[med-svn] [Git][med-team/ncbi-vdb][upstream] New upstream version 2.9.2-1+dfsg
Andreas Tille
gitlab at salsa.debian.org
Tue Aug 28 20:30:43 BST 2018
Andreas Tille pushed to branch upstream at Debian Med / ncbi-vdb
Commits:
bb5b4b8a by Andreas Tille at 2018-08-28T05:45:23Z
New upstream version 2.9.2-1+dfsg
- - - - -
11 changed files:
- CHANGES.md
- build/Makefile.vers
- libs/blast/blast-mgr.c
- libs/kdb/libkdb.vers.h
- libs/kfg/keystore.c
- libs/klib/release-vers.h
- libs/ncbi-vdb/libncbi-vdb.vers
- libs/vdb/cursor-cmn.c
- libs/vdb/libvdb.vers.h
- libs/vfs/manager.c
- test/vdb/test-vdb.cpp
Changes:
=====================================
CHANGES.md
=====================================
@@ -1,5 +1,16 @@
# NCBI External Developer Release:
+
+## NCBI VDB 2.9.2-1
+**July 31, 2018**
+ **vdb**: restored lost exported attribute on several entries in the private API
+
+
+## NCBI VDB 2.9.2
+**July 23, 2018**
+ **kfg, vfs**: Introduced enhanced handling of download-only NGC files that lack read/decrypt permissions
+
+
## NCBI VDB 2.9.1-1
**June 25, 2018**
=====================================
build/Makefile.vers
=====================================
@@ -23,4 +23,4 @@
# ===========================================================================
# NCBI-VDB and library version
-VERSION = 2.9.1
+VERSION = 2.9.2
=====================================
libs/blast/blast-mgr.c
=====================================
@@ -50,7 +50,7 @@
#include <stdio.h> /* fprintf */
#include <string.h> /* memset */
-#define TOOLKIT "sratoolkit2_9_1"
+#define TOOLKIT "sratoolkit2_9_2"
/******************************************************************************/
=====================================
libs/kdb/libkdb.vers.h
=====================================
@@ -24,4 +24,4 @@
*
*/
-#define LIBKDB_VERS 0x0207001A
+#define LIBKDB_VERS 0x0207001B
=====================================
libs/kfg/keystore.c
=====================================
@@ -174,6 +174,11 @@ rc_t ReadEncKey(const KFile* file, char* buf, size_t bufsize)
if (rc == 0)
{
+ char * pc;
+
+ /* ensure buffer is NUL terminated */
+ buf [ readNum ] = 0;
+
/* -----
* trim back the contents of the file to
* a single ASCII/UTF-8 text line
@@ -181,17 +186,20 @@ rc_t ReadEncKey(const KFile* file, char* buf, size_t bufsize)
* end of line characters so it could have other
* control characters...
*/
- char* pc = string_chr (buf, readNum, '\r');
- if (pc == NULL)
- pc = string_chr (buf, readNum, '\n');
-
+ pc = memchr ( buf, '\r', readNum );
+ if ( pc == NULL )
+ pc = memchr ( buf, '\n', readNum );
if (pc != NULL)
*pc = 0;
- else
- buf[readNum]=0;
-
- if (string_measure(buf, NULL) == 0)
+
+ /* disallow a length of 0 */
+ if ( buf [ 0 ] == 0 )
rc = RC (rcKFG, rcEncryptionKey, rcRetrieving, rcSize, rcTooShort);
+ else if ( memcmp ( buf, "n/a", 4 ) == 0 )
+ {
+ /* download-only NGC file */
+ rc = RC ( rcKFG, rcEncryptionKey, rcRetrieving, rcEncryptionKey, rcNoPerm );
+ }
}
return rc;
}
=====================================
libs/klib/release-vers.h
=====================================
@@ -28,7 +28,7 @@
/* Version of current SRA Toolkit Release */
-#define RELEASE_VERS 0x02090001
+#define RELEASE_VERS 0x02090002
/* Type of Version of current SRA Toolkit Release is one of:
=====================================
libs/ncbi-vdb/libncbi-vdb.vers
=====================================
@@ -1 +1 @@
-2.9.1
+2.9.2
=====================================
libs/vdb/cursor-cmn.c
=====================================
@@ -167,7 +167,7 @@ bool VCursorIsReadOnly ( const struct VCursor * self )
{
DISPATCH_VALUE ( isReadOnly ( self ), true );
}
-struct VSchema const * VCursorGetSchema ( struct VCursor const *self )
+LIB_EXPORT struct VSchema const * VCursorGetSchema(struct VCursor const *self)
{
DISPATCH_VALUE ( getSchema ( self ), NULL );
}
@@ -183,27 +183,27 @@ const struct KSymbol * VCursorFindOverride ( const VCursor *self, const struct V
{
DISPATCH_VALUE ( findOverride ( self, cid ), NULL );
}
-rc_t CC VCursorPermitPostOpenAdd ( struct VCursor const *self )
+LIB_EXPORT rc_t CC VCursorPermitPostOpenAdd(struct VCursor const *self)
{
DISPATCH ( permitPostOpenAdd ( self ) );
}
-rc_t CC VCursorSuspendTriggers ( struct VCursor const *self )
+LIB_EXPORT rc_t CC VCursorSuspendTriggers(struct VCursor const *self)
{
DISPATCH ( suspendTriggers ( self ) );
}
-rc_t CC VCursorLinkedCursorGet( const struct VCursor * self,const char * tbl, struct VCursor const ** curs)
+LIB_EXPORT rc_t CC VCursorLinkedCursorGet(const struct VCursor * self, const char * tbl, struct VCursor const ** curs)
{
DISPATCH ( linkedCursorGet ( self, tbl, curs ) );
}
-rc_t CC VCursorLinkedCursorSet( const struct VCursor * self,const char * tbl, struct VCursor const * curs)
+LIB_EXPORT rc_t CC VCursorLinkedCursorSet(const struct VCursor * self, const char * tbl, struct VCursor const * curs)
{
DISPATCH ( linkedCursorSet ( self, tbl, curs ) );
}
-uint64_t CC VCursorSetCacheCapacity ( struct VCursor * self,uint64_t capacity )
+LIB_EXPORT uint64_t CC VCursorSetCacheCapacity(struct VCursor * self, uint64_t capacity)
{
DISPATCH_VALUE ( setCacheCapacity ( self, capacity ), 0 );
}
-uint64_t CC VCursorGetCacheCapacity ( const struct VCursor * self )
+LIB_EXPORT uint64_t CC VCursorGetCacheCapacity(const struct VCursor * self)
{
DISPATCH_VALUE ( getCacheCapacity ( self ), 0 );
}
=====================================
libs/vdb/libvdb.vers.h
=====================================
@@ -24,4 +24,4 @@
*
*/
-#define LIBVDB_VERS 0x0207001A
+#define LIBVDB_VERS 0x0207001B
=====================================
libs/vfs/manager.c
=====================================
@@ -640,7 +640,7 @@ rc_t GetEncryptionKey(const VFSManager * self, const VPath * vpath, char* obuff,
rc = rc2;
}
}
-
+
if (rc == 0)
{
KEncryptionKey* enc_key = NULL;
@@ -677,6 +677,14 @@ rc_t GetEncryptionKey(const VFSManager * self, const VPath * vpath, char* obuff,
}
}
+ if ( GetRCState ( rc ) == rcNoPerm && GetRCObject ( rc ) == ( enum RCObject ) rcEncryptionKey )
+ {
+ LOGMSG ( klogErr, "You do not have read permissions to decrypt data from this project." );
+ LOGMSG ( klogErr, "Please contact your PI to request an NGC token with decrypt permissions." );
+ LOGMSG ( klogErr, "Import the new NGC file before decrypting again." );
+ LOGMSG ( klogErr, "If you continue to have problems, contact sra at ncbi.nlm.nih.gov for assistance." );
+ }
+
rc2 = KKeyStoreSetTemporaryKeyFromFile(self->keystore, NULL); /* forget the temp key if set */
if (rc == 0)
rc = rc2;
=====================================
test/vdb/test-vdb.cpp
=====================================
@@ -211,7 +211,7 @@ public:
throw logic_error ( "~VdbFixture: VCursorRelease failed" );
}
- rc_t Setup( const char * acc, const char* column[] )
+ rc_t Setup( const char * acc, const char* column[], bool open = true )
{
const VDatabase *db = NULL;
rc_t rc = VDBManagerOpenDBRead ( mgr, &db, NULL, acc );
@@ -255,7 +255,7 @@ public:
assert(i < N);
rc = VCursorAddColumn ( curs, col_idx + i, column[i] );
}
- if ( rc == 0 )
+ if ( rc == 0 && open )
{
rc = VCursorOpen(curs);
}
@@ -368,7 +368,6 @@ FIXTURE_TEST_CASE(VCursor_GetBlob_SRA, VdbFixture)
{ // multiple fragments per row (some are technical), multiple rows per blob
static char const *columns[] = { "READ", 0 };
REQUIRE_RC ( Setup ( "SRR000123", columns ) );
- REQUIRE_RC ( VCursorOpen (curs ) );
{
REQUIRE_RC ( VCursorSetRowId (curs, 1 ) );
@@ -439,7 +438,6 @@ FIXTURE_TEST_CASE(VCursor_GetBlob_WGS, VdbFixture)
{ // single fragment per row, multiple rows per blob
static char const *columns[] = { "READ", 0 };
REQUIRE_RC ( Setup ( "ALWZ01", columns ) );
- REQUIRE_RC ( VCursorOpen (curs ) );
{
REQUIRE_RC ( VCursorSetRowId (curs, 1 ) );
@@ -510,7 +508,6 @@ FIXTURE_TEST_CASE(VCursor_GetBlob_SequentialAccess, VdbFixture)
{ // VDB-2858: sequential access to blobs broken
static char const *columns[] = { "READ", 0 };
REQUIRE_RC ( Setup ( "ALAI01", columns ) );
- REQUIRE_RC ( VCursorOpen (curs ) );
int64_t first;
uint64_t count;
@@ -543,7 +540,6 @@ FIXTURE_TEST_CASE(VCursor_GetBlob_RandomAccess, VdbFixture)
{
static char const *columns[] = { "READ", 0 };
REQUIRE_RC ( Setup ( "SRR000001", columns ) );
- REQUIRE_RC ( VCursorOpen (curs ) );
// when accessing randomly, blob sizes stay very small
REQUIRE ( CheckBlobRange ( 1, 1, 4 ) );
@@ -561,7 +557,6 @@ FIXTURE_TEST_CASE(PageMapIterator_WGS, VdbFixture)
{ // single fragment per row, multiple rows per blob
static char const *columns[] = { "READ", 0 };
REQUIRE_RC ( Setup ( "ALWZ01", columns ) );
- REQUIRE_RC ( VCursorOpen (curs ) );
{
REQUIRE_RC ( VCursorSetRowId (curs, 1 ) );
@@ -602,7 +597,6 @@ FIXTURE_TEST_CASE ( VCursor_FindNextRowIdDirect, VdbFixture )
{
static char const *columns[] = { "SPOT_ID", "READ", 0 };
REQUIRE_RC ( Setup ( "SRR000001", columns ) );
- REQUIRE_RC ( VCursorOpen (curs ) );
int64_t next;
REQUIRE_RC ( VCursorFindNextRowIdDirect ( curs, 0, 1, & next ) );
REQUIRE_EQ ( (int64_t)1, next ) ;
@@ -610,6 +604,13 @@ FIXTURE_TEST_CASE ( VCursor_FindNextRowIdDirect, VdbFixture )
REQUIRE_EQ ( (int64_t)2, next ) ; // VDB-3075: next == 1
}
+FIXTURE_TEST_CASE(VCursor_PermitPostOpenAdd, VdbFixture)
+{
+ static char const *columns[] = { "SPOT_ID", 0 };
+ REQUIRE_RC(Setup("SRR000001", columns, false));
+ REQUIRE_RC(VCursorPermitPostOpenAdd(curs));
+}
+
//////////////////////////////////////////// Main
extern "C"
{
View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/commit/bb5b4b8a306a37952be1b4c58c7686aa983a1c05
--
View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/commit/bb5b4b8a306a37952be1b4c58c7686aa983a1c05
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