Merge branch 'master' of https://github.com/vscosta/yap-6.3
This commit is contained in:
Vitor Santos Costa
commit
b07a35a993
@ -885,7 +885,6 @@ static Int string_concat3(USES_REGS1) {
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Term t2, t3, ot;
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Term tf = 0;
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bool g1, g2, g3;
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Atom at;
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int l = push_text_stack();
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restart_aux:
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t1 = Deref(ARG1);
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@ -909,7 +908,6 @@ restart_aux:
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return cont_string_concat3(PASS_REGS1);
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} else {
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LOCAL_Error_TYPE = INSTANTIATION_ERROR;
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at = NULL;
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}
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if (tf) {
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if (Yap_unify(ot, tf)) {
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@ -1185,10 +1185,10 @@ Int YAP_ExecuteOnCut(PredEntry *pe, CPredicate exec_code,
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Yap_CloseSlots(CurSlot);
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PP = NULL;
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// B = LCL0-(CELL*)oB;
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if (false && Yap_RaiseException()) {
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if (!val && Yap_RaiseException()) {
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return false;
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} else { /* TRUE */
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return true;
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return val;
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}
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}
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@ -1371,12 +1371,16 @@ X_API Term YAP_NWideBufferToString(const wchar_t *s, size_t len) {
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/* copy a string to a buffer */
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X_API Term YAP_ReadBuffer(const char *s, Term *tp) {
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CACHE_REGS
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Term t;
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Term tv, t;
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BACKUP_H();
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if (*tp)
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tv = *tp;
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else
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tv = 0;
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LOCAL_ErrorMessage = NULL;
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while (!(t = Yap_StringToTerm(s, strlen(s) + 1, &LOCAL_encoding,
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GLOBAL_MaxPriority, tp))) {
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GLOBAL_MaxPriority, tv))) {
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if (LOCAL_ErrorMessage) {
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if (!strcmp(LOCAL_ErrorMessage, "Stack Overflow")) {
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if (!Yap_dogc(0, NULL PASS_REGS)) {
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@ -1447,11 +1447,7 @@ static int not_was_reconsulted(PredEntry *p, Term t, int mode) {
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static void addcl_permission_error(AtomEntry *ap, Int Arity, int in_use) {
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CACHE_REGS
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Term t, ti[2];
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ti[0] = MkAtomTerm(AbsAtom(ap));
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ti[1] = MkIntegerTerm(Arity);
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t = Yap_MkApplTerm(FunctorSlash, 2, ti);
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LOCAL_Error_TYPE = PERMISSION_ERROR_MODIFY_STATIC_PROCEDURE;
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LOCAL_ErrorMessage = Malloc( 256 );
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@ -1111,7 +1111,7 @@ static void c_bifun(basic_preds Op, Term t1, Term t2, Term t3, Term Goal,
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i2 = IntegerOfTerm(t2);
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if (i2 < 0) {
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Yap_ThrowError(DOMAIN_ERROR_NOT_LESS_THAN_ZERO, t2, 4,
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Yap_ThrowError(DOMAIN_ERROR_NOT_LESS_THAN_ZERO, t2,
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"compiling functor/3");
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save_machine_regs();
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siglongjmp(cglobs->cint.CompilerBotch, 1);
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@ -311,11 +311,11 @@ yap_error_descriptor_t *Yap_popErrorContext(void) {
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}
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void Yap_ThrowError__(const char *file, const char *function, int lineno,
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yap_error_number type, Term where, int code, ...) {
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yap_error_number type, Term where, ...) {
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va_list ap;
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char tmpbuf[MAXPATHLEN];
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va_start(ap, code);
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va_start(ap, where);
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char *format = va_arg(ap, char *);
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if (format != NULL) {
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#if HAVE_VSNPRINTF
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@ -328,7 +328,7 @@ Yap_Error__(file, function, lineno, type, where, tmpbuf);
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} else {
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Yap_Error__(file, function, lineno, type, where);
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}
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siglongjmp(LOCAL_RestartEnv, code);
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siglongjmp(LOCAL_RestartEnv, 4);
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}
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/**
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6
C/exec.c
6
C/exec.c
@ -1023,7 +1023,6 @@ static Int protect_stack(USES_REGS1) {
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static Int setup_call_catcher_cleanup(USES_REGS1) {
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Term Setup = Deref(ARG1);
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Term cmod = CurrentModule;
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Int oENV = LCL0 - ENV;
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choiceptr B0 = B;
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Term t3, t4;
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@ -1051,8 +1050,6 @@ static Int setup_call_catcher_cleanup(USES_REGS1) {
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prune_inner_computation(B0);
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}
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// at this point starts actual goal execution....
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cmod = CurrentModule;
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rc = Yap_RunTopGoal(Yap_GetFromSlot(h2), false);
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complete_inner_computation(B);
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t4 = Yap_GetFromSlot(h4);
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@ -2014,7 +2011,7 @@ bool is_cleanup_cp(choiceptr cp_b) {
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}
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static Int JumpToEnv() {
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choiceptr handler = B, oh = NULL;
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choiceptr handler = B;
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/* just keep the throwm object away, we don't need to care about it
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*/
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/* careful, previous step may have caused a stack shift,
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@ -2032,7 +2029,6 @@ static Int JumpToEnv() {
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handler->cp_b == NULL)) {
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break;
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}
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oh = handler;
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handler = handler->cp_b;
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}
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if (LOCAL_PrologMode & AsyncIntMode) {
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18
C/flags.c
18
C/flags.c
@ -182,7 +182,7 @@ static Term stream(Term inp) {
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}
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static bool
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static bool
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set_error_stream( Term inp ) {
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if( IsVarTerm(inp) )
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return Yap_unify( inp, Yap_StreamUserName( LOCAL_c_error_stream ) );
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@ -191,7 +191,7 @@ set_error_stream( Term inp ) {
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return true;
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}
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static bool
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static bool
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set_input_stream( Term inp ) {
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if( IsVarTerm(inp) )
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return Yap_unify( inp, Yap_StreamUserName( LOCAL_c_input_stream ) );
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@ -199,7 +199,7 @@ set_input_stream( Term inp ) {
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return true;
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}
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static bool
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static bool
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set_output_stream( Term inp ) {
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if( IsVarTerm(inp) )
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return Yap_unify( inp, Yap_StreamUserName( LOCAL_c_output_stream ) );
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@ -870,7 +870,7 @@ static Int cont_prolog_flag(USES_REGS1) {
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}
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EXTRA_CBACK_ARG(3, 1) = MkIntTerm(++i);
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flag = getYapFlag(f);
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if (!Yap_unify(f, ARG2))
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if (!Yap_unify(flag, ARG2))
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return false;
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return setYapFlag(f, Deref(ARG3));
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}
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@ -1175,7 +1175,7 @@ static Int source_mode(USES_REGS1) {
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if (!current && !Yap_unify_constant(ARG1, TermFalse))
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return false;
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targ = Deref(ARG2);
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setYapFlag(TermSource, ARG2);
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setYapFlag(TermSource, targ);
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return true;
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}
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@ -1319,7 +1319,7 @@ static bool setInitialValue(bool bootstrap, flag_func f, const char *s,
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CACHE_REGS
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encoding_t encoding = ENC_ISO_UTF8;
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t0 =
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Yap_StringToTerm(s, strlen(s) + 1, &encoding, GLOBAL_MaxPriority, NULL);
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Yap_StringToTerm(s, strlen(s) + 1, &encoding, GLOBAL_MaxPriority, 0L);
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if (!t0)
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return false;
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if (IsAtomTerm(t0) || IsIntTerm(t0)) {
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@ -1434,7 +1434,7 @@ do_prolog_flag_property(Term tflag,
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}
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}
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// UNLOCK(GLOBAL_Prolog_Flag[sno].prolog_flaglock);
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free(args);
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free(args);
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return rc;
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}
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@ -1540,7 +1540,7 @@ static Int do_create_prolog_flag(USES_REGS1) {
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if (fv) {
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if (args[PROLOG_FLAG_PROPERTY_KEEP].used &&
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args[PROLOG_FLAG_PROPERTY_KEEP].tvalue == TermTrue) {
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free(args);
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free(args);
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return true;
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}
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} else {
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@ -1633,7 +1633,7 @@ void Yap_InitFlags(bool bootstrap) {
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if (GLOBAL_Stream[StdInStream].status & Readline_Stream_f) {
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setBooleanGlobalPrologFlag(READLINE_FLAG, true);
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}
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if (!bootstrap) {
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Yap_InitCPredBack("current_prolog_flag", 2, 1, current_prolog_flag,
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cont_yap_flag, 0);
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6
C/text.c
6
C/text.c
@ -731,7 +731,7 @@ static Term write_number(unsigned char *s, seq_tv_t *out, int size, bool error_o
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static Term string_to_term(void *s, seq_tv_t *out, size_t leng USES_REGS) {
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Term o;
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o = out->val.t =
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Yap_StringToTerm(s, strlen(s) + 1, &out->enc, GLOBAL_MaxPriority, NULL);
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Yap_StringToTerm(s, strlen(s) + 1, &out->enc, GLOBAL_MaxPriority, 0L);
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return o;
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}
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@ -740,7 +740,7 @@ bool write_Text(unsigned char *inp, seq_tv_t *out, size_t leng USES_REGS) {
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if (out->type == 0) {
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return true;
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}
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if (out->type & YAP_STRING_TERM) {
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if ((out->val.t = string_to_term(inp, out, leng PASS_REGS)) != 0L)
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return out->val.t != 0;
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@ -948,7 +948,7 @@ bool Yap_Concat_Text(int tot, seq_tv_t inp[], seq_tv_t *out USES_REGS) {
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unsigned char *buf;
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int i;
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size_t leng;
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bufv = Malloc(tot * sizeof(unsigned char *));
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if (!bufv) {
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return NULL;
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@ -53,6 +53,8 @@ if(NOT COMMAND find_host_program)
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endmacro()
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endif()
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option(BUILD_SHARED_LIBS "Build shared library" ON)
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include(Prelims NO_POLICY_SCOPE)
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include(Sources NO_POLICY_SCOPE)
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@ -138,7 +138,7 @@ protected:
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BACKUP_MACHINE_REGS();
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Term *modp = NULL;
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out = Yap_StringToTerm(s0, strlen(s0) + 1, &LOCAL_encoding, 1200, &names);
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out = Yap_StringToTerm(s0, strlen(s0) + 1, &LOCAL_encoding, 1200, names);
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// extern char *s0;
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// fprintf(stderr,"ap=%p arity=%d text=%s", ap, ap->ArityOfPE, s);
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// Yap_DebugPlWrite(out);
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10
GIT
10
GIT
@ -1,10 +0,0 @@
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You need at least git-1.6 to install the development version.
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Please proceed as follows for the main branch:
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git clone git://gitorious.org/yap-git/mainline.git yap
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cd yap-6
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git submodule init
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git submodule update
|
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@ -70,6 +70,8 @@ add_subDIRECTORY (packages/ProbLog)
|
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|
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add_subDIRECTORY (packages/swi-minisat2)
|
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|
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add_subDIRECTORY (packages/clpqr)
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|
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|
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#todo: use cmake target builds
|
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# option (USE_MAXPERFORMANCE
|
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|
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337
Untitled
337
Untitled
@ -1,337 +0,0 @@
|
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Process: Python [88916]
|
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Path: /System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
|
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Identifier: Python
|
||||
Version: 2.7.10 (2.7.10)
|
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Code Type: X86-64 (Native)
|
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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
|
||||
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|
||||
0x7fff903c6000 - 0x7fff904eafff libsqlite3.dylib (216.4) <280D67B8-F93D-3587-A146-19F36C817548> /usr/lib/libsqlite3.dylib
|
||||
0x7fff90521000 - 0x7fff9055fff7 libGLImage.dylib (12.1) <BB1F1A93-5101-3906-AB17-8D83FCB200F9> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
|
||||
0x7fff90622000 - 0x7fff90667ff7 com.apple.coreservices.SharedFileList (24.4 - 24.5) <1D2AD77B-778F-3253-A295-3D0A32A8121C> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SharedFileList.framework/Versions/A/SharedFileList
|
||||
0x7fff90709000 - 0x7fff90717fff libxar.1.dylib (302) <03207F66-2C4A-3DBD-8D81-70F4C85903C4> /usr/lib/libxar.1.dylib
|
||||
0x7fff90e64000 - 0x7fff90e73ffb com.apple.LangAnalysis (1.7.0 - 1.7.0) <18D21123-A3E7-3851-974A-08E5D4540475> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/LangAnalysis.framework/Versions/A/LangAnalysis
|
||||
0x7fff90f0b000 - 0x7fff90f57fff com.apple.print.framework.PrintCore (11.2 - 472.2) <5AE8AA6B-CE09-397D-B0D4-0F9CCBF1F77D> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/PrintCore.framework/Versions/A/PrintCore
|
||||
0x7fff90f96000 - 0x7fff90fbafff com.apple.MultitouchSupport.framework (304.12 - 304.12) <65CB7653-EACD-3ADB-ABB6-2E0671708301> /System/Library/PrivateFrameworks/MultitouchSupport.framework/Versions/A/MultitouchSupport
|
||||
0x7fff91154000 - 0x7fff91165ff7 libsystem_trace.dylib (201.10.3) <F00E92E4-DBDA-3749-B5B3-0C3FBBABA1CB> /usr/lib/system/libsystem_trace.dylib
|
||||
0x7fff911f6000 - 0x7fff91254fff com.apple.SystemConfiguration (1.14 - 1.14) <D801FAD7-5A2D-3E5E-9F44-B6C9B8BEA747> /System/Library/Frameworks/SystemConfiguration.framework/Versions/A/SystemConfiguration
|
||||
0x7fff919db000 - 0x7fff919f2ff7 libsystem_coretls.dylib (83.40.5) <C90DAE38-4082-381C-A185-2A6A8B677628> /usr/lib/system/libsystem_coretls.dylib
|
||||
0x7fff919f3000 - 0x7fff919f3fff com.apple.ApplicationServices (48 - 48) <ADD57D3A-142F-3EF5-BFD8-EACD82164884> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
|
||||
0x7fff91b86000 - 0x7fff91bd2ffb com.apple.HIServices (1.22 - 550) <6B76B41C-CF5A-34C4-89F4-EFD7CA3D1C9D> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices
|
||||
0x7fff91c23000 - 0x7fff91c64ff7 libGLU.dylib (12.1) <CD7A5916-3E3C-3EF3-A275-B281016B99CB> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
|
||||
0x7fff91c65000 - 0x7fff91c96ff7 libncurses.5.4.dylib (46) <D4C10699-3E8F-3F42-A695-7490EA4B6B32> /usr/lib/libncurses.5.4.dylib
|
||||
0x7fff91ef6000 - 0x7fff91f49ff7 libc++.1.dylib (120.1) <8FC3D139-8055-3498-9AC5-6467CB7F4D14> /usr/lib/libc++.1.dylib
|
||||
0x7fff91f8c000 - 0x7fff91f8eff7 libquarantine.dylib (80) <0F4169F0-0C84-3A25-B3AE-E47B3586D908> /usr/lib/system/libquarantine.dylib
|
||||
0x7fff91fc3000 - 0x7fff91fddfff com.apple.Kerberos (3.0 - 1) <1B4744BF-E5AE-38E2-AA56-E22D3270F2E8> /System/Library/Frameworks/Kerberos.framework/Versions/A/Kerberos
|
||||
0x7fff9233c000 - 0x7fff9269ef3f libobjc.A.dylib (680) <7489D2D6-1EFD-3414-B18D-2AECCCC90286> /usr/lib/libobjc.A.dylib
|
||||
0x7fff926df000 - 0x7fff926f0fff libcmph.dylib (6) <BA4BF2C6-7F4E-33B8-9DD7-619C9EB83ECF> /usr/lib/libcmph.dylib
|
||||
0x7fff92756000 - 0x7fff9279bff3 libFontRegistry.dylib (155.2) <A70DD497-35F3-34DA-9C19-F4B90080E961> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.dylib
|
||||
0x7fff927b9000 - 0x7fff927c4ff7 libcommonCrypto.dylib (60075.50.1) <93732261-34B4-3914-B7A2-90A81A182DBA> /usr/lib/system/libcommonCrypto.dylib
|
||||
0x7fff927c5000 - 0x7fff927c6ffb libremovefile.dylib (41) <552EF39E-14D7-363E-9059-4565AC2F894E> /usr/lib/system/libremovefile.dylib
|
||||
0x7fff93126000 - 0x7fff93131ff7 libChineseTokenizer.dylib (16) <79B8C67A-3061-3C78-92CD-4650719E68D4> /usr/lib/libChineseTokenizer.dylib
|
||||
0x7fff93132000 - 0x7fff9313cfff com.apple.NetAuth (6.0 - 6.0) <D692B1EF-534F-3892-8E2F-2BBA7C8AFD74> /System/Library/PrivateFrameworks/NetAuth.framework/Versions/A/NetAuth
|
||||
0x7fff931b3000 - 0x7fff93240fff libsystem_c.dylib (1082.50.1) <B552D565-B798-3B9B-AE63-F623B42A5F01> /usr/lib/system/libsystem_c.dylib
|
||||
0x7fff93250000 - 0x7fff935e5fdb com.apple.vImage (8.0 - 8.0) <4BAC9B6F-7482-3580-8787-AB0A5B4D331B> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
|
||||
0x7fff9394a000 - 0x7fff939bffff com.apple.framework.IOKit (2.0.2 - 1179.50.2) <A509D3AE-9D48-31B7-89C7-326A7A2007B2> /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit
|
||||
0x7fff939e9000 - 0x7fff93a02fff com.apple.CFOpenDirectory (10.11 - 194) <11F95672-55E0-3F9D-9171-5E8C56AEE948> /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory
|
||||
0x7fff93ad9000 - 0x7fff93ae1fff libGFXShared.dylib (12.1) <5A0C2493-200C-30BE-97D5-8E8C0B8E604D> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib
|
||||
0x7fff93ae2000 - 0x7fff93aeafff libsystem_networkextension.dylib (385.40.36) <66095DC7-6539-38F2-95EE-458F15F6D014> /usr/lib/system/libsystem_networkextension.dylib
|
||||
0x7fff93d66000 - 0x7fff93d83ff7 com.apple.AppleVPAFramework (2.1.2 - 2.1.2) <41378C0B-B56A-3A73-9BD0-E06FA1F87B8C> /System/Library/PrivateFrameworks/AppleVPA.framework/Versions/A/AppleVPA
|
||||
0x7fff94496000 - 0x7fff9449efff com.apple.NetFS (6.0 - 4.0) <842A5346-24C3-3F22-9ECF-E586A10EA1F2> /System/Library/Frameworks/NetFS.framework/Versions/A/NetFS
|
||||
0x7fff9449f000 - 0x7fff944a4ff7 libmacho.dylib (875.1) <318264FA-58F1-39D8-8285-1F6254EE410E> /usr/lib/system/libmacho.dylib
|
||||
0x7fff944a5000 - 0x7fff944cefff libsystem_info.dylib (477.50.4) <FAA9226D-64DE-3769-A6D8-6CABA4B7FF4D> /usr/lib/system/libsystem_info.dylib
|
||||
0x7fff945f8000 - 0x7fff9466ffeb libcorecrypto.dylib (335.50.1) <B5C05FD7-A540-345A-87BF-8E41848A3C17> /usr/lib/system/libcorecrypto.dylib
|
||||
0x7fff94672000 - 0x7fff9467afef libsystem_platform.dylib (74.40.2) <29A905EF-6777-3C33-82B0-6C3A88C4BA15> /usr/lib/system/libsystem_platform.dylib
|
||||
0x7fff947a8000 - 0x7fff94835dd7 com.apple.AppleJPEG (1.0 - 1) <558ACADA-C41F-3EEF-82A0-C2D7B13C5428> /System/Library/PrivateFrameworks/AppleJPEG.framework/Versions/A/AppleJPEG
|
||||
0x7fff9490b000 - 0x7fff94914ff7 libsystem_pthread.dylib (138.10.4) <3DD1EF4C-1D1B-3ABF-8CC6-B3B1CEEE9559> /usr/lib/system/libsystem_pthread.dylib
|
||||
0x7fff94915000 - 0x7fff94923ff7 libbz2.1.0.dylib (38) <28E54258-C0FE-38D4-AB76-1734CACCB344> /usr/lib/libbz2.1.0.dylib
|
||||
0x7fff949d8000 - 0x7fff949e4fff com.apple.speech.synthesis.framework (5.4.12 - 5.4.12) <71DA00B8-5EA2-326B-8814-59DB25512F65> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis
|
||||
0x7fff949e5000 - 0x7fff94a43fff com.apple.CoreServices.OSServices (728.12 - 728.12) <776EBD4F-7052-377F-A70D-E2FDBD465A5E> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices
|
||||
0x7fff94c55000 - 0x7fff94c6dfef libcompression.dylib (28) <E7601B62-1053-369D-8A9E-91CF86239220> /usr/lib/libcompression.dylib
|
||||
0x7fff94d75000 - 0x7fff94d81ff7 com.apple.OpenDirectory (10.11 - 194) <31A67AD5-5CC2-350A-96D7-821DF4BC4196> /System/Library/Frameworks/OpenDirectory.framework/Versions/A/OpenDirectory
|
||||
0x7fff94dd2000 - 0x7fff94de9ff7 libsystem_asl.dylib (323.50.1) <41F8E11F-1BD0-3F1D-BA3A-AA1577ED98A9> /usr/lib/system/libsystem_asl.dylib
|
||||
0x7fff95efc000 - 0x7fff96372fff com.apple.CoreFoundation (6.9 - 1258.1) <943A1383-DA6A-3DC0-ABCD-D9AEB3D0D34D> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
|
||||
0x7fff96a8b000 - 0x7fff96a8cffb libSystem.B.dylib (1226.10.1) <C5D09FE1-CC70-383E-AC27-18602F2EDEC4> /usr/lib/libSystem.B.dylib
|
||||
0x7fff96b0b000 - 0x7fff96b67fff libTIFF.dylib (1450) <14EB7C03-7DDA-3276-BAC5-D597913AC9C4> /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib
|
||||
0x7fff9788c000 - 0x7fff97900ff3 com.apple.securityfoundation (6.0 - 55126) <130656AE-2711-3914-8736-D8B021C93FE0> /System/Library/Frameworks/SecurityFoundation.framework/Versions/A/SecurityFoundation
|
||||
0x7fff97901000 - 0x7fff9796fff7 com.apple.ApplicationServices.ATS (377 - 394.4) <9779E916-0788-3CAC-B1EC-F68BCB12A2B6> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS
|
||||
0x7fff97970000 - 0x7fff979c1ff7 libcups.2.dylib (435.2) <91584A40-214D-33E8-A613-CE22289037C8> /usr/lib/libcups.2.dylib
|
||||
0x7fff97acb000 - 0x7fff97ad4ff3 libsystem_notify.dylib (150.40.1) <D48BDE34-0F7E-34CA-A0FF-C578E39987CC> /usr/lib/system/libsystem_notify.dylib
|
||||
0x7fff97c56000 - 0x7fff97c58fff libCVMSPluginSupport.dylib (12.1) <D81B3D8D-B83F-3918-BD4B-6C794A30AF9F> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib
|
||||
0x7fff97c59000 - 0x7fff97c5cff7 libCoreFSCache.dylib (119.5) <2389D7DA-B8EF-3EB4-AAAF-FBEDE01CDECA> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreFSCache.dylib
|
||||
0x7fff97d7b000 - 0x7fff97d80ff7 libheimdal-asn1.dylib (453.40.10) <981DE40B-FA16-36F7-BE92-8C8A115D6CD9> /usr/lib/libheimdal-asn1.dylib
|
||||
0x7fff97d81000 - 0x7fff97d9fffb libedit.3.dylib (43) <1D3E3152-4001-3C19-B56A-7543F1BBA47C> /usr/lib/libedit.3.dylib
|
||||
0x7fff987b2000 - 0x7fff989bffff libicucore.A.dylib (551.51.3) <5BC80F94-C90D-3175-BD96-FF1DC222EC9C> /usr/lib/libicucore.A.dylib
|
||||
0x7fff989c0000 - 0x7fff989c0ff7 liblaunch.dylib (765.50.8) <834ED605-5114-3641-AA4D-ECF31B801C50> /usr/lib/system/liblaunch.dylib
|
||||
0x7fff98b55000 - 0x7fff98b8ffff com.apple.QD (3.12 - 302) <0FE53180-2895-3D14-A1E7-F82DE1D106E1> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/QD.framework/Versions/A/QD
|
||||
0x7fff98be1000 - 0x7fff98be1fff libenergytrace.dylib (10.40.1) <0A491CA7-3451-3FD5-999A-58AB4362682B> /usr/lib/libenergytrace.dylib
|
||||
0x7fff98c36000 - 0x7fff98c41fff libGL.dylib (12.1) <70D51643-04AC-3400-8F11-A6FC25985289> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
|
||||
0x7fff98c77000 - 0x7fff98ca0fff libc++abi.dylib (125) <DCCC8177-3D09-35BC-9784-2A04FEC4C71B> /usr/lib/libc++abi.dylib
|
||||
0x7fff98cb0000 - 0x7fff98cdfff7 com.apple.DictionaryServices (1.2 - 250.3) <30250542-CBAA-39C1-91AA-B57A5DE17594> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/DictionaryServices.framework/Versions/A/DictionaryServices
|
||||
0x7fff98ce0000 - 0x7fff98ce7ff7 libcompiler_rt.dylib (62) <A13ECF69-F59F-38AE-8609-7B731450FBCD> /usr/lib/system/libcompiler_rt.dylib
|
||||
0x7fff98d10000 - 0x7fff98fa6fff libmecabra.dylib (696.5) <EF6C0BD4-5FE8-34FB-8ADF-69A53CEC97A9> /usr/lib/libmecabra.dylib
|
||||
0x7fff99bdb000 - 0x7fff99bdbfff com.apple.Accelerate (1.10 - Accelerate 1.10) <185EC96A-5AF0-3620-A4ED-4D3654D25B39> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
|
||||
0x7fff99bdc000 - 0x7fff99bddfff libsystem_blocks.dylib (65) <1244D9D5-F6AA-35BB-B307-86851C24B8E5> /usr/lib/system/libsystem_blocks.dylib
|
||||
0x7fff99d2d000 - 0x7fff99e94fff libBLAS.dylib (1162.2) <A1398FE0-39D2-33EA-9A0F-B2644EEA29A0> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
|
||||
0x7fff99f74000 - 0x7fff9a259ffb com.apple.CoreServices.CarbonCore (1136.2 - 1136.2) <2DBAFC9A-6CD6-351D-B1F4-87D81AA6D640> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/Versions/A/CarbonCore
|
||||
0x7fff9a2cc000 - 0x7fff9a312ff7 libauto.dylib (186) <999E610F-41FC-32A3-ADCA-5EC049B65DFB> /usr/lib/libauto.dylib
|
||||
0x7fff9a359000 - 0x7fff9a35ffff com.apple.IOAccelerator (205.10 - 205.10) <E46ED853-C2CC-3F29-A7DD-5E9351A2E754> /System/Library/PrivateFrameworks/IOAccelerator.framework/Versions/A/IOAccelerator
|
||||
0x7fff9a40b000 - 0x7fff9a410ff3 libunwind.dylib (35.3) <F6EB48E5-4D12-359A-AB54-C937FBBE9043> /usr/lib/system/libunwind.dylib
|
||||
0x7fff9a833000 - 0x7fff9a923fff libJP2.dylib (1450) <FAFF00CD-1CF6-34DE-A06F-31D4BB9C8BA9> /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJP2.dylib
|
||||
0x7fff9ab94000 - 0x7fff9aba5fff libSparseBLAS.dylib (1162.2) <EBEB3848-3468-342A-91A6-5C47F2369CD9> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libSparseBLAS.dylib
|
||||
0x7fff9abea000 - 0x7fff9ac8afff com.apple.Metadata (10.7.0 - 972.34) <A93B485D-094C-3024-8CBB-D9E035FB83C4> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Versions/A/Metadata
|
||||
0x7fff9af5b000 - 0x7fff9af79ff7 libsystem_kernel.dylib (3248.50.21) <78E54D59-D2B0-3F54-9A4A-0A68D671F253> /usr/lib/system/libsystem_kernel.dylib
|
||||
0x7fff9b073000 - 0x7fff9b159ff7 libcrypto.0.9.8.dylib (59.40.2) <2486D801-C756-3488-B519-1AA6807E8948> /usr/lib/libcrypto.0.9.8.dylib
|
||||
0x7fff9b3c1000 - 0x7fff9b4bdff7 libFontParser.dylib (158.6) <267A9AE4-4138-3112-8D73-BDFDC96568FF> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.dylib
|
||||
0x7fff9b4c2000 - 0x7fff9b4ddff7 libCRFSuite.dylib (34) <078B4CD8-6A8C-3067-B2BA-0C2A0BAB8AC3> /usr/lib/libCRFSuite.dylib
|
||||
0x7fff9b625000 - 0x7fff9b8acff3 com.apple.CFNetwork (760.5.1 - 760.5.1) <EE9426D1-F11C-3DD4-AE08-EA29AEB27177> /System/Library/Frameworks/CFNetwork.framework/Versions/A/CFNetwork
|
||||
0x7fff9b928000 - 0x7fff9baeefe7 com.apple.ImageIO.framework (3.3.0 - 1450) <18ABA1F4-43EC-3990-9777-C91FD3D6AF71> /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
|
||||
0x7fff9bdf0000 - 0x7fff9be24ff7 com.apple.CoreVideo (1.8 - 191.3) <1AA24A1B-CB84-3F6B-B6DE-11494542649C> /System/Library/Frameworks/CoreVideo.framework/Versions/A/CoreVideo
|
||||
0x7fff9bf5b000 - 0x7fff9bf60fff com.apple.DiskArbitration (2.7 - 2.7) <F55902AA-5316-3255-A701-FDED5B553065> /System/Library/Frameworks/DiskArbitration.framework/Versions/A/DiskArbitration
|
||||
0x7fff9bf61000 - 0x7fff9c086fff com.apple.LaunchServices (728.12 - 728.12) <F5AB56CD-CF33-33F0-A48D-372551714E77> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices
|
||||
0x7fff9c0e4000 - 0x7fff9c0effff libkxld.dylib (3248.50.21) <99195052-038E-3490-ACF8-76F9AC43897E> /usr/lib/system/libkxld.dylib
|
||||
0x7fff9d382000 - 0x7fff9d386fff libpam.2.dylib (20) <CFCD19BD-87BC-3F2B-BB1C-4C23E8E55F1A> /usr/lib/libpam.2.dylib
|
||||
0x7fff9d4b7000 - 0x7fff9d4c8ff7 libz.1.dylib (61.20.1) <B3EBB42F-48E3-3287-9F0D-308E04D407AC> /usr/lib/libz.1.dylib
|
||||
0x7fff9d4ca000 - 0x7fff9d4f8ff7 com.apple.CoreServicesInternal (248.2 - 248.2) <6E111F0A-D7F1-3738-ADE7-CF983BD4EC8B> /System/Library/PrivateFrameworks/CoreServicesInternal.framework/Versions/A/CoreServicesInternal
|
||||
0x7fff9d4f9000 - 0x7fff9d4fbff7 libsystem_configuration.dylib (802.40.13) <3DEB7DF9-6804-37E1-BC83-0166882FF0FF> /usr/lib/system/libsystem_configuration.dylib
|
||||
0x7fff9d5ab000 - 0x7fff9d5acfff libsystem_secinit.dylib (20) <32B1A8C6-DC84-3F4F-B8CE-9A52B47C3E6B> /usr/lib/system/libsystem_secinit.dylib
|
||||
|
||||
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
152
callcount.yap
@ -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)).
|
||||
|
||||
%% @}
|
||||
|
||||
/**
|
||||
@}
|
||||
*/
|
||||
|
||||
@ -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 ${EXTRALIBS} unicode)
|
||||
@ -261,10 +265,8 @@ check_symbol_exists(flsll <string.h> HAVE_FLSLL)
|
||||
check_function_exists(fmemopen HAVE_FMEMOPEN)
|
||||
check_function_exists(fpclass HAVE_FPCLASS)
|
||||
check_function_exists(ftime HAVE_FTIME)
|
||||
check_function_exists(ftruncate HAVE_FTRUNCATE)
|
||||
check_function_exists(funopen HAVE_FUNOPEN)
|
||||
check_function_exists(gcc HAVE_GCC)
|
||||
check_function_exists(getcwd HAVE_GETCWD)
|
||||
check_function_exists(ftru
|
||||
wd HAVE_GETCWD)
|
||||
check_function_exists(getenv HAVE_GETENV)
|
||||
check_function_exists(getexecname HAVE_GETEXECNAME)
|
||||
check_function_exists(gethostbyname HAVE_GETHOSTBYNAME)
|
||||
@ -321,7 +323,8 @@ check_function_exists(setlocale HAVE_SETLOCALE)
|
||||
check_function_exists(setsid HAVE_SETSID)
|
||||
check_function_exists(shmat HAVE_SHMAT)
|
||||
check_function_exists(sigaction HAVE_SIGACTION)
|
||||
check_symbol_exists(SIGFPE signal.h HAVE_SIGFPE)
|
||||
check_symbol_exists(SI
|
||||
GFPE signal.h HAVE_SIGFPE)
|
||||
check_function_exists(siggetmask HAVE_SIGGETMASK)
|
||||
check_symbol_exists(SIGINFO signal.h HAVE_SIGINFO)
|
||||
check_function_exists(siginterrupt HAVE_SIGINTERRUPT)
|
||||
@ -400,5 +403,13 @@ configure_file(${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" )
|
||||
|
||||
@ -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} ${CUDD_INCLUDE_DIR} )
|
||||
|
||||
check_include_files( "stdio.h;cudd.h" HAVE_CUDD_H )
|
||||
check_include_files( "stdio.h;cudd/cudd.h" HAVE_CUDD_CUDD_H )
|
||||
check_include_files( "cuddInt.h" HAVE_CUDDINT_H )
|
||||
check_include_files( "cudd/cuddInt.h" HAVE_CUDD_CUDDINT_H )
|
||||
endif (CUDD_FOUND)
|
||||
|
||||
|
||||
endif(WITH_CUDD)
|
||||
|
||||
14
example.py
14
example.py
@ -1,14 +0,0 @@
|
||||
# python commands
|
||||
|
||||
import yap
|
||||
|
||||
engine = yap.YAPEngine();
|
||||
# engine = yap.YAPEngine(yap.YAPParams());
|
||||
|
||||
while True:
|
||||
s = raw_input("Prolog Query: ")
|
||||
q = engine.query(s)
|
||||
print "success"
|
||||
while q.next():
|
||||
ar = q.namedVars();
|
||||
print ar
|
||||
@ -42,7 +42,7 @@ struct yami *Yap_Error__(const char *file, const char *function, int lineno,
|
||||
yap_error_number err, YAP_Term wheret, ...);
|
||||
|
||||
void Yap_ThrowError__(const char *file, const char *function, int lineno,
|
||||
yap_error_number err, YAP_Term wheret, int code, ...) __attribute__ ((noreturn));
|
||||
yap_error_number err, YAP_Term wheret, ...) __attribute__ ((noreturn));
|
||||
|
||||
|
||||
#define Yap_NilError(id, ...) \
|
||||
@ -51,8 +51,8 @@ void Yap_ThrowError__(const char *file, const char *function, int lineno,
|
||||
#define Yap_Error(id, inp, ...) \
|
||||
Yap_Error__(__FILE__, __FUNCTION__, __LINE__, id, inp, __VA_ARGS__)
|
||||
|
||||
#define Yap_ThrowError(id, inp, code, ...) \
|
||||
Yap_ThrowError__(__FILE__, __FUNCTION__, __LINE__, id, inp, code, __VA_ARGS__)
|
||||
#define Yap_ThrowError(id, inp, ...) \
|
||||
Yap_ThrowError__(__FILE__, __FUNCTION__, __LINE__, id, inp, __VA_ARGS__)
|
||||
|
||||
#ifdef YAP_TERM_H
|
||||
/**
|
||||
|
||||
@ -57,7 +57,7 @@ ENDIF("${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)
|
||||
|
||||
@ -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;
|
||||
}
|
||||
|
||||
144
os/readterm.c
144
os/readterm.c
@ -1260,7 +1260,7 @@ X_API Term Yap_StringToTerm(const char *s, size_t len, encoding_t *encp,
|
||||
|
||||
if (len == 0) {
|
||||
Term rval = TermEof;
|
||||
pop_text_stack(lvl);
|
||||
pop_text_stack(lvl);
|
||||
return rval;
|
||||
}
|
||||
if (bindingsp) {
|
||||
@ -1276,7 +1276,7 @@ X_API Term Yap_StringToTerm(const char *s, size_t len, encoding_t *encp,
|
||||
Yap_CloseStream(stream);
|
||||
UNLOCK(GLOBAL_Stream[stream].streamlock);
|
||||
if (rval && bindingsp) {
|
||||
*bindingsp = ArgOfTerm(1,ctl);
|
||||
*bindingsp = ArgOfTerm(1, ctl);
|
||||
}
|
||||
pop_text_stack(lvl);
|
||||
return rval;
|
||||
@ -1326,107 +1326,6 @@ 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_ )
|
||||
*
|
||||
@ -1466,6 +1365,42 @@ 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);
|
||||
@ -1476,9 +1411,6 @@ 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);
|
||||
|
||||
@ -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)
|
||||
|
||||
|
||||
@ -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) *
|
||||
|
||||
@ -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);
|
||||
|
||||
|
||||
@ -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);
|
||||
|
||||
|
||||
27
packages/clpqr/CMakeLists.txt
Normal file
27
packages/clpqr/CMakeLists.txt
Normal file
@ -0,0 +1,27 @@
|
||||
################################################################
|
||||
# SWI-Prolog CLPQR package
|
||||
# Author: Jan Wielemaker. jan@swi.psy.uva.nl
|
||||
# Copyright: LGPL (see COPYING or www.gnu.org
|
||||
################################################################
|
||||
|
||||
|
||||
set (CLPRPRIV clpr/bb_r.pl clpr/bv_r.pl
|
||||
clpr/fourmotz_r.pl clpr/ineq_r.pl
|
||||
clpr/itf_r.pl clpr/nf_r.pl
|
||||
clpr/store_r.pl )
|
||||
set(CLPQPRIV clpq/bb_q.pl clpq/bv_q.pl
|
||||
clpq/fourmotz_q.pl clpq/ineq_q.pl
|
||||
clpq/itf_q.pl clpq/nf_q.pl
|
||||
clpq/store_q.pl)
|
||||
set (CLPQRPRIV clpqr/class.pl clpqr/dump.pl
|
||||
clpqr/geler.pl clpqr/itf.pl
|
||||
clpqr/ordering.pl
|
||||
clpqr/project.pl clpqr/redund.pl)
|
||||
set (LIBPL clpr.pl clpq.pl ${CLPRPRIV} ${CLPQPRIV} ${CLPQRPRIV} )
|
||||
|
||||
install ( FILES ${LIBPL} DESTINATION ${libpl} )
|
||||
|
||||
# $(PL) -q -f $(srcdir)/clpr_test.pl -g test,halt -t 'halt(1)'
|
||||
|
||||
|
||||
|
||||
@ -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
|
||||
)
|
||||
|
||||
|
||||
@ -46,6 +46,12 @@ src/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
|
||||
)
|
||||
|
||||
@ -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
652
x.py
@ -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
|
||||
Reference in New Issue
Block a user