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fix atom_to_term and increase sharing on CUDD stuff

This commit is contained in:
Vitor Santos Costa 2016-11-23 17:23:59 -06:00
parent 0be43c6525
commit f44ef18fed
32 changed files with 190 additions and 1579 deletions
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81
C/atomic.c
View File

@ -885,7 +885,6 @@ static Int string_concat3(USES_REGS1) {
Term t2, t3, ot;
Term tf = 0;
bool g1, g2, g3;
Atom at;
int l = push_text_stack();
restart_aux:
t1 = Deref(ARG1);
@ -909,7 +908,6 @@ restart_aux:
return cont_string_concat3(PASS_REGS1);
} else {
LOCAL_Error_TYPE = INSTANTIATION_ERROR;
at = NULL;
}
if (tf) {
if (Yap_unify(ot, tf)) {
@ -1880,14 +1878,13 @@ static Int cont_sub_atomic(USES_REGS1) {
size_t minv, len, after, sz;
wchar_t *wp = NULL;
const unsigned char *p = NULL, *p5 = NULL;
bool sub_atom = TRUE;
mask = IntegerOfTerm(EXTRA_CBACK_ARG(5, 1));
minv = IntegerOfTerm(EXTRA_CBACK_ARG(5, 2));
len = IntegerOfTerm(EXTRA_CBACK_ARG(5, 3));
after = IntegerOfTerm(EXTRA_CBACK_ARG(5, 4));
sz = IntegerOfTerm(EXTRA_CBACK_ARG(5, 5));
if (!IsVarTerm(tat1)) {
if (IsAtomTerm(tat1)) {
p = AtomOfTerm(tat1)->UStrOfAE;
@ -1907,7 +1904,7 @@ static Int cont_sub_atomic(USES_REGS1) {
bool found = false;
{
const unsigned char *p1 = p;
while (!found) {
p = skip_utf8(p1, minv);
if (cmpn_utf8(p, p5, len) == 0) {
@ -2219,6 +2216,73 @@ static Int cont_sub_atomic(USES_REGS1) {
return sub_atomic(false, true PASS_REGS);
}
static Int atomic_to_term(USES_REGS1) {
Term t1 = Deref(ARG1), rc;
const char *s;
size_t len;
if (IsVarTerm(t1)) {
Yap_Error(INSTANTIATION_ERROR, t1, "read_term_from_string/3");
return (FALSE);
} else if (!IsAtomicTerm(t1)) {
Yap_Error(TYPE_ERROR_ATOMIC, t1, "read_term_from_atomic/3");
return (FALSE);
} else {
Term t = Yap_AtomicToString(t1 PASS_REGS);
s = (const char *)UStringOfTerm(t);
len = strlen_utf8((unsigned char *)s);
}
encoding_t enc = ENC_ISO_UTF8;
rc = Yap_StringToTerm(s, len, &enc, 1200, ARG3);
if (!rc)
return false;
return Yap_unify(rc, ARG2);
}
static Int atom_to_term(USES_REGS1) {
Term t1 = Deref(ARG1), rc;
const char *s;
size_t len;
if (IsVarTerm(t1)) {
Yap_Error(INSTANTIATION_ERROR, t1, "read_term_from_string/3");
return (FALSE);
} else if (!IsAtomTerm(t1)) {
Yap_Error(TYPE_ERROR_ATOM, t1, "read_term_from_atomic/3");
return (FALSE);
} else {
Term t = Yap_AtomicToString(t1 PASS_REGS);
s = StringOfTerm(t);
len = strlen_utf8((const unsigned char *)s);
}
encoding_t enc = ENC_ISO_UTF8;
rc = Yap_StringToTerm(s, len, &enc, 1200, ARG3);
if (!rc)
return false;
return Yap_unify(rc, ARG2);
}
static Int string_to_term(USES_REGS1) {
Term t1 = Deref(ARG1), rc;
const char *s;
size_t len;
if (IsVarTerm(t1)) {
Yap_Error(INSTANTIATION_ERROR, t1, "read_term_from_string/3");
return (FALSE);
} else if (!IsStringTerm(t1)) {
Yap_Error(TYPE_ERROR_STRING, t1, "read_term_from_string/3");
return (FALSE);
} else {
s = StringOfTerm(t1);
len = strlen_utf8((const unsigned char *)s);
}
encoding_t enc = ENC_ISO_UTF8;
rc = Yap_StringToTerm(s, len, &enc, 1200, ARG3);
if (!rc)
return false;
return Yap_unify(rc, ARG2);
}
static Int cont_current_atom(USES_REGS1) {
Atom catom;
Int i = IntOfTerm(EXTRA_CBACK_ARG(1, 2));
@ -2357,6 +2421,11 @@ static Int cont_sub_atomic(USES_REGS1) {
*/
Yap_InitCPred("atom_to_term", 3, atom_to_term, 0);
Yap_InitCPred("atomic_to_term", 3, atomic_to_term, 0);
Yap_InitCPred("string_to_term", 3, string_to_term, 0);
Yap_InitCPred("atom_chars", 2, atom_chars, 0);
/** @pred atom_chars(? _A_,? _L_) is iso

13
C/c_interface.c
View File

@ -452,7 +452,7 @@ X_API Atom YAP_LookupAtom(const char *c) {
X_API Atom YAP_LookupWideAtom(const wchar_t *c) {
CACHE_REGS
Atom a;
while (TRUE) {
a = Yap_NWCharsToAtom(c, -1 USES_REGS);
@ -1187,10 +1187,10 @@ Int YAP_ExecuteOnCut(PredEntry *pe, CPredicate exec_code,
Yap_CloseSlots(CurSlot);
PP = NULL;
// B = LCL0-(CELL*)oB;
if (false && Yap_RaiseException()) {
if (!val && Yap_RaiseException()) {
return false;
} else { /* TRUE */
return true;
return val;
}
}
@ -1373,12 +1373,13 @@ X_API Term YAP_NWideBufferToString(const wchar_t *s, size_t len) {
/* copy a string to a buffer */
X_API Term YAP_ReadBuffer(const char *s, Term *tp) {
CACHE_REGS
Term t;
Term tv, t;
BACKUP_H();
if (*tp) tv = *tp; else tv = 0;
LOCAL_ErrorMessage = NULL;
while (!(t = Yap_StringToTerm(s, strlen(s) + 1, &LOCAL_encoding,
GLOBAL_MaxPriority, tp))) {
GLOBAL_MaxPriority,tv))) {
if (LOCAL_ErrorMessage) {
if (!strcmp(LOCAL_ErrorMessage, "Stack Overflow")) {
if (!Yap_dogc(0, NULL PASS_REGS)) {
@ -2306,7 +2307,7 @@ YAP_file_type_t YAP_Init(YAP_init_args *yap_init) {
GLOBAL_PrologShouldHandleInterrupts = yap_init->PrologShouldHandleInterrupts;
Yap_InitSysbits(0); /* init signal handling and time, required by later
functions */
GLOBAL_argv = yap_init->Argv;
GLOBAL_argv = yap_init->Argv;
GLOBAL_argc = yap_init->Argc;
if (0 && ((YAP_QLY && yap_init->SavedState) ||
(YAP_BOOT_PL && (yap_init->YapPrologBootFile)))) {

4
C/cdmgr.c
View File

@ -1447,11 +1447,7 @@ static int not_was_reconsulted(PredEntry *p, Term t, int mode) {
static void addcl_permission_error(AtomEntry *ap, Int Arity, int in_use) {
CACHE_REGS
Term t, ti[2];
ti[0] = MkAtomTerm(AbsAtom(ap));
ti[1] = MkIntegerTerm(Arity);
t = Yap_MkApplTerm(FunctorSlash, 2, ti);
LOCAL_Error_TYPE = PERMISSION_ERROR_MODIFY_STATIC_PROCEDURE;
LOCAL_ErrorMessage = Malloc( 256 );

5
C/compiler.c
View File

@ -1093,7 +1093,7 @@ static void c_bifun(basic_preds Op, Term t1, Term t2, Term t3, Term Goal,
char s[32];
Yap_bip_name(Op, s);
Yap_ThrowError(INSTANTIATION_ERROR , t2, "compiling %s/3", s);
Yap_ThrowError(INSTANTIATION_ERROR , t2, "compiling %s/3", s);
save_machine_regs();
siglongjmp(cglobs->cint.CompilerBotch, 1);
}
@ -1110,9 +1110,10 @@ static void c_bifun(basic_preds Op, Term t1, Term t2, Term t3, Term Goal,
i2 = IntegerOfTerm(t2);
if (i2 < 0) {
Yap_ThrowError(DOMAIN_ERROR_NOT_LESS_THAN_ZERO , t2,4, "compiling functor/3");
Yap_ThrowError(DOMAIN_ERROR_NOT_LESS_THAN_ZERO , t2, "compiling functor/3");
save_machine_regs();
siglongjmp(cglobs->cint.CompilerBotch, 1);
}
if (IsNumTerm(t1)) {
/* we will always fail */

6
C/errors.c
View File

@ -311,11 +311,11 @@ yap_error_descriptor_t *Yap_popErrorContext(void) {
}
void Yap_ThrowError__(const char *file, const char *function, int lineno,
yap_error_number type, Term where, int code, ...) {
yap_error_number type, Term where, ...) {
va_list ap;
char tmpbuf[MAXPATHLEN];
va_start(ap, code);
va_start(ap, where);
char *format = va_arg(ap, char *);
if (format != NULL) {
#if HAVE_VSNPRINTF
@ -328,7 +328,7 @@ Yap_Error__(file, function, lineno, type, where, tmpbuf);
} else {
Yap_Error__(file, function, lineno, type, where);
}
siglongjmp(LOCAL_RestartEnv, code);
siglongjmp(LOCAL_RestartEnv, 4);
}
/**

6
C/exec.c
View File

@ -1023,7 +1023,6 @@ static Int protect_stack(USES_REGS1) {
static Int setup_call_catcher_cleanup(USES_REGS1) {
Term Setup = Deref(ARG1);
Term cmod = CurrentModule;
Int oENV = LCL0 - ENV;
choiceptr B0 = B;
Term t3, t4;
@ -1051,8 +1050,6 @@ static Int setup_call_catcher_cleanup(USES_REGS1) {
prune_inner_computation(B0);
}
// at this point starts actual goal execution....
cmod = CurrentModule;
rc = Yap_RunTopGoal(Yap_GetFromSlot(h2), false);
complete_inner_computation(B);
t4 = Yap_GetFromSlot(h4);
@ -2010,7 +2007,7 @@ bool is_cleanup_cp(choiceptr cp_b) {
}
static Int JumpToEnv() {
choiceptr handler = B, oh = NULL;
choiceptr handler = B;
/* just keep the throwm object away, we don't need to care about it
*/
/* careful, previous step may have caused a stack shift,
@ -2028,7 +2025,6 @@ static Int JumpToEnv() {
handler->cp_b == NULL)) {
break;
}
oh = handler;
handler = handler->cp_b;
}
if (LOCAL_PrologMode & AsyncIntMode) {

18
C/flags.c
View File

@ -182,7 +182,7 @@ static Term stream(Term inp) {
}
static bool
static bool
set_error_stream( Term inp ) {
if( IsVarTerm(inp) )
return Yap_unify( inp, Yap_StreamUserName( LOCAL_c_error_stream ) );
@ -191,7 +191,7 @@ set_error_stream( Term inp ) {
return true;
}
static bool
static bool
set_input_stream( Term inp ) {
if( IsVarTerm(inp) )
return Yap_unify( inp, Yap_StreamUserName( LOCAL_c_input_stream ) );
@ -199,7 +199,7 @@ set_input_stream( Term inp ) {
return true;
}
static bool
static bool
set_output_stream( Term inp ) {
if( IsVarTerm(inp) )
return Yap_unify( inp, Yap_StreamUserName( LOCAL_c_output_stream ) );
@ -870,7 +870,7 @@ static Int cont_prolog_flag(USES_REGS1) {
}
EXTRA_CBACK_ARG(3, 1) = MkIntTerm(++i);
flag = getYapFlag(f);
if (!Yap_unify(f, ARG2))
if (!Yap_unify(flag, ARG2))
return false;
return setYapFlag(f, Deref(ARG3));
}
@ -1175,7 +1175,7 @@ static Int source_mode(USES_REGS1) {
if (!current && !Yap_unify_constant(ARG1, TermFalse))
return false;
targ = Deref(ARG2);
setYapFlag(TermSource, ARG2);
setYapFlag(TermSource, targ);
return true;
}
@ -1319,7 +1319,7 @@ static bool setInitialValue(bool bootstrap, flag_func f, const char *s,
CACHE_REGS
encoding_t encoding = ENC_ISO_UTF8;
t0 =
Yap_StringToTerm(s, strlen(s) + 1, &encoding, GLOBAL_MaxPriority, NULL);
Yap_StringToTerm(s, strlen(s) + 1, &encoding, GLOBAL_MaxPriority, 0L);
if (!t0)
return false;
if (IsAtomTerm(t0) || IsIntTerm(t0)) {
@ -1434,7 +1434,7 @@ do_prolog_flag_property(Term tflag,
}
}
// UNLOCK(GLOBAL_Prolog_Flag[sno].prolog_flaglock);
free(args);
free(args);
return rc;
}
@ -1540,7 +1540,7 @@ static Int do_create_prolog_flag(USES_REGS1) {
if (fv) {
if (args[PROLOG_FLAG_PROPERTY_KEEP].used &&
args[PROLOG_FLAG_PROPERTY_KEEP].tvalue == TermTrue) {
free(args);
free(args);
return true;
}
} else {
@ -1633,7 +1633,7 @@ void Yap_InitFlags(bool bootstrap) {
if (GLOBAL_Stream[StdInStream].status & Readline_Stream_f) {
setBooleanGlobalPrologFlag(READLINE_FLAG, true);
}
if (!bootstrap) {
Yap_InitCPredBack("current_prolog_flag", 2, 1, current_prolog_flag,
cont_yap_flag, 0);

6
C/text.c
View File

@ -731,7 +731,7 @@ static Term write_number(unsigned char *s, seq_tv_t *out, int size, bool error_o
static Term string_to_term(void *s, seq_tv_t *out, size_t leng USES_REGS) {
Term o;
o = out->val.t =
Yap_StringToTerm(s, strlen(s) + 1, &out->enc, GLOBAL_MaxPriority, NULL);
Yap_StringToTerm(s, strlen(s) + 1, &out->enc, GLOBAL_MaxPriority, 0L);
return o;
}
@ -740,7 +740,7 @@ bool write_Text(unsigned char *inp, seq_tv_t *out, size_t leng USES_REGS) {
if (out->type == 0) {
return true;
}
if (out->type & YAP_STRING_TERM) {
if ((out->val.t = string_to_term(inp, out, leng PASS_REGS)) != 0L)
return out->val.t != 0;
@ -948,7 +948,7 @@ bool Yap_Concat_Text(int tot, seq_tv_t inp[], seq_tv_t *out USES_REGS) {
unsigned char *buf;
int i;
size_t leng;
bufv = Malloc(tot * sizeof(unsigned char *));
if (!bufv) {
return NULL;

2
CMakeLists.txt
View File

@ -53,6 +53,8 @@ if(NOT COMMAND find_host_program)
endmacro()
endif()
option(BUILD_SHARED_LIBS "Build shared library" ON)
include(Prelims NO_POLICY_SCOPE)
include(Sources NO_POLICY_SCOPE)

2
CXX/yapdb.hh
View File

@ -138,7 +138,7 @@ protected:
BACKUP_MACHINE_REGS();
Term *modp = NULL;
out = Yap_StringToTerm(s0, strlen(s0) + 1, &LOCAL_encoding, 1200, &names);
out = Yap_StringToTerm(s0, strlen(s0) + 1, &LOCAL_encoding, 1200, names);
// extern char *s0;
// fprintf(stderr,"ap=%p arity=%d text=%s", ap, ap->ArityOfPE, s);
// Yap_DebugPlWrite(out);

10
GIT
View File

@ -1,10 +0,0 @@
You need at least git-1.6 to install the development version.
Please proceed as follows for the main branch:
git clone git://gitorious.org/yap-git/mainline.git yap
cd yap-6
git submodule init
git submodule update

337
Untitled
View File

@ -1,337 +0,0 @@
Process: Python [88916]
Path: /System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Identifier: Python
Version: 2.7.10 (2.7.10)
Code Type: X86-64 (Native)
Parent Process: Atom Helper [88821]
Responsible: Atom [88817]
User ID: 501
Date/Time: 2016-06-12 12:40:34.078 +0100
OS Version: Mac OS X 10.11.5 (15F34)
Report Version: 11
Anonymous UUID: B8085CAA-5C3C-7B89-D7A4-E30E7D5EAC9C
Sleep/Wake UUID: ABD12798-599D-4E2A-8BAF-24F5ACC919E7
Time Awake Since Boot: 220000 seconds
Time Since Wake: 4000 seconds
System Integrity Protection: enabled
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000008
VM Regions Near 0x8:
-->
__TEXT 0000000105287000-0000000105288000 [ 4K] r-x/rwx SM=COW /System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 org.python.python 0x000000010532ffce 0x10528f000 + 659406
1 org.python.python 0x0000000105330481 PyGILState_Ensure + 55
2 com.apple.LLDB.framework 0x0000000108b1e37a lldb_private::ScriptInterpreterPython::Locker::DoAcquireLock() + 28
3 com.apple.LLDB.framework 0x0000000108b23a6b lldb_private::ScriptInterpreterPython::Clear() + 37
4 com.apple.LLDB.framework 0x000000010885e510 lldb_private::Debugger::Clear() + 266
5 com.apple.LLDB.framework 0x000000010885f8ec lldb_private::Debugger::~Debugger() + 28
6 com.apple.LLDB.framework 0x000000010885fc0e lldb_private::Debugger::~Debugger() + 14
7 libc++.1.dylib 0x00007fff91f31cb8 std::__1::__shared_weak_count::__release_shared() + 44
8 com.apple.LLDB.framework 0x00000001068a06cf std::__1::__vector_base<std::__1::shared_ptr<lldb_private::TypeImpl>, std::__1::allocator<std::__1::shared_ptr<lldb_private::TypeImpl> > >::~__vector_base() + 49
9 libsystem_c.dylib 0x00007fff9321246b __cxa_finalize_ranges + 345
10 libsystem_c.dylib 0x00007fff9321276f exit + 55
11 org.python.python 0x000000010533200c 0x10528f000 + 667660
12 org.python.python 0x0000000105331c45 PyErr_PrintEx + 41
13 org.python.python 0x0000000105331668 PyRun_SimpleFileExFlags + 750
14 org.python.python 0x0000000105343011 Py_Main + 3137
15 libdyld.dylib 0x00007fff8d16d5ad start + 1
Thread 1:
0 libsystem_kernel.dylib 0x00007fff9af6bf72 mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff9af6b3b3 mach_msg + 55
2 com.apple.CoreFoundation 0x00007fff95f861c4 __CFRunLoopServiceMachPort + 212
3 com.apple.CoreFoundation 0x00007fff95f8568c __CFRunLoopRun + 1356
4 com.apple.CoreFoundation 0x00007fff95f84ed8 CFRunLoopRunSpecific + 296
5 com.apple.CoreFoundation 0x00007fff95fc69b1 CFRunLoopRun + 97
6 com.apple.DebugSymbols 0x00007fff87a2c69a SpotlightQueryThread(void*) + 346
7 libsystem_pthread.dylib 0x00007fff9490e99d _pthread_body + 131
8 libsystem_pthread.dylib 0x00007fff9490e91a _pthread_start + 168
9 libsystem_pthread.dylib 0x00007fff9490c351 thread_start + 13
Thread 2:
0 libsystem_kernel.dylib 0x00007fff9af725e2 __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff9490e578 _pthread_wqthread + 1283
2 libsystem_pthread.dylib 0x00007fff9490c341 start_wqthread + 13
Thread 3:
0 libsystem_kernel.dylib 0x00007fff9af725e2 __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff9490e578 _pthread_wqthread + 1283
2 libsystem_pthread.dylib 0x00007fff9490c341 start_wqthread + 13
Thread 4:: Dispatch queue: com.apple.libdispatch-manager
0 libsystem_kernel.dylib 0x00007fff9af72efa kevent_qos + 10
1 libdispatch.dylib 0x00007fff87927165 _dispatch_mgr_invoke + 216
2 libdispatch.dylib 0x00007fff87926dcd _dispatch_mgr_thread + 52
Thread 5:
0 libsystem_kernel.dylib 0x00007fff9af725e2 __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff9490e578 _pthread_wqthread + 1283
2 libsystem_pthread.dylib 0x00007fff9490c341 start_wqthread + 13
Thread 6:
0 libsystem_kernel.dylib 0x00007fff9af725e2 __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff9490e578 _pthread_wqthread + 1283
2 libsystem_pthread.dylib 0x00007fff9490c341 start_wqthread + 13
Thread 7:
0 libsystem_kernel.dylib 0x00007fff9af725e2 __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff9490e578 _pthread_wqthread + 1283
2 libsystem_pthread.dylib 0x00007fff9490c341 start_wqthread + 13
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000001 rbx: 0x00007fb1e266bdb0 rcx: 0x00000b0000000000 rdx: 0x00007fb1e2403388
rdi: 0x00007fb1e2403368 rsi: 0x00000b0000000b00 rbp: 0x00007fff5a9785a0 rsp: 0x00007fff5a978580
r8: 0x00000000fffffffc r9: 0x00007fb1e2403380 r10: 0x00000000ffffffff r11: 0xffffffff00000000
r12: 0x0000000000000001 r13: 0x0000000000000000 r14: 0x0000000000000000 r15: 0x0000000000000001
rip: 0x000000010532ffce rfl: 0x0000000000010206 cr2: 0x0000000000000008
Logical CPU: 6
Error Code: 0x00000004
Trap Number: 14
Binary Images:
0x105287000 - 0x105287fff org.python.python (2.7.10 - 2.7.10) <307E6E15-ECF7-3BB2-AF06-3E8D23DFDECA> /System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
0x10528f000 - 0x105380ff7 org.python.python (2.7.10 - 2.7.10) <83AFAAA7-BDFA-354D-8A7A-8F40A30ACB91> /System/Library/Frameworks/Python.framework/Versions/2.7/Python
0x105746000 - 0x105747fff _locale.so (94) <4394AC91-22AE-3D7D-85C4-792A4F35F3F2> /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_locale.so
0x10580c000 - 0x10580dff7 time.so (94) <94E8BF2A-7841-32AD-8722-6B2526999CA1> /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/time.so
0x105814000 - 0x105816fff select.so (94) <22170D1C-40EF-303A-8BB7-A48E783F9350> /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/select.so
0x10581d000 - 0x10581efff fcntl.so (94) <419069D5-A61F-3925-B320-EA7B9E38F44B> /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/fcntl.so
0x105823000 - 0x105826fff _struct.so (94) <0DCC6B47-A763-3AA6-82C5-B6A58073286B> /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_struct.so
0x10582d000 - 0x10582ffff binascii.so (94) <9044E1C3-221F-3B79-847A-C9C3D8FEA9FD> /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/binascii.so
0x105834000 - 0x105835fff cStringIO.so (94) <EC2054BE-E4CD-38B3-BBFB-4FEFB76CF1EF> /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/cStringIO.so
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External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 11
thread_create: 0
thread_set_state: 0
Calls made by this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by all processes on this machine:
task_for_pid: 199747
thread_create: 0
thread_set_state: 9181
VM Region Summary:
ReadOnly portion of Libraries: Total=231.3M resident=0K(0%) swapped_out_or_unallocated=231.3M(100%)
Writable regions: Total=112.3M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=112.3M(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Activity Tracing 2048K 2
Dispatch continuations 16.0M 2
Kernel Alloc Once 4K 2
MALLOC 75.5M 22
MALLOC guard page 32K 7
STACK GUARD 56.0M 9
Stack 11.1M 16
VM_ALLOCATE 7448K 21
__DATA 11.8M 183
__LINKEDIT 101.5M 32
__TEXT 129.8M 182
__UNICODE 552K 2
mapped file 47.0M 49
shared memory 324K 9
=========== ======= =======
TOTAL 458.9M 524
Model: MacBookPro11,5, BootROM MBP114.0172.B09, 4 processors, Intel Core i7, 2,5 GHz, 16 GB, SMC 2.30f2
Graphics: AMD Radeon R9 M370X, AMD Radeon R9 M370X, PCIe, 2048 MB
Graphics: Intel Iris Pro, Intel Iris Pro, Built-In
Memory Module: BANK 0/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D54343147533642465238412D50422020
Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D54343147533642465238412D50422020
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x152), Broadcom BCM43xx 1.0 (7.21.95.175.1a6)
Bluetooth: Version 4.4.5f3 17904, 3 services, 27 devices, 1 incoming serial ports
Network Service: Wi-Fi, AirPort, en0
Serial ATA Device: APPLE SSD SM0512G, 500,28 GB
USB Device: USB 3.0 Bus
USB Device: Card Reader
USB Device: Apple Internal Keyboard / Trackpad
USB Device: Bluetooth USB Host Controller
Thunderbolt Bus: MacBook Pro, Apple Inc., 27.1

152
callcount.yap
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@ -1,152 +0,0 @@
/*************************************************************************
* *
* YAP Prolog *
* *
* Yap Prolog was developed at NCCUP - Universidade do Porto *
* *
* Copyright L.Damas, V.S.Costa and Universidade do Porto 1985-1997 *
* *
**************************************************************************
* *
* File: callcount.yap *
* Last rev: 8/2/02 *
* mods: *
* comments: Some profiling predicates available in yap *
* *
*************************************************************************/
%% @{
/** @defgroup Profiling Profiling Prolog Programs
@ingroup extensions
YAP includes two profilers. The count profiler keeps information on the
number of times a predicate was called. This information can be used to
detect what are the most commonly called predicates in the program. The
count profiler can be compiled by setting YAP's flag profiling
to `on`. The time-profiler is a `gprof` profiler, and counts
how many ticks are being spent on specific predicates, or on other
system functions such as internal data-base accesses or garbage collects.
The YAP profiling sub-system is currently under
development. Functionality for this sub-system will increase with newer
implementation.
*/
%% @{
/** @defgroup Call_Counting Counting Calls
@ingroup Profiling
Predicates compiled with YAP's flag call_counting set to
`on` update counters on the numbers of calls and of
retries. Counters are actually decreasing counters, so that they can be
used as timers. Three counters are available:
+ `calls`: number of predicate calls since execution started or since
system was reset;
+ `retries`: number of retries for predicates called since
execution started or since counters were reset;
+ `calls_and_retries`: count both on predicate calls and
retries.
These counters can be used to find out how many calls a certain
goal takes to execute. They can also be used as timers.
The code for the call counters piggybacks on the profiling
code. Therefore, activating the call counters also activates the profiling
counters.
These are the predicates that access and manipulate the call counters.
*/
:- system_module( '$_callcount', [call_count/3,
call_count_data/3,
call_count_reset/0], []).
:- use_system_module( '$_errors', ['$do_error'/2]).
/** @pred call_count_data(- _Calls_, - _Retries_, - _CallsAndRetries_)
Give current call count data. The first argument gives the current value
for the _Calls_ counter, next the _Retries_ counter, and last
the _CallsAndRetries_ counter.
*/
call_count_data(Calls, Retries, Both) :-
'$call_count_info'(Calls, Retries, Both).
/** @pred call_count_reset
Reset call count counters. All timers are also reset.
*/
call_count_reset :-
'$call_count_reset'.
/** @pred call_count(? _CallsMax_, ? _RetriesMax_, ? _CallsAndRetriesMax_)
Set call counters as timers. YAP will generate an exception
if one of the instantiated call counters decreases to 0:
+ _CallsMax_
throw the exception `call_counter` when the
counter `calls` reaches 0;
+ _RetriesMax_
throw the exception `retry_counter` when the
counter `retries` reaches 0;
+ _CallsAndRetriesMax_
throw the exception
`call_and_retry_counter` when the counter `calls_and_retries`
reaches 0.
YAP will ignore counters that are called with unbound arguments.
Next, we show a simple example of how to use call counters:
~~~~~{.prolog}
?- yap_flag(call_counting,on), [-user]. l :- l. end_of_file. yap_flag(call_counting,off).
yes
yes
?- catch((call_count(10000,_,_),l),call_counter,format("limit_exceeded.~n",[])).
limit_exceeded.
yes
~~~~~
Notice that we first compile the looping predicate `l/0` with
call_counting `on`. Next, we catch/3 to handle an
exception when `l/0` performs more than 10000 reductions.
*/
call_count(Calls, Retries, Both) :-
'$check_if_call_count_on'(Calls, CallsOn),
'$check_if_call_count_on'(Retries, RetriesOn),
'$check_if_call_count_on'(Both, BothOn),
'$call_count_set'(Calls, CallsOn, Retries, RetriesOn, Both, BothOn).
'$check_if_call_count_on'(Calls, 1) :- integer(Calls), !.
'$check_if_call_count_on'(Calls, 0) :- var(Calls), !.
'$check_if_call_count_on'(Calls, A) :-
'$do_error'(type_error(integer,Calls),call_count(A)).
%% @}
/**
@}
*/

25
cmake/Config.cmake
View File

@ -15,13 +15,15 @@ include(TestBigEndian)
include(GetGitRevisionDescription)
# modern systems do this.
set(MALLOC_T "void *")
OPTION(WITH_SYSTEM_MALLOC
"use malloc to allocate memory" ON)
OPTION(WITH_DL_MALLOC
"use malloc to allocate memory" OFF)
OPTION(WITH_YAP_MALLOC
"use malloc to allocate memory" OFF)
"use malloc to allocate mem
ory" OFF)
if (WITH_SYSTEM_MALLOC)
set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS USE_SYSTEM_MALLOC=1)
@ -144,6 +146,7 @@ endif (HAVE_LIBDL)
if (WIN32)
check_library_exists(comdlg32 FindText "" HAVE_LIBCOMDLG32)
if (HAVE_LIBCOMDLG32)
set(EXTRALIBS ${EXTRALIBS} comdlg32)
endif (HAVE_LIBCOMDLG32)
check_library_exists(msvcrt strtok "" HAVE_LIBMSCRT)
@ -215,6 +218,7 @@ if (HAVE_LIBPTHREAD)
endif (HAVE_LIBPTHREAD)
check_library_exists(unicode main "" HAVE_LIBUNICODE)
if (HAVE_LIBUNICODE)
set(EXTRALIBS ${EXTRALIBS} unicode)
@ -261,10 +265,8 @@ check_symbol_exists(flsll <string.h> HAVE_FLSLL)
check_function_exists(fmemopen HAVE_FMEMOPEN)
check_function_exists(fpclass HAVE_FPCLASS)
check_function_exists(ftime HAVE_FTIME)
check_function_exists(ftruncate HAVE_FTRUNCATE)
check_function_exists(funopen HAVE_FUNOPEN)
check_function_exists(gcc HAVE_GCC)
check_function_exists(getcwd HAVE_GETCWD)
check_function_exists(ftru
wd HAVE_GETCWD)
check_function_exists(getenv HAVE_GETENV)
check_function_exists(getexecname HAVE_GETEXECNAME)
check_function_exists(gethostbyname HAVE_GETHOSTBYNAME)
@ -321,7 +323,8 @@ check_function_exists(setlocale HAVE_SETLOCALE)
check_function_exists(setsid HAVE_SETSID)
check_function_exists(shmat HAVE_SHMAT)
check_function_exists(sigaction HAVE_SIGACTION)
check_symbol_exists(SIGFPE signal.h HAVE_SIGFPE)
check_symbol_exists(SI
GFPE signal.h HAVE_SIGFPE)
check_function_exists(siggetmask HAVE_SIGGETMASK)
check_symbol_exists(SIGINFO signal.h HAVE_SIGINFO)
check_function_exists(siginterrupt HAVE_SIGINTERRUPT)
@ -396,5 +399,13 @@ configure_file(${CMAKE_CURRENT_LIST_DIR}/../YapTermConfig.h.cmake
configure_file(${CMAKE_CURRENT_LIST_DIR}/../config.h.cmake
${CMAKE_BINARY_DIR}/config.h)
configure_file(${CMAKE_CURRENT_LIST_DIR}/../GitSHA1.c.in GitSHA1.c @ONLY)
configure_file(${CMAKE_CURRENT_LIST_DIR}/../os/YapIOConfig.h.cmake ${CMAKE_BINARY_DIR}/os/YapIOConfig.h)
check_include_files( "stdio.h;cudd.h" HAVE_CTYPE_HUDD_H )
check_include_files( "stdio.h;cuddI.h" HAVE_CUDD_H )
check_include_files( "cudd.h;cuddInt.h" HAVE_CUDDINT_H )
check_include_files( "stdio.h;cudd/cudd.h" HAVE_CUDD_CUDD_H )
check_include_files( "stdio.h;cudd/cuddInt.h" HAVE_CUDD_CUDDINT_H )
configure_file (cmake/cudd_config.h.cmake
"${CMAKE_CURRENT_BINARY_DIR}/cudd_config.h" )

7
cmake/cudd.cmake
View File

@ -1,5 +1,5 @@
option (WITH_CUDD "BDD CUDD package" ON)
if (WITH_CUDD)
@ -18,10 +18,7 @@ if (CUDD_FOUND)
set( CMAKE_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES} ${CUDD_INCLUDE_DIR} )
check_include_files( "stdio.h;cudd.h" HAVE_CUDD_H )
check_include_files( "stdio.h;cudd/cudd.h" HAVE_CUDD_CUDD_H )
check_include_files( "cuddInt.h" HAVE_CUDDINT_H )
check_include_files( "cudd/cuddInt.h" HAVE_CUDD_CUDDINT_H )
endif (CUDD_FOUND)
endif(WITH_CUDD)

0
packages/bdd/cudd_config.h.cmake → cmake/cudd_config.h.cmake
View File

14
example.py
View File

@ -1,14 +0,0 @@
# python commands
import yap
engine = yap.YAPEngine();
# engine = yap.YAPEngine(yap.YAPParams());
while True:
s = raw_input("Prolog Query: ")
q = engine.query(s)
print "success"
while q.next():
ar = q.namedVars();
print ar

0
heap_top_
View File

6
include/YapError.h
View File

@ -42,7 +42,7 @@ struct yami *Yap_Error__(const char *file, const char *function, int lineno,
yap_error_number err, YAP_Term wheret, ...);
void Yap_ThrowError__(const char *file, const char *function, int lineno,
yap_error_number err, YAP_Term wheret, int code, ...) __attribute__ ((noreturn));
yap_error_number err, YAP_Term wheret, ...) __attribute__ ((noreturn));
#define Yap_NilError(id, ...) \
@ -51,8 +51,8 @@ void Yap_ThrowError__(const char *file, const char *function, int lineno,
#define Yap_Error(id, inp, ...) \
Yap_Error__(__FILE__, __FUNCTION__, __LINE__, id, inp, __VA_ARGS__)
#define Yap_ThrowError(id, inp, code, ...) \
Yap_ThrowError__(__FILE__, __FUNCTION__, __LINE__, id, inp, code, __VA_ARGS__)
#define Yap_ThrowError(id, inp, ...) \
Yap_ThrowError__(__FILE__, __FUNCTION__, __LINE__, id, inp, __VA_ARGS__)
#ifdef YAP_TERM_H
/**

2
libYap.cmake
View File

@ -57,7 +57,7 @@ ENDIF("${isSystemDir}" STREQUAL "-1")
include_directories (H
H/generated
include os OPTYap utf8proc JIT/HPP)
include_directories (BEFORE ${CMAKE_BINARY_DIR})
include_directories (BEFORE ${CMAKE_BINARY_DIR} ${CMAKE_TOP_BINARY_DIR})
if (ANDROID)
include_directories (CXX ${CMAKE_SOURCE_DIR}/../generated/src/jni)

3
os/fmem.c
View File

@ -110,11 +110,10 @@ static char SccsId[] = "%W% %G%";
bool Yap_set_stream_to_buf(StreamDesc *st, const char *buf, size_t nchars) {
FILE *f;
stream_flags_t flags;
// like any file stream.
st->file = f = fmemopen((void *)buf, nchars, "r");
flags = Input_Stream_f | InMemory_Stream_f | Seekable_Stream_f;
st->status = Input_Stream_f | InMemory_Stream_f | Seekable_Stream_f;
Yap_DefaultStreamOps(st);
return true;
}

156
os/readterm.c
View File

@ -1211,26 +1211,23 @@ static Int style_checker(USES_REGS1) {
}
X_API Term Yap_StringToTerm(const char *s, size_t len, encoding_t *encp,
int prio, Term *bindings) {
int prio, Term bindings) {
CACHE_REGS
Term bvar = MkVarTerm(), ctl;
yhandle_t sl;
int lvl = push_text_stack();
Term ctl;
int lvl = push_text_stack();
if (len == 0) {
Term rval = TermEof;
if (rval && bindings) {
*bindings = TermNil;
rval = Yap_unify(bindings , TermNil );
}
pop_text_stack(lvl);
return rval;
}
if (bindings) {
ctl = Yap_MkApplTerm(Yap_MkFunctor(AtomVariableNames, 1), 1, &bvar);
sl = Yap_PushHandle(bvar);
ctl = Yap_MkApplTerm(Yap_MkFunctor(AtomVariableNames, 1), 1, &bindings);
} else {
ctl = TermNil;
sl = 0;
}
Term rval;
@ -1239,9 +1236,6 @@ X_API Term Yap_StringToTerm(const char *s, size_t len, encoding_t *encp,
rval = Yap_read_term(stream, ctl, 3);
Yap_CloseStream(stream);
UNLOCK(GLOBAL_Stream[stream].streamlock);
if (rval && bindings) {
*bindings = Yap_PopHandle(sl);
}
pop_text_stack(lvl);
return rval;
}
@ -1290,107 +1284,6 @@ Term Yap_AtomToTerm(Atom a, Term opts) {
return rval;
}
/**
* @pred read_term_from_string( +_String_ , - _T_ , + _Options_
*
* read a term _T_ stored in constant _String_ according to _Options_
*
* @param _String_ the source _String_
* @param _T_ the output term _T_, may be any term
* @param _Options_ read_term/3 options.
*
* @notes Idea from SWI-Prolog, in YAP only works with strings
* Check read_term_from_atomic/3 for the general version.
*/
static Int read_term_from_string(USES_REGS1) {
Term t1 = Deref(ARG1), rc;
const unsigned char *s;
size_t len;
if (IsVarTerm(t1)) {
Yap_Error(INSTANTIATION_ERROR, t1, "read_term_from_string/3");
return (FALSE);
} else if (!IsStringTerm(t1)) {
Yap_Error(TYPE_ERROR_STRING, t1, "read_term_from_string/3");
return (FALSE);
} else {
s = UStringOfTerm(t1);
len = strlen_utf8(s);
}
char *ss = (char *)s;
encoding_t enc = ENC_ISO_UTF8;
int sno = Yap_open_buf_read_stream(ss, len, &enc, MEM_BUF_USER);
rc = Yap_read_term(sno, Deref(ARG3), 3);
Yap_CloseStream(sno);
if (!rc)
return false;
return Yap_unify(rc, ARG2);
}
static Int string_to_term(USES_REGS1) {
Term t1 = Deref(ARG1), rc;
const char *s;
size_t len;
if (IsVarTerm(t1)) {
Yap_Error(INSTANTIATION_ERROR, t1, "read_term_from_string/3");
return (FALSE);
} else if (!IsStringTerm(t1)) {
Yap_Error(TYPE_ERROR_STRING, t1, "read_term_from_string/3");
return (FALSE);
} else {
s = StringOfTerm(t1);
len = strlen_utf8((const unsigned char *)s);
}
encoding_t enc = ENC_ISO_UTF8;
rc = Yap_StringToTerm(s, len, &enc, 1200, &ARG3);
if (!rc)
return false;
return Yap_unify(rc, ARG2);
}
static Int atomic_to_term(USES_REGS1) {
Term t1 = Deref(ARG1), rc;
const char *s;
size_t len;
if (IsVarTerm(t1)) {
Yap_Error(INSTANTIATION_ERROR, t1, "read_term_from_string/3");
return (FALSE);
} else if (!IsAtomicTerm(t1)) {
Yap_Error(TYPE_ERROR_ATOMIC, t1, "read_term_from_atomic/3");
return (FALSE);
} else {
Term t = Yap_AtomicToString(t1 PASS_REGS);
s = (const char *)UStringOfTerm(t);
len = strlen_utf8((unsigned char *)s);
}
encoding_t enc = ENC_ISO_UTF8;
rc = Yap_StringToTerm(s, len, &enc, 1200, &ARG3);
if (!rc)
return false;
return Yap_unify(rc, ARG2);
}
static Int atom_to_term(USES_REGS1) {
Term t1 = Deref(ARG1), rc;
const char *s;
size_t len;
if (IsVarTerm(t1)) {
Yap_Error(INSTANTIATION_ERROR, t1, "read_term_from_string/3");
return (FALSE);
} else if (!IsAtomTerm(t1)) {
Yap_Error(TYPE_ERROR_ATOM, t1, "read_term_from_atomic/3");
return (FALSE);
} else {
Term t = Yap_AtomicToString(t1 PASS_REGS);
s = StringOfTerm(t);
len = strlen_utf8((const unsigned char *)s);
}
encoding_t enc = ENC_ISO_UTF8;
rc = Yap_StringToTerm(s, len, &enc, 1200, &ARG3);
if (!rc)
return false;
return Yap_unify(rc, ARG2);
}
/**
* @pred read_term_from_atomic( +_Atomic_ , - _T_ , + _Options_ )
*
@ -1430,6 +1323,42 @@ static Int read_term_from_atomic(USES_REGS1) {
return Yap_unify(rc, ARG2);
}
/**
* @pred read_term_from_string( +_String_ , - _T_ , + _Options_
*
* read a term _T_ stored in constant _String_ according to _Options_
*
* @param _String_ the source _String_
* @param _T_ the output term _T_, may be any term
* @param _Options_ read_term/3 options.
*
* @notes Idea from SWI-Prolog, in YAP only works with strings
* Check read_term_from_atomic/3 for the general version.
*/
static Int read_term_from_string(USES_REGS1) {
Term t1 = Deref(ARG1), rc;
const unsigned char *s;
size_t len;
if (IsVarTerm(t1)) {
Yap_Error(INSTANTIATION_ERROR, t1, "read_term_from_string/3");
return (FALSE);
} else if (!IsStringTerm(t1)) {
Yap_Error(TYPE_ERROR_STRING, t1, "read_term_from_string/3");
return (FALSE);
} else {
s = UStringOfTerm(t1);
len = strlen_utf8(s);
}
char *ss = (char *)s;
encoding_t enc = ENC_ISO_UTF8;
int sno = Yap_open_buf_read_stream(ss, len, &enc, MEM_BUF_USER);
rc = Yap_read_term(sno, Deref(ARG3), 3);
Yap_CloseStream(sno);
if (!rc)
return false;
return Yap_unify(rc, ARG2);
}
void Yap_InitReadTPreds(void) {
Yap_InitCPred("read", 1, read1, SyncPredFlag);
Yap_InitCPred("read", 2, read2, SyncPredFlag);
@ -1440,9 +1369,6 @@ void Yap_InitReadTPreds(void) {
Yap_InitCPred("read_term_from_atom", 3, read_term_from_atom, 0);
Yap_InitCPred("read_term_from_atomic", 3, read_term_from_atomic, 0);
Yap_InitCPred("read_term_from_string", 3, read_term_from_string, 0);
Yap_InitCPred("atom_to_term", 3, atom_to_term, 0);
Yap_InitCPred("atomic_to_term", 3, atomic_to_term, 0);
Yap_InitCPred("string_to_term", 3, string_to_term, 0);
Yap_InitCPred("fileerrors", 0, fileerrors, SyncPredFlag);
Yap_InitCPred("nofileeleerrors", 0, nofileerrors, SyncPredFlag);

3
os/yapio.h
View File

@ -105,8 +105,7 @@ typedef enum mem_buf_source {
extern char *Yap_MemStreamBuf(int sno);
extern X_API Term Yap_StringToTerm(const char *s, size_t len, encoding_t *encp,
int prio, Term *bindings_p);
extern X_API Term Yap_StringToTerm(const char *s, size_t len, encoding_t *encp,int prio, Term bindings);
extern Term Yap_StringToNumberTerm(const char *s, encoding_t *encp, bool error_on);
extern int Yap_FormatFloat(Float f, char **s, size_t sz);
extern int Yap_open_buf_read_stream(const char *buf, size_t nchars,

5
packages/bdd/CMakeLists.txt
View File

@ -32,10 +32,6 @@ IF (CUDD_FOUND)
${CMAKE_CURRENT_BINARY_DIR}
)
configure_file ("${PROJECT_SOURCE_DIR}/cudd_config.h.cmake"
"${CMAKE_CURRENT_BINARY_DIR}/cudd_config.h" )
if(DEFINED YAP_MAJOR_VERSION)
TARGET_LINK_LIBRARIES(cudd
${CUDD_LIBRARIES}
@ -66,4 +62,3 @@ IF (CUDD_FOUND)
INSTALL(FILES trie_sp.yap DESTINATION ${libpl})
ENDIF (CUDD_FOUND)

222
packages/bdd/simplecudd/simplecudd.c
View File

@ -1,224 +1,4 @@
/****************************************************************************** \
/*********************************************************************vii
* *
* SimpleCUDD library (www.cs.kuleuven.be/~theo/tools/simplecudd.html) *
* SimpleCUDD was developed at Katholieke Universiteit Leuven(www.kuleuven.be) *

3
packages/bdd/simplecudd/simplecudd.h
View File

@ -193,7 +193,7 @@
#include <math.h>
#include <time.h>
#include "config.h"
#include "../cudd_config.h"
#include "cudd_config.h"
#if HAVE_CUDD_UTIL_H
#include <cudd/util.h>
@ -352,4 +352,3 @@ void ExpandNodes(hisqueue *Nodes, int index, int nodenum);
int simpleBDDtoDot(DdManager *manager, DdNode *bdd, char *filename);
int simpleNamedBDDtoDot(DdManager *manager, namedvars varmap, DdNode *bdd, char *filename);

3
packages/bdd/simplecudd_lfi/simplecudd.h
View File

@ -192,7 +192,7 @@
#include <time.h>
#include "pqueue.h"
#include "config.h"
#include "../cudd_config.h"
#include "cudd_config.h"
#if HAVE_CUDD_UTIL_H
#include <cudd/util.h>
#elif HAVE_UTIL_H
@ -353,4 +353,3 @@ void ExpandNodes(hisqueue *Nodes, int index, int nodenum);
int simpleBDDtoDot(DdManager *manager, DdNode *bdd, const char *filename);
int simpleNamedBDDtoDot(DdManager *manager, namedvars varmap, DdNode *bdd, const char *filename);

8
packages/cplint/CMakeLists.txt
View File

@ -1,4 +1,4 @@
# Be sure to also update these in Makefile!
set(SO_MAJOR 1)
set(SO_MINOR 0)
@ -63,7 +63,7 @@ IF (CUDD_FOUND)
slipcover/revise_sl.pl
slipcover/slipcover.pl
)
set (CPLINT_TEST_PROGRAMS
testcpl.pl
testlpad.pl
@ -151,7 +151,7 @@ IF (CUDD_FOUND)
ARCHIVE DESTINATION ${dlls}
)
add_library (cplint SHARED
${CPLINT_SOURCES}
)
@ -162,7 +162,7 @@ IF (CUDD_FOUND)
)
TARGET_LINK_LIBRARIES(cplint
${CUDD_LIBRARIES}
${CUDD_LIBRARIES}
libYap
)

8
packages/myddas/sqlite3/CMakeLists.txt
View File

@ -45,6 +45,12 @@ Android/jni/sqlite/nativehelper/ScopedLocalRef.h
endif (ANDROID)
add_component( Yapsqlite3
add_component( Yapsqlite3
${YAPSQLITE3_SOURCES} )
MY_set_target_properties(Yapsqlite3
PROPERTIES
# RPATH ${libdir} VERSION ${LIBYAPTAI_FULL_VERSION}
# SOVERSION ${LIBYAPTAI_MAJOR_VERSION}.${LIBYAPTAI_MINOR_VERSION}
POSITION_INDEPENDENT_CODE TRUE
)

10
pl/dbload.yap
View File

@ -25,11 +25,11 @@
:- use_system_module( attributes, [get_module_atts/2,
put_module_atts/2]).
:- dynamic dbloading/6, dbprocess/2.
dbload_from_stream(R, M0, rdf, term ) :-
'$lines_in_file'(R, Lines),
'$input_lines'(R, Type, Lines).
load_mega_clause( Stream ) :-
line_spec( Stream, Line),
repeat,
( fact( Stream ), fail ;
stream_property(Stream, at_end_of_file( on )).
'$input_lines'(R, csv, yeLines ) :-
'$process_lines'(R, Lines, Type ),

652
x.py
View File

@ -1,652 +0,0 @@
#! /usr/bin/env python3
#
# druwid is machine learning tool for adverse drug discovery
#
# It relies on the Aleph ILP learner, written and maintained by Ashwin Srinivasan\
#
# Authos: Vitor Santos Costa, David Page
# Bugs are from Vitor Santos Costa
#
import matplotlib
import matplotlib.image as mpimg
#matplotlib.use('Agg')
import argparse
import csv
import heapq
import logging
import networkx as nx
import os
import numpy as np
import pandas as pd
import sys
import threading
import time
import yap
graphics_ability = False
if graphics_ability:
import PIL
def display_pdf(id):
im = Image.open(self.shown_clause[id])
im.show()
logging.basicConfig(level=logging.DEBUG,
format='[%(levelname)s] (%(threadName)-10s) %(message)s',
)
from collections import namedtuple
from enum import IntEnum
from queue import Queue
from dru.druplot import plotClause
from dru.shell import alephShell
# class Console(InteractiveConsole):
# def __init__(*args): InteractiveConsole.__init__(*args)
compile = namedtuple('consult', 'FileName')
ensure_loaded = namedtuple('ensure_loaded', 'FileName')
loadFile = namedtuple('load_file', 'FileName Opts')
add_example = namedtuple('add_example', 'polarity case id b e')
set = namedtuple('set', 'key val')
setting = namedtuple('setting', ' key')
clsrc = namedtuple('clsrc', ' key ids')
clgraph = namedtuple('clgraph', ' key')
clhist = namedtuple('clhist', ' key first pos')
clause_info = namedtuple('clause_info', ' key Text Symbs H1Pos H2Pos CH1Pos CH2Pos ')
learn = namedtuple('learn', 'example')
learn_in_thread = namedtuple('learn_in_thread', 'example')
#learner = namedtuple('learn', 'class')
# assert = namedtuple('assert', 'fact')
load_ptable = namedtuple('load_ptable', 'File')
load_files = namedtuple('load_files', 'File Opts')
# prolog engine
class y:
E = None
def run(g):
y.E.goal(g)
def f(g):
y.E.fun(g)
# Schema information on Marshfiel mode table ( 2016 data )
#
# TBD: make it match/ genrate a mode declaration
#
# column headers, StudyId refers to the study participant
#
class DiagFields:
StudyID = 0
DX_CODE= 1
AGE= 2
FACILITY_NUM= 3
PROV_ID= 4
DX_DESC= 5
DX_TYPE_ID= 6
DX_TYPE_DESC= 7
DX_SUB_TYPE_ID= 8
DX_SUB_TYPE_DESC= 9
DX_CODE_CATEGORY= 10
DX_CODE_CATEGORY_DESC= 11
DX_CODE_SUBCATEGORY= 12
DX_CODE_SUBCATEGORY_DESC= 13
DATA_SOURCE= 14
#
# operations to fetch data from meds
#
class DiagOps(DiagFields):
''' Selects age, id, and one descriptor: we chose to use DX_DESC so that people
can understand the rules easily. '''
def import_row( self ):
return ( DiagFields.StudyID, DiagFields.AGE, DiagFields.DX_DESC )
def pred(self):
return yap.YAPPrologPredicate( self.name, 3 )
def __init__(self, name, ids):
self.name = name
self.ids = ids
# column headers, StudyId refers to the study participant
#
class MedFields( IntEnum ):
StudyID = 0
AGE = 1
GCN_SEQ_NUM= 2
DRUG_NAME= 3
GENERIC_NAME= 4
DOSAGE= 5
FREQUENCY= 6
ACTION_ATTRIBUTE_DESC= 7
ACTION_VALUE_DESC = 8
ACTION_IN_PLAN_CODE= 9
THERAPEUTIC_GENERIC_ID= 10
THERAPEUTIC_GENERIC_DESC= 11
THERAPEUTIC_SPECIFIC_ID= 12
THERAPEUTIC_SPECIFIC_DESC= 13
DRUG_SOURCE= 14
DATA_SOURCE = 15
#
# operations to fetch data from meds
#
class MedOps:
''' Operations as designed for the Marshfield meds table'''
arity = 3
def import_row( self ):
return ( MedFields.StudyID, MedFields.AGE, MedFields.DRUG_NAME )
def pred( self ):
return yap.YAPPredicate( self.name, 3 )
def __init__(self, name, ids):
self.name = name
self.ids = ids
class PrologTable:
'''Access tables in Prolog format'''
def query( self ):
args = [ 0 for x in range(self.arity) ]
return self.pname._make( args )
def __init__(self, p, name):
self.p = p
self.name = name
self.arity = p.arity()
ArgNames = [ "A" + str(x+1) for x in range(self.arity) ]
self.pname = namedtuple(self.name, ArgNames)
def __iter__(self):
goal = self.pname._make( )
return PrologTableIter(self, e, goal)
class PrologTableIter:
def __init__(self, e, goal):
try:
self.e = e
self.q = e.YAPQuery(goal)
except:
print('Error')
def __iter__(self):
# Iterators are iterables too.
# Adding this functions to make them so.
return self
def next(self):
if self.q.next():
return goal
else:
self.q.close()
self.q = None
raise StopIteration()
class DBStore:
'''store operations: csv to pl, and so on'''
def filter ( self, row ):
id = int(row[self.StudyID])
if id in self.ids:
ex1 = self.ids[ id ]
ex2 = self.ids[ -id ]
age = int(float(row[self.AGE])*1000)
if ex2[1] <= age and age <= ex2[2]:
id = -id
elif ex1[1] > age or age > ex1[2]:
return None
desc = row[self.DESC]
return id, age, desc
def __init__(self, File, dbi, ids ):
self.ids = ids
OFile = "data/" + dbi.name + '.yap'
if os.path.isfile(OFile) :
print("loading db from "+OFile)
y.run( load_files( OFile , []) )
return
with open(File) as csvfile:
print("Converting db from "+File+ " to "+OFile)
with open( OFile, "w") as out:
csvfile.seek(0)
reader = csv.reader(csvfile, delimiter = '|', quoting = csv.QUOTE_MINIMAL )
( self.StudyID, self.AGE, self.DESC ) = dbi.import_row()
P = dbi.pred()
reader.__next__()
for row in reader:
tuple = self.filter( row )
if tuple:
out.write( dbi.name + "( " + str(tuple[0]) +" , " + str(tuple[1])+ ", \'" + str(tuple[2]) + "\').\n" )
print("loading db from "+OFile)
y.E.reSet()
y.run( load_ptable( OFile ) )
def save_table(self, File, name):
p = self.YAPPredicate(name, 3)
with open(File, 'w', newline='') as csvfile:
fieldnames = ['Id', 'Age', 'Attribute' ]
writer = csv.writer(csvfile, delimiter='|', fieldnames=fieldnames)
writer.writerows(PrologTable(p, name))
class Examples:
''' Support for the manipulation and processing of examples.
So far, only loadng examples'''
ids = {}
def __init__(self, File):
if File.lower().endswith(('.yap','.pl','.pro','.prolog')):
E.run( add_prolog( File ) )
return
print("loading examples from "+File)
with open(File) as csvfile:
dialect = csv.Sniffer().sniff(csvfile.read(1024))
dialect.delimiter = '|'
dialect.quoting = csv.QUOTE_MINIMAL
csvfile.seek(0)
reader = csv.reader(csvfile, dialect)
reader.__next__()
for row in reader:
( cdb, pdb, id, b, e ) = row
case = cdb == "1" or cdb == 't' or cdb == '+'
Type = pdb == "1" or pdb == 't' or pdb == '+'
if Type:
id = int(id)
ti = 1
else:
id = -int(id)
ti = 0
if case:
ci = 1
else:
ci = 0
b = int(float(b)*1000)
e = int(float(e)*1000)
y.run( add_example(ti, ci, id, b, e) )
self.ids[id] = ( case, b, e )
cols = ['Id', 'Ref', 'Parent', 'TPP', 'TPN', 'TNN', ' CPP', 'CPN', 'CNN']
indx= ['Id']
class ClauseQueue:
'''Auxiliary class that represents the list of visited clauses.'''
''' queue size '''
size = 1024*256
best = 8
q = []
count = 0
def parentText(self, parent):
[row] = self.DF.loc[self.DF.Id==parent].values.tolist( )
return "Parent "+str(parent)+", cases " +repr(row[3:6])+", controls " +repr(row[6:9])
def showQueue(self, n):
L = heapq.nlargest(n, self.q)
S = "[ *********************************************************************\nbest rules at " + repr(self.count) +" nodes:\n"
S += "Node".rjust(6) + "Score".rjust(10) + "Parent".rjust(6) +" | " +"Matches on Cases".center(24) +" | " +"Matches on Controls".center(24) + '|\n'
S += "".rjust(6) + "".rjust(10) + "".rjust(6) + " | " +"Generic".center(8) + "Both".center(8) + "Brand".center(8) + " | " +"Generic".center(8) + "Both".center(8) + "Brand".center(8) + '|\n'
S += "".rjust(6) + "".rjust(10) + "".rjust(6) + " | " + "Only".center(8) + "".center(8) + "Only".center(8) + " | " +"Only".center(8) + "".center(8) + "Only".center(8) + '|\n'
for cl in L:
S += self.clauseToStringRow( cl )
S += "\n[ ********************************************************************* ]\n\n"
for cl in L:
S += self.PrintClbyId( cl )
return S
def loadHists(self):
hists = {}
if self.ipcs[0]:
hists["case_after_first"] = self.histpcs[0][0:self.ipcs[0]]
if self.ipcs[1]:
hists["case_after_last"] = self.histpcs[1][0:self.ipcs[1]]
if self.ipcs[2]:
hists["case_bef_first"] = self.histpcs[2][0:self.ipcs[2]]
if self.ipcs[3]:
hists["case_bef_last"] = self.histpcs[3][0:self.ipcs[3]]
if self.ipcs[4]:
hists["control_after_first"] = self.histpcs[4][0:self.ipcs[4]]
if self.ipcs[5]:
hists["control_after_last"] = self.histpcs[5][0:self.ipcs[5]]
if self.ipcs[6]:
hists["control_bef_first"] = self.histpcs[6][0:self.ipcs[6]]
if self.ipcs[7]:
hists["control_bef_last"] = self.histpcs[7][0:self.ipcs[7]]
return hists
def attendRequests(self):
while not self.command_q.empty():
msg = self.command_q.get()
if msg[0] == "show_clause":
row = msg[1]
y.run( clsrc( row[1], self ) )
parent = row[2]
parentDesc = self.parentText(parent)
self.hists = self.loadHists()
print( hists)
self.reply_q.put( ("show_clause", parentDesc ) )
# this method implements PrintCl if YAP is running
def printClWithThreads(self, row):
try:
id = row[0]
# if id in self.shown_clause:
# im = Image.open(self.shown_clause[id])
# im.show()
# return
#Prolog does the firat half
self.queue.prolog_q.put( ( "show_clause" , row ) )
( x, parentDesc )= self.queue.reply_q.get()
self.shown_clause[id] = plotClause(row[0],parentDesc, row[3:6], row[3:9], Text, (self.GraphV,self.d), self.hists)
except Exception as e:
print( 'trieref = ' + trieref )
raise
# this method implements PrintCl if YAP is not running
def printClNoThreads(self, row):
try:
id = row[0]
if graphics_ability and id in self.shown_clause:
display_pdf( id )
im = Image.open(self.shown_clause[id])
im.show()
return
#Prolog does the real work
y.run( clsrc( row[1], self ) )
parent = row[2]
self.hists = self.loadHists()
parentDesc = self.parentText(parent)
# and then sealib
self.shown_clause[id] = plotClause(row[0],parentDesc, row[3:6], row[6:9], self.Text )
except Exception as e:
print( 'trieref = ' + trieref )
raise
def clauseToStringRow(self, id):
try:
[row] = self.DF.loc[self.DF.Id==id].values.tolist( )
S = "" + repr(id).rjust(6) + "{:10.3f}".format(cl[0]) + repr(row[2]).rjust(6) +" | " + repr(row[3]).rjust(6) + repr(row[4]).rjust(6) + repr(row[5]).rjust(6) + ' | '+ repr(row[6]).rjust(6) + repr(row[7]).rjust(6) + repr(row[8]).rjust(6) + '|\n'
return S
except Exception as e:
print( str(e) )
raise
def printClauseAsRow(self, id):
print( self.clauseToStringRow( id ) )
def printClbyId(self, id):
try:
[row] = self.DF.loc[self.DF.Id==id].values.tolist( )
self.printClause( row )
except Exception as e:
print( str(e) )
raise
def printClbyTrieRef(self, trieref):
try:
[row] = self.DF.loc[self.DF.Ref==trieref].values.tolist()
self.printClause( row )
except Exception as e:
print( str(e) )
raise
def idFromTrieRef( self, trieref ):
try:
row = self.DF.loc[self.DF.Ref==trieref]
return int(row.at['Id','Id' ])
except Exception as e:
print("node = "+str(trieref))
print(self.DF)
raise
def add(self, parent, score, trieref, c):
try:
#import pdb
#pdb.set_trace()
self.count += 1
k = [self.count,trieref,parent,c[0],c[1],c[2],c[3],c[4],c[5]]
heapq.heappush(self.q, (score, self.count))
self.DF = self.DF.append(pd.DataFrame([k],columns=cols,index=indx))
if not self.command_q.empty():
self.attendRequests()
except Exception as e:
print("new node = "+str(self.count))
print("parent = "+str(parent))
print(self.DF)
raise
def link(self, parent, trieref):
try:
row = self.DF.loc[self.DF.Ref==trieref]
if not self.command_q.empty():
self.attendRequests()
except Exception as e:
print("new node = "+str(trieref))
print("parent = "+str(parent))
print(self.DF)
raise
def pushHistogram( self, i, val):
try:
x = self.ipcs[i]
self.histpcs[i][x] = val
self.ipcs[i] = x+1
except Exception as e:
print("i = "+str(i))
print("x = "+str(x))
print(self.DF)
raise
def initHistograms( self ):
self.histpcs = ( [None]*2400, [None]*2400, [None]*2400, [None]*2400,
[None]*2400, [None]*2400, [None]*2400, [None]*2400)
self.resetHistograms()
def resetHistograms( self ):
self.ipcs = [ 0, 0, 0, 0, 0, 0, 0, 0 ]
def setClauseText( self, txt ):
self.Text = txt
def setClauseGraph( self, labels,edges ):
G=nx.DiGraph()
dict = {}
for (i,l) in labels:
G.add_node(i,label=i)
dict[i] = l.strip()[0].lower()
for (i,j) in edges:
G.add_edge(i,j)
self.GraphV = G
self.d = dict
return G
def __repr__(self):
l = heapq.nlargest(self.q, 10)
for i in l:
print( l )
def __init__(self):
self.command_q = Queue()
self.reply_q = Queue()
self.GraphV=nx.Graph()
self.count = 0
self.DF = pd.DataFrame([[0,88998993,0,4,3,2,1,160,400]],columns=cols, index=indx)
self.shown_clause = {}
class LineSettings:
'''Isolate interface with argparse '''
opts = None
def __init__(self):
parser = argparse.ArgumentParser(description='''Search for ADRs using EHR data.
The arguments are CSV files for the databases, with at least 3 fields:
- an integer giving the patient id, called key
- a float point giving the patient\'s age in years, called age
- a string describing the diagnosis, called data
dppb
The case and control files are alos in CSV form, withe the following fields:
Key,AgeBefStart,AgeStartEnd,AgeAfterStart,AGeAfterEnd
p ''')
parser.add_argument('--save-db', dest='save', default=None, help="save the processed DB in Prolog, CSV, pickle")
parser.add_argument('--meds', dest='meds', default="data/meds.csv", help="CSV or Tab like with the medications database")
parser.add_argument('--diags', dest='diags', default="data/diags.csv", help="CSV or Tab like with the medications database")
parser.add_argument('--examples', dest='examples', default="data/exs.csv" , help="CSV or Tab like with the cases and controls")
parser.add_argument('--labs', type=argparse.FileType('r'), default=None, help="unsupported for now")
parser.add_argument('--min_examples', type=int, default=20, help="minimal number of examples to cover")
parser.add_argument('--seed', type=int, default=0, help="examples to start search, 0 if tries to cinsider all")
parser.add_argument('-f', default=" " , help="jupyter notebook")
parser.add_argument('--interactive', type = bool, default=True, help="run as line mode, or run as closed script ()")
self.opts = parser.parse_args()
def map(self):
return vars(self.opts)
class Aleph:
e = None
def add_db(self, p, t):
queue.addClause(t)
def set_options( self, xargs):
if 'min-examples' in xargs:
self.set('minpos', xargs[ 'min_examples' ] )
if 'verbosity' in xargs:
self.set('verbosity', xargs[ 'verbosity' ] )
if 'search' in xargs:
self.set('search', xargs[ 'search' ] )
if 'nodes' in xargs:
self.set('nodes', xargs[ 'nodes' ] )
def set( self, parameter, value):
'''Set an integer parameter, eg nodes, seeds or noise'''
y.run(set(parameter, value))
def setting( self, parameter):
'''Return the Aleph setting for parameter p, or show all
the current settings'''
if parameter:
value = yap.YAPVarTerm()
y.run(setting(parameter, value))
# return value
y.run( settings )
def induce( self, index = 0):
'''Learn clauses'''
y.run( learn( index ) )
def induceInThread( self, index = 0):
'''Learn clauses as a separe thread'''
if self.learning:
print("Already learning" )
return
self.learning = True
y.run( learn_in_thread( index ) )
def query_prolog( self, y, Query):
y.run( Query )
def rule( self, id ):
self.queue.printClause( id )
def histogram( self, Dict ):
pass
def induceInThread( self, index = 0 ):
kw = {}
kw["index"] = index
t = threading.Thread(target=self.induceInThread, kwargs=kw)
t.setDaemon = True
self.queue.printClause = self.queue.printClWithThreads
t.start()
self.queue.printClause = self.queue.printClNoThreads
def rules( self, count = 100 ):
self.queue.showQueue()
def golearn( self ):
try:
# import pdb
# pdb.set_trace()
self.learning = False
alephShell( self ).cmdloop()
q.close()
except SyntaxError as err:
print("Syntax Error error: {0}".format(err))
print( sys.exc_info()[0] )
except EOFError:
return
except RuntimeError as err:
print("YAP Execution Error: {0}".format(err))
print( sys.exc_info()[0] )
except ValueError as err:
print("Could not convert data to an integer: {0}.", format(rr))
print( sys.exc_info()[0] )
except NameError as err:
print("Bad Name: {0}.", format(err))
print( sys.exc_info()[0] )
except Exception as err:
print("Unexpected error:" + sys.exc_info() )
print( sys.exc_info()[0] )
def learn( self ):
while True:
self.golearn()
def __init__(self, queue):
''' Initialize Aleph by loading the data-bases and the example'''
if y.E == None:
y.E = yap.YAPEngine()
y.run( ensure_loaded( sys.druwid_root +'/druwid.yap' ) )
y.E.reSet()
x_args = LineSettings().map()
exf = x_args['examples']
exs = Examples(exf)
di = x_args['diags']
exmap = exs.ids
diags = DBStore( di, DiagOps( "diags", exmap ), exmap )
md = x_args['meds']
meds = DBStore(md, MedOps( "meds", exmap ) , exmap )
y.E.reSet()
save_db = x_args['save']
self.set_options( x_args )
self.interactive = x_args['interactive']
self.queue = queue
self.learning = False
self.queue.initHistograms( )
self.queue.printClause = self.queue.printClNoThreads

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