Changeset: 3a940cccfc2a for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=3a940cccfc2a
Modified Files:
monetdb5/extras/rapi/rapi.c
monetdb5/extras/rapi/rapi.h
monetdb5/extras/rapi/rapi.mal
sql/backends/monet5/Tests/All
sql/backends/monet5/Tests/rapi00.sql
sql/backends/monet5/Tests/rapi01.sql
sql/backends/monet5/Tests/rapi02.sql
Branch: RIntegration
Log Message:
R API: select rfunc(a,b) from sometable; select * from rfunc(); now working.
diffs (truncated from 862 to 300 lines):
diff --git a/monetdb5/extras/rapi/rapi.c b/monetdb5/extras/rapi/rapi.c
--- a/monetdb5/extras/rapi/rapi.c
+++ b/monetdb5/extras/rapi/rapi.c
@@ -117,6 +117,7 @@ static int rapiInitialized = FALSE;
void writeConsole(const char * buf, int buflen) {
(void) buflen;
THRprintf(GDKout, "%s", buf);
+ fprintf(stderr, "%s", buf);
}
void writeConsoleEx(const char * buf, int buflen, int foo) {
(void) buflen;
@@ -131,39 +132,35 @@ static int RAPIinitialize(void) {
ParseStatus status;
char rlibs[BUFSIZ];
char rapiinclude[BUFSIZ];
+ MT_lock_init(&rapiLock, "rapi_lock");
// adapted from Rinit.c (JRI package)
- MT_lock_init(&rapiLock, "rapi_lock");
-
- if (!getenv("R_HOME")) {
- return 1;
- }
+ if (!getenv("R_HOME")) {
+ return 1;
+ }
// TODO: put this into dbfarm
snprintf(rlibs, BUFSIZ, "%s%c%s%c%s%c%s",
- LOCALSTATEDIR, DIR_SEP, "monetdb5", DIR_SEP, "rapi",
- DIR_SEP, "libs");
-
-
- setenv("R_LIBS_USER",rlibs,TRUE);
+ LOCALSTATEDIR, DIR_SEP, "monetdb5", DIR_SEP, "rapi",
+ DIR_SEP, "libs");
+ setenv("R_LIBS_USER", rlibs, TRUE);
#ifdef RIF_HAS_RSIGHAND
- R_SignalHandlers=0;
+ R_SignalHandlers=0;
#endif
- {
- int stat=Rf_initialize_R(rargc, rargv);
- if (stat<0) {
- return 2;
- }
- }
+ {
+ int stat = Rf_initialize_R(rargc, rargv);
+ if (stat < 0) {
+ return 2;
+ }
+ }
#ifdef RIF_HAS_RSIGHAND
- R_SignalHandlers=0;
+ R_SignalHandlers=0;
#endif
- /* disable stack checking, because threads will thow it off */
- R_CStackLimit = (uintptr_t) -1;
-
- R_Interactive = 0;
+ /* disable stack checking, because threads will thow it off */
+ R_CStackLimit = (uintptr_t) -1;
+ R_Interactive = FALSE;
ptr_R_WriteConsole = writeConsole;
ptr_R_WriteConsoleEx = writeConsoleEx;
R_Outputfile = NULL;
@@ -174,23 +171,21 @@ static int RAPIinitialize(void) {
// run the R environment initialization script rapi.R
snprintf(rapiinclude, BUFSIZ, "source(\"%s\")",
- locate_file("rapi",".R",0));
- R_tryEval(
- VECTOR_ELT(
- R_ParseVector(
- mkString(rapiinclude),1, &status, R_NilValue),
0),R_GlobalEnv,&evalErr);
+ locate_file("rapi", ".R", 0));
+ R_tryEval(VECTOR_ELT(R_ParseVector(
+ mkString(rapiinclude), 1, &status, R_NilValue), 0), R_GlobalEnv,
&evalErr);
rapiInitialized++;
return 0;
}
-str RAPIparser(int *ret, str *rcall){
+str RAPIparser(int *ret, str *rcall) {
ParseStatus status;
str msg = NULL;
(void) ret;
(void) R_ParseVector(mkString(*rcall), INT_MAX, &status, R_NilValue);
- if (status != PARSE_OK)
+ if (status != PARSE_OK)
msg = createException(MAL, "rapi.eval", "%s", *rcall);
free(*rcall);
return msg;
@@ -198,11 +193,11 @@ str RAPIparser(int *ret, str *rcall){
str RAPIeval(Client cntxt, MalBlkPtr mb, MalStkPtr stk, InstrPtr pci) {
str exprStr = *(str*) getArgReference(stk, pci, pci->retc);
- SEXP x, env,retval;
+ SEXP x, env, retval;
SEXP varname = R_NilValue;
SEXP varvalue = R_NilValue;
ParseStatus status;
- int i,j, k=1;
+ int i, j, k = 1;
char buf[64] = "rapi";
char argnames[1000] = "";
char* rcall;
@@ -215,14 +210,13 @@ str RAPIeval(Client cntxt, MalBlkPtr mb,
BUN cnt;
int initstatus = 0;
-
rcall = malloc(strlen(exprStr) + sizeof(argnames) + 100);
- if (rcall==NULL) {
+ if (rcall == NULL) {
throw(MAL, "rapi.eval", MAL_MALLOC_FAIL);
}
args = (str*) GDKzalloc(sizeof(str) * pci->argc);
- if (args == NULL){
+ if (args == NULL) {
free(rcall);
throw(MAL, "rapi.eval", MAL_MALLOC_FAIL);
}
@@ -232,7 +226,7 @@ str RAPIeval(Client cntxt, MalBlkPtr mb,
initstatus = RAPIinitialize();
if (initstatus != 0) {
msg = createException(MAL, "rapi.eval",
- "failed to initialize R environment
(%i)",initstatus);
+ "failed to initialize R environment
(%i)", initstatus);
goto wrapup;
}
}
@@ -252,21 +246,22 @@ str RAPIeval(Client cntxt, MalBlkPtr mb,
for (i = pci->retc + 1; i < pci->argc; i++) {
// check for BAT or scalar first, keep code left
if (!isaBatType(getArgType(mb,pci,i))) {
- b = BATnew(TYPE_void, getArgType(mb,pci,i),0);
- if (b == NULL){
- msg= createException(MAL, "rapi.eval",
MAL_MALLOC_FAIL);
+ b = BATnew(TYPE_void, getArgType(mb, pci, i), 0);
+ if (b == NULL) {
+ msg = createException(MAL, "rapi.eval",
MAL_MALLOC_FAIL);
goto wrapup;
}
if ( getArgType(mb,pci,i) == TYPE_str)
- BUNappend(b, *(str*)
getArgReference(stk,pci,i), FALSE);
- else BUNappend(b, getArgReference(stk,pci,i), FALSE);
- BATsetcount(b,1);
- BATseqbase(b,0);
+ BUNappend(b, *(str*) getArgReference(stk, pci,
i), FALSE);
+ else
+ BUNappend(b, getArgReference(stk, pci, i),
FALSE);
+ BATsetcount(b, 1);
+ BATseqbase(b, 0);
BATsettrivprop(b);
} else {
b = BATdescriptor(*(int*) getArgReference(stk, pci, i));
- if (b == NULL){
- msg= createException(MAL, "rapi.eval",
MAL_MALLOC_FAIL);
+ if (b == NULL) {
+ msg = createException(MAL, "rapi.eval",
MAL_MALLOC_FAIL);
goto wrapup;
}
}
@@ -276,43 +271,49 @@ str RAPIeval(Client cntxt, MalBlkPtr mb,
switch (ATOMstorage(getTailType(getArgType(mb,pci,i)))) {
case TYPE_bte:
- BAT_TO_INTSXP(b,bte,varvalue);
+ BAT_TO_INTSXP(b, bte, varvalue)
+ ;
break;
case TYPE_sht:
- BAT_TO_INTSXP(b,sht,varvalue);
+ BAT_TO_INTSXP(b, sht, varvalue)
+ ;
break;
case TYPE_int:
- BAT_TO_INTSXP(b,int,varvalue);
+ BAT_TO_INTSXP(b, int, varvalue)
+ ;
break;
case TYPE_flt:
- BAT_TO_REALSXP(b,flt,varvalue);
+ BAT_TO_REALSXP(b, flt, varvalue)
+ ;
break;
case TYPE_dbl:
- BAT_TO_REALSXP(b,dbl,varvalue);
+ BAT_TO_REALSXP(b, dbl, varvalue)
+ ;
break;
case TYPE_lng: /* R's integers are stored as int, so we cannot
be sure long will fit */
- BAT_TO_REALSXP(b,lng,varvalue);
+ BAT_TO_REALSXP(b, lng, varvalue)
+ ;
break;
case TYPE_str: { // there is only one string type, thus no
macro here
- BUN p = 0, q = 0, j=0;
+ BUN p = 0, q = 0, j = 0;
BATiter li;
li = bat_iterator(b);
varvalue = PROTECT(NEW_STRING(BATcount(b)));
- BATloop(b, p, q) {
- const char *t = (const char *)
BUNtail(li, p);
- if (t == str_nil) {
- SET_STRING_ELT(varvalue, j,
NA_STRING);
- } else {
- SET_STRING_ELT(varvalue, j,
mkCharCE(t,CE_UTF8));
- }
- j++;
+ BATloop(b, p, q)
+ {
+ const char *t = (const char *) BUNtail(li, p);
+ if (t == str_nil) {
+ SET_STRING_ELT(varvalue, j, NA_STRING);
+ } else {
+ SET_STRING_ELT(varvalue, j, mkCharCE(t,
CE_UTF8));
}
+ j++;
}
+ }
break;
default:
// no clue what type to consider
- msg = createException(MAL, "rapi.eval",
- "unknown argument type");
+ msg = createException(MAL, "rapi.eval", "unknown
argument type");
goto wrapup;
}
BBPreleaseref(b->batCacheid);
@@ -329,17 +330,18 @@ str RAPIeval(Client cntxt, MalBlkPtr mb,
* this is also compatible with PL/R
*/
for (i = pci->retc + 1; i < pci->argc; i++) {
- strcat(argnames,args[i]);
- if (i < pci->argc-1) {
- strcat(argnames,",");
+ strcat(argnames, args[i]);
+ if (i < pci->argc - 1) {
+ strcat(argnames, ",");
}
}
- sprintf(rcall, "ret <-
as.data.frame((function(%s){%s})(%s),nm=NA,stringsAsFactors=F)\n", argnames,
- exprStr, argnames);
+ sprintf(rcall,
+ "ret <-
as.data.frame((function(%s){%s})(%s),nm=NA,stringsAsFactors=F)\n",
+ argnames, exprStr, argnames);
- #ifdef _RAPI_DEBUG_
- mnstr_printf(cntxt->fdout, "# Executed R expression %s\n",
rcall);
- #endif
+#ifdef _RAPI_DEBUG_
+ mnstr_printf(cntxt->fdout, "# Executed R expression %s\n", rcall);
+#endif
x = R_ParseVector(mkString(rcall), INT_MAX, &status, R_NilValue);
if (status != PARSE_OK) {
@@ -350,12 +352,12 @@ str RAPIeval(Client cntxt, MalBlkPtr mb,
/* parsing creates a separate call for each statement, since our r code
can consist of multiple statements, we need to evaluate each vector entry */
if (LENGTH(x) != 1) {
msg = createException(MAL, "rapi.eval", "%s", exprStr);
- goto wrapup;
+ goto wrapup;
}
- retval = R_tryEval(VECTOR_ELT(x, 0), env,&evalErr);
+ retval = R_tryEval(VECTOR_ELT(x, 0), env, &evalErr);
if (evalErr != FALSE) {
msg = createException(MAL, "rapi.eval", "%s", exprStr);
- goto wrapup;
+ goto wrapup;
}
// ret should be a data frame with exactly as many columns as we need
from retc
@@ -371,75 +373,86 @@ str RAPIeval(Client cntxt, MalBlkPtr mb,
for (i = 0; i < pci->retc; i++) {
SEXP ret_col = VECTOR_ELT(retval, i);
int bat_type = ATOMstorage(getTailType(getArgType(mb,pci,i)));
- int *ret = (int *)getArgReference(stk, pci, i);
- cnt = (BUN)ret_rows;
+ int *ret = (int *) getArgReference(stk, pci, i);
+ cnt = (BUN) ret_rows;
// check if return type is indeed a BAT
if (!isaBatType(getArgType(mb,pci,i))) {
- msg = createException(MAL, "rapi.eval","I only like BAT
return types");
+ msg = createException(MAL, "rapi.eval",
+ "I only like BAT return types");
goto wrapup;
}
// hand over the vector into a BAT
switch (bat_type) {
- case TYPE_int: {
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