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// =============================================================== //
// //
// File : adquery.cxx //
// Purpose : //
// //
// Institute of Microbiology (Technical University Munich) //
// http://www.arb-home.de/ //
// //
// =============================================================== //
#include "gb_aci.h"
#include "gb_comm.h"
#include "gb_index.h"
#include "gb_key.h"
#include "gb_localdata.h"
#include "gb_ta.h"
#include <algorithm>
#include <arb_strbuf.h>
#include <arb_match.h>
#include <cctype>
#define GB_PATH_MAX 1024
static void build_GBDATA_path(GBDATA *gbd, char **buffer) {
GBCONTAINER *gbc = GB_FATHER(gbd);
if (gbc) {
build_GBDATA_path(gbc, buffer);
const char *key = GB_KEY(gbd);
char *bp = *buffer;
*bp++ = '/';
while (*key) *bp++ = *key++;
*bp = 0;
*buffer = bp;
}
}
#define BUFFERSIZE 1024
static const char *GB_get_GBDATA_path(GBDATA *gbd) {
static char *orgbuffer = NULL;
char *buffer;
if (!orgbuffer) orgbuffer = (char*)malloc(BUFFERSIZE);
buffer = orgbuffer;
build_GBDATA_path(gbd, &buffer);
assert_or_exit((buffer-orgbuffer) < BUFFERSIZE); // buffer overflow
return orgbuffer;
}
// ----------------
// QUERIES
static bool gb_find_value_equal(GBDATA *gb, GB_TYPES type, const char *val, GB_CASE case_sens) {
bool equal = false;
#if defined(DEBUG)
GB_TYPES realtype = gb->type();
gb_assert(val);
if (type == GB_STRING) {
gb_assert(gb->is_a_string()); // gb_find_internal called with wrong type
}
else {
gb_assert(realtype == type); // gb_find_internal called with wrong type
}
#endif // DEBUG
switch (type) {
case GB_STRING:
case GB_LINK:
equal = GBS_string_matches(GB_read_char_pntr(gb), val, case_sens);
break;
case GB_INT: {
int i = GB_read_int(gb);
if (i == *(int*)val) equal = true;
break;
}
case GB_FLOAT: {
GBK_terminate("cant search float by value"); // @@@ search by comparing floats is nonsense - should be removed/replaced/rewritten
double d = GB_read_float(gb);
if (d == *(double*)(void*)val) equal = true; // (no aliasing problem here; char* -> double* ok)
break;
}
default: {
const char *err = GBS_global_string("Value search not supported for data type %i (%i)", gb->type(), type);
GB_internal_error(err);
break;
}
}
return equal;
}
static GBDATA *find_sub_by_quark(GBCONTAINER *father, GBQUARK key_quark, GB_TYPES type, const char *val, GB_CASE case_sens, GBDATA *after, size_t skip_over) {
/* search an entry with a key 'key_quark' below a container 'father'
after position 'after'
if 'skip_over' > 0 search skips 'skip_over' entries
if (val != NULL) search for entry with value 'val':
GB_STRING/GB_LINK: compares string (case_sensitive or not)
GB_INT: compares values
GB_FLOAT: ditto (val MUST be a 'double*')
others: not implemented yet
Note: to search for non-char*-values use GB_find_int()
for other types write a new similar function
if key_quark<0 search everything
*/
int end = father->d.nheader;
gb_header_list *header = GB_DATA_LIST_HEADER(father->d);
int index;
if (after) index = (int)after->index+1; else index = 0;
if (key_quark<0) { // unspecific key quark (i.e. search all)
gb_assert(!val); // search for val not possible if searching all keys!
if (!val) {
for (; index < end; index++) {
if (header[index].flags.key_quark != 0) {
if (header[index].flags.changed >= GB_DELETED) continue;
GBDATA *gb = GB_HEADER_LIST_GBD(header[index]);
if (!gb) {
// @@@ DRY here versus below
gb_unfold(father, 0, index);
header = GB_DATA_LIST_HEADER(father->d);
gb = GB_HEADER_LIST_GBD(header[index]);
if (!gb) {
const char *err = GBS_global_string("Database entry #%u is missing (in '%s')", index, GB_get_GBDATA_path(father));
GB_internal_error(err);
continue;
}
}
if (!skip_over--) return gb;
}
}
}
}
else { // specific key quark
for (; index < end; index++) {
if (key_quark == header[index].flags.key_quark) {
if (header[index].flags.changed >= GB_DELETED) continue;
GBDATA *gb = GB_HEADER_LIST_GBD(header[index]);
if (!gb) {
// @@@ DRY here versus section above
gb_unfold(father, 0, index);
header = GB_DATA_LIST_HEADER(father->d);
gb = GB_HEADER_LIST_GBD(header[index]);
if (!gb) {
const char *err = GBS_global_string("Database entry #%u is missing (in '%s')", index, GB_get_GBDATA_path(father));
GB_internal_error(err);
continue;
}
}
if (val) {
if (!gb) {
GB_internal_error("Cannot unfold data");
continue;
}
else {
if (!gb_find_value_equal(gb, type, val, case_sens)) continue;
}
}
if (!skip_over--) return gb;
}
}
}
return NULL;
}
GBDATA *GB_find_sub_by_quark(GBDATA *father, GBQUARK key_quark, GBDATA *after, size_t skip_over) {
return find_sub_by_quark(father->expect_container(), key_quark, GB_NONE, NULL, GB_MIND_CASE, after, skip_over);
}
static GBDATA *GB_find_subcontent_by_quark(GBDATA *father, GBQUARK key_quark, GB_TYPES type, const char *val, GB_CASE case_sens, GBDATA *after, size_t skip_over) {
return find_sub_by_quark(father->expect_container(), key_quark, type, val, case_sens, after, skip_over);
}
static GBDATA *find_sub_sub_by_quark(GBCONTAINER *const father, const char *key, GBQUARK sub_key_quark, GB_TYPES type, const char *val, GB_CASE case_sens, GBDATA *after) {
gb_index_files *ifs = NULL;
GB_MAIN_TYPE *Main = GBCONTAINER_MAIN(father);
int end = father->d.nheader;
gb_header_list *header = GB_DATA_LIST_HEADER(father->d);
int index;
if (after) index = (int)after->index+1; else index = 0;
GBDATA *res;
// ****** look for any hash index tables ********
// ****** no wildcards allowed *******
if (Main->is_client()) {
if (father->flags2.folded_container) {
// do the query in the server
if (GB_ARRAY_FLAGS(father).changed) {
if (!father->flags2.update_in_server) {
GB_ERROR error = Main->send_update_to_server(father);
if (error) {
GB_export_error(error);
return NULL;
}
}
}
}
if (father->d.size > GB_MAX_LOCAL_SEARCH && val) {
if (after) res = GBCMC_find(after, key, type, val, case_sens, SEARCH_CHILD_OF_NEXT);
else res = GBCMC_find(father, key, type, val, case_sens, SEARCH_GRANDCHILD);
return res;
}
}
if (val &&
(ifs=GBCONTAINER_IFS(father))!=NULL &&
(!strchr(val, '*')) &&
(!strchr(val, '?')))
{
for (; ifs; ifs = GB_INDEX_FILES_NEXT(ifs)) {
if (ifs->key != sub_key_quark) continue;
// ***** We found the index table *****
res = gb_index_find(father, ifs, sub_key_quark, val, case_sens, index);
return res;
}
}
GBDATA *gb = after ? after : NULL;
for (; index < end; index++) {
GBDATA *gbn = GB_HEADER_LIST_GBD(header[index]);
if (header[index].flags.changed >= GB_DELETED) continue;
if (!gbn) {
if (Main->is_client()) {
if (gb) res = GBCMC_find(gb, key, type, val, case_sens, SEARCH_CHILD_OF_NEXT);
else res = GBCMC_find(father, key, type, val, case_sens, SEARCH_GRANDCHILD);
return res;
}
GB_internal_error("Empty item in server");
continue;
}
gb = gbn;
if (gb->is_container()) {
res = GB_find_subcontent_by_quark(gb, sub_key_quark, type, val, case_sens, NULL, 0);
if (res) return res;
}
}
return NULL;
}
static GBDATA *gb_find_internal(GBDATA *gbd, const char *key, GB_TYPES type, const char *val, GB_CASE case_sens, GB_SEARCH_TYPE gbs) {
GBDATA *result = NULL;
if (gbd) {
GBDATA *after = NULL;
GBCONTAINER *gbc = NULL;
switch (gbs) {
case SEARCH_NEXT_BROTHER:
after = gbd;
case SEARCH_BROTHER:
gbs = SEARCH_CHILD;
gbc = GB_FATHER(gbd);
break;
case SEARCH_CHILD:
case SEARCH_GRANDCHILD:
if (gbd->is_container()) gbc = gbd->as_container();
break;
case SEARCH_CHILD_OF_NEXT:
after = gbd;
gbs = SEARCH_GRANDCHILD;
gbc = GB_FATHER(gbd);
break;
}
if (gbc) {
GBQUARK key_quark = GB_find_existing_quark(gbd, key);
if (key_quark) { // only search if 'key' is known to db
if (gbs == SEARCH_CHILD) {
result = GB_find_subcontent_by_quark(gbc, key_quark, type, val, case_sens, after, 0);
}
else {
gb_assert(gbs == SEARCH_GRANDCHILD);
result = find_sub_sub_by_quark(gbc, key, key_quark, type, val, case_sens, after);
}
}
}
}
return result;
}
GBDATA *GB_find(GBDATA *gbd, const char *key, GB_SEARCH_TYPE gbs) {
// normally you should not need to use GB_find!
// better use one of the replacement functions
// (GB_find_string, GB_find_int, GB_child, GB_nextChild, GB_entry, GB_nextEntry, GB_brother)
return gb_find_internal(gbd, key, GB_NONE, NULL, GB_CASE_UNDEFINED, gbs);
}
GBDATA *GB_find_string(GBDATA *gbd, const char *key, const char *str, GB_CASE case_sens, GB_SEARCH_TYPE gbs) {
// search for a subentry of 'gbd' that has
// - fieldname 'key'
// - type GB_STRING and
// - content matching 'str'
// if 'case_sensitive' is true, content is matched case sensitive.
// GBS_string_matches is used to compare (supports wildcards)
return gb_find_internal(gbd, key, GB_STRING, str, case_sens, gbs);
}
NOT4PERL GBDATA *GB_find_int(GBDATA *gbd, const char *key, long val, GB_SEARCH_TYPE gbs) {
// search for a subentry of 'gbd' that has
// - fieldname 'key'
// - type GB_INT
// - and value 'val'
return gb_find_internal(gbd, key, GB_INT, (const char *)&val, GB_CASE_UNDEFINED, gbs);
}
// ----------------------------------------------------
// iterate over ALL subentries of a container
GBDATA *GB_child(GBDATA *father) {
// return first child (or NULL if no children)
return GB_find(father, NULL, SEARCH_CHILD);
}
GBDATA *GB_nextChild(GBDATA *child) {
// return next child after 'child' (or NULL if no more children)
return GB_find(child, NULL, SEARCH_NEXT_BROTHER);
}
// ------------------------------------------------------------------------------
// iterate over all subentries of a container that have a specified key
GBDATA *GB_entry(GBDATA *father, const char *key) {
// return first child of 'father' that has fieldname 'key'
// (or NULL if none found)
return GB_find(father, key, SEARCH_CHILD);
}
GBDATA *GB_nextEntry(GBDATA *entry) {
// return next child after 'entry', that has the same fieldname
// (or NULL if 'entry' is last one)
return GB_find_sub_by_quark(GB_FATHER(entry), GB_get_quark(entry), entry, 0);
}
GBDATA *GB_followingEntry(GBDATA *entry, size_t skip_over) {
// return following child after 'entry', that has the same fieldname
// (or NULL if no such entry)
// skips 'skip_over' entries (skip_over == 0 behaves like GB_nextEntry)
return GB_find_sub_by_quark(GB_FATHER(entry), GB_get_quark(entry), entry, skip_over);
}
GBDATA *GB_brother(GBDATA *entry, const char *key) {
// searches (first) brother (before or after) of 'entry' which has field 'key'
// i.e. does same as GB_entry(GB_get_father(entry), key)
return GB_find(entry, key, SEARCH_BROTHER);
}
GBDATA *gb_find_by_nr(GBCONTAINER *father, int index) {
/* get a subentry by its internal number:
Warning: This subentry must exists, otherwise internal error */
gb_header_list *header = GB_DATA_LIST_HEADER(father->d);
if (index >= father->d.nheader || index <0) {
GB_internal_errorf("Index '%i' out of range [%i:%i[", index, 0, father->d.nheader);
return NULL;
}
if (header[index].flags.changed >= GB_DELETED || !header[index].flags.key_quark) {
GB_internal_error("Entry already deleted");
return NULL;
}
GBDATA *gb = GB_HEADER_LIST_GBD(header[index]);
if (!gb) {
gb_unfold(father, 0, index);
header = GB_DATA_LIST_HEADER(father->d);
gb = GB_HEADER_LIST_GBD(header[index]);
if (!gb) {
GB_internal_error("Could not unfold data");
return NULL;
}
}
return gb;
}
class keychar_table {
bool table[256];
public:
keychar_table() {
for (int i=0; i<256; i++) {
table[i] = islower(i) || isupper(i) || isdigit(i) || i=='_' || i=='@';
}
}
const char *first_non_key_character(const char *str) const {
while (1) {
int c = *str;
if (!table[c]) {
if (c == 0) break;
return str;
}
str++;
}
return NULL;
}
};
static keychar_table keychars;
const char *GB_first_non_key_char(const char *str) {
return keychars.first_non_key_character(str);
}
inline GBDATA *find_or_create(GBCONTAINER *gb_parent, const char *key, GB_TYPES create, bool internflag) {
gb_assert(!keychars.first_non_key_character(key));
GBDATA *gbd = GB_entry(gb_parent, key);
if (create) {
if (gbd) {
GB_TYPES oldType = gbd->type();
if (create != oldType) { // type mismatch
GB_export_errorf("Inconsistent type for field '%s' (existing=%i, expected=%i)", key, oldType, create);
gbd = NULL;
}
}
else {
if (create == GB_CREATE_CONTAINER) {
gbd = internflag ? gb_create_container(gb_parent, key) : GB_create_container(gb_parent, key);
}
else {
gbd = gb_create(gb_parent, key, create);
}
gb_assert(gbd || GB_have_error());
}
}
return gbd;
}
GBDATA *gb_search(GBCONTAINER *gbc, const char *key, GB_TYPES create, int internflag) {
/* finds a hierarchical key,
* if create != GB_FIND(==0), then create the key
* force types if ! internflag
*/
gb_assert(!GB_have_error()); // illegal to enter this function when an error is exported!
GB_test_transaction(gbc);
if (!key) return NULL; // was allowed in the past (and returned the 1st child). now returns NULL
if (key[0] == '/') {
gbc = gb_get_root(gbc);
key++;
}
if (!key[0]) {
return gbc;
}
GBDATA *gb_result = NULL;
const char *separator = keychars.first_non_key_character(key);
if (!separator) gb_result = find_or_create(gbc, key, create, internflag);
else {
int len = separator-key;
char firstKey[len+1];
memcpy(firstKey, key, len);
firstKey[len] = 0;
char invalid_char = 0;
switch (separator[0]) {
case '/': {
GBDATA *gb_sub = find_or_create(gbc, firstKey, create ? GB_CREATE_CONTAINER : GB_FIND, internflag);
if (gb_sub) {
if (gb_sub->is_container()) {
if (separator[1] == '/') {
GB_export_errorf("Invalid '//' in key '%s'", key);
}
else {
gb_result = gb_search(gb_sub->as_container(), separator+1, create, internflag);
}
}
else {
GB_export_errorf("terminal entry '%s' cannot be used as container", firstKey);
}
}
break;
}
case '.': {
if (separator[1] != '.') invalid_char = separator[0];
else {
GBCONTAINER *gb_parent = gbc->get_father();
if (gb_parent) {
switch (separator[2]) {
case 0: gb_result = gb_parent; break;
case '/': gb_result = gb_search(gb_parent, separator+3, create, internflag); break;
default:
GB_export_errorf("Expected '/' after '..' in key '%s'", key);
break;
}
}
else { // ".." at root-node
if (create) {
GB_export_error("cannot use '..' at root node");
}
}
}
break;
}
case '-':
if (separator[1] != '>') invalid_char = separator[0];
else {
if (firstKey[0]) {
GBDATA *gb_link = GB_entry(gbc, firstKey);
if (!gb_link) {
if (create) {
GB_export_error("Cannot create links on the fly in gb_search");
}
}
else {
if (gb_link->type() == GB_LINK) {
GBDATA *gb_target = GB_follow_link(gb_link);
if (!gb_target) GB_export_errorf("Link '%s' points nowhere", firstKey);
else gb_result = gb_search(gb_target->as_container(), separator+2, create, internflag);
}
else GB_export_errorf("'%s' exists, but is not a link", firstKey);
}
}
else GB_export_errorf("Missing linkname before '->' in '%s'", key);
}
break;
default:
invalid_char = separator[0];
break;
}
if (invalid_char) {
gb_assert(!gb_result);
GB_export_errorf("Invalid char '%c' in key '%s'", invalid_char, key);
}
}
gb_assert(!(gb_result && GB_have_error()));
return gb_result;
}
GBDATA *GB_search(GBDATA *gbd, const char *fieldpath, GB_TYPES create) {
return gb_search(gbd->expect_container(), fieldpath, create, 0);
}
static GBDATA *gb_expect_type(GBDATA *gbd, GB_TYPES expected_type, const char *fieldname) {
gb_assert(expected_type != GB_FIND); // impossible
GB_TYPES type = gbd->type();
if (type != expected_type) {
GB_export_errorf("Field '%s' has wrong type (found=%i, expected=%i)", fieldname, type, expected_type);
gbd = 0;
}
return gbd;
}
GBDATA *GB_searchOrCreate_string(GBDATA *gb_container, const char *fieldpath, const char *default_value) {
gb_assert(!GB_have_error()); // illegal to enter this function when an error is exported!
GBDATA *gb_str = GB_search(gb_container, fieldpath, GB_FIND);
if (!gb_str) {
GB_clear_error();
gb_str = GB_search(gb_container, fieldpath, GB_STRING);
GB_ERROR error;
if (!gb_str) error = GB_await_error();
else error = GB_write_string(gb_str, default_value);
if (error) {
gb_str = 0;
GB_export_error(error);
}
}
else {
gb_str = gb_expect_type(gb_str, GB_STRING, fieldpath);
}
return gb_str;
}
GBDATA *GB_searchOrCreate_int(GBDATA *gb_container, const char *fieldpath, long default_value) {
gb_assert(!GB_have_error()); // illegal to enter this function when an error is exported!
GBDATA *gb_int = GB_search(gb_container, fieldpath, GB_FIND);
if (!gb_int) {
gb_int = GB_search(gb_container, fieldpath, GB_INT);
GB_ERROR error;
if (!gb_int) error = GB_await_error();
else error = GB_write_int(gb_int, default_value);
if (error) { // @@@ in case GB_search returned 0, gb_int already is 0 and error is exported. just assert error is exported
gb_int = 0;
GB_export_error(error);
}
}
else {
gb_int = gb_expect_type(gb_int, GB_INT, fieldpath);
}
return gb_int;
}
GBDATA *GB_searchOrCreate_float(GBDATA *gb_container, const char *fieldpath, double default_value) {
gb_assert(!GB_have_error()); // illegal to enter this function when an error is exported!
GBDATA *gb_float = GB_search(gb_container, fieldpath, GB_FIND);
if (!gb_float) {
gb_float = GB_search(gb_container, fieldpath, GB_FLOAT);
GB_ERROR error;
if (!gb_float) error = GB_await_error();
else error = GB_write_float(gb_float, default_value);
if (error) {
gb_float = 0;
GB_export_error(error);
}
}
else {
gb_float = gb_expect_type(gb_float, GB_FLOAT, fieldpath);
}
return gb_float;
}
static GBDATA *gb_search_marked(GBCONTAINER *gbc, GBQUARK key_quark, int firstindex, size_t skip_over) {
int userbit = GBCONTAINER_MAIN(gbc)->users[0]->userbit;
int index;
int end = gbc->d.nheader;
gb_header_list *header = GB_DATA_LIST_HEADER(gbc->d);
for (index = firstindex; index<end; index++) {
GBDATA *gb;
if (! (userbit & header[index].flags.flags)) continue;
if ((key_quark>=0) && (header[index].flags.key_quark != key_quark)) continue;
if (header[index].flags.changed >= GB_DELETED) continue;
if ((gb=GB_HEADER_LIST_GBD(header[index]))==NULL) {
gb_unfold(gbc, 0, index);
header = GB_DATA_LIST_HEADER(gbc->d);
gb = GB_HEADER_LIST_GBD(header[index]);
}
if (!skip_over--) return gb;
}
return NULL;
}
long GB_number_of_marked_subentries(GBDATA *gbd) {
long count = 0;
if (gbd->is_container()) {
GBCONTAINER *gbc = gbd->as_container();
gb_header_list *header = GB_DATA_LIST_HEADER(gbc->d);
int userbit = GBCONTAINER_MAIN(gbc)->users[0]->userbit;
int end = gbc->d.nheader;
for (int index = 0; index<end; index++) {
if (!(userbit & header[index].flags.flags)) continue;
if (header[index].flags.changed >= GB_DELETED) continue;
count++;
}
}
return count;
}
GBDATA *GB_first_marked(GBDATA *gbd, const char *keystring) {
GBCONTAINER *gbc = gbd->expect_container();
GBQUARK key_quark = GB_find_existing_quark(gbd, keystring);
GB_test_transaction(gbc);
return key_quark ? gb_search_marked(gbc, key_quark, 0, 0) : NULL;
}
GBDATA *GB_following_marked(GBDATA *gbd, const char *keystring, size_t skip_over) {
GBCONTAINER *gbc = GB_FATHER(gbd);
GBQUARK key_quark = GB_find_existing_quark(gbd, keystring);
GB_test_transaction(gbc);
return key_quark ? gb_search_marked(gbc, key_quark, (int)gbd->index+1, skip_over) : NULL;
}
GBDATA *GB_next_marked(GBDATA *gbd, const char *keystring) {
return GB_following_marked(gbd, keystring, 0);
}
// ----------------------------
// Command interpreter
void gb_install_command_table(GBDATA *gb_main, struct GBL_command_table *table, size_t table_size) {
GB_MAIN_TYPE *Main = GB_MAIN(gb_main);
if (!Main->command_hash) Main->command_hash = GBS_create_hash(table_size, GB_IGNORE_CASE);
for (; table->command_identifier; table++) {
GBS_write_hash(Main->command_hash, table->command_identifier, (long)table->function);
}
gb_assert((GBS_hash_count_elems(Main->command_hash)+1) == table_size);
}
static char *gbs_search_second_x(const char *str) {
int c;
for (; (c=*str); str++) {
if (c=='\\') { // escaped characters
str++;
if (!(c=*str)) return NULL;
continue;
}
if (c=='"') return (char *)str;
}
return NULL;
}
char *gbs_search_second_bracket(const char *source) {
int c;
int deep = 0;
if (*source != '(') deep --; // first bracket
for (; (c=*source); source++) {
if (c=='\\') { // escaped characters
source++;
if (!*source) break;
continue;
}
if (c=='(') deep--;
else if (c==')') deep++;
if (!deep) return (char *)source;
if (c=='"') { // search the second "
source = gbs_search_second_x(source);
if (!source) return NULL;
}
}
if (!c) return NULL;
return (char *)source;
}
static char *gbs_search_next_separator(const char *source, const char *seps) {
// search the next separator
static char tab[256];
static int flag = 0;
int c;
const char *p;
if (!flag) {
flag = 1;
memset(tab, 0, 256);
}
for (p = seps; (c=*p); p++) tab[c] = 1; // tab[seps[x]] = 1
tab['('] = 1; // exclude () pairs
tab['"'] = 1; // exclude " pairs
tab['\\'] = 1; // exclude \-escaped chars
for (; (c=*source); source++) {
if (tab[c]) {
if (c=='\\') {
source++;
continue;
}
if (c=='(') {
source = gbs_search_second_bracket(source);
if (!source) break;
continue;
}
if (c=='"') {
source = gbs_search_second_x(source+1);
if (!source) break;
continue;
}
for (p = seps; (c=*p); p++) tab[c] = 0;
return (char *)source;
}
}
for (p = seps; (c=*p); p++) tab[c] = 0; // clear tab
return NULL;
}
static void dumpStreams(const char *name, const GBL_streams& streams) {
int count = streams.size();
printf("%s=%i\n", name, count);
if (count > 0) {
for (int c = 0; c<count; c++) {
printf(" %02i='%s'\n", c, streams.get(c));
}
}
}
static const char *shortenLongString(const char *str, size_t wanted_len) {
// shortens the string 'str' to 'wanted_len' (appends '[..]' if string was shortened)
const char *result;
size_t len = strlen(str);
gb_assert(wanted_len>4);
if (len>wanted_len) {
static char *shortened_str;
static size_t short_len = 0;
if (short_len >= wanted_len) {
memcpy(shortened_str, str, wanted_len-4);
}
else {
freeset(shortened_str, GB_strpartdup(str, str+wanted_len));
short_len = wanted_len;
}
strcpy(shortened_str+wanted_len-4, "[..]");
result = shortened_str;
}
else {
result = str;
}
return result;
}
static char *apply_ACI(GBDATA *gb_main, const char *commands, const char *str, GBDATA *gbd, const char *default_tree_name) {
int trace = GB_get_ACISRT_trace();
GB_MAIN_TYPE *Main = GB_MAIN(gb_main);
gb_local->gbl.gb_main = gb_main;
char *buffer = strdup(commands);
// ********************** remove all spaces and tabs *******************
{
const char *s1;
char *s2;
s1 = commands;
s2 = buffer;
{
int c;
for (; (c = *s1); s1++) {
if (c=='\\') {
*(s2++) = c;
if (!(c=*++s1)) { break; }
*(s2++) = c;
continue;
}
if (c=='"') { // search the second "
const char *hp = gbs_search_second_x(s1+1);
if (!hp) {
GB_export_errorf("unbalanced '\"' in '%s'", commands);
free(buffer);
return NULL;
}
while (s1 <= hp) *(s2++) = *(s1++);
s1--;
continue;
}
if (c!=' ' && c!='\t') *(s2++) = c;
}
}
*s2 = 0;
}
GBL_streams orig;
orig.insert(strdup(str));
GB_ERROR error = NULL;
GBL_streams out;
{
char *s1, *s2;
s1 = buffer;
if (*s1 == '|') s1++;
// ** loop over all commands **
for (; s1; s1 = s2) {
int separator;
GBL_COMMAND command;
s2 = gbs_search_next_separator(s1, "|;,");
if (s2) {
separator = *(s2);
*(s2++) = 0;
}
else {
separator = 0;
}
// collect the parameters
GBL_streams in;
if (*s1 == '"') { // copy "text" to out
char *end = gbs_search_second_x(s1+1);
if (!end) {
UNCOVERED(); // seems unreachable (balancing is already ensured by gbs_search_next_separator)
error = "Missing second '\"'";
break;
}
*end = 0;
out.insert(strdup(s1+1));
}
else {
char *bracket = strchr(s1, '(');
if (bracket) { // I got the parameter list
int slen;
*(bracket++) = 0;
slen = strlen(bracket);
if (bracket[slen-1] != ')') {
error = "Missing ')'";
}
else {
// go through the parameters
char *p1, *p2;
bracket[slen-1] = 0;
for (p1 = bracket; p1; p1 = p2) {
p2 = gbs_search_next_separator(p1, ";,");
if (p2) {
*(p2++) = 0;
}
if (p1[0] == '"') { // remove "" pairs
int len2;
p1++;
len2 = strlen(p1)-1;
if (p1[len2] != '\"') {
error = "Missing '\"'";
}
else {
p1[len2] = 0;
}
}
in.insert(strdup(p1));
}
}
}
if (!error && (bracket || *s1)) {
char *p = s1;
int c;
while ((c = *p)) { // command to lower case
if (c>='A' && c<='Z') {
c += 'a'-'A';
*p = c;
}
p++;
}
command = (GBL_COMMAND)GBS_read_hash(Main->command_hash, s1);
if (!command) {
error = GBS_global_string("Unknown command '%s'", s1);
}
else {
GBL_command_arguments args(gbd, default_tree_name, orig, in, out);
args.command = s1;
if (trace) {
printf("-----------------------\nExecution of command '%s':\n", args.command);
dumpStreams("Arguments", args.param);
dumpStreams("InputStreams", args.input);
}
error = command(&args); // execute the command
if (!error && trace) dumpStreams("OutputStreams", args.output);
if (error) {
char *dup_error = strdup(error);
#define MAX_PRINT_LEN 200
char *paramlist = 0;
for (int j = 0; j<args.param.size(); ++j) {
const char *param = args.param.get(j);
const char *param_short = shortenLongString(param, MAX_PRINT_LEN);
if (!paramlist) paramlist = strdup(param_short);
else freeset(paramlist, GBS_global_string_copy("%s,%s", paramlist, param_short));
}
char *inputstreams = 0;
for (int j = 0; j<args.input.size(); ++j) {
const char *input = args.input.get(j);
const char *input_short = shortenLongString(input, MAX_PRINT_LEN);
if (!inputstreams) inputstreams = strdup(input_short);
else freeset(inputstreams, GBS_global_string_copy("%s;%s", inputstreams, input_short));
}
#undef MAX_PRINT_LEN
if (paramlist) {
error = GBS_global_string("while applying '%s(%s)'\nto '%s':\n%s", s1, paramlist, inputstreams, dup_error);
}
else {
error = GBS_global_string("while applying '%s'\nto '%s':\n%s", s1, inputstreams, dup_error);
}
free(inputstreams);
free(paramlist);
free(dup_error);
}
}
}
}
if (error) break;
if (separator == '|') { // out -> in pipe; clear in
out.swap(orig);
out.erase();
}
}
}
{
char *s1 = out.concatenated();
free(buffer);
if (!error) {
if (trace) printf("GB_command_interpreter: result='%s'\n", s1);
return s1;
}
free(s1);
}
GB_export_errorf("Command '%s' failed:\nReason: %s", commands, error);
return NULL;
}
// --------------------------------------------------------------------------------
char *GBL_streams::concatenated() const {
int count = size();
if (!count) return strdup("");
if (count == 1) return strdup(get(0));
GBS_strstruct *strstruct = GBS_stropen(1000);
for (int i=0; i<count; i++) {
const char *s = get(i);
if (s) GBS_strcat(strstruct, s);
}
return GBS_strclose(strstruct);
}
char *GB_command_interpreter(GBDATA *gb_main, const char *str, const char *commands, GBDATA *gbd, const char *default_tree_name) {
/* simple command interpreter returns NULL on error (which should be exported in that case)
* if first character is == ':' run string parser
* if first character is == '/' run regexpr
* else run ACI
*/
int trace = GB_get_ACISRT_trace();
SmartMallocPtr(char) heapstr;
if (!str) {
if (!gbd) {
GB_export_error("ACI: no input streams found");
return NULL;
}
if (GB_read_type(gbd) == GB_STRING) {
str = GB_read_char_pntr(gbd);
}
else {
char *asstr = GB_read_as_string(gbd);
if (!asstr) {
GB_export_error("Can't read this DB entry as string");
return NULL;
}
heapstr = asstr;
str = &*heapstr;
}
}
if (trace) {
printf("GB_command_interpreter: str='%s'\n"
" command='%s'\n", str, commands);
}
if (!commands || !commands[0]) { // empty command -> do not modify string
return strdup(str);
}
if (commands[0] == ':') { // ':' -> string parser
return GBS_string_eval(str, commands+1, gbd);
}
if (commands[0] == '/') { // regular expression
GB_ERROR err = 0;
char *result = GBS_regreplace(str, commands, &err);
if (!result) {
if (strcmp(err, "Missing '/' between search and replace string") == 0) {
// if GBS_regreplace didn't find a third '/' -> silently use GBS_regmatch:
size_t matchlen;
err = 0;
const char *matched = GBS_regmatch(str, commands, &matchlen, &err);
if (matched) result = GB_strndup(matched, matchlen);
else if (!err) result = strdup("");
}
if (!result && err) result = GBS_global_string_copy("<Error: %s>", err);
}
return result;
}
return apply_ACI(gb_main, commands, str, gbd, default_tree_name);
}
// --------------------------------------------------------------------------------
#ifdef UNIT_TESTS
#include <test_unit.h>
#define TEST_CI__INTERNAL(input,cmd,expected,got,TEST_RESULT) do { \
char *result; \
TEST_EXPECT_RESULT__NOERROREXPORTED(result = GB_command_interpreter(gb_main, input, cmd, gb_data, NULL)); \
TEST_RESULT(result,expected,got); \
free(result); \
} while(0)
#define TEST_CI(input,cmd,expected) TEST_CI__INTERNAL(input,cmd,expected,narg, TEST_EXPECT_EQUAL__IGNARG)
#define TEST_CI__BROKEN(input,cmd,expected,regr) TEST_CI__INTERNAL(input,cmd,expected,regr, TEST_EXPECT_EQUAL__BROKEN)
#define TEST_CI_NOOP(inandout,cmd) TEST_CI__INTERNAL(inandout,cmd,inandout,narg,TEST_EXPECT_EQUAL__IGNARG)
#define TEST_CI_NOOP__BROKEN(inandout,regr,cmd) TEST_CI__INTERNAL(inandout,cmd,inandout,regr,TEST_EXPECT_EQUAL__BROKEN)
#define TEST_CI_INVERSE(in,cmd,inv_cmd,out) do { \
TEST_CI(in, cmd, out); \
TEST_CI(out, inv_cmd, in); \
} while(0)
#define TEST_CI_ERROR_CONTAINS(input,cmd,errorpart_expected) \
TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_command_interpreter(gb_main, input, cmd, gb_data, NULL), errorpart_expected)
#define ACI_SPLIT "|split(\",\",0)"
#define ACI_MERGE "|merge(\",\")"
#define WITH_SPLITTED(aci) ACI_SPLIT aci ACI_MERGE
void TEST_GB_command_interpreter() {
GB_shell shell;
GBDATA *gb_main = GB_open("TEST_nuc.arb", "rw"); // ../UNIT_TESTER/run/TEST_nuc.arb
GBT_set_default_alignment(gb_main, "ali_16s"); // for sequence ACI command (@@@ really needed ? )
int old_trace = GB_get_ACISRT_trace();
#if 0
GB_set_ACISRT_trace(1); // used to detect coverage and for debugging purposes
#endif
{
GB_transaction ta(gb_main);
GBDATA *gb_data = GBT_find_species(gb_main, "LcbReu40");
TEST_CI_NOOP("bla", "");
TEST_CI("bla", ":a=u", "blu"); // simple SRT
TEST_CI("bla", "/a/u/", "blu"); // simple regExp replace
TEST_CI("blabla", "/l.*b/", "lab"); // simple regExp match
TEST_CI("blabla", "/b.b/", ""); // simple regExp match (failing)
// escape / quote
TEST_CI_INVERSE("ac", "|quote", "|unquote", "\"ac\"");
TEST_CI_INVERSE("ac", "|escape", "|unescape", "ac");
TEST_CI_INVERSE("ac", "|escape|quote", "|unquote|unescape", "\"ac\"");
TEST_CI_INVERSE("ac", "|quote|escape", "|unescape|unquote", "\\\"ac\\\"");
TEST_CI_INVERSE("a\"b\\c", "|quote", "|unquote", "\"a\"b\\c\"");
TEST_CI_INVERSE("a\"b\\c", "|escape", "|unescape", "a\\\"b\\\\c");
TEST_CI_INVERSE("a\"b\\c", "|escape|quote", "|unquote|unescape", "\"a\\\"b\\\\c\"");
TEST_CI_INVERSE("a\"b\\c", "|quote|escape", "|unescape|unquote", "\\\"a\\\"b\\\\c\\\"");
TEST_CI_NOOP("ac", "|unquote");
TEST_CI_NOOP("\"ac", "|unquote");
TEST_CI_NOOP("ac\"", "|unquote");
TEST_CI("blabla", "|coUNT(ab)", "4"); // simple ACI
TEST_CI("l", "|\"b\";dd;\"a\"|dd", "bla"); // ACI with muliple streams
TEST_CI("bla", "|count()", "0"); // one empty parameter
TEST_CI("bla", "|count(\"\")", "0"); // empty parameter
TEST_CI("b a", "|count(\" \")", "1"); // space in quotes
TEST_CI("b\\a", "|count(\\a)", "2"); // count '\\' and 'a' (ok)
TEST_CI__BROKEN("b\\a", "|count(\"\\a\")", "1", "2"); // should only count 'a' (which is escaped in param)
TEST_CI("b\\a", "|count(\"\a\")", "0"); // does not contain '\a'
TEST_CI("b\a", "|count(\"\a\")", "1"); // counts '\a'
// escaping (@@@ wrong behavior?)
TEST_CI("b\\a", "|count(\\a)", "2"); // i would expect '1' as result (the 'a'), but it counts '\\' and 'a'
TEST_CI("b\\a", "|contains(\"\\\\\")", "0"); // searches for 2 backslashes, finds none
TEST_CI__BROKEN("b\\a", "|contains(\"\")", "0", "1"); // search for nothing, but reports 1 hit
TEST_CI__BROKEN("b\\a", "|contains(\\)", "1", "2"); // searches for 1 backslash (ok), but reports two hits instead of one
TEST_CI__BROKEN("b\\\\a", "|contains(\"\\\\\")", "1", "2"); // searches for 2 backslashes (ok), but reports two hits instead of one
TEST_CI_ERROR_CONTAINS("b\\a", "|contains(\"\\\")", "ARB ERROR: unbalanced '\"' in '|contains(\"\\\")'"); // raises error (should search for 1 backslash)
// test binary ops
TEST_CI("", "\"5\";\"7\"|minus", "-2");
TEST_CI("", "\"5\"|minus(\"7\")", "-2");
TEST_CI("", "|minus(\"\"5\"\", \"\"7\"\")", "-2"); // @@@ syntax needed here 'minus(""5"", ""7"")' is broken - need to unescape correctly after parsing parameters!
TEST_CI_NOOP("ab,bcb,abac", WITH_SPLITTED(""));
TEST_CI ("ab,bcb,abac", WITH_SPLITTED("|len"), "2,3,4");
TEST_CI ("ab,bcb,abac", WITH_SPLITTED("|count(a)"), "1,0,2");
TEST_CI ("ab,bcb,abac", WITH_SPLITTED("|minus(len,count(a))"), "1,3,2");
TEST_CI ("ab,bcb,abac", WITH_SPLITTED("|minus(\"\"5\"\",count(a))"), "4,5,3"); // @@@ escaping broken here as well
// test other recursive uses of GB_command_interpreter
TEST_CI("one", "|dd;\"two\";dd|command(\"dd;\"_\";dd;\"-\"\")", "one_one-two_two-one_one-");
TEST_CI("", "|sequence|command(\"/^([\\\\.-]*)[A-Z].*/\\\\1/\")|len", "9"); // count gaps at start of sequence
TEST_CI("one", "|dd;dd|eval(\"\"up\";\"per\"|merge\")", "ONEONE");
TEST_CI("1,2,3", WITH_SPLITTED("|select(\"\", \"\"one\"\", \"\"two\"\", \"\"three\"\")"), "one,two,three");
TEST_CI_ERROR_CONTAINS("1,4", WITH_SPLITTED("|select(\"\", \"\"one\"\", \"\"two\"\", \"\"three\"\")"), "Illegal param number '4' (allowed [0..3])");
// test define and do (@@@ SLOW)
TEST_CI("ignored", "define(d4, \"dd;dd;dd;dd\")", "");
TEST_CI("ignored", "define(d16, \"do(d4)|do(d4)\")", "");
TEST_CI("ignored", "define(d64, \"do(d4)|do(d16)\")", "");
TEST_CI("ignored", "define(d4096, \"do(d64)|do(d64)\")", "");
TEST_CI("x", "do(d4)", "xxxx");
TEST_CI("xy", "do(d4)", "xyxyxyxy");
TEST_CI("x", "do(d16)", "xxxxxxxxxxxxxxxx");
TEST_CI("x", "do(d64)|len", "64");
TEST_CI("xy", "do(d4)|len", "8");
TEST_CI("xy", "do(d4)|len()", "8");
TEST_CI("xy", "do(d4)|len(x)", "4");
TEST_CI("x", "do(d4096)|len", "4096");
{
int prev_trace = GB_get_ACISRT_trace();
GB_set_ACISRT_trace(0); // do not trace here
// create 4096 streams:
TEST_CI("x", "dd;dd|dd;dd|dd;dd|dd;dd|dd;dd|dd;dd|dd;dd|dd;dd|dd;dd|dd;dd|dd;dd|dd;dd|streams", "4096");
GB_set_ACISRT_trace(prev_trace);
}
// other commands
// streams
TEST_CI("x", "dd;dd|streams", "2");
TEST_CI("x", "dd;dd|dd;dd|streams", "4");
TEST_CI("x", "dd;dd|dd;dd|dd;dd|streams", "8");
TEST_CI("x", "do(d4)|streams", "1"); // stream is merged when do() returns
TEST_CI("", "ali_name", "ali_16s"); // ask for default-alignment name
TEST_CI("", "sequence_type", "rna"); // ask for sequence_type of default-alignment
// format
TEST_CI("acgt", "format", " acgt");
TEST_CI("acgt", "format(firsttab=1)", " acgt");
TEST_CI("acgt", "format(firsttab=1, width=2)",
" ac\n"
" gt");
TEST_CI("acgt", "format(firsttab=1,tab=1,width=2)",
" ac\n"
" gt");
TEST_CI("acgt", "format(firsttab=0,tab=0,width=2)",
"ac\n"
"gt");
TEST_CI("acgt", "format(firsttab=0,tab=0,width=1)",
"a\n"
"c\n"
"g\n"
"t");
TEST_CI_ERROR_CONTAINS("acgt", "format(gap=0)", "Unknown Parameter 'gap=0' in command 'format'");
TEST_CI_ERROR_CONTAINS("acgt", "format(numleft)", "Unknown Parameter 'numleft' in command 'format'");
// format_sequence
TEST_CI("acgt", "format_sequence(firsttab=5,tab=5,width=1,numleft=1)",
"1 a\n"
"2 c\n"
"3 g\n"
"4 t");
TEST_CI("acgt", "format_sequence(firsttab=0,tab=0,width=2,gap=1)",
"a c\n"
"g t");
TEST_CI("acgt", "format_sequence(firsttab=0,tab=0,width=4,gap=1)", "a c g t");
TEST_CI("acgt", "format_sequence(firsttab=0,tab=0,width=4,gap=2)", "ac gt");
TEST_CI("acgtacgt", "format_sequence(firsttab=0,width=10,gap=4)", "acgt acgt");
TEST_CI("acgtacgt", "format_sequence(firsttab=1,width=10,gap=4)", " acgt acgt");
TEST_CI_ERROR_CONTAINS("acgt", "format_sequence(nl=c)", "Unknown Parameter 'nl=c' in command 'format_sequence'");
TEST_CI_ERROR_CONTAINS("acgt", "format_sequence(forcenl=)", "Unknown Parameter 'forcenl=' in command 'format_sequence'");
// TEST_CI_ERROR_CONTAINS("acgt", "format(width=0)", "should_raise_some_error"); // @@@ crashes
// remove + keep
TEST_CI_NOOP("acgtacgt", "remove(-.)");
TEST_CI ("..acg--ta-cgt...", "remove(-.)", "acgtacgt");
TEST_CI ("..acg--ta-cgt...", "remove(acgt)", "..---...");
TEST_CI_NOOP("acgtacgt", "keep(acgt)");
TEST_CI ("..acg--ta-cgt...", "keep(-.)", "..---...");
TEST_CI ("..acg--ta-cgt...", "keep(acgt)", "acgtacgt");
// compare + icompare
TEST_CI("x,z,y,y,z,x,x,Z,y,Y,Z,x", WITH_SPLITTED("|compare"), "-1,0,1,1,1,-1");
TEST_CI("x,z,y,y,z,x,x,Z,y,Y,Z,x", WITH_SPLITTED("|icompare"), "-1,0,1,-1,0,1");
TEST_CI("x,y,z", WITH_SPLITTED("|compare(\"y\")"), "-1,0,1");
// equals + iequals
TEST_CI("a,b,a,a,a,A", WITH_SPLITTED("|equals"), "0,1,0");
TEST_CI("a,b,a,a,a,A", WITH_SPLITTED("|iequals"), "0,1,1");
// contains + icontains
TEST_CI("abc,bcd,BCD", WITH_SPLITTED("|contains(\"bc\")"), "2,1,0");
TEST_CI("abc,bcd,BCD", WITH_SPLITTED("|icontains(\"bc\")"), "2,1,1");
TEST_CI("abc,bcd,BCD", WITH_SPLITTED("|icontains(\"d\")"), "0,3,3");
// partof + ipartof
TEST_CI("abc,BCD,def,deg", WITH_SPLITTED("|partof(\"abcdefg\")"), "1,0,4,0");
TEST_CI("abc,BCD,def,deg", WITH_SPLITTED("|ipartof(\"abcdefg\")"), "1,2,4,0");
// translate
TEST_CI("abcdefgh", "translate(abc,cba)", "cbadefgh");
TEST_CI("abcdefgh", "translate(cba,abc)", "cbadefgh");
TEST_CI("abcdefgh", "translate(hcba,abch,-)", "hcb----a");
TEST_CI("abcdefgh", "translate(aceg,aceg,-)", "a-c-e-g-");
TEST_CI("abbaabba", "translate(ab,ba,-)", "baabbaab");
TEST_CI("abbaabba", "translate(a,x,-)", "x--xx--x");
TEST_CI("abbaabba", "translate(,,-)", "--------");
// echo
TEST_CI("", "echo", "");
TEST_CI("", "echo(x,y,z)", "xyz");
TEST_CI("", "echo(x;y,z)", "xyz"); // check ';' as param-separator
TEST_CI("", "echo(x;y;z)", "xyz");
TEST_CI("", "echo(x,y,z)|streams", "3");
// upper, lower + caps
TEST_CI("the QUICK brOwn Fox", "lower", "the quick brown fox");
TEST_CI("the QUICK brOwn Fox", "upper", "THE QUICK BROWN FOX");
TEST_CI("the QUICK brOwn FoX", "caps", "The Quick Brown Fox");
// head, tail + mid/mid0
TEST_CI ("1234567890", "head(3)", "123");
TEST_CI ("1234567890", "head(9)", "123456789");
TEST_CI_NOOP("1234567890", "head(10)");
TEST_CI_NOOP("1234567890", "head(20)");
TEST_CI ("1234567890", "tail(4)", "7890");
TEST_CI ("1234567890", "tail(9)", "234567890");
TEST_CI_NOOP("1234567890", "tail(10)");
TEST_CI_NOOP("1234567890", "tail(20)");
TEST_CI("1234567890", "tail(0)", "");
TEST_CI("1234567890", "head(0)", "");
TEST_CI("1234567890", "tail(-2)", "");
TEST_CI("1234567890", "head(-2)", "");
TEST_CI("1234567890", "mid(3,5)", "345");
TEST_CI("1234567890", "mid(2,2)", "2");
TEST_CI("1234567890", "mid0(3,5)", "456");
TEST_CI("1234567890", "mid(9,20)", "90");
TEST_CI("1234567890", "mid(20,20)", "");
TEST_CI("1234567890", "tail(3)", "890"); // example from ../HELP_SOURCE/oldhelp/commands.hlp@mid0
TEST_CI("1234567890", "mid(-2,0)", "890");
TEST_CI("1234567890", "mid0(-3,-1)", "890");
// tab + pretab
TEST_CI("x,xx,xxx", WITH_SPLITTED("|tab(2)"), "x ,xx,xxx");
TEST_CI("x,xx,xxx", WITH_SPLITTED("|tab(3)"), "x ,xx ,xxx");
TEST_CI("x,xx,xxx", WITH_SPLITTED("|tab(4)"), "x ,xx ,xxx ");
TEST_CI("x,xx,xxx", WITH_SPLITTED("|pretab(2)"), " x,xx,xxx");
TEST_CI("x,xx,xxx", WITH_SPLITTED("|pretab(3)"), " x, xx,xxx");
TEST_CI("x,xx,xxx", WITH_SPLITTED("|pretab(4)"), " x, xx, xxx");
// crop
TEST_CI(" x x ", "crop(\" \")", "x x");
TEST_CI("\n \t x x \n \t", "crop(\"\t\n \")", "x x");
// cut, drop, dropempty and dropzero
TEST_CI("one,two,three,four,five,six", WITH_SPLITTED("|cut(2,3,5)"), "two,three,five");
TEST_CI("one,two,three,four,five,six", WITH_SPLITTED("|drop(2,3,5)"), "one,four,six");
TEST_CI_ERROR_CONTAINS("a", "drop(2)", "Illegal stream number '2' (allowed [1..1])");
TEST_CI_ERROR_CONTAINS("a", "drop(0)", "Illegal stream number '0' (allowed [1..1])");
TEST_CI_ERROR_CONTAINS("a", "cut(2)", "Illegal stream number '2' (allowed [1..1])");
TEST_CI_ERROR_CONTAINS("a", "cut(0)", "Illegal stream number '0' (allowed [1..1])");
TEST_CI("one,two,three,four,five,six", WITH_SPLITTED("|dropempty|streams"), "6");
TEST_CI("one,two,,,five,six", WITH_SPLITTED("|dropempty|streams"), "4");
TEST_CI(",,,,,", WITH_SPLITTED("|dropempty"), "");
TEST_CI(",,,,,", WITH_SPLITTED("|dropempty|streams"), "0");
TEST_CI("1,0,0,2,3,0", WITH_SPLITTED("|dropzero"), "1,2,3");
TEST_CI("0,0,0,0,0,0", WITH_SPLITTED("|dropzero"), "");
TEST_CI("0,0,0,0,0,0", WITH_SPLITTED("|dropzero|streams"), "0");
// swap
TEST_CI("1,2,3,four,five,six", WITH_SPLITTED("|swap"), "1,2,3,four,six,five");
TEST_CI("1,2,3,four,five,six", WITH_SPLITTED("|swap(2,3)"), "1,3,2,four,five,six");
TEST_CI("1,2,3,four,five,six", WITH_SPLITTED("|swap(2,3)|swap(4,3)"), "1,3,four,2,five,six");
TEST_CI_NOOP("1,2,3,four,five,six", WITH_SPLITTED("|swap(3,3)"));
TEST_CI_NOOP("1,2,3,four,five,six", WITH_SPLITTED("|swap(3,2)|swap(2,3)"));
TEST_CI_NOOP("1,2,3,four,five,six", WITH_SPLITTED("|swap(3,2)|swap(3,1)|swap(2,1)|swap(1,3)"));
TEST_CI_ERROR_CONTAINS("a", "swap", "need at least two input streams");
TEST_CI_ERROR_CONTAINS("a,b", WITH_SPLITTED("|swap(2,3)"), "Illegal stream number '3' (allowed [1..2])");
TEST_CI_ERROR_CONTAINS("a,b", WITH_SPLITTED("|swap(3,2)"), "Illegal stream number '3' (allowed [1..2])");
// toback + tofront
TEST_CI ("front,mid,back", WITH_SPLITTED("|toback(2)"), "front,back,mid");
TEST_CI ("front,mid,back", WITH_SPLITTED("|tofront(2)"), "mid,front,back");
TEST_CI_NOOP("front,mid,back", WITH_SPLITTED("|toback(3)"));
TEST_CI_NOOP("front,mid,back", WITH_SPLITTED("|tofront(1)"));
TEST_CI_NOOP("a", WITH_SPLITTED("|tofront(1)"));
TEST_CI_NOOP("a", WITH_SPLITTED("|toback(1)"));
TEST_CI_ERROR_CONTAINS("a,b", WITH_SPLITTED("|tofront(3)"), "Illegal stream number '3' (allowed [1..2])");
TEST_CI_ERROR_CONTAINS("a,b", WITH_SPLITTED("|toback(3)"), "Illegal stream number '3' (allowed [1..2])");
// split (default)
TEST_CI("a\nb", "|split" ACI_MERGE, "a,b");
// extract_words + extract_sequence
TEST_CI("1,2,3,four,five,six", "extract_words(\"0123456789\",1)", "1 2 3");
TEST_CI("1,2,3,four,five,six", "extract_words(\"abcdefghijklmnopqrstuvwxyz\", 3)", "five four six");
TEST_CI("1,2,3,four,five,six", "extract_words(\"abcdefghijklmnopqrstuvwxyz\", 4)", "five four");
TEST_CI("1,2,3,four,five,six", "extract_words(\"abcdefghijklmnopqrstuvwxyz\", 5)", "");
TEST_CI ("1,2,3,four,five,six", "extract_sequence(\"acgtu\", 1.0)", "");
TEST_CI ("1,2,3,four,five,six", "extract_sequence(\"acgtu\", 0.5)", "");
TEST_CI ("1,2,3,four,five,six", "extract_sequence(\"acgtu\", 0.0)", "four five six");
TEST_CI ("..acg--ta-cgt...", "extract_sequence(\"acgtu\", 1.0)", "");
TEST_CI_NOOP("..acg--ta-cgt...", "extract_sequence(\"acgtu-.\", 1.0)");
TEST_CI_NOOP("..acg--ta-ygt...", "extract_sequence(\"acgtu-.\", 0.7)");
TEST_CI ("70 ..acg--ta-cgt... 70", "extract_sequence(\"acgtu-.\", 1.0)", "..acg--ta-cgt...");
// checksum + gcgchecksum
TEST_CI("", "sequence|checksum", "4C549A5F");
TEST_CI("", "sequence | gcgchecksum", "4308");
// SRT
TEST_CI( "The quick brown fox", "srt(\"quick=lazy:brown fox=dog\")", "The lazy dog");
TEST_CI__BROKEN("The quick brown fox", "srt(quick=lazy:brown fox=dog)",
"The lazy dog", // @@@ parsing problem ?
"The lazy brown fox"); // document current (unwanted behavior)
TEST_CI_ERROR_CONTAINS("x", "srt(x=y,z)", "SRT ERROR: no '=' found in command");
// REG
TEST_CI("stars*to*stripes", "/\\*/--/", "stars--to--stripes");
TEST_CI("sImILaRWIllBE,GonEEASIly", WITH_SPLITTED("|command(/[A-Z]//)"), "small,only");
TEST_CI("sthBIGinside,FATnotCAP", WITH_SPLITTED("|command(/([A-Z])+/)"), "BIG,FAT");
// calculator
TEST_CI("", "echo(9,3)|plus", "12");
TEST_CI("", "echo(9,3)|minus", "6");
TEST_CI("", "echo(9,3)|mult", "27");
TEST_CI("", "echo(9,3)|div", "3");
TEST_CI("", "echo(9,3)|rest", "0");
TEST_CI("", "echo(9,3)|per_cent", "300");
TEST_CI("", "echo(1,2,3)|plus(1)" ACI_MERGE, "2,3,4");
TEST_CI("", "echo(1,2,3)|minus(2)" ACI_MERGE, "-1,0,1");
TEST_CI("", "echo(1,2,3)|mult(42)" ACI_MERGE, "42,84,126");
TEST_CI("", "echo(1,2,3)|div(2)" ACI_MERGE, "0,1,1");
TEST_CI("", "echo(1,2,3)|rest(2)" ACI_MERGE, "1,0,1");
TEST_CI("", "echo(1,2,3)|per_cent(3)" ACI_MERGE, "33,66,100");
// readdb
TEST_CI("", "readdb(name)", "LcbReu40");
TEST_CI("", "readdb(acc)", "X76328");
// taxonomy
TEST_CI("", "taxonomy(1)", "No default tree");
TEST_CI("", "taxonomy(tree_nuc, 1)", "group1");
TEST_CI("", "taxonomy(tree_nuc, 5)", "top/lower-red/group1");
TEST_CI_ERROR_CONTAINS("", "taxonomy", "syntax: taxonomy([tree_name,]count)");
// diff, filter + change
TEST_CI("..acg--ta-cgt..." ","
"..acg--ta-cgt...", WITH_SPLITTED("|diff(pairwise=1)"),
"................");
TEST_CI("..acg--ta-cgt..." ","
"..cgt--ta-acg...", WITH_SPLITTED("|diff(pairwise=1,equal==)"),
"==cgt=====acg===");
TEST_CI("..acg--ta-cgt..." ","
"..cgt--ta-acg...", WITH_SPLITTED("|diff(pairwise=1,differ=X)"),
"..XXX.....XXX...");
TEST_CI("", "sequence|diff(species=LcbFruct)|checksum", "645E3107");
TEST_CI("..XXX.....XXX..." ","
"..acg--ta-cgt...", WITH_SPLITTED("|filter(pairwise=1,exclude=X)"),
"..--ta-...");
TEST_CI("..XXX.....XXX..." ","
"..acg--ta-cgt...", WITH_SPLITTED("|filter(pairwise=1,include=X)"),
"acgcgt");
TEST_CI("", "sequence|filter(species=LcbFruct,include=.-)", "-----------T----T-------G----------C-----T----T...");
TEST_CI("...XXX....XXX..." ","
"..acg--ta-cgt...", WITH_SPLITTED("|change(pairwise=1,include=X,to=C,change=100)"),
"..aCC--ta-CCC...");
TEST_CI("...XXXXXXXXX...." ","
"..acg--ta-cgt...", WITH_SPLITTED("|change(pairwise=1,include=X,to=-,change=100)"),
"..a---------t...");
// exec
TEST_CI("c,b,c,b,a,a", WITH_SPLITTED("|exec(\"(sort|uniq)\")|split|dropempty"), "a,b,c");
TEST_CI("a,aba,cac", WITH_SPLITTED("|exec(\"perl\",-pe,s/([bc])/$1$1/g)|split|dropempty"), "a,abba,ccacc");
// error cases
TEST_CI_ERROR_CONTAINS("", "nocmd", "Unknown command 'nocmd'");
TEST_CI_ERROR_CONTAINS("", "|nocmd", "Unknown command 'nocmd'");
TEST_CI_ERROR_CONTAINS("", "caps(x)", "syntax: caps (no parameters)");
TEST_CI_ERROR_CONTAINS("", "trace", "syntax: trace(0|1)");
TEST_CI_ERROR_CONTAINS("", "count", "syntax: count(\"characters to count\")");
TEST_CI_ERROR_CONTAINS("", "count(a,b)", "syntax: count(\"characters to count\")");
TEST_CI_ERROR_CONTAINS("", "len(a,b)", "syntax: len[(\"characters not to count\")]");
TEST_CI_ERROR_CONTAINS("", "plus(a,b,c)", "syntax: plus[(Expr1[,Expr2])]");
TEST_CI_ERROR_CONTAINS("", "count(a,b", "Reason: Missing ')'");
TEST_CI_ERROR_CONTAINS("", "count(a,\"b)", "unbalanced '\"' in 'count(a,\"b)'");
TEST_CI_ERROR_CONTAINS("", "count(a,\"b)\"", "Reason: Missing ')'");
TEST_CI_ERROR_CONTAINS("", "dd;dd|count", "syntax: count(\"characters to count\")");
TEST_CI_ERROR_CONTAINS("", "|count(\"a\"x)", "Reason: Missing '\"'");
TEST_CI_ERROR_CONTAINS("", "|count(\"a)", "unbalanced '\"' in '|count(\"a)'");
TEST_CI_ERROR_CONTAINS("", "translate(a)", "syntax: translate(old,new[,other])");
TEST_CI_ERROR_CONTAINS("", "translate(a,b,c,d)", "syntax: translate(old,new[,other])");
TEST_CI_ERROR_CONTAINS(NULL, "whatever", "ARB ERROR: Can't read this DB entry as string"); // here gb_data is the species container
gb_data = GB_entry(gb_data, "full_name"); // execute ACI on 'full_name' from here on ------------------------------
TEST_CI(NULL, "", "Lactobacillus reuteri"); // noop
TEST_CI(NULL, "|len", "21");
TEST_CI(NULL, ":tobac=", "Lacillus reuteri");
TEST_CI(NULL, "/ba.*us/B/", "LactoB reuteri");
TEST_CI(NULL, "|taxonomy(1)", "No default tree");
TEST_CI_ERROR_CONTAINS(NULL, "|taxonomy(tree_nuc,2)", "Container has neither 'name' nor 'group_name' entry - can't detect container type");
gb_data = NULL;
TEST_CI_ERROR_CONTAINS(NULL, "", "no input streams found");
}
GB_set_ACISRT_trace(old_trace); // avoid side effect of TEST_GB_command_interpreter
GB_close(gb_main);
}
const char *GBT_get_name(GBDATA *gb_item);
struct TestDB : virtual Noncopyable {
GB_shell shell;
GBDATA *gb_main;
GB_ERROR error;
GBDATA *gb_cont1;
GBDATA *gb_cont2;
GBDATA *gb_cont_empty;
GBDATA *gb_cont_misc;
GB_ERROR create_many_items(GBDATA *gb_parent, const char **item_key_list, int item_count) {
int k = 0;
for (int i = 0; i<item_count && !error; i++) {
const char *item_key = item_key_list[k++];
if (!item_key) { item_key = item_key_list[0]; k = 1; }
GBDATA *gb_child = GB_create_container(gb_parent, item_key);
if (!gb_child) {
error = GB_await_error();
}
else {
if ((i%7) == 0) GB_write_flag(gb_child, 1); // mark some
GBDATA *gb_name = GB_create(gb_child, "name", GB_STRING);
error = GB_write_string(gb_name, GBS_global_string("%s %i", item_key, i));
}
}
return error;
}
TestDB() {
gb_main = GB_open("nosuch.arb", "c");
error = gb_main ? NULL : GB_await_error();
if (!error) {
GB_transaction ta(gb_main);
gb_cont1 = GB_create_container(gb_main, "container1");
gb_cont2 = GB_create_container(gb_main, "container2");
gb_cont_empty = GB_create_container(gb_main, "empty");
gb_cont_misc = GB_create_container(gb_main, "misc");
if (!gb_cont1 || !gb_cont2) error = GB_await_error();
const char *single_key[] = { "entry", NULL };
const char *mixed_keys[] = { "item", "other", NULL };
if (!error) error = create_many_items(gb_cont1, single_key, 100);
if (!error) error = create_many_items(gb_cont2, mixed_keys, 20);
}
TEST_EXPECT_NO_ERROR(error);
}
~TestDB() {
GB_close(gb_main);
}
};
void TEST_DB_search() {
TestDB db;
TEST_EXPECT_NO_ERROR(db.error);
{
GB_transaction ta(db.gb_main);
TEST_EXPECT_EQUAL(GB_number_of_subentries(db.gb_cont1), 100);
TEST_EXPECT_EQUAL(GB_number_of_subentries(db.gb_cont2), 20);
{
GBDATA *gb_any_child = GB_child(db.gb_cont1);
TEST_REJECT_NULL(gb_any_child);
TEST_EXPECT_EQUAL(gb_any_child, GB_entry(db.gb_cont1, "entry"));
TEST_EXPECT_EQUAL(gb_any_child, GB_search(db.gb_main, "container1/entry", GB_FIND));
TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(db.gb_main, "zic-zac", GB_FIND), "Invalid char '-' in key 'zic-zac'");
// check link-syntax
TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(db.gb_main, "->entry", GB_FIND), "Missing linkname before '->' in '->entry'");
TEST_EXPECT_NORESULT__NOERROREXPORTED(GB_search(db.gb_main, "entry->bla", GB_FIND));
TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(db.gb_main, "container1/entry->nowhere", GB_FIND), "'entry' exists, but is not a link");
TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(db.gb_main, "container1/nosuchentry->nowhere", GB_STRING), "Cannot create links on the fly in gb_search");
TEST_EXPECT_NORESULT__NOERROREXPORTED(GB_search(db.gb_main, "entry->", GB_FIND)); // valid ? just deref link
// check ..
TEST_EXPECT_EQUAL(GB_search(gb_any_child, "..", GB_FIND), db.gb_cont1);
TEST_EXPECT_EQUAL(GB_search(gb_any_child, "../..", GB_FIND), db.gb_main);
// above main entry
TEST_EXPECT_NORESULT__NOERROREXPORTED(GB_search(gb_any_child, "../../..", GB_FIND));
TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(gb_any_child, "../../../impossible", GB_STRING), "cannot use '..' at root node");
TEST_EXPECT_EQUAL(GB_search(gb_any_child, "", GB_FIND), gb_any_child); // return self
TEST_EXPECT_EQUAL(GB_search(gb_any_child, "/container1/", GB_FIND), db.gb_cont1); // accept trailing slash for container ..
TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(gb_any_child, "/container1/entry/name/", GB_FIND), "terminal entry 'name' cannot be used as container"); // .. but not for normal entries
TEST_EXPECT_EQUAL(GB_search(gb_any_child, "/", GB_FIND), db.gb_main);
TEST_EXPECT_EQUAL(GB_search(gb_any_child, "/container1/..", GB_FIND), db.gb_main);
TEST_EXPECT_NORESULT__NOERROREXPORTED(GB_search(gb_any_child, "/..", GB_FIND)); // main has no parent
}
{
GBDATA *gb_child1 = GB_child(db.gb_cont2); TEST_REJECT_NULL(gb_child1);
GBDATA *gb_child2 = GB_nextChild(gb_child1); TEST_REJECT_NULL(gb_child2);
GBDATA *gb_child3 = GB_nextChild(gb_child2); TEST_REJECT_NULL(gb_child3);
GBDATA *gb_child4 = GB_nextChild(gb_child3); TEST_REJECT_NULL(gb_child4);
TEST_EXPECT_EQUAL(GB_read_key_pntr(gb_child1), "item");
TEST_EXPECT_EQUAL(GB_read_key_pntr(gb_child2), "other");
TEST_EXPECT_EQUAL(GB_read_key_pntr(gb_child3), "item");
TEST_EXPECT_EQUAL(GB_read_key_pntr(gb_child4), "other");
TEST_EXPECT_NORESULT__NOERROREXPORTED(GB_entry(db.gb_cont2, "entry"));
TEST_EXPECT_EQUAL(GB_entry(db.gb_cont2, "item"), gb_child1);
TEST_EXPECT_EQUAL(GB_entry(db.gb_cont2, "other"), gb_child2);
TEST_EXPECT_EQUAL(GB_nextEntry(gb_child1), gb_child3);
TEST_EXPECT_EQUAL(GB_nextEntry(gb_child2), gb_child4);
// check ..
TEST_EXPECT_EQUAL(GB_search(gb_child3, "../item", GB_FIND), gb_child1);
TEST_EXPECT_EQUAL(GB_search(gb_child3, "../other", GB_FIND), gb_child2);
TEST_EXPECT_EQUAL(GB_search(gb_child3, "../other/../item", GB_FIND), gb_child1);
}
// ------------------------
// single entries
{
GBDATA *gb_str = GB_searchOrCreate_string(db.gb_cont_misc, "str", "bla"); TEST_REJECT_NULL(gb_str);
GBDATA *gb_str_same = GB_searchOrCreate_string(db.gb_cont_misc, "str", "blub");
TEST_EXPECT_EQUAL(gb_str, gb_str_same);
TEST_EXPECT_EQUAL(GB_read_char_pntr(gb_str), "bla");
GBDATA *gb_int = GB_searchOrCreate_int(db.gb_cont_misc, "int", 4711); TEST_REJECT_NULL(gb_int);
GBDATA *gb_int_same = GB_searchOrCreate_int(db.gb_cont_misc, "int", 2012);
TEST_EXPECT_EQUAL(gb_int, gb_int_same);
TEST_EXPECT_EQUAL(GB_read_int(gb_int), 4711);
GBDATA *gb_float = GB_searchOrCreate_float(db.gb_cont_misc, "float", 0.815); TEST_REJECT_NULL(gb_float);
GBDATA *gb_float_same = GB_searchOrCreate_float(db.gb_cont_misc, "float", 3.1415);
TEST_EXPECT_EQUAL(gb_float, gb_float_same);
TEST_EXPECT_SIMILAR(GB_read_float(gb_float), 0.815, 0.0001);
TEST_EXPECT_EQUAL (GB_read_char_pntr(GB_searchOrCreate_string(db.gb_cont_misc, "sub1/str", "blub")), "blub");
TEST_EXPECT_EQUAL (GB_read_int (GB_searchOrCreate_int (db.gb_cont_misc, "sub2/int", 2012)), 2012);
TEST_EXPECT_SIMILAR(GB_read_float (GB_searchOrCreate_float (db.gb_cont_misc, "sub3/float", 3.1415)), 3.1415, 0.0001);
TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_searchOrCreate_float (db.gb_cont_misc, "int", 0.815), "has wrong type");
TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_searchOrCreate_float (db.gb_cont_misc, "str", 0.815), "has wrong type");
TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_searchOrCreate_int (db.gb_cont_misc, "float", 4711), "has wrong type");
TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_searchOrCreate_int (db.gb_cont_misc, "str", 4711), "has wrong type");
TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_searchOrCreate_string(db.gb_cont_misc, "float", "bla"), "has wrong type");
TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_searchOrCreate_string(db.gb_cont_misc, "int", "bla"), "has wrong type");
TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_searchOrCreate_string(db.gb_cont_misc, "*", "bla"), "Invalid char '*' in key '*'");
TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_searchOrCreate_string(db.gb_cont_misc, "int*", "bla"), "Invalid char '*' in key 'int*'");
TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_searchOrCreate_string(db.gb_cont_misc, "sth_else*", "bla"), "Invalid char '*' in key 'sth_else*'");
GBDATA *gb_entry;
TEST_EXPECT_NORESULT__NOERROREXPORTED(GB_search(db.gb_cont_misc, "subcont/entry", GB_FIND));
TEST_EXPECT_RESULT__NOERROREXPORTED(gb_entry = GB_search(db.gb_cont_misc, "subcont/entry", GB_INT));
TEST_EXPECT_EQUAL(GB_read_int(gb_entry), 0);
GBDATA *gb_cont1;
TEST_EXPECT_RESULT__NOERROREXPORTED(gb_cont1 = GB_search(db.gb_cont_misc, "subcont", GB_CREATE_CONTAINER));
TEST_EXPECT_EQUAL(GB_child(gb_cont1), gb_entry); // test GB_search found the container created implicitely above
GBDATA *gb_cont2;
TEST_EXPECT_RESULT__NOERROREXPORTED(gb_cont2 = GB_search(db.gb_cont_misc, "subcont2", GB_CREATE_CONTAINER)); // create new container
// -----------------------
// search values
GBDATA *gb_4711;
TEST_EXPECT_RESULT__NOERROREXPORTED(gb_4711 = GB_find_int(db.gb_cont_misc, "int", 4711, SEARCH_CHILD));
TEST_EXPECT_EQUAL(gb_4711, gb_int);
TEST_EXPECT_NULL(GB_find_int(db.gb_cont_misc, "int", 2012, SEARCH_CHILD));
GBDATA *gb_bla;
TEST_EXPECT_RESULT__NOERROREXPORTED(gb_bla = GB_find_string(db.gb_cont_misc, "str", "bla", GB_MIND_CASE, SEARCH_CHILD));
TEST_EXPECT_EQUAL(gb_bla, gb_str);
TEST_EXPECT_RESULT__NOERROREXPORTED(gb_bla = GB_find_string(gb_4711, "str", "bla", GB_MIND_CASE, SEARCH_BROTHER));
TEST_EXPECT_EQUAL(gb_bla, gb_str);
TEST_EXPECT_NULL(GB_find_string(db.gb_cont_misc, "str", "blub", GB_MIND_CASE, SEARCH_CHILD));
GBDATA *gb_name;
TEST_REJECT_NULL (GB_find_string (db.gb_cont1, "name", "entry 77", GB_MIND_CASE, SEARCH_GRANDCHILD));
TEST_REJECT_NULL (GB_find_string (db.gb_cont1, "name", "entry 99", GB_MIND_CASE, SEARCH_GRANDCHILD));
TEST_EXPECT_NORESULT__NOERROREXPORTED(GB_find_string (db.gb_cont1, "name", "entry 100", GB_MIND_CASE, SEARCH_GRANDCHILD));
TEST_EXPECT_NORESULT__NOERROREXPORTED(GB_find_string (db.gb_cont1, "name", "ENTRY 13", GB_MIND_CASE, SEARCH_GRANDCHILD));
TEST_REJECT_NULL (gb_name = GB_find_string(db.gb_cont1, "name", "ENTRY 13", GB_IGNORE_CASE, SEARCH_GRANDCHILD));
GBDATA *gb_sub;
TEST_REJECT_NULL(gb_sub = GB_get_father(gb_name)); TEST_EXPECT_EQUAL(GBT_get_name(gb_sub), "entry 13");
TEST_REJECT_NULL(gb_sub = GB_followingEntry(gb_sub, 0)); TEST_EXPECT_EQUAL(GBT_get_name(gb_sub), "entry 14");
TEST_REJECT_NULL(gb_sub = GB_followingEntry(gb_sub, 1)); TEST_EXPECT_EQUAL(GBT_get_name(gb_sub), "entry 16");
TEST_REJECT_NULL(gb_sub = GB_followingEntry(gb_sub, 10)); TEST_EXPECT_EQUAL(GBT_get_name(gb_sub), "entry 27");
TEST_EXPECT_NORESULT__NOERROREXPORTED(GB_followingEntry(gb_sub, -1U));
TEST_REJECT_NULL(gb_sub = GB_brother(gb_sub, "entry")); TEST_EXPECT_EQUAL(GBT_get_name(gb_sub), "entry 0");
TEST_EXPECT_EQUAL(gb_bla = GB_search(gb_cont1, "/misc/str", GB_FIND), gb_str); // fullpath (ignores passed GBDATA)
// keyless search
TEST_EXPECT_NORESULT__NOERROREXPORTED(GB_search(db.gb_cont_misc, NULL, GB_FIND));
// ----------------------------
// GB_get_GBDATA_path
TEST_EXPECT_EQUAL(GB_get_GBDATA_path(gb_int), "/main/misc/int");
TEST_EXPECT_EQUAL(GB_get_GBDATA_path(gb_str), "/main/misc/str");
TEST_EXPECT_EQUAL(GB_get_GBDATA_path(gb_entry), "/main/misc/subcont/entry");
TEST_EXPECT_EQUAL(GB_get_GBDATA_path(gb_cont2), "/main/misc/subcont2");
// -----------------------------------------
// search/create with changed type
TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(db.gb_cont_misc, "str", GB_INT), "Inconsistent type for field");
TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(db.gb_cont_misc, "subcont", GB_STRING), "Inconsistent type for field");
// ---------------------------------------------
// search containers with trailing '/'
GBDATA *gb_cont2_slash;
TEST_EXPECT_RESULT__NOERROREXPORTED(gb_cont2_slash = GB_search(db.gb_cont_misc, "subcont2/", GB_FIND));
TEST_EXPECT_EQUAL(gb_cont2_slash, gb_cont2);
GBDATA *gb_rootcont;
GBDATA *gb_rootcont_slash;
TEST_EXPECT_RESULT__NOERROREXPORTED(gb_rootcont = GB_search(db.gb_main, "/container1", GB_FIND));
TEST_EXPECT_RESULT__NOERROREXPORTED(gb_rootcont_slash = GB_search(db.gb_main, "/container1/", GB_FIND));
TEST_EXPECT_EQUAL(gb_rootcont_slash, gb_rootcont);
}
{
// check invalid searches
TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(db.gb_cont_misc, "sub/inva*lid", GB_INT), "Invalid char '*' in key 'inva*lid'");
TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(db.gb_cont_misc, "sub/1 3", GB_INT), "Invalid char ' ' in key '1 3'");
TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(db.gb_cont_misc, "sub//sub", GB_INT), "Invalid '//' in key 'sub//sub'");
TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(db.gb_cont_misc, "subcont2//", GB_FIND), "Invalid '//' in key 'subcont2//'");
TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(db.gb_cont_misc, "sub/..sub", GB_INT), "Expected '/' after '..' in key '..sub'");
TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(db.gb_cont_misc, "subcont/entry/", GB_FIND), "terminal entry 'entry' cannot be used as container");
}
// ---------------
// marks
TEST_EXPECT_EQUAL(GB_number_of_marked_subentries(db.gb_cont1), 15);
TEST_EXPECT_EQUAL(GB_number_of_marked_subentries(db.gb_cont2), 3);
TEST_EXPECT_NORESULT__NOERROREXPORTED(GB_first_marked(db.gb_cont2, "entry"));
GBDATA *gb_marked;
TEST_REJECT_NULL(gb_marked = GB_first_marked(db.gb_cont2, "item"));
TEST_EXPECT_EQUAL(GBT_get_name(gb_marked), "item 0");
TEST_EXPECT_NORESULT__NOERROREXPORTED(GB_following_marked(gb_marked, "item", 1)); // skip over last
TEST_REJECT_NULL(gb_marked = GB_next_marked(gb_marked, "item")); // find last
TEST_EXPECT_EQUAL(GBT_get_name(gb_marked), "item 14");
}
// @@@ delete some species, then search again
TEST_EXPECT_NO_ERROR(db.error);
}
#endif // UNIT_TESTS
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