Changeset: 6fe592bdf6cc for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=6fe592bdf6cc
Added Files:
monetdb5/extras/pyapi/Tests/pyapi01.malC
Modified Files:
monetdb5/extras/pyapi/Tests/All
monetdb5/extras/pyapi/Tests/pyapi02.malC
monetdb5/extras/pyapi/pyapi.c
Branch: pyapi
Log Message:
Fixed strings to work properly. Fixed a bug caused by multiple PyInterpreters.
It is now possible to return a single array rather than a list containing a
single array.
diffs (truncated from 470 to 300 lines):
diff --git a/monetdb5/extras/pyapi/Tests/All b/monetdb5/extras/pyapi/Tests/All
--- a/monetdb5/extras/pyapi/Tests/All
+++ b/monetdb5/extras/pyapi/Tests/All
@@ -1,2 +1,3 @@
HAVE_LIBPY?pyapi00
+HAVE_LIBPY?pyapi01
HAVE_LIBPY?pyapi02
diff --git a/monetdb5/extras/pyapi/Tests/pyapi01.malC
b/monetdb5/extras/pyapi/Tests/pyapi01.malC
new file mode 100644
--- /dev/null
+++ b/monetdb5/extras/pyapi/Tests/pyapi01.malC
@@ -0,0 +1,8 @@
+#strings testing
+bstr:= bat.new(:oid,:str);
+bat.append(bstr,"asdf":str);
+bat.append(bstr,"sd asd asd asd asd a":str);
+bat.append(bstr,"":str);
+bat.append(bstr,"test":str);
+rstr:bat[:oid,:str] := pyapi.eval(nil:ptr,"return(arg1)",bstr);
+io.print(rstr);
diff --git a/monetdb5/extras/pyapi/Tests/pyapi02.malC
b/monetdb5/extras/pyapi/Tests/pyapi02.malC
--- a/monetdb5/extras/pyapi/Tests/pyapi02.malC
+++ b/monetdb5/extras/pyapi/Tests/pyapi02.malC
@@ -2,14 +2,14 @@
# inty types
-bbit:= bat.new(:oid,:bit);
-bat.append(bbit,1:bit);
-bat.append(bbit,0:bit);
-bat.append(bbit,1:bit);
-bat.append(bbit,0:bit);
-bat.append(bbit,nil:bit);
-rbit:bat[:oid,:dbl] :=
pyapi.eval(nil:ptr,"print(arg1)\nreturn([numpy.add(arg1.filled(0),42)])",bbit);
-io.print(rbit);
+#bbit:= bat.new(:oid,:bit);
+#bat.append(bbit,1:bit);
+#bat.append(bbit,0:bit);
+#bat.append(bbit,1:bit);
+#bat.append(bbit,0:bit);
+#bat.append(bbit,nil:bit);
+#rbit:bat[:oid,:dbl] :=
pyapi.eval(nil:ptr,"return([numpy.add(arg1.filled(0),1)])",bbit);
+#io.print(rbit);
bbte:= bat.new(:oid,:bte);
bat.append(bbte,42:bte);
@@ -17,14 +17,15 @@ bat.append(bbte,84:bte);
bat.append(bbte,111:bte);
bat.append(bbte,0:bte);
bat.append(bbte,nil:bte);
-rbte:bat[:oid,:dbl] := pyapi.eval(nil:ptr,"return([[42,43]])",bbte);
+io.print(bbte);
+rbte:bat[:oid,:dbl] := pyapi.eval(nil:ptr,"return numpy.add(arg1, 99)",bbte);
io.print(rbte);
bsht:= bat.new(:oid,:sht);
bat.append(bsht,42:sht);
bat.append(bsht,82:sht);
bat.append(bsht,0:sht);
-bat.append(bsht,3276:sht);
+bat.append(bsht,240:sht);
bat.append(bsht,nil:sht);
rsht:bat[:oid,:dbl] :=
pyapi.eval(nil:ptr,"return([numpy.add(arg1.filled(0),1)])",bsht);
io.print(rsht);
@@ -43,6 +44,7 @@ bat.append(bwrd,1804289383:wrd);
bat.append(bwrd,846930886:wrd);
bat.append(bwrd,1681692777:wrd);
bat.append(bwrd,1714636915:wrd);
+bat.append(bwrd,nil:wrd);
rwrd:bat[:oid,:dbl] :=
pyapi.eval(nil:ptr,"return([numpy.add(arg1.filled(0),1)])",bwrd);
io.print(rwrd);
@@ -70,7 +72,8 @@ bat.append(bflt,18042.89383:flt);
bat.append(bflt,846.930886:flt);
bat.append(bflt,16.81692777:flt);
bat.append(bflt,1714636.915:flt);
-rflt:bat[:oid,:dbl] := pyapi.eval(nil:ptr,"return([numpy.add(arg1,1)])",bflt);
+bat.append(bflt,nil:flt);
+rflt:bat[:oid,:dbl] :=
pyapi.eval(nil:ptr,"return([numpy.add(arg1.filled(0),1)])",bflt);
io.print(rflt);
bdbl:= bat.new(:oid,:dbl);
@@ -79,18 +82,18 @@ bat.append(bdbl,84.6930886:dbl);
bat.append(bdbl,168169.2777:dbl);
bat.append(bdbl,17146369.15:dbl);
bat.append(bdbl,nil:dbl);
-rdbl:bat[:oid,:dbl] := pyapi.eval(nil:ptr,"return([numpy.add(arg1,1)])",bdbl);
+rdbl:bat[:oid,:dbl] :=
pyapi.eval(nil:ptr,"return([numpy.add(arg1.filled(0),1)])",bdbl);
io.print(rdbl);
# strings
-bstr:= bat.new(:oid,:str);
-bat.append(bstr,"asdf":str);
-bat.append(bstr,"sd asd asd asd asd a":str);
-bat.append(bstr,"":str);
-bat.append(bstr,nil:str);
-rstr:bat[:oid,:int] := pyapi.eval(nil:ptr,"unlist(lapply(arg1,nchar))",bstr);
-io.print(rstr);
+#bstr:= bat.new(:oid,:str);
+#bat.append(bstr,"asdf":str);
+#bat.append(bstr,"sd asd asd asd asd a":str);
+#bat.append(bstr,"":str);
+#bat.append(bstr,"test":str);
+#rstr:bat[:oid,:int] :=
pyapi.eval(nil:ptr,"print(arg1);\nreturn([arg1])",bstr);
+#io.print(rstr);
@@ -103,26 +106,26 @@ bat.append(binto,1681692777:int);
bat.append(binto,1714636915:int);
bat.append(binto,nil:int);
-rintbi:bat[:oid,:int] := pyapi.eval(nil:ptr,"arg1",binto);
+rintbi:bat[:oid,:int] := pyapi.eval(nil:ptr,"return [arg1.filled(0)]",binto);
io.print(rintbi);
-rintbi2:bat[:oid,:int] := pyapi.eval(nil:ptr,"as.integer(arg1)",binto);
-io.print(rintbi2);
+# rintbi2:bat[:oid,:int] := pyapi.eval(nil:ptr,"as.integer(arg1)",binto);
+# io.print(rintbi2);
-rintbl:bat[:oid,:lng] := pyapi.eval(nil:ptr,"as.integer(arg1)",binto);
-io.print(rintbl);
+# rintbl:bat[:oid,:lng] := pyapi.eval(nil:ptr,"as.integer(arg1)",binto);
+# io.print(rintbl);
-rintbh:bat[:oid,:hge] := pyapi.eval(nil:ptr,"as.integer(arg1)",binto);
-io.print(rintbh);
+# rintbh:bat[:oid,:hge] := pyapi.eval(nil:ptr,"as.integer(arg1)",binto);
+# io.print(rintbh);
-rintbd:bat[:oid,:dbl] := pyapi.eval(nil:ptr,"as.numeric(arg1)",binto);
-io.print(rintbd);
+# rintbd:bat[:oid,:dbl] := pyapi.eval(nil:ptr,"as.numeric(arg1)",binto);
+# io.print(rintbd);
-rintbs:bat[:oid,:str] := pyapi.eval(nil:ptr,"as.character(arg1)",binto);
-io.print(rintbs);
+# rintbs:bat[:oid,:str] := pyapi.eval(nil:ptr,"as.character(arg1)",binto);
+# io.print(rintbs);
-# factors should be strings
-rintbf:bat[:oid,:str] := pyapi.eval(nil:ptr,"as.factor(arg1)",binto);
-io.print(rintbf);
+# # factors should be strings
+# rintbf:bat[:oid,:str] := pyapi.eval(nil:ptr,"as.factor(arg1)",binto);
+# io.print(rintbf);
diff --git a/monetdb5/extras/pyapi/pyapi.c b/monetdb5/extras/pyapi/pyapi.c
--- a/monetdb5/extras/pyapi/pyapi.c
+++ b/monetdb5/extras/pyapi/pyapi.c
@@ -27,12 +27,15 @@
#include <string.h>
const char* pyapi_enableflag = "embedded_py";
+char *NPYConstToString(int);
+bool IsPyArrayObject(PyObject *);
int PyAPIEnabled(void) {
return (GDKgetenv_istrue(pyapi_enableflag)
|| GDKgetenv_isyes(pyapi_enableflag));
}
+
// TODO: exclude pyapi from mergetable, too
// TODO: add to SQL layer
// TODO: can we call the Python interpreter in a multi-thread environment?
@@ -49,7 +52,14 @@ static int pyapiInitialized = FALSE;
PyArrayObject* pCol = (PyArrayObject*) PyArray_FromAny(pColO, \
PyArray_DescrFromType(nptpe), 1, 1, NPY_ARRAY_CARRAY |
\
NPY_ARRAY_FORCECAST, NULL);
\
- size_t cnt = PyArray_DIMS(pCol)[0], j; \
+ size_t cnt = 0; \
+ if (pCol == NULL)
\
+ {
\
+ pCol = (PyArrayObject*) PyArray_FromAny(pColO, NULL, 1,
1, NPY_ARRAY_CARRAY, NULL); \
+ msg = createException(MAL, "pyapi.eval", "Wrong return
type in python function. Expected an array of type \"%s\" as return value, but
the python function returned an array of type \"%s\".", #mtpe,
NPYConstToString(PyArray_DTYPE(pCol)->type_num)); \
+ goto wrapup;
\
+ }
\
+ cnt = PyArray_DIMS(pCol)[0], j; \
bat = BATnew(TYPE_void, TYPE_##mtpe, cnt, TRANSIENT); \
BATseqbase(bat, 0); bat->T->nil = 0; bat->T->nonil = 1; \
bat->tkey = 0; bat->tsorted = 0; bat->trevsorted = 0; \
@@ -58,6 +68,7 @@ static int pyapiInitialized = FALSE;
*(mtpe*) PyArray_GETPTR1(pCol, j); }
\
BATsetcount(bat, cnt); }
+//todo: NULL
// TODO: also handle the case if someone returns a masked array
#define _PYAPI_DEBUG_
@@ -97,8 +108,12 @@ str PyAPIeval(MalBlkPtr mb, MalStkPtr st
node * argnode;
int seengrp = FALSE;
PyObject *pArgs, *pResult; // this is going to be the parameter tuple
- PyThreadState* tstate;
+ BUN p = 0, q = 0;
+ BATiter li;
+ size_t count;
+ size_t maxsize;
+ size_t j;
if (!PyAPIEnabled()) {
throw(MAL, "pyapi.eval",
@@ -120,7 +135,7 @@ str PyAPIeval(MalBlkPtr mb, MalStkPtr st
// this isolates our interpreter, so it's safe to run pyapi
multithreaded
// TODO: verify this
- tstate = Py_NewInterpreter();
+ /*tstate = Py_NewInterpreter();*/
// first argument after the return contains the pointer to the sql_func
structure
if (sqlfun != NULL && sqlfun->ops->cnt > 0) {
@@ -178,7 +193,6 @@ str PyAPIeval(MalBlkPtr mb, MalStkPtr st
}
}
-
switch (ATOMstorage(getColumnType(getArgType(mb,pci,i)))) {
case TYPE_bte:
vararray = BAT_TO_NP(b, bte, NPY_INT8);
@@ -198,8 +212,49 @@ str PyAPIeval(MalBlkPtr mb, MalStkPtr st
case TYPE_dbl:
vararray = BAT_TO_NP(b, dbl, NPY_FLOAT64);
break;
+ case TYPE_str:
+ li = bat_iterator(b);
- // TODO: implement other types (strings, boolean)
+ //we first loop over all the strings in the BAT to find
the maximum length of a single string
+ //this is because NUMPY only supports strings with a
fixed maximum length
+ maxsize = 0;
+ count = BATcount(b);
+ BATloop(b, p, q)
+ {
+ const char *t = (const char *) BUNtail(li, p);
+ const size_t length = (const size_t) strlen(t);
+
+ if (strlen(t) > maxsize)
+ maxsize = length;
+
+ }
+
+ //create a NPY_STRING array object
+ vararray = PyArray_New(
+ &PyArray_Type,
+ 1,
+ (npy_intp[1]) {count},
+ NPY_STRING,
+ NULL,
+ NULL,
+ maxsize,
+ 0,
+ NULL);
+
+ //fill the NPY_STRING array object using the
PyArray_SETITEM function
+ j = 0;
+ BATloop(b, p, q)
+ {
+ const char *t = (const char *) BUNtail(li, p);
+ PyArray_SETITEM((PyArrayObject*)vararray,
PyArray_GETPTR1((PyArrayObject*)vararray, j), PyString_FromString(t));
+ j++;
+ }
+ break;
+ case TYPE_hge:
+ vararray = BAT_TO_NP(b, hge, NPY_LONGLONG);
+ break;
+
+ // TODO: implement other types (boolean)
default:
msg = createException(MAL, "pyapi.eval", "unknown
argument type ");
goto wrapup;
@@ -218,7 +273,8 @@ str PyAPIeval(MalBlkPtr mb, MalStkPtr st
int (*atomcmp)(const void *, const void *) =
ATOMcompare(b->ttype);
BATiter bi = bat_iterator(b);
- if (b->T->nil) {
+ if (b->T->nil)
+ {
size_t j;
for (j = 0; j < BATcount(b); j++) {
if ((*atomcmp)(BUNtail(bi, BUNfirst(b)
+ j), nil) == 0) {
@@ -227,8 +283,10 @@ str PyAPIeval(MalBlkPtr mb, MalStkPtr st
}
}
}
+
PyTuple_SetItem(maargs, 0, vararray);
PyTuple_SetItem(maargs, 1, (PyObject*) nullmask);
+
vararray = PyObject_CallObject(mafunc, maargs);
if (!vararray) {
msg = createException(MAL, "pyapi.eval",
"UUUH");
@@ -241,7 +299,6 @@ str PyAPIeval(MalBlkPtr mb, MalStkPtr st
// TODO: do this later
BBPunfix(b->batCacheid);
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