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Don't allocate error messages
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@cornett
cornett committed Jan 11, 2019
1 parent 6751052 commit 85b409d
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Showing 4 changed files with 55 additions and 33 deletions.
2 changes: 1 addition & 1 deletion coho.h
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Original file line number Diff line number Diff line change
Expand Up @@ -84,7 +84,7 @@ struct coho_smiles {
const char *smiles;
int position;
int end;
char *error;
char error[32];
int error_position;

int atom_count;
Expand Down
2 changes: 1 addition & 1 deletion python/coho/smiles.pxd
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Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,7 @@ cdef extern from "coho.h":
int bond_count
coho_smiles_atom *atoms
coho_smiles_bond *bonds
char *error
char error[32]
int error_position

void coho_smiles_free(coho_smiles *)
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11 changes: 7 additions & 4 deletions python/coho/smiles.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -34,16 +34,19 @@ cdef class Parser:
def __dealloc__(self):
coho_smiles_free(&self._x)

cdef _has_error(self):
return self._x.error_position >= 0

def error(self):
"""Error message if last parse failed"""
if self._x.error != NULL:
if self._has_error():
return self._x.error.decode()

error = property(error, doc=error.__doc__)

def error_position(self):
"""Error position if last parse failed"""
if self._x.error != NULL:
if self._has_error():
return self._x.error_position

error_position = property(error_position, doc=error_position.__doc__)
Expand All @@ -59,7 +62,7 @@ cdef class Parser:

def atoms(self):
"""Atom information produced by the last parse."""
if self._x.error != NULL:
if self._has_error():
return None
x = []
def noneif(x, mark):
Expand Down Expand Up @@ -87,7 +90,7 @@ cdef class Parser:

def bonds(self):
"""Bond information produced by the last parse."""
if self._x.error != NULL:
if self._has_error():
return None
x = []
for i in range(self._x.bond_count):
Expand Down
73 changes: 46 additions & 27 deletions smiles.c
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Original file line number Diff line number Diff line change
Expand Up @@ -112,7 +112,6 @@ static int standard_valences[][4] = {
void
coho_smiles_free(struct coho_smiles *x)
{
free(x->error);
free(x->atoms);
free(x->bonds);
free(x->paren_stack);
Expand All @@ -126,7 +125,7 @@ coho_smiles_init(struct coho_smiles *x)
x->smiles = NULL;
x->position = 0;
x->end = 0;
x->error = NULL;
x->error[0] = '\0';
x->error_position = -1;

x->atom_count = 0;
Expand Down Expand Up @@ -164,7 +163,7 @@ coho_smiles_parse(struct coho_smiles *x, const char *smiles, size_t sz)

end = sz ? sz : strlen(smiles);
if (sz > INT_MAX) {
x->error = strdup("SMILES too long");
strlcpy(x->error, "SMILES too long", sizeof(x->error));
return COHO_NOMEM;
}
coho_smiles_reinit(x, smiles, end);
Expand All @@ -187,7 +186,9 @@ coho_smiles_parse(struct coho_smiles *x, const char *smiles, size_t sz)
*/
case INIT:
if (eos) {
x->error = strdup("empty SMILES");
strlcpy(x->error,
"empty SMILES",
sizeof(x->error));
goto err;
}

Expand All @@ -197,7 +198,9 @@ coho_smiles_parse(struct coho_smiles *x, const char *smiles, size_t sz)
}

else {
x->error = strdup("atom expected");
strlcpy(x->error,
"atom expected",
sizeof(x->error));
goto err;
}
state = ATOM_READ;
Expand Down Expand Up @@ -278,7 +281,9 @@ coho_smiles_parse(struct coho_smiles *x, const char *smiles, size_t sz)
if (rc == -1)
goto err;
} else {
x->error = strdup("atom must follow dot");
strlcpy(x->error,
"atom must follow dot",
sizeof(x->error));
goto err;
}
state = ATOM_READ;
Expand All @@ -294,7 +299,9 @@ coho_smiles_parse(struct coho_smiles *x, const char *smiles, size_t sz)
if (rc == -1)
goto err;
} else {
x->error = strdup("atom must follow bond");
strlcpy(x->error,
"atom must follow bond",
sizeof(x->error));
goto err;
}
state = ATOM_READ;
Expand All @@ -307,7 +314,9 @@ coho_smiles_parse(struct coho_smiles *x, const char *smiles, size_t sz)
case OPEN_PAREN_READ:

if (eos) {
x->error = strdup("unbalanced parenthesis");
strlcpy(x->error,
"unbalanced parenthesis",
sizeof(x->error));
x->error_position = x->position - 1;
goto err;
}
Expand All @@ -329,8 +338,9 @@ coho_smiles_parse(struct coho_smiles *x, const char *smiles, size_t sz)
}

else {
x->error = strdup("atom, bond, or dot "
"expected");
strlcpy(x->error,
"atom, bond, or dot expected",
sizeof(x->error));
goto err;
}
break;
Expand Down Expand Up @@ -385,7 +395,7 @@ coho_smiles_parse(struct coho_smiles *x, const char *smiles, size_t sz)
goto err;

if (x->paren_stack_count > 0) {
x->error = strdup("unbalanced parenthesis");
strlcpy(x->error, "unbalanced parenthesis", sizeof(x->error));
x->error_position = x->paren_stack[0].position;
goto err;
}
Expand All @@ -396,7 +406,7 @@ coho_smiles_parse(struct coho_smiles *x, const char *smiles, size_t sz)
return COHO_OK;

unexpected:
x->error = strdup("unexpected character");
strlcpy(x->error, "unexpected character", sizeof(x->error));
err:
if (x->error_position == -1)
x->error_position = x->position;
Expand All @@ -421,10 +431,10 @@ atom_class(struct coho_smiles *x, struct coho_smiles_atom *a)
a->length += t.n;

if ((n = integer(x, 8, &a->atom_class)) == -1) {
x->error = strdup("atom class too large");
strlcpy(x->error, "atom class too large", sizeof(x->error));
return -1;
} else if (n == 0) {
x->error = strdup("atom class expected");
strlcpy(x->error, "atom class expected", sizeof(x->error));
return -1;
}

Expand Down Expand Up @@ -485,7 +495,7 @@ add_bond(struct coho_smiles *x, struct coho_smiles_bond *bond)
else if (nb.atom1 < b->atom1)
continue;
else {
x->error = strdup("duplicate bond");
strlcpy(x->error, "duplicate bond", sizeof(x->error));
x->error_position = nb.position;
return -1;
}
Expand Down Expand Up @@ -537,7 +547,9 @@ add_ringbond(struct coho_smiles *x, int rnum, struct coho_smiles_bond *b)
/* Close the open bond */

if (rb->atom0 == b->atom0) {
x->error = strdup("Atom ring-bonded to itself");
strlcpy(x->error,
"atom ring-bonded to itself",
sizeof(x->error));
x->error_position = x->atoms[b->atom0].position;
return -1;
}
Expand All @@ -547,7 +559,9 @@ add_ringbond(struct coho_smiles *x, int rnum, struct coho_smiles_bond *b)
else if (b->order == COHO_SMILES_BOND_UNSPECIFIED)
; /* pass */
else if (rb->order != b->order) {
x->error = strdup("conflicting ring bond orders");
strlcpy(x->error,
"conflicting ring bond orders",
sizeof(x->error));
x->error_position = x->atoms[b->atom0].position;
return -1;
}
Expand Down Expand Up @@ -775,7 +789,7 @@ bracket_atom(struct coho_smiles *x, struct coho_smiles_atom *a)
return -1;

if (symbol(x, a) == 0) {
x->error = strdup("atom symbol expected");
strlcpy(x->error, "atom symbol expected", sizeof(x->error));
return -1;
}

Expand All @@ -792,7 +806,9 @@ bracket_atom(struct coho_smiles *x, struct coho_smiles_atom *a)
return -1;

if (!match(x, &t, 0, BRACKET_CLOSE)) {
x->error = strdup("bracket atom syntax error");
strlcpy(x->error,
"bracket atom syntax error",
sizeof(x->error));
return -1;
}
a->length += t.n;
Expand All @@ -811,7 +827,7 @@ check_ring_closures(struct coho_smiles *x)
if (x->open_ring_closures == 0)
return 0;

x->error = strdup("unclosed ring bond");
strlcpy(x->error, "unclosed ring bond", sizeof(x->error));

for (i = 0; i < 100; i++) {
if (x->ring_bonds[i].atom0 != -1) {
Expand Down Expand Up @@ -843,7 +859,7 @@ charge(struct coho_smiles *x, struct coho_smiles_atom *a)
length = t.n;

if ((n = integer(x, 2, &a->charge)) == -1) {
x->error = strdup("charge too large");
strlcpy(x->error, "charge too large", sizeof(x->error));
return -1;
} else if (n) {
a->charge *= sign;
Expand Down Expand Up @@ -1027,7 +1043,7 @@ isotope(struct coho_smiles *x, struct coho_smiles_atom *a)
int n;

if ((n = integer(x, 5, &a->isotope)) == -1) {
x->error = strdup("isotope too large");
strlcpy(x->error, "isotope too large", sizeof(x->error));
return -1;
}
a->length += n;
Expand Down Expand Up @@ -1095,7 +1111,7 @@ static int
pop_paren_stack(struct coho_smiles *x, int position, struct coho_smiles_bond *b)
{
if (!x->paren_stack_count) {
x->error = strdup("unbalanced parenthesis");
strlcpy(x->error, "unbalanced parenthesis", sizeof(x->error));
x->error_position = position;
return -1;
}
Expand Down Expand Up @@ -1164,13 +1180,17 @@ ringbond(struct coho_smiles *x, int anum)

if (t.type == PERCENT) {
if (!match(x, &t, 0, DIGIT)) {
x->error = strdup("ring bond expected");
strlcpy(x->error,
"ring bond expected",
sizeof(x->error));
return -1;
}
rnum = t.intval * 10;

if (!match(x, &t, 0, DIGIT)) {
x->error = strdup("2 digit ring bond expected");
strlcpy(x->error,
"2 digit ring bond expected",
sizeof(x->error));
return -1;
}
rnum += t.intval;
Expand Down Expand Up @@ -1260,8 +1280,7 @@ coho_smiles_reinit(struct coho_smiles *x, const char *smiles, size_t end)
x->smiles = smiles;
x->position = 0;
x->end = end;
free(x->error);
x->error = NULL;
x->error[0] = '\0';
x->error_position = -1;
x->atom_count = 0;
x->bond_count = 0;
Expand Down

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