--- /dev/null
+From d615c51fb9fe6172a84feea47906abd164198fd5 Mon Sep 17 00:00:00 2001
+From: ucko <ucko@ncbi.nlm.nih.gov>
+Date: Thu, 18 Jul 2024 18:33:56 +0000
+Subject: [PATCH] Allow substituting PCRE2 for legacy PCRE by explicit request.
+
+- For now, require opt-in via --with-components="...;PCRE2;..." (CMake),
+ --with-pcre2 (traditional Unix build system), or uncommenting the
+ relevant ThirdParty_PCRE2 setting in project_tree_builder.ini
+ (traditional Windows build system).
+- Likewise, hold off on switching the bundled copy to PCRE2 or checking
+ for any functions or headers that will become of interest.
+- Redundantly (for now) shun external PCRE2 in bin-release configurations.
+- Otherwise favor (allowed!) external installations over the bundled
+ copy, preferring PCRE2 over legacy PCRE when both are found and
+ allowed but (in due course) external legacy PCRE over bundled PCRE2 in
+ the absence of external PCRE2.
+- In the traditional build system, have the widely used PCRE_LIBS macro
+ correspond to whichever PCRE is default (when not falling back on a
+ bundled copy), and add a PCRE_LEGACY_LIBS macro for the sake of
+ anything using legacy PCRE directly (very occasionally seen).
+
+JIRA: CXX-12761,
+
+git-svn-id: https://anonsvn.ncbi.nlm.nih.gov/repos/v1/trunk/c++@102806 78c7ea69-d796-4a43-9a09-de51944f1b03
+
+Irrelevant (and inapplicable) changes to c++/src/build-system/cmake/,
+c++/src/build-system/configure (which will be regenerated anyway), and
+c++/src/build-system/project_tree_builder.ini elided.
+---
+ include/util/xregexp/regexp.hpp | 13 +-
+ src/build-system/Makefile.mk.in | 3 +
+ .../cmake/CMake.NCBIComponents.cmake | 2 +-
+ .../cmake/CMake.NCBIComponentsMSVC.cmake | 17 +-
+ .../cmake/CMake.NCBIComponentsPackage.cmake | 10 +-
+ .../cmake/CMake.NCBIComponentsUNIXex.cmake | 18 +-
+ .../cmake/CMake.NCBIComponentsXCODE.cmake | 9 +
+ .../cmake/CMakeChecks.compiler.cmake | 1 +
+ src/build-system/cmake/conanfile.py | 2 +
+ src/build-system/cmake/config.cmake.h.in | 3 +
+ src/build-system/config.h.in | 3 +
+ src/build-system/configure | 181 +++++++++++++++++-
+ src/build-system/configure.ac | 34 +++-
+ src/build-system/project_tree_builder.ini | 21 ++
+ src/util/xregexp/CMakeLists.txt | 7 +-
+ src/util/xregexp/Makefile.xregexp.lib | 6 +-
+ src/util/xregexp/regexp.cpp | 69 ++++++-
+ 17 files changed, 376 insertions(+), 23 deletions(-)
+
+--- a/c++/include/util/xregexp/regexp.hpp
++++ b/c++/include/util/xregexp/regexp.hpp
+@@ -70,7 +70,11 @@ class NCBI_XREGEXP_EXPORT CRegexp
+ {
+ public:
+ /// Element type for GetResults().
++#ifdef HAVE_LIBPCRE2
++ typedef size_t TOffset;
++#else
+ typedef int TOffset;
++#endif
+
+ /// Type definitions used for code clarity.
+ typedef unsigned int TCompile; ///< Compilation options.
+@@ -287,13 +291,20 @@ private:
+ void x_Match(CTempString str, size_t offset, TMatch flags);
+
+ void* m_PReg; /// Pointer to compiled PCRE pattern.
+- void* m_Extra; /// Pointer to extra structure used for pattern study.
+
++#ifdef HAVE_LIBPCRE2
++ void* m_MatchData;
++ TOffset* m_Results;
++ int m_JITStatus;
++#else
++ void* m_Extra; /// Pointer to extra structure used for pattern study.
+
+ /// Array of locations of patterns/subpatterns resulting from
+ /// the last call to GetMatch(). Also contains 1/3 extra space used
+ /// internally by the PCRE C library.
+ int m_Results[(kRegexpMaxSubPatterns +1) * 3];
++#endif
++
+
+ /// The total number of pattern + subpatterns resulting from
+ /// the last call to GetMatch.
+--- a/c++/src/build-system/Makefile.mk.in
++++ b/c++/src/build-system/Makefile.mk.in
+@@ -390,6 +390,9 @@ CMPRS_LIB = $(Z_LIB) $(BZ2_LIB) $(ZS
+ # wrapper and goes by the name "regexp".
+ PCRE_INCLUDE = @PCRE_INCLUDE@
+ PCRE_LIBS = @PCRE_LIBS@
++PCRE_LEGACY_LIBS = @PCRE_LEGACY_LIBS@
++PCRE2_INCLUDE = @PCRE2_INCLUDE@
++PCRE2_LIBS = @PCRE2_LIBS@
+ PCREPOSIX_LIBS = @PCREPOSIX_LIBS@
+ PCRE_LIB = @PCRE_LIB@
+
+--- a/c++/src/build-system/config.h.in
++++ b/c++/src/build-system/config.h.in
+@@ -486,6 +486,9 @@
+ /* Define to 1 if libpcre is available. */
+ #undef HAVE_LIBPCRE
+
++/* Define to 1 if libpcre2 is available. */
++#undef HAVE_LIBPCRE2
++
+ /* Define to 1 if libpng is available. */
+ #undef HAVE_LIBPNG
+
+--- a/c++/src/build-system/configure.ac
++++ b/c++/src/build-system/configure.ac
+@@ -90,7 +90,7 @@ case "$with_3psw" in
+ with_yaml_cpp=no
+ fi
+ m4_foreach(X, [sss, sssutils, sssdb, vdb, ngs, ncbicrypt, libunwind,
+- z, bz2, lzo, zstd, pcre, mbedtls,
++ z, bz2, lzo, zstd, pcre, pcre2, mbedtls,
+ gmp, gcrypt, nettle, gnutls, openssl, krb5, boost, lmdb,
+ sybase, ftds, mysql, opengl, mesa, glut, glew, gl2ps,
+ wxwidgets, freetype, ftgl, fastcgi, fastcgipp,
+@@ -324,6 +324,10 @@ AC_ARG_WITH(pcre,
+ [ --with-pcre=DIR use PCRE installation in DIR])
+ AC_ARG_WITH(pcre,
+ [ --without-pcre use internal copy of PCRE])
++AC_ARG_WITH(pcre2,
++ [ --with-pcre2=DIR use PCRE2 installation in DIR])
++AC_ARG_WITH(pcre,
++ [ --without-pcre2 do not use PCRE2])
+ AC_ARG_WITH(mbedtls,
+ [ --with-mbedtls(=DIR) use external mbedTLS installation (in DIR)])
+ AC_ARG_WITH(gmp,
+@@ -728,7 +732,7 @@ ncbi-c wxwidgets wxwidgets-ucs fastcgi f
+ sss sssdb sssutils included-sss \
+ geo included-geo vdb downloaded-vdb static-vdb ngs ncbicrypt libunwind libdw \
+ backward-cpp backward-cpp-sig \
+-z bz2 lzo zstd pcre mbedtls \
++z bz2 lzo zstd pcre pcre2 mbedtls \
+ gmp gcrypt nettle gnutls static-gnutls openssl krb5 \
+ sybase sybase-local sybase-new ftds mysql \
+ orbacus freetype ftgl opengl mesa glut glew glew-mx gl2ps \
+@@ -798,7 +802,7 @@ for x_arg in "$@" ; do
+ | --with-ncbicrypt=* \
+ | --with-libunwind=* | --with-libdw=* | --with-backward-cpp=* \
+ | --with-z=* | --with-bz2=* | --with-lzo=* | --with-zstd=* \
+- | --with-pcre=* | --with-mbedtls=* \
++ | --with-pcre=* | --with-pcre2=* | --with-mbedtls=* \
+ | --with-gmp=* | --with-gcrypt=* | --with-nettle=* \
+ | --with-gnutls=* | --with-openssl=* | --with-krb5=* \
+ | --with-sybase-local=* | --with-ftds=*/* | --with-mysql=* \
+@@ -892,6 +896,7 @@ if test "$with_bin_release" = "yes" ; th
+ : ${with_libdw=no}
+ : ${with_ncbicrypt=no}
+ : ${with_pcre=no} # Too much variation across distributions.
++ : ${with_pcre2=no}
+ : ${with_sse42=no}
+ AC_DEFINE(NCBI_BIN_RELEASE, 1,
+ [Define to 1 when building binaries for public release.])
+@@ -4832,7 +4837,18 @@ fi
+ NCBI_CHECK_THIRD_PARTY_LIB(pcre,
+ [AC_LANG_PROGRAM([@%:@include <pcre.h>],
+ [[const char*s[]={"x"}; pcre* p; pcre_extra* x = pcre_study(p, 1, s);]])])
+-if test -z "$PCRE_LIBS"; then
++
++: ${with_pcre2=no}
++NCBI_CHECK_THIRD_PARTY_LIB_EX(pcre2, PCRE2, pcre2-8,
++ [AC_LANG_PROGRAM([@%:@define PCRE2_CODE_UNIT_WIDTH 8
++ @%:@include <pcre2.h>],
++ [[pcre2_config(123, NULL);]])])
++PCRE_LEGACY_LIBS=$PCRE_LIBS
++if test "x$with_pcre2" != xno; then
++ PCRE_LIBS=$PCRE2_LIBS
++fi
++
++if test -z "$PCRE_LIBS" -a -z "$PCRE2_LIBS"; then
+ pcrelocal=util/regexp
+ AC_MSG_NOTICE([using local PCRE copy in $pcrelocal])
+ PCRE_PATH="<$pcrelocal>"
+@@ -4841,8 +4857,15 @@ if test -z "$PCRE_LIBS"; then
+ # PCREPOSIX_LIBS="-lregexp"
+ PCRE_LIB="regexp"
+ AC_DEFINE(USE_LOCAL_PCRE, 1, [Define to 1 if using a local copy of PCRE.])
+- NCBI_PACKAGE(PCRE)
++ if test -f $srcdir/include/$pcrelocal/pcre2.h; then
++ AC_DEFINE(HAVE_LIBPCRE2, 1, [Define to 1 if libpcre2 is available.])
++ NCBI_PACKAGE(PCRE2)
++ else
++ NCBI_PACKAGE(PCRE)
++ fi
+ NCBI_PACKAGE(LocalPCRE)
++elif test -n "$PCRE2_LIBS"; then
++ PCREPOSIX_LIBS=`echo "$PCRE2_LIBS" | sed -e 's/-lpcre2-8/-lpcre2posix &/'`
+ else
+ PCREPOSIX_LIBS=`echo "$PCRE_LIBS" | sed -e 's/-lpcre/-lpcreposix -lpcre/'`
+ fi
+@@ -9765,6 +9788,7 @@ AC_SUBST(BZ2_LIB)
+ AC_SUBST(ZSTD_STATIC_LIBS)
+ AC_SUBST(PCREPOSIX_LIBS)
+ AC_SUBST(PCRE_LIB)
++AC_SUBST(PCRE_LEGACY_LIBS)
+ AC_SUBST(OPENSSL_STATIC_LIBS)
+ AC_SUBST(CURL_STATIC_LIBS)
+ AC_SUBST(SYBASE_PATH)
+--- a/c++/src/util/xregexp/CMakeLists.txt
++++ b/c++/src/util/xregexp/CMakeLists.txt
+@@ -1,6 +1,11 @@
+ # $Id: CMakeLists.txt 621427 2020-12-11 14:26:55Z ivanov $
+
+ NCBI_project_tags(core)
+-NCBI_requires(PCRE)
++# NCBI_optional_components(PCRE PCRE2)
++if(NCBI_COMPONENT_PCRE2_FOUND)
++ NCBI_REQUIRES(PCRE2)
++else()
++ NCBI_REQUIRES(PCRE)
++endif()
+ NCBI_add_library(xregexp xregexp_template_tester)
+
+--- a/c++/src/util/xregexp/Makefile.xregexp.lib
++++ b/c++/src/util/xregexp/Makefile.xregexp.lib
+@@ -3,12 +3,12 @@
+ SRC = regexp arg_regexp mask_regexp convert_dates_iso8601
+ LIB = xregexp
+
+-CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
++CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE) $(PCRE2_INCLUDE)
+
+ DLL_LIB = $(PCRE_LIB) xutil
+-LIBS = $(PCRE_LIBS)
++LIBS = $(PCRE_LIBS) $(PCRE2_LIBS)
+
+ USES_LIBRARIES = \
+- $(PCRE_LIB) $(PCRE_LIBS) xncbi
++ $(PCRE_LIB) $(PCRE_LIBS) $(PCRE2_LIBS) xncbi
+
+ WATCHERS = ivanov
+--- a/c++/src/util/xregexp/regexp.cpp
++++ b/c++/src/util/xregexp/regexp.cpp
+@@ -34,8 +34,14 @@
+ #include <corelib/ncbi_limits.h>
+ #include <corelib/ncbistl.hpp>
+ #include <util/xregexp/regexp.hpp>
+-#include <pcre.h>
+-#define PCRE_FLAG(x) PCRE_##x
++#ifdef HAVE_LIBPCRE2
++# define PCRE2_CODE_UNIT_WIDTH 8
++# include <pcre2.h>
++# define PCRE_FLAG(x) PCRE2_##x
++#else
++# include <pcre.h>
++# define PCRE_FLAG(x) PCRE_##x
++#endif
+
+ #include <memory>
+ #include <stdlib.h>
+@@ -103,7 +109,15 @@ static int s_GetRealMatchFlags(CRegexp::
+
+
+ CRegexp::CRegexp(CTempStringEx pattern, TCompile flags)
+- : m_PReg(NULL), m_Extra(NULL), m_NumFound(0)
++ : m_PReg(NULL),
++#ifdef HAVE_LIBPCRE2
++ m_MatchData(NULL),
++ m_Results(NULL),
++ m_JITStatus(PCRE2_ERROR_UNSET),
++#else
++ m_Extra(NULL),
++#endif
++ m_NumFound(0)
+ {
+ Set(pattern, flags);
+ }
+@@ -111,33 +125,63 @@ CRegexp::CRegexp(CTempStringEx pattern,
+
+ CRegexp::~CRegexp()
+ {
++#ifdef HAVE_LIBPCRE2
++ pcre2_code_free((pcre2_code*)m_PReg);
++ pcre2_match_data_free((pcre2_match_data*)m_MatchData);
++#else
+ (*pcre_free)(m_PReg);
+ (*pcre_free)(m_Extra);
++#endif
+ }
+
+
+ void CRegexp::Set(CTempStringEx pattern, TCompile flags)
+ {
+ if ( m_PReg ) {
++#ifdef HAVE_LIBPCRE2
++ pcre2_code_free((pcre2_code*)m_PReg);
++#else
+ (*pcre_free)(m_PReg);
++#endif
+ }
++#ifdef HAVE_LIBPCRE2
++ int err_num;
++#else
+ const char *err;
++#endif
+ TOffset err_offset;
+ int x_flags = s_GetRealCompileFlags(flags);
+
++#ifdef HAVE_LIBPCRE2
++ m_PReg = pcre2_compile((PCRE2_SPTR) pattern.data(), pattern.size(),
++ x_flags, &err_num, &err_offset, NULL);
++#else
+ if ( pattern.HasZeroAtEnd() ) {
+ m_PReg = pcre_compile(pattern.data(), x_flags, &err, &err_offset, NULL);
+ } else {
+ m_PReg = pcre_compile(string(pattern).c_str(), x_flags, &err, &err_offset, NULL);
+ }
++#endif
+ if ( !m_PReg ) {
++#ifdef HAVE_LIBPCRE2
++ char err[120];
++ pcre2_get_error_message(err_num, (PCRE2_UCHAR*) err, ArraySize(err));
++#endif
+ NCBI_THROW(CRegexpException, eCompile, "Compilation of the pattern '" +
+ string(pattern) + "' failed: " + err);
+ }
++#ifdef HAVE_LIBPCRE2
++ pcre2_match_data_free((pcre2_match_data*)m_MatchData);
++ m_MatchData = pcre2_match_data_create_from_pattern((pcre2_code*)m_PReg,
++ NULL);
++ // Too heavyweight to use by default; a flag may be in order.
++ // m_JITStatus = pcre2_jit_compile((pcre2_code*)m_PReg, PCRE2_JIT_COMPLETE);
++#else
+ if ( m_Extra ) {
+ (*pcre_free)(m_Extra);
+ }
+ m_Extra = pcre_study((pcre*)m_PReg, 0, &err);
++#endif
+ }
+
+
+@@ -158,8 +202,12 @@ CTempString CRegexp::GetSub(CTempString
+ if ( (int)idx >= m_NumFound ) {
+ return CTempString();
+ }
++#ifdef HAVE_LIBPCRE2
++ static const PCRE2_SIZE kNotFound = PCRE2_UNSET;
++#else
+ static const int kNotFound = -1;
+- const int * offsets = m_Results;
++#endif
++ const auto * offsets = m_Results;
+ auto start = offsets[2 * idx];
+ auto end = offsets[2 * idx + 1];
+ if (start == kNotFound || end == kNotFound) {
+@@ -172,10 +220,23 @@ CTempString CRegexp::GetSub(CTempString
+ void CRegexp::x_Match(CTempString str, size_t offset, TMatch flags)
+ {
+ int x_flags = s_GetRealMatchFlags(flags);
++#ifdef HAVE_LIBPCRE2
++ auto f = (m_JITStatus == 0) ? &pcre2_jit_match : &pcre2_match;
++ auto *match_data = (pcre2_match_data*) m_MatchData;
++ int rc = (*f)((pcre2_code*) m_PReg, (PCRE2_UCHAR*)str.data(), str.length(),
++ offset, x_flags, match_data, NULL);
++ m_Results = pcre2_get_ovector_pointer(match_data);
++ if (rc >= 0) {
++ m_NumFound = pcre2_get_ovector_count(match_data);
++ } else {
++ m_NumFound = -1;
++ }
++#else
+ m_NumFound = pcre_exec((pcre*)m_PReg, (pcre_extra*)m_Extra, str.data(),
+ (int)str.length(), (int)offset,
+ x_flags, m_Results,
+ (int)(kRegexpMaxSubPatterns +1) * 3);
++#endif
+ }
+
+
projects / ncbi-blast+.git / commitdiff