3.0.2 RELEASE: Merge branch '3.0.1rc'

CHANGES.md

@@ -1,6 +1,12 @@
 # NCBI External Developer Release:
 
 
+## SRA Toolkit 3.0.2
+**December 12, 2022**
+
+  **prefetch**: extended URL buffer size that caused 'buffer insufficient while converting string within text module' failure on Mac  
+
+
 ## SRA Toolkit 3.0.1
 **November 15, 2022**
 

README.md

@@ -15,7 +15,13 @@ Please check the [CHANGES.md](CHANGES.md) file for change history.
 The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for
 using data in the INSDC Sequence Read Archives.
 
-November 15, 2022 : SRA Toolkit 3.0.1
+_December 12, 2022_ : **SRA Toolkit 3.0.2**
+
+Fixed 'buffer insufficient while converting string within text module' failure of prefetch on Mac.
+
+----
+
+_November 15, 2022_ : **SRA Toolkit 3.0.1**
 
 Removed interactive requirement to configure SRA Toolkit.
 
@@ -39,13 +45,13 @@ The build flags shown above can be combined on the same command line, for instan
 
 ----
 
-August 4, 2022 : Security Update
+_August 4, 2022_ : Security Update
 
 Due to updated security at NCBI, versions of the SRA Toolkit 2.9.6 and older will no longer be able to connect to the NCBI data location service. We advise impacted users to update to the [latest version](https://github.com/ncbi/sra-tools/wiki/01.-Downloading-SRA-Toolkit) of the SRA Toolkit.
 
 ----
 
-February 10, 2022 : SRA Toolkit 3.0.0
+_February 10, 2022_ : **SRA Toolkit 3.0.0**
 
 NCBI's SRA changed the source build system to use CMake in toolkit release 3.0.0. This change is an important step to improve developers' productivity as it provides unified cross platform access to support multiple build systems. This change affects developers building NCBI SRA tools from source. Old makefiles and build systems are no longer supported.
 

build/Makefile.vers

@@ -23,4 +23,4 @@
 # ===========================================================================
 
 # SRA-TOOLS and library version
-VERSION = 3.0.1
+VERSION = 3.0.2

ngs/ngs-bam/Makefile.vers

@@ -23,4 +23,4 @@
 # ===========================================================================
 
 # NGS-BAM and library version
-VERSION = 3.0.1
+VERSION = 3.0.2

ngs/ngs-java/Makefile.vers

@@ -23,4 +23,4 @@
 # ===========================================================================
 
 # NGS-JAVA and library version
-VERSION = 3.0.1
+VERSION = 3.0.2

ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java

@@ -28,7 +28,7 @@
 
 public class LibDependencies {
     public final static String NGS_SDK  = "ngs-sdk";
-    final static String NGS_SDK_VERSION = "3.0.1";
+    final static String NGS_SDK_VERSION = "3.0.2";
 
  // this is an sra-tools library that includes libncbi-vdb and its JNI wrapper
     public final static String NCBI_VDB = "ncbi-ngs";

ngs/ngs-python/Makefile.vers

@@ -23,4 +23,4 @@
 # ===========================================================================
 
 # NGS-PYTHON and library version
-VERSION = 3.0.1
+VERSION = 3.0.2

ngs/ngs-sdk/Makefile.vers

@@ -23,4 +23,4 @@
 # ===========================================================================
 
 # NGS-SDK and library version
-VERSION = 3.0.1
+VERSION = 3.0.2

ngs/ngs-sdk/dispatch/version.h

@@ -1 +1 @@
-#define NGS_SDK_VERSION "3.0.1"
+#define NGS_SDK_VERSION "3.0.2"

shared/toolkit.vers

@@ -1 +1 @@
-3.0.1
+3.0.2

shared/toolkit.vers.h

@@ -1 +1 @@
-#define TOOLKIT_VERS 0x03000001
+#define TOOLKIT_VERS 0x03000002

test/internal/vdb-diff/CMakeLists.txt

@@ -43,7 +43,7 @@ endif()
 
 if( NOT WIN32 )
 	add_test( NAME Test_VDB_Diff_Check_success
-		COMMAND test_success.sh "${DIRTOTEST}" ${ACCESSION} vdb-diff
+		COMMAND sh test_success.sh "${DIRTOTEST}" ${ACCESSION} vdb-diff
 		WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
 	if( RUN_SANITIZER_TESTS )
 		add_test( NAME Test_VDB_Diff_Check_success-asan
@@ -55,7 +55,7 @@ if( NOT WIN32 )
 	endif()
 
 	add_test( NAME Test_VDB_Diff_Check_failure
-		COMMAND test_failure.sh "${DIRTOTEST}" ${ACCESSION} vdb-diff
+		COMMAND sh test_failure.sh "${DIRTOTEST}" ${ACCESSION} vdb-diff
 		WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
 	if( RUN_SANITIZER_TESTS )
 		add_test( NAME Test_VDB_Diff_Check_failure-asan
@@ -69,4 +69,4 @@ endif()
 
 else()
     message(WARNING "${DIRTOTEST}/vdb-diff${EXE} is not found. The corresponding tests are skipped." )
-endif()
+endif()

tools/external/prefetch/PrfMain.c

@@ -50,14 +50,10 @@
 #include <vfs/resolver.h> /* VResolverRelease */
 
 #include "PrfMain.h"
+#include "PrfOutFile.h" /* PATH_MAX */
 
 #include <time.h> /* time */
 
-#include <limits.h> /* PATH_MAX */
-#ifndef PATH_MAX
-#define PATH_MAX 4096
-#endif
-
 bool _StringIsXYZ(const String *self, const char **withoutScheme,
     const char * scheme, size_t scheme_size)
 {

tools/external/prefetch/prefetch.c

@@ -91,6 +91,8 @@
 #define USE_CURL 0
 #define ALLOW_STRIP_QUALS 0
 
+#define URL_MAX 4096
+
 #define rcResolver   rcTree
 static bool NotFoundByResolver(rc_t rc) {
     if (GetRCModule(rc) == rcVFS) {
@@ -579,7 +581,7 @@ static rc_t V_ResolverRemote(const VResolver *self,
                 }
 
                 if ( rc == 0 ) {
-                    char path [ PATH_MAX ] = "";
+                    char path [ URL_MAX ] = "";
                     size_t len = 0;
                     rc = VPathReadUri ( v -> path,
                                         path, sizeof path, & len );
@@ -1082,7 +1084,7 @@ static rc_t ResolvedLocal(const Resolved *self,
             const VPath * http = NULL;
             rc = KSrvRespFileGetHttp(self->respFile, &http);
             if (rc == 0 && http != NULL) {
-                char path[PATH_MAX] = "";
+                char path[URL_MAX] = "";
                 size_t len = 0;
                 rc = VPathReadUri(http, path, sizeof path, &len);
                 if (rc == 0) {
@@ -1286,11 +1288,9 @@ static rc_t PrfMainDownloadHttpFile(Resolved *self,
 
     progressbar * pb = NULL;
 
-    const VPathStr * remote = NULL;
-
     KStsLevel lvl = STAT_PWR;
 
-    char spath[PATH_MAX] = "";
+    char spath[URL_MAX] = "";
     size_t len = 0;
 
     String src;
@@ -1311,9 +1311,12 @@ static rc_t PrfMainDownloadHttpFile(Resolved *self,
     else
         StringInit(&src, spath, len, (uint32_t)len);
 
+/*
+    const VPathStr * remote = NULL;
     remote = self -> remoteHttp . path != NULL ? & self -> remoteHttp
                                                : & self -> remoteHttps;
     assert(remote);
+*/
 
     if (rc == 0 && !mane->dryRun)
         rc = PrfOutFileOpen(pof, mane->force == eForceALL);
@@ -1547,7 +1550,7 @@ static rc_t PrfMainDownloadAscp(const Resolved *self, PrfMain *mane,
     const char *src = NULL;
     AscpOptions opt;
 
-    char spath[PATH_MAX] = "";
+    char spath[URL_MAX] = "";
     size_t len = 0;
 
     assert ( self && mane );
@@ -1730,7 +1733,7 @@ static rc_t PrfMainDoDownload(Resolved *self, const Item * item,
     mane = item->mane;
     assert(mane && pof);
     {
-        char spath[PATH_MAX] = "";
+        char spath[URL_MAX] = "";
         KStsLevel lvl = STS_DBG;
         rc_t r = VPathReadUri(path, spath, sizeof spath, NULL);
         if (mane->dryRun)
@@ -2288,7 +2291,7 @@ static rc_t ItemSetDependency(Item *self,
                 v->path = remote;
             }
             if (rc == 0) {
-                char path[PATH_MAX] = "";
+                char path[URL_MAX] = "";
                 size_t len = 0;
                 rc = VPathReadUri(v->path,
                     path, sizeof path, &len);
@@ -2383,7 +2386,7 @@ static rc_t _ItemSetResolverAndAccessionInResolved(Item *item,
                 else if ( StringEqual ( & scheme, & fasp ) )
                     remote = & resolved -> remoteFasp ;
                 if ( remote != NULL ) {
-                    char path[PATH_MAX] = "";
+                    char path[URL_MAX] = "";
                     size_t len = 0;
                     remote -> path = resolved -> accession;
                     rc = VPathReadUri(resolved->accession,

tools/external/ref-variation/test/CMakeLists.txt

@@ -23,6 +23,6 @@
 # ===========================================================================
 
 if ( NOT WIN32)
-	add_test ( NAME Ref-Variation-1.0 WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND ./have-access.sh ${CMAKE_RUNTIME_OUTPUT_DIRECTORY} ref-variation )
-	add_test ( NAME Var-Expand-1.0    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND ./have-access.sh ${CMAKE_RUNTIME_OUTPUT_DIRECTORY} var-expand )
+	add_test ( NAME Ref-Variation-1.0 WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND sh ./have-access.sh ${CMAKE_RUNTIME_OUTPUT_DIRECTORY} ref-variation )
+	add_test ( NAME Var-Expand-1.0    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND sh ./have-access.sh ${CMAKE_RUNTIME_OUTPUT_DIRECTORY} var-expand )
 endif()