expected (100%)
create mode 100644 test/kns/test-proxy/env-with-schema/environment
create mode 100644 test/kns/test-proxy/env-with-schema/expected
create mode 100644 test/kns/test-proxy/kfg-with-schema-and-port/config
copy test/kns/test-proxy/{http_proxy => kfg-with-schema-and-port}/expected (100%)
create mode 100644 test/kns/test-proxy/kfg-with-schema/config
create mode 100644 test/kns/test-proxy/kfg-with-schema/expected
create mode 100644 test/ngs/ngstest_byteblob.cpp
create mode 100644 test/ngs/ngstest_referenceblob.cpp
create mode 100644 test/vdb/test-VDB-3305.cpp
create mode 100644 test/vfs/test-names-30.cpp
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