END_TEST
START_TEST (test_L3FormulaFormatter_parseUnits)
{
StringBuffer_t *sb = StringBuffer_create(42);
char *s = StringBuffer_getBuffer(sb);
ASTNode_t *n = ASTNode_create();
L3ParserSettings_t* l3ps = L3ParserSettings_create();
ASTNode_setReal(n, 1.1);
ASTNode_setUnits(n, "mL");
//default (true)
s = SBML_formulaToL3StringWithSettings(n, l3ps);
fail_unless( !strcmp(s, "1.1 mL"), NULL );
safe_free(s);
//explicit false
L3ParserSettings_setParseUnits(l3ps, 0);
s = SBML_formulaToL3StringWithSettings(n, l3ps);
fail_unless( !strcmp(s, "1.1"), NULL );
safe_free(s);
//explicit true
L3ParserSettings_setParseUnits(l3ps, 1);
s = SBML_formulaToL3StringWithSettings(n, l3ps);
fail_unless( !strcmp(s, "1.1 mL"), NULL );
safe_free(s);
ASTNode_free(n);
L3ParserSettings_free(l3ps);
}
END_TEST
START_TEST (test_L3FormulaFormatter_multiGT)
{
StringBuffer_t *sb = StringBuffer_create(42);
char *s = StringBuffer_getBuffer(sb);
ASTNode_t *n = ASTNode_create();
ASTNode_t *c = ASTNode_create();
ASTNode_setType(n, AST_RELATIONAL_GT);
s = SBML_formulaToL3String(n);
fail_unless( !strcmp(s, "gt()"), NULL );
ASTNode_setName(c, "x");
ASTNode_addChild(n, c);
s = SBML_formulaToL3String(n);
fail_unless( !strcmp(s, "gt(x)"), NULL );
safe_free(s);
c = ASTNode_create();
ASTNode_setName(c, "y");
ASTNode_addChild(n, c);
s = SBML_formulaToL3String(n);
fail_unless( !strcmp(s, "x > y"), NULL );
safe_free(s);
c = ASTNode_create();
ASTNode_setName(c, "z");
ASTNode_addChild(n, c);
s = SBML_formulaToL3String(n);
fail_unless( !strcmp(s, "gt(x, y, z)"), NULL );
safe_free(s);
ASTNode_free(n);
}
/**
* Post event or status data message to mmonit
* @param E An event object or NULL for status data
* @return If failed, return HANDLER_MMONIT flag or HANDLER_SUCCEEDED flag if succeeded
*/
int handle_mmonit(Event_T E) {
int rv = HANDLER_MMONIT;
Socket_T socket = NULL;
Mmonit_T C = Run.mmonits;
/* The event is sent to mmonit just once - only in the case that the state changed */
if (! C || (E && ! E->state_changed))
return HANDLER_SUCCEEDED;
StringBuffer_T sb = StringBuffer_create(256);
for (; C; C = C->next) {
if (! (socket = socket_create_t(C->url->hostname, C->url->port, SOCKET_TCP, C->ssl, C->timeout))) {
LogError("M/Monit: cannot open a connection to %s -- %s\n", C->url->url, STRERROR);
goto error;
}
status_xml(sb, E, E ? LEVEL_SUMMARY : LEVEL_FULL, 2, socket_get_local_host(socket));
if (! data_send(socket, C, StringBuffer_toString(sb))) {
LogError("M/Monit: cannot send %s message to %s\n", E ? "event" : "status", C->url->url);
goto error;
}
StringBuffer_clear(sb);
socket_shutdown_write(socket);
if (! data_check(socket, C)) {
LogError("M/Monit: %s message to %s failed\n", E ? "event" : "status", C->url->url);
goto error;
}
rv = HANDLER_SUCCEEDED; // Return success if at least one M/Monit succeeded
DEBUG("M/Monit: %s message sent to %s\n", E ? "event" : "status", C->url->url);
error:
if (socket)
socket_free(&socket);
}
StringBuffer_free(&sb);
return rv;
}
END_TEST
START_TEST (test_FormulaFormatter_multiPlusTimes)
{
StringBuffer_t *sb = StringBuffer_create(42);
char *s = StringBuffer_getBuffer(sb);
ASTNode_t *n = ASTNode_create();
ASTNode_t *c = ASTNode_create();
ASTNode_setType(n, AST_PLUS);
ASTNode_setName(c, "x");
ASTNode_addChild(n, c);
c = ASTNode_create();
ASTNode_setName(c, "y");
ASTNode_addChild(n, c);
c = ASTNode_create();
ASTNode_setName(c, "z");
ASTNode_addChild(n, c);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, "x + y + z"), NULL );
ASTNode_setType(n, AST_TIMES);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, "x * y * z"), NULL );
safe_free(s);
ASTNode_free(n);
}
END_TEST
START_TEST (test_FormulaFormatter_multiDivide)
{
StringBuffer_t *sb = StringBuffer_create(42);
char *s = StringBuffer_getBuffer(sb);
ASTNode_t *n = ASTNode_create();
ASTNode_t *c = ASTNode_create();
ASTNode_setType(n, AST_DIVIDE);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, " / "), NULL );
ASTNode_setName(c, "x");
ASTNode_addChild(n, c);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, " / (x)"), NULL );
safe_free(s);
c = ASTNode_create();
ASTNode_setName(c, "y");
ASTNode_addChild(n, c);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, "x / y"), NULL );
safe_free(s);
c = ASTNode_create();
ASTNode_setName(c, "z");
ASTNode_addChild(n, c);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, "x / y / z"), NULL );
safe_free(s);
ASTNode_free(n);
}
END_TEST
START_TEST (test_FormulaFormatter_multiOr)
{
StringBuffer_t *sb = StringBuffer_create(42);
char *s = StringBuffer_getBuffer(sb);
ASTNode_t *n = ASTNode_create();
ASTNode_t *c = ASTNode_create();
ASTNode_setType(n, AST_LOGICAL_OR);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, "or()"), NULL );
ASTNode_setName(c, "x");
ASTNode_addChild(n, c);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, "or(x)"), NULL );
safe_free(s);
c = ASTNode_create();
ASTNode_setName(c, "y");
ASTNode_addChild(n, c);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, "or(x, y)"), NULL );
safe_free(s);
c = ASTNode_create();
ASTNode_setName(c, "z");
ASTNode_addChild(n, c);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, "or(x, y, z)"), NULL );
safe_free(s);
ASTNode_free(n);
}
END_TEST
START_TEST (test_L3FormulaFormatter_multiAnd)
{
StringBuffer_t *sb = StringBuffer_create(42);
char *s = StringBuffer_getBuffer(sb);
ASTNode_t *n = ASTNode_create();
ASTNode_t *c = ASTNode_create();
ASTNode_setType(n, AST_LOGICAL_AND);
s = SBML_formulaToL3String(n);
fail_unless( !strcmp(s, "and()"), NULL );
ASTNode_setName(c, "x");
ASTNode_addChild(n, c);
s = SBML_formulaToL3String(n);
fail_unless( !strcmp(s, "and(x)"), NULL );
safe_free(s);
c = ASTNode_create();
ASTNode_setName(c, "y");
ASTNode_addChild(n, c);
s = SBML_formulaToL3String(n);
fail_unless( !strcmp(s, "x && y"), NULL );
safe_free(s);
c = ASTNode_create();
ASTNode_setName(c, "z");
ASTNode_addChild(n, c);
s = SBML_formulaToL3String(n);
fail_unless( !strcmp(s, "x && y && z"), NULL );
safe_free(s);
ASTNode_free(n);
}
/**
* @return the given formula AST as a directed graph. The caller
* owns the returned string and is responsible for freeing it.
*/
char *
SBML_formulaToDot (const ASTNode_t *tree)
{
StringBuffer_t *sb = StringBuffer_create(128);
char *name;
char *s;
if (FormulaGraphvizFormatter_isFunction(tree)
|| ASTNode_isOperator(tree))
{
FormulaGraphvizFormatter_visit(NULL, tree, sb);
}
else
{
name = FormulaGraphvizFormatter_format(tree);
StringBuffer_append(sb, name);
}
StringBuffer_append(sb, "}\n");
s = StringBuffer_getBuffer(sb);
free(sb);
return s;
}
T SqlServerConnection_new(URL_T url, char **error) {
T C;
SqlServer_T db;
assert(url);
assert(error);
if (! (db = doConnect(url, error)))
return NULL;
NEW(C);
C->db = db;
C->url = url;
C->timeout = SQL_DEFAULT_TIMEOUT;
C->sb = StringBuffer_create(STRLEN);
C->err = StringBuffer_create(STRLEN);
// if (! setProperties(C, error))
// SqlServerConnection_free(&C);
return C;
}
/**
* Since graphviz will interpret identical names as referring to
* the same node presentation-wise it is better if each function node
* has a unique name.
*
* Returns the name of the function with the name of the first child
* prepended
*
* THIS COULD BE DONE BETTER
*/
char *
FormulaGraphvizFormatter_FunctionGetUniqueName (const ASTNode_t *node)
{
char *s;
StringBuffer_t *p = StringBuffer_create(128);
ASTNodeType_t type = ASTNode_getType(node);
if (ASTNode_getNumChildren(node) != 0)
{
const char* name = ASTNode_getName(ASTNode_getChild(node,0));
if (name != NULL)
StringBuffer_append(p, name);
}
else
{
StringBuffer_append(p, "unknown");
}
switch (type)
{
case AST_FUNCTION_ARCCOS:
StringBuffer_append(p, "acos");
break;
case AST_FUNCTION_ARCSIN:
StringBuffer_append(p, "asin");
break;
case AST_FUNCTION_ARCTAN:
StringBuffer_append(p, "atan");
break;
case AST_FUNCTION_CEILING:
StringBuffer_append(p, "ceil");
break;
case AST_FUNCTION_LN:
StringBuffer_append(p, "log");
break;
case AST_FUNCTION_POWER:
StringBuffer_append(p, "pow");
break;
default:
if (ASTNode_getName(node) != NULL)
{
StringBuffer_append(p, ASTNode_getName(node));
}
break;
}
s = StringBuffer_toString(p);
free(p);
return s;
}
void
StringBufferTest_setup (void)
{
SB = StringBuffer_create(10);
if (SB == NULL)
{
fail("StringBuffer_create(10) returned a NULL pointer.");
}
}
/**
* Read all processes to initialize the information tree.
* @param reference reference of ProcessTree
* @return treesize>0 if succeeded otherwise =0.
*/
int initprocesstree_sysdep(ProcessTree_T **reference) {
int treesize;
static kvm_t *kvm_handle;
ProcessTree_T *pt;
struct kinfo_proc *pinfo;
if (! (kvm_handle = kvm_open(NULL, _PATH_DEVNULL, NULL, O_RDONLY, prog))) {
LogError("system statistic error -- cannot initialize kvm interface\n");
return 0;
}
pinfo = kvm_getprocs(kvm_handle, KERN_PROC_PROC, 0, &treesize);
if (! pinfo || (treesize < 1)) {
LogError("system statistic error -- cannot get process tree\n");
kvm_close(kvm_handle);
return 0;
}
pt = CALLOC(sizeof(ProcessTree_T), treesize);
for (int i = 0; i < treesize; i++) {
StringBuffer_T cmdline = StringBuffer_create(64);
pt[i].pid = pinfo[i].ki_pid;
pt[i].ppid = pinfo[i].ki_ppid;
pt[i].uid = pinfo[i].ki_ruid;
pt[i].euid = pinfo[i].ki_uid;
pt[i].gid = pinfo[i].ki_rgid;
pt[i].starttime = pinfo[i].ki_start.tv_sec;
pt[i].cputime = (long)(pinfo[i].ki_runtime / 100000);
pt[i].mem_kbyte = (unsigned long)(pinfo[i].ki_rssize * pagesize_kbyte);
int flags = pinfo[i].ki_stat;
char * procname = pinfo[i].ki_comm;
if (flags == SZOMB)
pt[i].zombie = true;
pt[i].cpu_percent = 0;
pt[i].time = get_float_time();
char **args;
if ((args = kvm_getargv(kvm_handle, &pinfo[i], 0))) {
for (int j = 0; args[j]; j++)
StringBuffer_append(cmdline, args[j + 1] ? "%s " : "%s", args[j]);
pt[i].cmdline = Str_dup(StringBuffer_toString(StringBuffer_trim(cmdline)));
}
StringBuffer_free(&cmdline);
if (! pt[i].cmdline || ! *pt[i].cmdline) {
FREE(pt[i].cmdline);
pt[i].cmdline = Str_dup(procname);
}
}
*reference = pt;
kvm_close(kvm_handle);
return treesize;
}
/**
* Read all processes to initialize the information tree.
* @param reference reference of ProcessTree
* @param pflags Process engine flags
* @return treesize > 0 if succeeded otherwise 0.
*/
int initprocesstree_sysdep(ProcessTree_T **reference, ProcessEngine_Flags pflags) {
kvm_t *kvm_handle = kvm_open(NULL, _PATH_DEVNULL, NULL, O_RDONLY, prog);
if (! kvm_handle) {
LogError("system statistic error -- cannot initialize kvm interface\n");
return 0;
}
int treesize;
struct kinfo_proc *pinfo = kvm_getprocs(kvm_handle, KERN_PROC_ALL, 0, &treesize);
if (! pinfo || (treesize < 1)) {
LogError("system statistic error -- cannot get process tree\n");
kvm_close(kvm_handle);
return 0;
}
ProcessTree_T *pt = CALLOC(sizeof(ProcessTree_T), treesize);
StringBuffer_T cmdline = NULL;
if (pflags & ProcessEngine_CollectCommandLine)
cmdline = StringBuffer_create(64);
for (int i = 0; i < treesize; i++) {
pt[i].pid = pinfo[i].kp_pid;
pt[i].ppid = pinfo[i].kp_ppid;
pt[i].cred.uid = pinfo[i].kp_ruid;
pt[i].cred.euid = pinfo[i].kp_uid;
pt[i].cred.gid = pinfo[i].kp_rgid;
pt[i].threads = pinfo[i].kp_nthreads;
pt[i].uptime = systeminfo.time / 10. - pinfo[i].kp_start.tv_sec;
pt[i].cpu.time = (double)((pinfo[i].kp_lwp.kl_uticks + pinfo[i].kp_lwp.kl_sticks + pinfo[i].kp_lwp.kl_iticks) / 1000000.);
pt[i].memory.usage = (uint64_t)pinfo[i].kp_vm_rssize * (uint64_t)pagesize;
pt[i].zombie = pinfo[i].kp_stat == SZOMB ? true : false;
if (pflags & ProcessEngine_CollectCommandLine) {
char **args = kvm_getargv(kvm_handle, &pinfo[i], 0);
if (args) {
StringBuffer_clear(cmdline);
for (int j = 0; args[j]; j++)
StringBuffer_append(cmdline, args[j + 1] ? "%s " : "%s", args[j]);
if (StringBuffer_length(cmdline))
pt[i].cmdline = Str_dup(StringBuffer_toString(StringBuffer_trim(cmdline)));
}
if (! pt[i].cmdline || ! *pt[i].cmdline) {
FREE(pt[i].cmdline);
pt[i].cmdline = Str_dup(pinfo[i].kp_comm);
}
}
}
if (pflags & ProcessEngine_CollectCommandLine)
StringBuffer_free(&cmdline);
*reference = pt;
kvm_close(kvm_handle);
return treesize;
}
T PostgresqlConnection_new(URL_T url, char **error) {
T C;
assert(url);
assert(error);
NEW(C);
C->url = url;
C->sb = StringBuffer_create(STRLEN);
C->timeout = SQL_DEFAULT_TIMEOUT;
if (! _doConnect(C, error))
PostgresqlConnection_free(&C);
return C;
}
/**
* Returns a new HttpResponse object wrapping a default response. Use
* the set_XXX methods to change the object.
*/
static HttpResponse create_HttpResponse(Socket_T S) {
HttpResponse res= NULL;
NEW(res);
res->S= S;
res->status= SC_OK;
res->outputbuffer= StringBuffer_create(256);
res->is_committed= FALSE;
res->protocol= SERVER_PROTOCOL;
res->status_msg= get_status_string(SC_OK);
return res;
}
/**
* Formats the given ASTNode as a directed graph function name and returns the
* result as a string.
*/
char *
FormulaGraphvizFormatter_formatFunction (const ASTNode_t *node)
{
char *s;
StringBuffer_t *p = StringBuffer_create(128);
ASTNodeType_t type = ASTNode_getType(node);
switch (type)
{
case AST_FUNCTION_ARCCOS:
s = "acos";
break;
case AST_FUNCTION_ARCSIN:
s = "asin";
break;
case AST_FUNCTION_ARCTAN:
s = "atan";
break;
case AST_FUNCTION_CEILING:
s = "ceil";
break;
case AST_FUNCTION_LN:
s = "log";
break;
case AST_FUNCTION_POWER:
s = "pow";
break;
default:
if (ASTNode_getName(node) == NULL)
{
StringBuffer_append(p, "unknown");
}
else
{
StringBuffer_append(p, ASTNode_getName(node));
}
s = StringBuffer_toString(p);
break;
}
free(p);
return s;
}
T MysqlConnection_new(URL_T url, char **error) {
T C;
MYSQL *db;
assert(url);
assert(error);
if (! (db = doConnect(url, error)))
return NULL;
NEW(C);
C->db = db;
C->url = url;
C->sb = StringBuffer_create(STRLEN);
C->timeout = SQL_DEFAULT_TIMEOUT;
return C;
}
T OracleConnection_new(URL_T url, char **error) {
T C;
assert(url);
assert(error);
NEW(C);
C->url = url;
C->sb = StringBuffer_create(STRLEN);
C->timeout = SQL_DEFAULT_TIMEOUT;
if (! doConnect(C, url, error)) {
OracleConnection_free(&C);
return NULL;
}
C->txnhp = NULL;
return C;
}
LIBSBML_EXTERN
char *
SBML_formulaToL3StringWithSettings (const ASTNode_t *tree, const L3ParserSettings_t *settings)
{
char *s;
StringBuffer_t *sb = StringBuffer_create(128);
if (tree == NULL)
{
return NULL;
}
L3FormulaFormatter_visit(NULL, tree, sb, settings);
s = StringBuffer_getBuffer(sb);
safe_free(sb);
return s;
}
int check_http(Socket_T socket) {
Port_T P;
char host[STRLEN];
char auth[STRLEN] = {};
const char *request = NULL;
const char *hostheader = NULL;
ASSERT(socket);
P = socket_get_Port(socket);
ASSERT(P);
request = P->request ? P->request : "/";
hostheader = _findHostHeaderIn(P->http_headers);
hostheader = hostheader ? hostheader : P->request_hostheader
? P->request_hostheader : Util_getHTTPHostHeader(socket, host, STRLEN); // Otherwise use deprecated request_hostheader or default host
StringBuffer_T sb = StringBuffer_create(168);
StringBuffer_append(sb,
"GET %s HTTP/1.1\r\n"
"Host: %s\r\n"
"Accept: */*\r\n"
"User-Agent: Monit/%s\r\n"
"%s",
request, hostheader, VERSION,
get_auth_header(P, auth, STRLEN));
// Add headers if we have them
if (P->http_headers) {
for (list_t p = P->http_headers->head; p; p = p->next) {
if (Str_startsWith(p->e, "Host")) // Already set contrived above
continue;
StringBuffer_append(sb, "%s\r\n", p->e);
}
}
StringBuffer_append(sb, "\r\n");
int send_status = socket_write(socket, (void*)StringBuffer_toString(sb), StringBuffer_length(sb));
StringBuffer_free(&sb);
if (send_status < 0) {
socket_setError(socket, "HTTP: error sending data -- %s", STRERROR);
return FALSE;
}
return check_request(socket, P);
}
/**
* Formats the given ASTNode as a directed graph token and returns the result as
* a string.
*/
char *
FormulaGraphvizFormatter_format (const ASTNode_t *node)
{
StringBuffer_t *p = StringBuffer_create(128);
char *s = NULL;
if (ASTNode_isOperator(node))
{
s = FormulaGraphvizFormatter_formatOperator(node);
}
else if (ASTNode_isFunction(node))
{
s = FormulaGraphvizFormatter_formatFunction(node);
}
else if (ASTNode_isInteger(node))
{
StringBuffer_appendInt(p, ASTNode_getInteger(node));
s = StringBuffer_toString(p);
}
else if (ASTNode_isRational(node))
{
s = FormulaGraphvizFormatter_formatRational(node);
}
else if (ASTNode_isReal(node))
{
s = FormulaGraphvizFormatter_formatReal(node);
}
else if ( !ASTNode_isUnknown(node) )
{
if (ASTNode_getName(node) == NULL)
{
StringBuffer_append(p, "unknown");
}
else
{
StringBuffer_append(p, ASTNode_getName(node));
}
s = StringBuffer_toString(p);
}
free(p);
return s;
}
/**
* Formats the given ASTNode as a rational number and returns the result as
* a string. This amounts to:
*
* "(numerator/denominator)"
*/
char *
FormulaGraphvizFormatter_formatRational (const ASTNode_t *node)
{
char *s;
StringBuffer_t *p = StringBuffer_create(128);
StringBuffer_appendChar( p, '(');
StringBuffer_appendInt ( p, ASTNode_getNumerator(node) );
StringBuffer_appendChar( p, '/');
StringBuffer_appendInt ( p, ASTNode_getDenominator(node) );
StringBuffer_appendChar( p, ')');
s = StringBuffer_toString(p);
free(p);
return s;
}
END_TEST
START_TEST (test_L3FormulaFormatter_collapseMinus)
{
StringBuffer_t *sb = StringBuffer_create(42);
char *s = StringBuffer_getBuffer(sb);
ASTNode_t *n = ASTNode_create();
ASTNode_t *c = ASTNode_create();
ASTNode_t *c2 = ASTNode_create();
ASTNode_t *c3 = ASTNode_create();
ASTNode_t *c4 = ASTNode_create();
L3ParserSettings_t* l3ps = L3ParserSettings_create();
ASTNode_setType(n, AST_MINUS);
ASTNode_setType(c, AST_MINUS);
ASTNode_addChild(n, c);
ASTNode_setType(c2, AST_MINUS);
ASTNode_addChild(c, c2);
ASTNode_setType(c3, AST_MINUS);
ASTNode_addChild(c2, c3);
ASTNode_setName(c4, "x");
ASTNode_addChild(c3, c4);
//default (false)
s = SBML_formulaToL3StringWithSettings(n, l3ps);
fail_unless( !strcmp(s, "----x"), NULL );
safe_free(s);
//explicit false
L3ParserSettings_setParseCollapseMinus(l3ps, 0);
s = SBML_formulaToL3StringWithSettings(n, l3ps);
fail_unless( !strcmp(s, "----x"), NULL );
safe_free(s);
//explicit true
L3ParserSettings_setParseCollapseMinus(l3ps, 1);
s = SBML_formulaToL3StringWithSettings(n, l3ps);
fail_unless( !strcmp(s, "x"), NULL );
safe_free(s);
ASTNode_free(n);
L3ParserSettings_free(l3ps);
}
/**
* Converts an AST to a string representation of a formula using a syntax
* basically derived from SBML Level 1.
*
* @if clike The text-string form of mathematical formulas produced by
* SBML_formulaToString() and read by SBML_parseFormula() and SBML_parseL3Formula()
* are in a C-inspired infix notation. A formula in
* this text-string form therefore can be handed to a program that
* understands SBML mathematical expressions, or used as part
* of a formula translation system. The syntax is described in detail in
* the documentation for ASTNode. @endif@if java The text-string form of
* mathematical formulas produced by <code><a
* href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">
* libsbml.formulaToString()</a></code> and read by
* <code><a href="libsbml.html#parseFormula(java.lang.String)">
* libsbml.parseFormula()</a></code> and
* <code><a href="libsbml.html#parseL3Formula(java.lang.String)">
* libsbml.parseL3Formula()</a></code> are in a
* simple C-inspired infix notation. A
* formula in this text-string form therefore can be handed to a program
* that understands SBML mathematical expressions, or used as
* part of a formula translation system. The syntax is described in detail
* in the documentation for ASTNode. @endif
*
* Note that this facility is provided as a convenience by libSBML—the
* MathML standard does not actually define a "string-form" equivalent to
* MathML expression trees, so the choice of formula syntax is somewhat
* arbitrary. The approach taken by libSBML is to use the syntax defined by
* SBML Level 1 (which in fact used a text-string representation of
* formulas and not MathML). This formula syntax is based mostly on C
* programming syntax, and may contain operators, function calls, symbols,
* and white space characters. The following table provides the precedence
* rules for the different entities that may appear in formula strings.
*
* @htmlinclude math-precedence-table.html
*
* In the table above, @em operand implies the construct is an operand, @em
* prefix implies the operation is applied to the following arguments, @em
* unary implies there is one argument, and @em binary implies there are
* two arguments. The values in the <b>Precedence</b> column show how the
* order of different types of operation are determined. For example, the
* expression <code>a * b + c</code> is evaluated as <code>(a * b) +
* c</code> because the @c * operator has higher precedence. The
* <b>Associates</b> column shows how the order of similar precedence
* operations is determined; for example, <code>a - b + c</code> is
* evaluated as <code>(a - b) + c</code> because the @c + and @c -
* operators are left-associative.
*
* The function call syntax consists of a function name, followed by optional
* white space, followed by an opening parenthesis token, followed by a
* sequence of zero or more arguments separated by commas (with each comma
* optionally preceded and/or followed by zero or more white space
* characters, followed by a closing parenthesis token. The function name
* must be chosen from one of the pre-defined functions in SBML or a
* user-defined function in the model. The following table lists the names
* of certain common mathematical functions; this table corresponds to
* Table 6 in the <a target="_blank" href="http://sbml.org/Documents/Specifications#SBML_Level_1_Version_2">SBML Level 1 Version 2 specification</a>:
*
* @htmlinclude string-functions-table.html
*
* @warning There are differences between the symbols used to represent the
* common mathematical functions and the corresponding MathML token names.
* This is a potential source of incompatibilities. Note in particular that
* in this text-string syntax, <code>log(x)</code> represents the natural
* logarithm, whereas in MathML, the natural logarithm is
* <code><ln/></code>. Application writers are urged to be careful
* when translating between text forms and MathML forms, especially if they
* provide a direct text-string input facility to users of their software
* systems.<br><br>
* @htmlinclude L1-math-syntax-warning.html
*
* @param tree the AST to be converted.
*
* @return the formula from the given AST as an SBML Level 1 text-string
* mathematical formula. The caller owns the returned string and is
* responsible for freeing it when it is no longer needed.
*
* @see SBML_parseFormula()
* @see SBML_parseL3Formula()
*/
LIBSBML_EXTERN
char *
SBML_formulaToString (const ASTNode_t *tree)
{
char *s;
if (tree == NULL)
{
s = NULL;
}
else
{
StringBuffer_t *sb = StringBuffer_create(128);
FormulaFormatter_visit(NULL, tree, sb);
s = StringBuffer_getBuffer(sb);
safe_free(sb);
}
return s;
}
END_TEST
START_TEST (test_FormulaFormatter_formatRational)
{
StringBuffer_t *sb = StringBuffer_create(10);
ASTNode_t *n = ASTNode_create();
char *s;
ASTNode_setRational(n, 1, 2);
FormulaFormatter_formatRational(sb, n);
s = StringBuffer_toString(sb);
fail_unless( !strcmp(s, "(1/2)"), NULL );
safe_free(s);
ASTNode_free(n);
StringBuffer_free(sb);
}
/**
* Formats the given ASTNode as a directed graph operator and returns the result
* as a string.
*/
char *
FormulaGraphvizFormatter_formatOperator (const ASTNode_t *node)
{
char *s;
ASTNodeType_t type = ASTNode_getType(node);
StringBuffer_t *p = StringBuffer_create(128);
switch (type)
{
case AST_TIMES:
s = "times";
break;
case AST_DIVIDE:
s = "divide";
break;
case AST_PLUS:
s = "plus";
break;
case AST_MINUS:
s = "minus";
break;
case AST_POWER:
s = "power";
break;
default:
StringBuffer_appendChar(p, ASTNode_getCharacter(node));
s = StringBuffer_toString(p);
break;
}
free(p);
return s;
}
/**
* Formats the given ASTNode as a real number and returns the result as
* a string.
*/
char *
FormulaGraphvizFormatter_formatReal (const ASTNode_t *node)
{
StringBuffer_t *p = StringBuffer_create(128);
double value = ASTNode_getReal(node);
int sign;
char *s;
if (util_isNaN(value))
{
s = "NaN";
}
else if ((sign = util_isInf(value)) != 0)
{
if (sign == -1)
{
s = "-INF";
}
else
{
s = "INF";
}
}
else if (util_isNegZero(value))
{
s = "-0";
}
else
{
StringBuffer_appendReal(p, value);
s = StringBuffer_toString(p);
}
free(p);
return s;
}
/**
* Since graphviz will interpret identical names as referring to
* the same node presentation-wise it is better if each function node
* has a unique name.
*
* Returns the name of the operator with the name of the first child
* prepended
*
* THIS COULD BE DONE BETTER
*/
char *
FormulaGraphvizFormatter_OperatorGetUniqueName (const ASTNode_t *node)
{
char *s;
char number[10];
StringBuffer_t *p = StringBuffer_create(128);
ASTNodeType_t type = ASTNode_getType(node);
if (FormulaGraphvizFormatter_isFunction(ASTNode_getChild(node,0))
|| ASTNode_isOperator(ASTNode_getChild(node,0)))
{
StringBuffer_append(p, "func");
}
else
{
if (ASTNode_isInteger(ASTNode_getChild(node, 0)))
{
sprintf(number, "%d", (int)ASTNode_getInteger(ASTNode_getChild(node, 0)));
StringBuffer_append(p, number);
}
else if (ASTNode_isReal(ASTNode_getChild(node, 0)))
{
sprintf(number, "%ld", ASTNode_getNumerator(ASTNode_getChild(node, 0)));
StringBuffer_append(p, number);
}
else
{
StringBuffer_append(p, ASTNode_getName(ASTNode_getChild(node,0)));
}
}
switch (type)
{
case AST_TIMES:
StringBuffer_append(p, "times");
break;
case AST_DIVIDE:
StringBuffer_append(p, "divide");
break;
case AST_PLUS:
StringBuffer_append(p, "plus");
break;
case AST_MINUS:
StringBuffer_append(p, "minus");
break;
case AST_POWER:
StringBuffer_append(p, "power");
break;
default:
StringBuffer_appendChar(p, ASTNode_getCharacter(node));
break;
}
s = StringBuffer_toString(p);
free(p);
return s;
}
END_TEST
START_TEST (test_FormulaFormatter_formatReal)
{
StringBuffer_t *sb = StringBuffer_create(42);
char *s = StringBuffer_getBuffer(sb);
ASTNode_t *n = ASTNode_create();
/** 1.2 **/
ASTNode_setReal(n, 1.2);
FormulaFormatter_formatReal(sb, n);
fail_unless( !strcmp(s, "1.2"), NULL );
StringBuffer_reset(sb);
/** 1e-100 **/
ASTNode_setRealWithExponent(n, 1, -100);
FormulaFormatter_formatReal(sb, n);
fail_unless( !strcmp(s, "1.000000e-100"), NULL );
StringBuffer_reset(sb);
/** NaN **/
ASTNode_setReal(n, util_NaN());
FormulaFormatter_formatReal(sb, n);
fail_unless( !strcmp(s, "NaN"), NULL );
StringBuffer_reset(sb);
/** Inf **/
ASTNode_setReal(n, util_PosInf());
FormulaFormatter_formatReal(sb, n);
fail_unless( !strcmp(s, "INF"), NULL );
StringBuffer_reset(sb);
/** -Inf **/
ASTNode_setReal(n, util_NegInf());
FormulaFormatter_formatReal(sb, n);
fail_unless( !strcmp(s, "-INF"), NULL );
StringBuffer_reset(sb);
/** -0 **/
ASTNode_setReal(n, util_NegZero());
FormulaFormatter_formatReal(sb, n);
fail_unless( !strcmp(s, "-0"), NULL );
StringBuffer_reset(sb);
StringBuffer_free(sb);
ASTNode_free(n);
}
int main(void) {
StringBuffer_T sb;
Bootstrap(); // Need to initialize library
printf("============> Start StringBuffer Tests\n\n");
printf("=> Test1: create/destroy\n");
{
sb= StringBuffer_new("");
assert(sb);
assert(StringBuffer_length(sb)==0);
StringBuffer_free(&sb);
assert(sb==NULL);
sb= StringBuffer_create(1024);
assert(sb);
StringBuffer_free(&sb);
assert(sb==NULL);
}
printf("=> Test1: OK\n\n");
printf("=> Test2: Append NULL value\n");
{
sb= StringBuffer_new("");
assert(sb);
StringBuffer_append(sb, NULL);
assert(StringBuffer_length(sb)==0);
StringBuffer_free(&sb);
assert(sb==NULL);
}
printf("=> Test2: OK\n\n");
printf("=> Test3: Create with string\n");
{
sb= StringBuffer_new("abc");
assert(sb);
assert(StringBuffer_length(sb)==3);
StringBuffer_free(&sb);
assert(sb==NULL);
}
printf("=> Test3: OK\n\n");
printf("=> Test4: Append string value\n");
{
sb= StringBuffer_new("abc");
assert(sb);
printf("\tTesting StringBuffer_append:..");
StringBuffer_append(sb, "def");
assert(StringBuffer_length(sb)==6);
printf("ok\n");
printf("\tTesting StringBuffer_vappend:..");
append(sb, "%c%s", 'g', "hi");
assert(StringBuffer_length(sb)==9);
assert(Str_isEqual(StringBuffer_toString(sb), "abcdefghi"));
printf("ok\n");
StringBuffer_free(&sb);
assert(sb==NULL);
}
printf("=> Test4: OK\n\n");
printf("=> Test5: trim\n");
{
sb= StringBuffer_new("\t 'foo bar' \n ");
assert(Str_isEqual(StringBuffer_toString(StringBuffer_trim(sb)), "'foo bar'"));
StringBuffer_clear(sb);
StringBuffer_append(sb, "'foo bar'");
StringBuffer_trim(sb);
assert(Str_isEqual(StringBuffer_toString(sb), "'foo bar'"));
StringBuffer_clear(sb);
StringBuffer_append(sb, "\t \r \n ");
assert(Str_isEqual(StringBuffer_toString(StringBuffer_trim(sb)), ""));
StringBuffer_free(&sb);
sb = StringBuffer_create(10);
StringBuffer_trim(sb);
assert(StringBuffer_toString(sb)[0] == 0);
StringBuffer_free(&sb);
}
printf("=> Test5: OK\n\n");
printf("=> Test6: deleteFrom\n");
{
sb= StringBuffer_new("abcdefgh");
assert(sb);
StringBuffer_delete(sb,3);
assert(StringBuffer_length(sb)==3);
StringBuffer_free(&sb);
assert(sb==NULL);
}
printf("=> Test6: OK\n\n");
printf("=> Test7: indexOf and lastIndexOf\n");
{
sb= StringBuffer_new("jan-henrik haukeland");
assert(sb);
assert(StringBuffer_indexOf(sb, "henrik")==4);
assert(StringBuffer_indexOf(sb, "an")==1);
assert(StringBuffer_indexOf(sb, "-")==3);
assert(StringBuffer_lastIndexOf(sb, "an")==17);
assert(StringBuffer_indexOf(sb, "")==-1);
assert(StringBuffer_indexOf(sb, 0)==-1);
assert(StringBuffer_indexOf(sb, "d")==19);
assert(StringBuffer_indexOf(sb, "j")==0);
assert(StringBuffer_lastIndexOf(sb, "d")==19);
assert(StringBuffer_lastIndexOf(sb, "j")==0);
assert(StringBuffer_lastIndexOf(sb, "x")==-1);
assert(StringBuffer_indexOf(sb, "jane")==-1);
assert(StringBuffer_indexOf(sb, "jan-henrik haukeland")==0);
assert(StringBuffer_indexOf(sb, "haukeland")==11);
StringBuffer_free(&sb);
assert(sb==NULL);
}
printf("=> Test7: OK\n\n");
printf("=> Test8: length and clear\n");
{
sb= StringBuffer_new("jan-henrik haukeland");
assert(sb);
assert(StringBuffer_length(sb)==20);
StringBuffer_clear(sb);
assert(StringBuffer_length(sb)==0);
StringBuffer_free(&sb);
assert(sb==NULL);
}
printf("=> Test8: OK\n\n");
printf("=> Test9: toString value\n");
{
sb= StringBuffer_new("abc");
assert(sb);
StringBuffer_append(sb, "def");
assert(Str_isEqual(StringBuffer_toString(sb), "abcdef"));
StringBuffer_free(&sb);
assert(sb==NULL);
}
printf("=> Test9: OK\n\n");
printf("=> Test10: internal resize\n");
{
int i;
sb= StringBuffer_new("");
assert(sb);
for (i= 0; i<1024; i++)
StringBuffer_append(sb, "a");
assert(StringBuffer_length(sb)==1024);
assert(StringBuffer_toString(sb)[1023]=='a');
assert(StringBuffer_toString(sb)[1024]==0);
StringBuffer_free(&sb);
assert(sb==NULL);
}
printf("=> Test10: OK\n\n");
printf("=> Test11: substring\n");
{
sb= StringBuffer_new("jan-henrik haukeland");
assert(sb);
assert(Str_isEqual(StringBuffer_substring(sb, StringBuffer_indexOf(sb, "-")),
"-henrik haukeland"));
StringBuffer_free(&sb);
assert(sb==NULL);
}
printf("=> Test11: OK\n\n");
printf("=> Test12: replace\n");
{
printf("\tNothing to replace\n");
sb= StringBuffer_new("abc?def?");
assert(sb);
StringBuffer_replace(sb, "x", "$x");
assert(Str_isEqual(StringBuffer_toString(sb), "abc?def?"));
StringBuffer_free(&sb);
assert(sb==NULL);
printf("\tReplace and expand\n");
sb= StringBuffer_new("abc?def?");
assert(sb);
StringBuffer_replace(sb, "?", "$x");
assert(Str_isEqual(StringBuffer_toString(sb), "abc$xdef$x"));
StringBuffer_free(&sb);
assert(sb==NULL);
printf("\tReplace and shrink\n");
sb= StringBuffer_new("abc$xdef$x");
assert(sb);
StringBuffer_replace(sb, "$x", "?");
assert(Str_isEqual(StringBuffer_toString(sb), "abc?def?"));
StringBuffer_free(&sb);
assert(sb==NULL);
printf("\tReplace with empty string\n");
sb= StringBuffer_new("abc$xdef$x");
assert(sb);
StringBuffer_replace(sb, "$x", "");
assert(Str_isEqual(StringBuffer_toString(sb), "abcdef"));
StringBuffer_free(&sb);
assert(sb==NULL);
printf("\tReplace with same length\n");
sb= StringBuffer_new("foo bar baz foo bar baz");
assert(sb);
StringBuffer_replace(sb, "baz", "bar");
assert(Str_isEqual(StringBuffer_toString(sb), "foo bar bar foo bar bar"));
StringBuffer_free(&sb);
assert(sb==NULL);
printf("\tRemove words and test traceback\n");
sb= StringBuffer_new("foo bar baz foo foo bar baz");
assert(sb);
StringBuffer_replace(sb, "baz", "bar");
assert(Str_isEqual(StringBuffer_toString(sb), "foo bar bar foo foo bar bar"));
StringBuffer_replace(sb, "foo bar ", "");
assert(Str_isEqual(StringBuffer_toString(sb), "bar foo bar"));
StringBuffer_free(&sb);
assert(sb==NULL);
printf("\tReplace all elements\n");
sb= StringBuffer_new("aaaaaaaaaaaaaaaaaaaaaaaa");
assert(sb);
StringBuffer_replace(sb, "a", "b");
assert(Str_isEqual(StringBuffer_toString(sb), "bbbbbbbbbbbbbbbbbbbbbbbb"));
StringBuffer_free(&sb);
assert(sb==NULL);
printf("\tReplace and expand with resize of StringBuffer\n");
sb= StringBuffer_new("insert into(?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?) values (1,2,3,4,5,6,7,8,9,0,1,2,3,4,5,6,7,8,9,01,2,3);");
assert(sb);
StringBuffer_replace(sb, "?", "$x");
assert(Str_isEqual(StringBuffer_toString(sb), "insert into($x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x, $x) values (1,2,3,4,5,6,7,8,9,0,1,2,3,4,5,6,7,8,9,01,2,3);"));
StringBuffer_free(&sb);
assert(sb==NULL);
}
printf("=> Test12: OK\n\n");
printf("============> StringBuffer Tests: OK\n\n");
return 0;
}
