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source: tags/ms_r16q4/ARBDB/adquery.cxx

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Last change on this file was 15176, checked in by westram, 9 years ago
reintegrates 'fixres' into 'trunk' fixes #715 adds: log:branches/fixres@15127:15175
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File size: 76.1 KB

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1	// =============================================================== //
2	// //
3	// File : adquery.cxx //
4	// Purpose : //
5	// //
6	// Institute of Microbiology (Technical University Munich) //
7	// http://www.arb-home.de/ //
8	// //
9	// =============================================================== //
10
11	#include "gb_aci.h"
12	#include "gb_comm.h"
13	#include "gb_index.h"
14	#include "gb_key.h"
15	#include "gb_localdata.h"
16	#include "gb_ta.h"
17	#include <algorithm>
18
19	#include <arb_strbuf.h>
20	#include <arb_match.h>
21
22	#include <cctype>
23
24	#define GB_PATH_MAX 1024
25
26	static void build_GBDATA_path(GBDATA gbd, char *buffer) {
27	GBCONTAINER *gbc = GB_FATHER(gbd);
28	if (gbc) {
29	build_GBDATA_path(gbc, buffer);
30
31	const char *key = GB_KEY(gbd);
32	char bp = buffer;
33
34	*bp++ = '/';
35	while (key) bp++ = *key++;
36	*bp = 0;
37
38	*buffer = bp;
39	}
40	}
41
42	#define BUFFERSIZE 1024
43
44	static const char GB_get_GBDATA_path(GBDATA gbd) {
45	static char *orgbuffer = NULL;
46	char *buffer;
47
48	if (!orgbuffer) ARB_alloc(orgbuffer, BUFFERSIZE);
49	buffer = orgbuffer;
50
51	build_GBDATA_path(gbd, &buffer);
52	assert_or_exit((buffer-orgbuffer) < BUFFERSIZE); // buffer overflow
53
54	return orgbuffer;
55	}
56
57	// ----------------
58	// QUERIES
59
60	static bool gb_find_value_equal(GBDATA gb, GB_TYPES type, const char val, GB_CASE case_sens) {
61	bool equal = false;
62
63	#if defined(DEBUG)
64	GB_TYPES realtype = gb->type();
65	gb_assert(val);
66	if (type == GB_STRING) {
67	gb_assert(gb->is_a_string()); // gb_find_internal called with wrong type
68	}
69	else {
70	gb_assert(realtype == type); // gb_find_internal called with wrong type
71	}
72	#endif // DEBUG
73
74	switch (type) {
75	case GB_STRING:
76	case GB_LINK:
77	equal = GBS_string_matches(GB_read_char_pntr(gb), val, case_sens);
78	break;
79
80	case GB_INT: {
81	int i = GB_read_int(gb);
82	if (i == (int)val) equal = true;
83	break;
84	}
85	default: {
86	const char *err = GBS_global_string("Value search not supported for data type %i (%i)", gb->type(), type);
87	GB_internal_error(err);
88	break;
89	}
90	}
91
92	return equal;
93	}
94
95	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) {
96	/* search an entry with a key 'key_quark' below a container 'father'
97	after position 'after'
98
99	if 'skip_over' > 0 search skips 'skip_over' entries
100
101	if (val != NULL) search for entry with value 'val':
102
103	GB_STRING/GB_LINK: compares string (case_sensitive or not)
104	GB_INT: compares values
105	GB_FLOAT: ditto (val MUST be a 'double*')
106	others: not implemented yet
107
108	Note: to search for non-char*-values use GB_find_int()
109	for other types write a new similar function
110
111	if key_quark<0 search everything
112	*/
113
114	int end = father->d.nheader;
115	gb_header_list *header = GB_DATA_LIST_HEADER(father->d);
116
117	int index;
118	if (after) index = (int)after->index+1; else index = 0;
119
120	if (key_quark<0) { // unspecific key quark (i.e. search all)
121	gb_assert(!val); // search for val not possible if searching all keys!
122	if (!val) {
123	for (; index < end; index++) {
124	if (header[index].flags.key_quark != 0) {
125	if (header[index].flags.changed >= GB_DELETED) continue;
126	GBDATA *gb = GB_HEADER_LIST_GBD(header[index]);
127	if (!gb) {
128	// @@@ DRY here versus below
129	gb_unfold(father, 0, index);
130	header = GB_DATA_LIST_HEADER(father->d);
131	gb = GB_HEADER_LIST_GBD(header[index]);
132	if (!gb) {
133	const char *err = GBS_global_string("Database entry #%u is missing (in '%s')", index, GB_get_GBDATA_path(father));
134	GB_internal_error(err);
135	continue;
136	}
137	}
138	if (!skip_over--) return gb;
139	}
140	}
141	}
142	}
143	else { // specific key quark
144	for (; index < end; index++) {
145	if (key_quark == header[index].flags.key_quark) {
146	if (header[index].flags.changed >= GB_DELETED) continue;
147	GBDATA *gb = GB_HEADER_LIST_GBD(header[index]);
148	if (!gb) {
149	// @@@ DRY here versus section above
150	gb_unfold(father, 0, index);
151	header = GB_DATA_LIST_HEADER(father->d);
152	gb = GB_HEADER_LIST_GBD(header[index]);
153	if (!gb) {
154	const char *err = GBS_global_string("Database entry #%u is missing (in '%s')", index, GB_get_GBDATA_path(father));
155	GB_internal_error(err);
156	continue;
157	}
158	}
159	if (val) {
160	if (!gb) {
161	GB_internal_error("Cannot unfold data");
162	continue;
163	}
164	else {
165	if (!gb_find_value_equal(gb, type, val, case_sens)) continue;
166	}
167	}
168	if (!skip_over--) return gb;
169	}
170	}
171	}
172	return NULL;
173	}
174
175	GBDATA GB_find_sub_by_quark(GBDATA father, GBQUARK key_quark, GBDATA *after, size_t skip_over) {
176	return find_sub_by_quark(father->expect_container(), key_quark, GB_NONE, NULL, GB_MIND_CASE, after, skip_over);
177	}
178
179	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) {
180	return find_sub_by_quark(father->expect_container(), key_quark, type, val, case_sens, after, skip_over);
181	}
182
183	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) {
184	gb_index_files *ifs = NULL;
185	GB_MAIN_TYPE *Main = GBCONTAINER_MAIN(father);
186	int end = father->d.nheader;
187	gb_header_list *header = GB_DATA_LIST_HEADER(father->d);
188
189	int index;
190	if (after) index = (int)after->index+1; else index = 0;
191
192	GBDATA *res;
193	// **** look for any hash index tables ******
194	// **** no wildcards allowed *****
195	if (Main->is_client()) {
196	if (father->flags2.folded_container) {
197	// do the query in the server
198	if (GB_ARRAY_FLAGS(father).changed) {
199	if (!father->flags2.update_in_server) {
200	GB_ERROR error = Main->send_update_to_server(father);
201	if (error) {
202	GB_export_error(error);
203	return NULL;
204	}
205	}
206	}
207	}
208	if (father->d.size > GB_MAX_LOCAL_SEARCH && val) {
209	if (after) res = GBCMC_find(after, key, type, val, case_sens, SEARCH_CHILD_OF_NEXT);
210	else res = GBCMC_find(father, key, type, val, case_sens, SEARCH_GRANDCHILD);
211	return res;
212	}
213	}
214	if (val &&
215	(ifs=GBCONTAINER_IFS(father))!=NULL &&
216	(!strchr(val, '*')) &&
217	(!strchr(val, '?')))
218	{
219	for (; ifs; ifs = GB_INDEX_FILES_NEXT(ifs)) {
220	if (ifs->key != sub_key_quark) continue;
221	// *** We found the index table ***
222	res = gb_index_find(father, ifs, sub_key_quark, val, case_sens, index);
223	return res;
224	}
225	}
226
227	GBDATA *gb = after ? after : NULL;
228	for (; index < end; index++) {
229	GBDATA *gbn = GB_HEADER_LIST_GBD(header[index]);
230
231	if (header[index].flags.changed >= GB_DELETED) continue;
232	if (!gbn) {
233	if (Main->is_client()) {
234	if (gb) res = GBCMC_find(gb, key, type, val, case_sens, SEARCH_CHILD_OF_NEXT);
235	else res = GBCMC_find(father, key, type, val, case_sens, SEARCH_GRANDCHILD);
236	return res;
237	}
238	GB_internal_error("Empty item in server");
239	continue;
240	}
241	gb = gbn;
242	if (gb->is_container()) {
243	res = GB_find_subcontent_by_quark(gb, sub_key_quark, type, val, case_sens, NULL, 0);
244	if (res) return res;
245	}
246	}
247	return NULL;
248	}
249
250
251	static GBDATA gb_find_internal(GBDATA gbd, const char key, GB_TYPES type, const char val, GB_CASE case_sens, GB_SEARCH_TYPE gbs) {
252	GBDATA *result = NULL;
253
254	if (gbd) {
255	GBDATA *after = NULL;
256	GBCONTAINER *gbc = NULL;
257
258	switch (gbs) {
259	case SEARCH_NEXT_BROTHER:
260	after = gbd;
261	case SEARCH_BROTHER:
262	gbs = SEARCH_CHILD;
263	gbc = GB_FATHER(gbd);
264	break;
265
266	case SEARCH_CHILD:
267	case SEARCH_GRANDCHILD:
268	if (gbd->is_container()) gbc = gbd->as_container();
269	break;
270
271	case SEARCH_CHILD_OF_NEXT:
272	after = gbd;
273	gbs = SEARCH_GRANDCHILD;
274	gbc = GB_FATHER(gbd);
275	break;
276	}
277
278	if (gbc) {
279	GBQUARK key_quark = GB_find_existing_quark(gbd, key);
280
281	if (key_quark) { // only search if 'key' is known to db
282	if (gbs == SEARCH_CHILD) {
283	result = GB_find_subcontent_by_quark(gbc, key_quark, type, val, case_sens, after, 0);
284	}
285	else {
286	gb_assert(gbs == SEARCH_GRANDCHILD);
287	result = find_sub_sub_by_quark(gbc, key, key_quark, type, val, case_sens, after);
288	}
289	}
290	}
291	}
292	return result;
293	}
294
295	GBDATA GB_find(GBDATA gbd, const char *key, GB_SEARCH_TYPE gbs) {
296	// normally you should not need to use GB_find!
297	// better use one of the replacement functions
298	// (GB_find_string, GB_find_int, GB_child, GB_nextChild, GB_entry, GB_nextEntry, GB_brother)
299	return gb_find_internal(gbd, key, GB_NONE, NULL, GB_CASE_UNDEFINED, gbs);
300	}
301
302	GBDATA GB_find_string(GBDATA gbd, const char key, const char str, GB_CASE case_sens, GB_SEARCH_TYPE gbs) {
303	// search for a subentry of 'gbd' that has
304	// - fieldname 'key'
305	// - type GB_STRING and
306	// - content matching 'str'
307	// if 'case_sensitive' is true, content is matched case sensitive.
308	// GBS_string_matches is used to compare (supports wildcards)
309	return gb_find_internal(gbd, key, GB_STRING, str, case_sens, gbs);
310	}
311	NOT4PERL GBDATA GB_find_int(GBDATA gbd, const char *key, long val, GB_SEARCH_TYPE gbs) {
312	// search for a subentry of 'gbd' that has
313	// - fieldname 'key'
314	// - type GB_INT
315	// - and value 'val'
316	return gb_find_internal(gbd, key, GB_INT, (const char *)&val, GB_CASE_UNDEFINED, gbs);
317	}
318
319	// ----------------------------------------------------
320	// iterate over ALL subentries of a container
321
322	GBDATA GB_child(GBDATA father) {
323	// return first child (or NULL if no children)
324	return GB_find(father, NULL, SEARCH_CHILD);
325	}
326	GBDATA GB_nextChild(GBDATA child) {
327	// return next child after 'child' (or NULL if no more children)
328	return GB_find(child, NULL, SEARCH_NEXT_BROTHER);
329	}
330
331	// ------------------------------------------------------------------------------
332	// iterate over all subentries of a container that have a specified key
333
334	GBDATA GB_entry(GBDATA father, const char *key) {
335	// return first child of 'father' that has fieldname 'key'
336	// (or NULL if none found)
337	return GB_find(father, key, SEARCH_CHILD);
338	}
339	GBDATA GB_nextEntry(GBDATA entry) {
340	// return next child after 'entry', that has the same fieldname
341	// (or NULL if 'entry' is last one)
342	return GB_find_sub_by_quark(GB_FATHER(entry), GB_get_quark(entry), entry, 0);
343	}
344	GBDATA GB_followingEntry(GBDATA entry, size_t skip_over) {
345	// return following child after 'entry', that has the same fieldname
346	// (or NULL if no such entry)
347	// skips 'skip_over' entries (skip_over == 0 behaves like GB_nextEntry)
348	return GB_find_sub_by_quark(GB_FATHER(entry), GB_get_quark(entry), entry, skip_over);
349	}
350
351	GBDATA GB_brother(GBDATA entry, const char *key) {
352	// searches (first) brother (before or after) of 'entry' which has field 'key'
353	// i.e. does same as GB_entry(GB_get_father(entry), key)
354	return GB_find(entry, key, SEARCH_BROTHER);
355	}
356
357	GBDATA gb_find_by_nr(GBCONTAINER father, int index) {
358	/* get a subentry by its internal number:
359	Warning: This subentry must exists, otherwise internal error */
360
361	gb_header_list *header = GB_DATA_LIST_HEADER(father->d);
362	if (index >= father->d.nheader \|\| index <0) {
363	GB_internal_errorf("Index '%i' out of range [%i:%i[", index, 0, father->d.nheader);
364	return NULL;
365	}
366	if (header[index].flags.changed >= GB_DELETED \|\| !header[index].flags.key_quark) {
367	GB_internal_error("Entry already deleted");
368	return NULL;
369	}
370
371	GBDATA *gb = GB_HEADER_LIST_GBD(header[index]);
372	if (!gb) {
373	gb_unfold(father, 0, index);
374	header = GB_DATA_LIST_HEADER(father->d);
375	gb = GB_HEADER_LIST_GBD(header[index]);
376	if (!gb) {
377	GB_internal_error("Could not unfold data");
378	return NULL;
379	}
380	}
381	return gb;
382	}
383
384	class keychar_table {
385	bool table[256];
386	public:
387	keychar_table() {
388	for (int i=0; i<256; i++) {
389	table[i] = islower(i) \|\| isupper(i) \|\| isdigit(i) \|\| i=='_' \|\| i=='@';
390	}
391	}
392	const char first_non_key_character(const char str) const {
393	while (1) {
394	int c = *str;
395	if (!table[c]) {
396	if (c == 0) break;
397	return str;
398	}
399	str++;
400	}
401	return NULL;
402	}
403	};
404	static keychar_table keychars;
405
406	const char GB_first_non_key_char(const char str) {
407	return keychars.first_non_key_character(str);
408	}
409
410	inline GBDATA find_or_create(GBCONTAINER gb_parent, const char *key, GB_TYPES create, bool internflag) {
411	gb_assert(!keychars.first_non_key_character(key));
412
413	GBDATA *gbd = GB_entry(gb_parent, key);
414	if (create) {
415	if (gbd) {
416	GB_TYPES oldType = gbd->type();
417	if (create != oldType) { // type mismatch
418	GB_export_errorf("Inconsistent type for field '%s' (existing=%i, expected=%i)", key, oldType, create);
419	gbd = NULL;
420	}
421	}
422	else {
423	if (create == GB_CREATE_CONTAINER) {
424	gbd = internflag ? gb_create_container(gb_parent, key) : GB_create_container(gb_parent, key);
425	}
426	else {
427	gbd = gb_create(gb_parent, key, create);
428	}
429	gb_assert(gbd \|\| GB_have_error());
430	}
431	}
432	return gbd;
433	}
434
435	GBDATA gb_search(GBCONTAINER gbc, const char *key, GB_TYPES create, int internflag) {
436	/* finds a hierarchical key,
437	* if create != GB_FIND(==0), then create the key
438	* force types if ! internflag
439	*/
440
441	gb_assert(!GB_have_error()); // illegal to enter this function when an error is exported!
442
443	GB_test_transaction(gbc);
444
445	if (!key) return NULL; // was allowed in the past (and returned the 1st child). now returns NULL
446
447	if (key[0] == '/') {
448	gbc = gb_get_root(gbc);
449	key++;
450	}
451
452	if (!key[0]) {
453	return gbc;
454	}
455
456	GBDATA *gb_result = NULL;
457	const char *separator = keychars.first_non_key_character(key);
458	if (!separator) gb_result = find_or_create(gbc, key, create, internflag);
459	else {
460	int len = separator-key;
461	char firstKey[len+1];
462	memcpy(firstKey, key, len);
463	firstKey[len] = 0;
464
465	char invalid_char = 0;
466
467	switch (separator[0]) {
468	case '/': {
469	GBDATA *gb_sub = find_or_create(gbc, firstKey, create ? GB_CREATE_CONTAINER : GB_FIND, internflag);
470	if (gb_sub) {
471	if (gb_sub->is_container()) {
472	if (separator[1] == '/') {
473	GB_export_errorf("Invalid '//' in key '%s'", key);
474	}
475	else {
476	gb_result = gb_search(gb_sub->as_container(), separator+1, create, internflag);
477	}
478	}
479	else {
480	GB_export_errorf("terminal entry '%s' cannot be used as container", firstKey);
481	}
482	}
483	break;
484	}
485	case '.': {
486	if (separator[1] != '.') invalid_char = separator[0];
487	else {
488	GBCONTAINER *gb_parent = gbc->get_father();
489	if (gb_parent) {
490	switch (separator[2]) {
491	case 0: gb_result = gb_parent; break;
492	case '/': gb_result = gb_search(gb_parent, separator+3, create, internflag); break;
493	default:
494	GB_export_errorf("Expected '/' after '..' in key '%s'", key);
495	break;
496	}
497	}
498	else { // ".." at root-node
499	if (create) {
500	GB_export_error("cannot use '..' at root node");
501	}
502	}
503	}
504	break;
505	}
506	case '-':
507	if (separator[1] != '>') invalid_char = separator[0];
508	else {
509	if (firstKey[0]) {
510	GBDATA *gb_link = GB_entry(gbc, firstKey);
511	if (!gb_link) {
512	if (create) {
513	GB_export_error("Cannot create links on the fly in gb_search");
514	}
515	}
516	else {
517	if (gb_link->type() == GB_LINK) {
518	GBDATA *gb_target = GB_follow_link(gb_link);
519	if (!gb_target) GB_export_errorf("Link '%s' points nowhere", firstKey);
520	else gb_result = gb_search(gb_target->as_container(), separator+2, create, internflag);
521	}
522	else GB_export_errorf("'%s' exists, but is not a link", firstKey);
523	}
524	}
525	else GB_export_errorf("Missing linkname before '->' in '%s'", key);
526	}
527	break;
528
529	default:
530	invalid_char = separator[0];
531	break;
532	}
533
534	if (invalid_char) {
535	gb_assert(!gb_result);
536	GB_export_errorf("Invalid char '%c' in key '%s'", invalid_char, key);
537	}
538	}
539	gb_assert(!(gb_result && GB_have_error()));
540	return gb_result;
541	}
542
543
544	GBDATA GB_search(GBDATA gbd, const char *fieldpath, GB_TYPES create) {
545	return gb_search(gbd->expect_container(), fieldpath, create, 0);
546	}
547
548	static GBDATA gb_expect_type(GBDATA gbd, GB_TYPES expected_type, const char *fieldname) {
549	gb_assert(expected_type != GB_FIND); // impossible
550
551	GB_TYPES type = gbd->type();
552	if (type != expected_type) {
553	GB_export_errorf("Field '%s' has wrong type (found=%i, expected=%i)", fieldname, type, expected_type);
554	gbd = 0;
555	}
556	return gbd;
557	}
558
559	GBDATA GB_searchOrCreate_string(GBDATA gb_container, const char fieldpath, const char default_value) {
560	gb_assert(!GB_have_error()); // illegal to enter this function when an error is exported!
561
562	GBDATA *gb_str = GB_search(gb_container, fieldpath, GB_FIND);
563	if (!gb_str) {
564	GB_clear_error();
565	gb_str = GB_search(gb_container, fieldpath, GB_STRING);
566	GB_ERROR error;
567
568	if (!gb_str) error = GB_await_error();
569	else error = GB_write_string(gb_str, default_value);
570
571	if (error) {
572	gb_str = 0;
573	GB_export_error(error);
574	}
575	}
576	else {
577	gb_str = gb_expect_type(gb_str, GB_STRING, fieldpath);
578	}
579	return gb_str;
580	}
581
582	GBDATA GB_searchOrCreate_int(GBDATA gb_container, const char *fieldpath, long default_value) {
583	gb_assert(!GB_have_error()); // illegal to enter this function when an error is exported!
584
585	GBDATA *gb_int = GB_search(gb_container, fieldpath, GB_FIND);
586	if (!gb_int) {
587	gb_int = GB_search(gb_container, fieldpath, GB_INT);
588	GB_ERROR error;
589
590	if (!gb_int) error = GB_await_error();
591	else error = GB_write_int(gb_int, default_value);
592
593	if (error) { // @@@ in case GB_search returned 0, gb_int already is 0 and error is exported. just assert error is exported
594	gb_int = 0;
595	GB_export_error(error);
596	}
597	}
598	else {
599	gb_int = gb_expect_type(gb_int, GB_INT, fieldpath);
600	}
601	return gb_int;
602	}
603
604	GBDATA GB_searchOrCreate_float(GBDATA gb_container, const char *fieldpath, float default_value) {
605	gb_assert(!GB_have_error()); // illegal to enter this function when an error is exported!
606
607	GBDATA *gb_float = GB_search(gb_container, fieldpath, GB_FIND);
608	if (!gb_float) {
609	gb_float = GB_search(gb_container, fieldpath, GB_FLOAT);
610	GB_ERROR error;
611
612	if (!gb_float) error = GB_await_error();
613	else error = GB_write_float(gb_float, default_value);
614
615	if (error) {
616	gb_float = 0;
617	GB_export_error(error);
618	}
619	}
620	else {
621	gb_float = gb_expect_type(gb_float, GB_FLOAT, fieldpath);
622	}
623	return gb_float;
624	}
625
626	static GBDATA gb_search_marked(GBCONTAINER gbc, GBQUARK key_quark, int firstindex, size_t skip_over) {
627	int userbit = GBCONTAINER_MAIN(gbc)->users[0]->userbit;
628	int index;
629	int end = gbc->d.nheader;
630	gb_header_list *header = GB_DATA_LIST_HEADER(gbc->d);
631
632	for (index = firstindex; index<end; index++) {
633	GBDATA *gb;
634
635	if (! (userbit & header[index].flags.flags)) continue;
636	if ((key_quark>=0) && (header[index].flags.key_quark != key_quark)) continue;
637	if (header[index].flags.changed >= GB_DELETED) continue;
638	if ((gb=GB_HEADER_LIST_GBD(header[index]))==NULL) {
639	gb_unfold(gbc, 0, index);
640	header = GB_DATA_LIST_HEADER(gbc->d);
641	gb = GB_HEADER_LIST_GBD(header[index]);
642	}
643	if (!skip_over--) return gb;
644	}
645	return NULL;
646	}
647
648	long GB_number_of_marked_subentries(GBDATA *gbd) {
649	long count = 0;
650	if (gbd->is_container()) {
651	GBCONTAINER *gbc = gbd->as_container();
652	gb_header_list *header = GB_DATA_LIST_HEADER(gbc->d);
653
654	int userbit = GBCONTAINER_MAIN(gbc)->users[0]->userbit;
655	int end = gbc->d.nheader;
656
657	for (int index = 0; index<end; index++) {
658	if (!(userbit & header[index].flags.flags)) continue;
659	if (header[index].flags.changed >= GB_DELETED) continue;
660	count++;
661	}
662	}
663	return count;
664	}
665
666
667
668	GBDATA GB_first_marked(GBDATA gbd, const char *keystring) {
669	GBCONTAINER *gbc = gbd->expect_container();
670	GBQUARK key_quark = GB_find_existing_quark(gbd, keystring);
671	GB_test_transaction(gbc);
672	return key_quark ? gb_search_marked(gbc, key_quark, 0, 0) : NULL;
673	}
674
675
676	GBDATA GB_following_marked(GBDATA gbd, const char *keystring, size_t skip_over) {
677	GBCONTAINER *gbc = GB_FATHER(gbd);
678	GBQUARK key_quark = GB_find_existing_quark(gbd, keystring);
679	GB_test_transaction(gbc);
680	return key_quark ? gb_search_marked(gbc, key_quark, (int)gbd->index+1, skip_over) : NULL;
681	}
682
683	GBDATA GB_next_marked(GBDATA gbd, const char *keystring) {
684	return GB_following_marked(gbd, keystring, 0);
685	}
686
687	// ----------------------------
688	// Command interpreter
689
690	void gb_install_command_table(GBDATA gb_main, struct GBL_command_table table, size_t table_size) {
691	GB_MAIN_TYPE *Main = GB_MAIN(gb_main);
692	if (!Main->command_hash) Main->command_hash = GBS_create_hash(table_size, GB_IGNORE_CASE);
693
694	for (; table->command_identifier; table++) {
695	GBS_write_hash(Main->command_hash, table->command_identifier, (long)table->function);
696	}
697
698	gb_assert((GBS_hash_elements(Main->command_hash)+1) == table_size);
699	}
700
701	static char gbs_search_second_x(const char str) {
702	int c;
703	for (; (c=*str); str++) {
704	if (c=='\\') { // escaped characters
705	str++;
706	if (!(c=*str)) return NULL;
707	continue;
708	}
709	if (c=='"') return (char *)str;
710	}
711	return NULL;
712	}
713
714	char gbs_search_second_bracket(const char source) {
715	int c;
716	int deep = 0;
717	if (*source != '(') deep --; // first bracket
718	for (; (c=*source); source++) {
719	if (c=='\\') { // escaped characters
720	source++;
721	if (!*source) break;
722	continue;
723	}
724	if (c=='(') deep--;
725	else if (c==')') deep++;
726	if (!deep) return (char *)source;
727	if (c=='"') { // search the second "
728	source = gbs_search_second_x(source);
729	if (!source) return NULL;
730	}
731	}
732	if (!c) return NULL;
733	return (char *)source;
734	}
735
736
737	static char gbs_search_next_separator(const char source, const char *seps) {
738	// search the next separator
739	static char tab[256];
740	static int flag = 0;
741	int c;
742	const char *p;
743	if (!flag) {
744	flag = 1;
745	memset(tab, 0, 256);
746	}
747	for (p = seps; (c=*p); p++) tab[c] = 1; // tab[seps[x]] = 1
748	tab['('] = 1; // exclude () pairs
749	tab['"'] = 1; // exclude " pairs
750	tab['\\'] = 1; // exclude \-escaped chars
751
752	for (; (c=*source); source++) {
753	if (tab[c]) {
754	if (c=='\\') {
755	source++;
756	continue;
757	}
758	if (c=='(') {
759	source = gbs_search_second_bracket(source);
760	if (!source) break;
761	continue;
762	}
763	if (c=='"') {
764	source = gbs_search_second_x(source+1);
765	if (!source) break;
766	continue;
767	}
768	for (p = seps; (c=*p); p++) tab[c] = 0;
769	return (char *)source;
770	}
771	}
772	for (p = seps; (c=*p); p++) tab[c] = 0; // clear tab
773	return NULL;
774	}
775
776	static void dumpStreams(const char *name, const GBL_streams& streams) {
777	int count = streams.size();
778	printf("%s=%i\n", name, count);
779	if (count > 0) {
780	for (int c = 0; c<count; c++) {
781	printf(" %02i='%s'\n", c, streams.get(c));
782	}
783	}
784	}
785
786	static const char shortenLongString(const char str, size_t wanted_len) {
787	// shortens the string 'str' to 'wanted_len' (appends '[..]' if string was shortened)
788
789	const char *result;
790	size_t len = strlen(str);
791
792	gb_assert(wanted_len>4);
793
794	if (len>wanted_len) {
795	static char *shortened_str;
796	static size_t short_len = 0;
797
798	if (short_len >= wanted_len) {
799	memcpy(shortened_str, str, wanted_len-4);
800	}
801	else {
802	freeset(shortened_str, ARB_strpartdup(str, str+wanted_len));
803	short_len = wanted_len;
804	}
805	strcpy(shortened_str+wanted_len-4, "[..]");
806	result = shortened_str;
807	}
808	else {
809	result = str;
810	}
811	return result;
812	}
813
814	static char apply_ACI(GBDATA gb_main, const char commands, const char str, GBDATA gbd, const char default_tree_name) {
815	int trace = GB_get_ACISRT_trace();
816
817	GB_MAIN_TYPE *Main = GB_MAIN(gb_main);
818	gb_local->gbl.gb_main = gb_main;
819
820	char *buffer = ARB_strdup(commands);
821
822	// ******************** remove all spaces and tabs *****************
823	{
824	const char *s1;
825	char *s2;
826	s1 = commands;
827	s2 = buffer;
828	{
829	int c;
830	for (; (c = *s1); s1++) {
831	if (c=='\\') {
832	*(s2++) = c;
833	if (!(c=*++s1)) { break; }
834	*(s2++) = c;
835	continue;
836	}
837
838	if (c=='"') { // search the second "
839	const char *hp = gbs_search_second_x(s1+1);
840	if (!hp) {
841	GB_export_errorf("unbalanced '\"' in '%s'", commands);
842	free(buffer);
843	return NULL;
844	}
845	while (s1 <= hp) (s2++) = (s1++);
846	s1--;
847	continue;
848	}
849	if (c!=' ' && c!='\t') *(s2++) = c;
850	}
851	}
852	*s2 = 0;
853	}
854
855	GBL_streams orig;
856
857	orig.insert(ARB_strdup(str));
858
859	GB_ERROR error = NULL;
860	GBL_streams out;
861	{
862	char s1, s2;
863	s1 = buffer;
864	if (*s1 == '\|') s1++;
865
866	// loop over all commands
867	for (; s1; s1 = s2) {
868	int separator;
869	GBL_COMMAND command;
870	s2 = gbs_search_next_separator(s1, "\|;,");
871	if (s2) {
872	separator = *(s2);
873	*(s2++) = 0;
874	}
875	else {
876	separator = 0;
877	}
878	// collect the parameters
879	GBL_streams in;
880	if (*s1 == '"') { // copy "text" to out
881	char *end = gbs_search_second_x(s1+1);
882	if (!end) {
883	UNCOVERED(); // seems unreachable (balancing is already ensured by gbs_search_next_separator)
884	error = "Missing second '\"'";
885	break;
886	}
887	*end = 0;
888
889	out.insert(ARB_strdup(s1+1));
890	}
891	else {
892	char *bracket = strchr(s1, '(');
893
894	if (bracket) { // I got the parameter list
895	int slen;
896	*(bracket++) = 0;
897	slen = strlen(bracket);
898	if (bracket[slen-1] != ')') {
899	error = "Missing ')'";
900	}
901	else {
902	// go through the parameters
903	char p1, p2;
904	bracket[slen-1] = 0;
905	for (p1 = bracket; p1; p1 = p2) {
906	p2 = gbs_search_next_separator(p1, ";,");
907	if (p2) {
908	*(p2++) = 0;
909	}
910	if (p1[0] == '"') { // remove "" pairs
911	int len2;
912	p1++;
913	len2 = strlen(p1)-1;
914
915	if (p1[len2] != '\"') {
916	error = "Missing '\"'";
917	}
918	else {
919	p1[len2] = 0;
920	}
921	}
922	in.insert(ARB_strdup(p1));
923	}
924	}
925	}
926	if (!error && (bracket \|\| *s1)) {
927	char *p = s1;
928	int c;
929	while ((c = *p)) { // command to lower case
930	if (c>='A' && c<='Z') {
931	c += 'a'-'A';
932	*p = c;
933	}
934	p++;
935	}
936
937	command = (GBL_COMMAND)GBS_read_hash(Main->command_hash, s1);
938	if (!command) {
939	error = GBS_global_string("Unknown command '%s'", s1);
940	}
941	else {
942	GBL_command_arguments args(gbd, default_tree_name, orig, in, out);
943
944	args.command = s1;
945
946	if (trace) {
947	printf("-----------------------\nExecution of command '%s':\n", args.command);
948	dumpStreams("Arguments", args.param);
949	dumpStreams("InputStreams", args.input);
950	}
951
952	error = command(&args); // execute the command
953
954	if (!error && trace) dumpStreams("OutputStreams", args.output);
955
956	if (error) {
957	char *dup_error = ARB_strdup(error);
958
959	#define MAX_PRINT_LEN 200
960
961	char *paramlist = 0;
962	for (int j = 0; j<args.param.size(); ++j) {
963	const char *param = args.param.get(j);
964	const char *param_short = shortenLongString(param, MAX_PRINT_LEN);
965
966	if (!paramlist) paramlist = ARB_strdup(param_short);
967	else freeset(paramlist, GBS_global_string_copy("%s,%s", paramlist, param_short));
968	}
969	char *inputstreams = 0;
970	for (int j = 0; j<args.input.size(); ++j) {
971	const char *input = args.input.get(j);
972	const char *input_short = shortenLongString(input, MAX_PRINT_LEN);
973
974	if (!inputstreams) inputstreams = ARB_strdup(input_short);
975	else freeset(inputstreams, GBS_global_string_copy("%s;%s", inputstreams, input_short));
976	}
977	#undef MAX_PRINT_LEN
978	if (paramlist) {
979	error = GBS_global_string("while applying '%s(%s)'\nto '%s':\n%s", s1, paramlist, inputstreams, dup_error);
980	}
981	else {
982	error = GBS_global_string("while applying '%s'\nto '%s':\n%s", s1, inputstreams, dup_error);
983	}
984
985	free(inputstreams);
986	free(paramlist);
987	free(dup_error);
988	}
989	}
990	}
991	}
992
993	if (error) break;
994
995	if (separator == '\|') { // out -> in pipe; clear in
996	out.swap(orig);
997	out.erase();
998	}
999	}
1000	}
1001
1002	{
1003	char *s1 = out.concatenated();
1004	free(buffer);
1005
1006	if (!error) {
1007	if (trace) printf("GB_command_interpreter: result='%s'\n", s1);
1008	return s1;
1009	}
1010	free(s1);
1011	}
1012
1013	GB_export_errorf("Command '%s' failed:\nReason: %s", commands, error);
1014	return NULL;
1015	}
1016	// --------------------------------------------------------------------------------
1017
1018	char *GBL_streams::concatenated() const {
1019	int count = size();
1020	if (!count) return ARB_strdup("");
1021	if (count == 1) return ARB_strdup(get(0));
1022
1023	GBS_strstruct *strstruct = GBS_stropen(1000);
1024	for (int i=0; i<count; i++) {
1025	const char *s = get(i);
1026	if (s) GBS_strcat(strstruct, s);
1027	}
1028	return GBS_strclose(strstruct);
1029	}
1030
1031	char GB_command_interpreter(GBDATA gb_main, const char str, const char commands, GBDATA gbd, const char default_tree_name) {
1032	/* simple command interpreter returns NULL on error (which should be exported in that case)
1033	* if first character is == ':' run string parser
1034	* if first character is == '/' run regexpr
1035	* else run ACI
1036	*/
1037
1038	int trace = GB_get_ACISRT_trace();
1039	SmartMallocPtr(char) heapstr;
1040
1041	if (!str) {
1042	if (!gbd) {
1043	GB_export_error("ACI: no input streams found");
1044	return NULL;
1045	}
1046
1047	if (GB_read_type(gbd) == GB_STRING) {
1048	str = GB_read_char_pntr(gbd);
1049	}
1050	else {
1051	char *asstr = GB_read_as_string(gbd);
1052	if (!asstr) {
1053	GB_export_error("Can't read this DB entry as string");
1054	return NULL;
1055	}
1056
1057	heapstr = asstr;
1058	str = &*heapstr;
1059	}
1060	}
1061
1062	if (trace) {
1063	printf("GB_command_interpreter: str='%s'\n"
1064	" command='%s'\n", str, commands);
1065	}
1066
1067	if (!commands \|\| !commands[0]) { // empty command -> do not modify string
1068	return ARB_strdup(str);
1069	}
1070
1071	if (commands[0] == ':') { // ':' -> string parser
1072	return GBS_string_eval(str, commands+1, gbd);
1073	}
1074
1075	if (commands[0] == '/') { // regular expression
1076	GB_ERROR err = 0;
1077	char *result = GBS_regreplace(str, commands, &err);
1078
1079	if (!result) {
1080	if (strcmp(err, "Missing '/' between search and replace string") == 0) {
1081	// if GBS_regreplace didn't find a third '/' -> silently use GBS_regmatch:
1082	size_t matchlen;
1083	err = 0;
1084	const char *matched = GBS_regmatch(str, commands, &matchlen, &err);
1085
1086	if (matched) result = ARB_strndup(matched, matchlen);
1087	else if (!err) result = ARB_strdup("");
1088	}
1089
1090	if (!result && err) result = GBS_global_string_copy("<Error: %s>", err);
1091	}
1092	return result;
1093	}
1094
1095	return apply_ACI(gb_main, commands, str, gbd, default_tree_name);
1096	}
1097
1098	// --------------------------------------------------------------------------------
1099
1100	#ifdef UNIT_TESTS
1101	#include <test_unit.h>
1102
1103	#define TEST_CI__INTERNAL(input,cmd,expected,got,TEST_RESULT) do { \
1104	char *result; \
1105	TEST_EXPECT_RESULT__NOERROREXPORTED(result = GB_command_interpreter(gb_main, input, cmd, gb_data, NULL)); \
1106	TEST_RESULT(result,expected,got); \
1107	free(result); \
1108	} while(0)
1109
1110	#define TEST_CI(input,cmd,expected) TEST_CI__INTERNAL(input,cmd,expected,narg, TEST_EXPECT_EQUAL__IGNARG)
1111	#define TEST_CI__BROKEN(input,cmd,expected,regr) TEST_CI__INTERNAL(input,cmd,expected,regr, TEST_EXPECT_EQUAL__BROKEN)
1112	#define TEST_CI_NOOP(inandout,cmd) TEST_CI__INTERNAL(inandout,cmd,inandout,narg,TEST_EXPECT_EQUAL__IGNARG)
1113	#define TEST_CI_NOOP__BROKEN(inandout,regr,cmd) TEST_CI__INTERNAL(inandout,cmd,inandout,regr,TEST_EXPECT_EQUAL__BROKEN)
1114
1115	#define TEST_CI_INVERSE(in,cmd,inv_cmd,out) do { \
1116	TEST_CI(in, cmd, out); \
1117	TEST_CI(out, inv_cmd, in); \
1118	} while(0)
1119
1120	#define TEST_CI_ERROR_CONTAINS(input,cmd,errorpart_expected) \
1121	TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_command_interpreter(gb_main, input, cmd, gb_data, NULL), errorpart_expected)
1122
1123	#define ACI_SPLIT "\|split(\",\",0)"
1124	#define ACI_MERGE "\|merge(\",\")"
1125	#define WITH_SPLITTED(aci) ACI_SPLIT aci ACI_MERGE
1126
1127	void TEST_GB_command_interpreter() {
1128	GB_shell shell;
1129	GBDATA *gb_main = GB_open("TEST_nuc.arb", "rw"); // ../UNIT_TESTER/run/TEST_nuc.arb
1130
1131	GBT_set_default_alignment(gb_main, "ali_16s"); // for sequence ACI command (@@@ really needed ? )
1132
1133	int old_trace = GB_get_ACISRT_trace();
1134	#if 0
1135	GB_set_ACISRT_trace(1); // used to detect coverage and for debugging purposes
1136	#endif
1137	{
1138	GB_transaction ta(gb_main);
1139	GBDATA *gb_data = GBT_find_species(gb_main, "LcbReu40");
1140
1141	TEST_CI_NOOP("bla", "");
1142
1143	TEST_CI("bla", ":a=u", "blu"); // simple SRT
1144
1145	TEST_CI("bla", "/a/u/", "blu"); // simple regExp replace
1146	TEST_CI("blabla", "/l.*b/", "lab"); // simple regExp match
1147	TEST_CI("blabla", "/b.b/", ""); // simple regExp match (failing)
1148
1149	// escape / quote
1150	TEST_CI_INVERSE("ac", "\|quote", "\|unquote", "\"ac\"");
1151	TEST_CI_INVERSE("ac", "\|escape", "\|unescape", "ac");
1152	TEST_CI_INVERSE("ac", "\|escape\|quote", "\|unquote\|unescape", "\"ac\"");
1153	TEST_CI_INVERSE("ac", "\|quote\|escape", "\|unescape\|unquote", "\\\"ac\\\"");
1154
1155	TEST_CI_INVERSE("a\"b\\c", "\|quote", "\|unquote", "\"a\"b\\c\"");
1156	TEST_CI_INVERSE("a\"b\\c", "\|escape", "\|unescape", "a\\\"b\\\\c");
1157	TEST_CI_INVERSE("a\"b\\c", "\|escape\|quote", "\|unquote\|unescape", "\"a\\\"b\\\\c\"");
1158	TEST_CI_INVERSE("a\"b\\c", "\|quote\|escape", "\|unescape\|unquote", "\\\"a\\\"b\\\\c\\\"");
1159
1160	TEST_CI_NOOP("ac", "\|unquote");
1161	TEST_CI_NOOP("\"ac", "\|unquote");
1162	TEST_CI_NOOP("ac\"", "\|unquote");
1163
1164	TEST_CI("blabla", "\|coUNT(ab)", "4"); // simple ACI
1165	TEST_CI("l", "\|\"b\";dd;\"a\"\|dd", "bla"); // ACI with muliple streams
1166	TEST_CI("bla", "\|count()", "0"); // one empty parameter
1167	TEST_CI("bla", "\|count(\"\")", "0"); // empty parameter
1168	TEST_CI("b a", "\|count(\" \")", "1"); // space in quotes
1169	TEST_CI("b\\a", "\|count(\\a)", "2"); // count '\\' and 'a' (ok)
1170	TEST_CI__BROKEN("b\\a", "\|count(\"\\a\")", "1", "2"); // should only count 'a' (which is escaped in param)
1171	TEST_CI("b\\a", "\|count(\"\a\")", "0"); // does not contain '\a'
1172	TEST_CI("b\a", "\|count(\"\a\")", "1"); // counts '\a'
1173
1174	// escaping (@@@ wrong behavior?)
1175	TEST_CI("b\\a", "\|count(\\a)", "2"); // i would expect '1' as result (the 'a'), but it counts '\\' and 'a'
1176	TEST_CI("b\\a", "\|contains(\"\\\\\")", "0"); // searches for 2 backslashes, finds none
1177	TEST_CI__BROKEN("b\\a", "\|contains(\"\")", "0", "1"); // search for nothing, but reports 1 hit
1178	TEST_CI__BROKEN("b\\a", "\|contains(\\)", "1", "2"); // searches for 1 backslash (ok), but reports two hits instead of one
1179	TEST_CI__BROKEN("b\\\\a", "\|contains(\"\\\\\")", "1", "2"); // searches for 2 backslashes (ok), but reports two hits instead of one
1180	TEST_CI_ERROR_CONTAINS("b\\a", "\|contains(\"\\\")", "ARB ERROR: unbalanced '\"' in '\|contains(\"\\\")'"); // raises error (should search for 1 backslash)
1181
1182	// test binary ops
1183	TEST_CI("", "\"5\";\"7\"\|minus", "-2");
1184	TEST_CI("", "\"5\"\|minus(\"7\")", "-2");
1185	TEST_CI("", "\|minus(\"\"5\"\", \"\"7\"\")", "-2"); // @@@ syntax needed here 'minus(""5"", ""7"")' is broken - need to unescape correctly after parsing parameters!
1186
1187
1188	TEST_CI_NOOP("ab,bcb,abac", WITH_SPLITTED(""));
1189	TEST_CI ("ab,bcb,abac", WITH_SPLITTED("\|len"), "2,3,4");
1190	TEST_CI ("ab,bcb,abac", WITH_SPLITTED("\|count(a)"), "1,0,2");
1191	TEST_CI ("ab,bcb,abac", WITH_SPLITTED("\|minus(len,count(a))"), "1,3,2");
1192	TEST_CI ("ab,bcb,abac", WITH_SPLITTED("\|minus(\"\"5\"\",count(a))"), "4,5,3"); // @@@ escaping broken here as well
1193
1194	// test other recursive uses of GB_command_interpreter
1195	TEST_CI("one", "\|dd;\"two\";dd\|command(\"dd;\"_\";dd;\"-\"\")", "one_one-two_two-one_one-");
1196	TEST_CI("", "\|sequence\|command(\"/^([\\\\.-])[A-Z]./\\\\1/\")\|len", "9"); // count gaps at start of sequence
1197	TEST_CI("one", "\|dd;dd\|eval(\"\"up\";\"per\"\|merge\")", "ONEONE");
1198	TEST_CI("1,2,3", WITH_SPLITTED("\|select(\"\", \"\"one\"\", \"\"two\"\", \"\"three\"\")"), "one,two,three");
1199	TEST_CI_ERROR_CONTAINS("1,4", WITH_SPLITTED("\|select(\"\", \"\"one\"\", \"\"two\"\", \"\"three\"\")"), "Illegal param number '4' (allowed [0..3])");
1200
1201	// test define and do (@@@ SLOW)
1202	TEST_CI("ignored", "define(d4, \"dd;dd;dd;dd\")", "");
1203	TEST_CI("ignored", "define(d16, \"do(d4)\|do(d4)\")", "");
1204	TEST_CI("ignored", "define(d64, \"do(d4)\|do(d16)\")", "");
1205	TEST_CI("ignored", "define(d4096, \"do(d64)\|do(d64)\")", "");
1206
1207	TEST_CI("x", "do(d4)", "xxxx");
1208	TEST_CI("xy", "do(d4)", "xyxyxyxy");
1209	TEST_CI("x", "do(d16)", "xxxxxxxxxxxxxxxx");
1210	TEST_CI("x", "do(d64)\|len", "64");
1211	TEST_CI("xy", "do(d4)\|len", "8");
1212	TEST_CI("xy", "do(d4)\|len()", "8");
1213	TEST_CI("xy", "do(d4)\|len(x)", "4");
1214	TEST_CI("x", "do(d4096)\|len", "4096");
1215
1216	{
1217	int prev_trace = GB_get_ACISRT_trace();
1218	GB_set_ACISRT_trace(0); // do not trace here
1219	// create 4096 streams:
1220	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");
1221	GB_set_ACISRT_trace(prev_trace);
1222	}
1223
1224	// other commands
1225
1226	// streams
1227	TEST_CI("x", "dd;dd\|streams", "2");
1228	TEST_CI("x", "dd;dd\|dd;dd\|streams", "4");
1229	TEST_CI("x", "dd;dd\|dd;dd\|dd;dd\|streams", "8");
1230	TEST_CI("x", "do(d4)\|streams", "1"); // stream is merged when do() returns
1231
1232	TEST_CI("", "ali_name", "ali_16s"); // ask for default-alignment name
1233	TEST_CI("", "sequence_type", "rna"); // ask for sequence_type of default-alignment
1234
1235	// format
1236	TEST_CI("acgt", "format", " acgt");
1237	TEST_CI("acgt", "format(firsttab=1)", " acgt");
1238	TEST_CI("acgt", "format(firsttab=1, width=2)",
1239	" ac\n"
1240	" gt");
1241	TEST_CI("acgt", "format(firsttab=1,tab=1,width=2)",
1242	" ac\n"
1243	" gt");
1244	TEST_CI("acgt", "format(firsttab=0,tab=0,width=2)",
1245	"ac\n"
1246	"gt");
1247	TEST_CI("acgt", "format(firsttab=0,tab=0,width=1)",
1248	"a\n"
1249	"c\n"
1250	"g\n"
1251	"t");
1252
1253	TEST_CI_ERROR_CONTAINS("acgt", "format(gap=0)", "Unknown Parameter 'gap=0' in command 'format'");
1254	TEST_CI_ERROR_CONTAINS("acgt", "format(numleft)", "Unknown Parameter 'numleft' in command 'format'");
1255
1256	// format_sequence
1257	TEST_CI_ERROR_CONTAINS("acgt", "format_sequence(numright=5, numleft)", "You may only specify 'numleft' OR 'numright', not both");
1258
1259	TEST_CI("acgtacgtacgtacg", "format_sequence(firsttab=5,tab=5,width=4,numleft=1)",
1260	"1 acgt\n"
1261	"5 acgt\n"
1262	"9 acgt\n"
1263	"13 acg");
1264
1265	TEST_CI("acgtacgtacgtacg", "format_sequence(firsttab=5,tab=5,width=4,numright=9)", // test EMBL sequence formatting
1266	" acgt 4\n"
1267	" acgt 8\n"
1268	" acgt 12\n"
1269	" acg 15");
1270
1271	TEST_CI("acgtacgtacgtac", "format_sequence(firsttab=5,tab=5,width=4,gap=2,numright=-1)", // autodetect width for 'numright'
1272	" ac gt 4\n"
1273	" ac gt 8\n"
1274	" ac gt 12\n"
1275	" ac 14");
1276
1277	TEST_CI("acgt", "format_sequence(firsttab=0,tab=0,width=2,gap=1)",
1278	"a c\n"
1279	"g t");
1280	TEST_CI("acgt", "format_sequence(firsttab=0,tab=0,width=4,gap=1)", "a c g t");
1281	TEST_CI("acgt", "format_sequence(firsttab=0,tab=0,width=4,gap=2)", "ac gt");
1282	TEST_CI("acgtacgt", "format_sequence(firsttab=0,width=10,gap=4)", "acgt acgt");
1283	TEST_CI("acgtacgt", "format_sequence(firsttab=1,width=10,gap=4)", " acgt acgt");
1284
1285	TEST_CI_ERROR_CONTAINS("acgt", "format_sequence(nl=c)", "Unknown Parameter 'nl=c' in command 'format_sequence'");
1286	TEST_CI_ERROR_CONTAINS("acgt", "format_sequence(forcenl=)", "Unknown Parameter 'forcenl=' in command 'format_sequence'");
1287
1288	TEST_CI_ERROR_CONTAINS("acgt", "format(width=0)", "Illegal zero width");
1289	TEST_CI_ERROR_CONTAINS("acgt", "format_sequence(width=0)", "Illegal zero width");
1290
1291	// remove + keep
1292	TEST_CI_NOOP("acgtacgt", "remove(-.)");
1293	TEST_CI ("..acg--ta-cgt...", "remove(-.)", "acgtacgt");
1294	TEST_CI ("..acg--ta-cgt...", "remove(acgt)", "..---...");
1295
1296	TEST_CI_NOOP("acgtacgt", "keep(acgt)");
1297	TEST_CI ("..acg--ta-cgt...", "keep(-.)", "..---...");
1298	TEST_CI ("..acg--ta-cgt...", "keep(acgt)", "acgtacgt");
1299
1300	// compare + icompare
1301	TEST_CI("x,z,y,y,z,x,x,Z,y,Y,Z,x", WITH_SPLITTED("\|compare"), "-1,0,1,1,1,-1");
1302	TEST_CI("x,z,y,y,z,x,x,Z,y,Y,Z,x", WITH_SPLITTED("\|icompare"), "-1,0,1,-1,0,1");
1303
1304	TEST_CI("x,y,z", WITH_SPLITTED("\|compare(\"y\")"), "-1,0,1");
1305
1306	// equals + iequals
1307	TEST_CI("a,b,a,a,a,A", WITH_SPLITTED("\|equals"), "0,1,0");
1308	TEST_CI("a,b,a,a,a,A", WITH_SPLITTED("\|iequals"), "0,1,1");
1309
1310	// contains + icontains
1311	TEST_CI("abc,bcd,BCD", WITH_SPLITTED("\|contains(\"bc\")"), "2,1,0");
1312	TEST_CI("abc,bcd,BCD", WITH_SPLITTED("\|icontains(\"bc\")"), "2,1,1");
1313	TEST_CI("abc,bcd,BCD", WITH_SPLITTED("\|icontains(\"d\")"), "0,3,3");
1314
1315	// partof + ipartof
1316	TEST_CI("abc,BCD,def,deg", WITH_SPLITTED("\|partof(\"abcdefg\")"), "1,0,4,0");
1317	TEST_CI("abc,BCD,def,deg", WITH_SPLITTED("\|ipartof(\"abcdefg\")"), "1,2,4,0");
1318
1319	// translate
1320	TEST_CI("abcdefgh", "translate(abc,cba)", "cbadefgh");
1321	TEST_CI("abcdefgh", "translate(cba,abc)", "cbadefgh");
1322	TEST_CI("abcdefgh", "translate(hcba,abch,-)", "hcb----a");
1323	TEST_CI("abcdefgh", "translate(aceg,aceg,-)", "a-c-e-g-");
1324	TEST_CI("abbaabba", "translate(ab,ba,-)", "baabbaab");
1325	TEST_CI("abbaabba", "translate(a,x,-)", "x--xx--x");
1326	TEST_CI("abbaabba", "translate(,,-)", "--------");
1327
1328	// echo
1329	TEST_CI("", "echo", "");
1330	TEST_CI("", "echo(x,y,z)", "xyz");
1331	TEST_CI("", "echo(x;y,z)", "xyz"); // check ';' as param-separator
1332	TEST_CI("", "echo(x;y;z)", "xyz");
1333	TEST_CI("", "echo(x,y,z)\|streams", "3");
1334
1335	// upper, lower + caps
1336	TEST_CI("the QUICK brOwn Fox", "lower", "the quick brown fox");
1337	TEST_CI("the QUICK brOwn Fox", "upper", "THE QUICK BROWN FOX");
1338	TEST_CI("the QUICK brOwn FoX", "caps", "The Quick Brown Fox");
1339
1340	// head, tail + mid/mid0
1341	TEST_CI ("1234567890", "head(3)", "123");
1342	TEST_CI ("1234567890", "head(9)", "123456789");
1343	TEST_CI_NOOP("1234567890", "head(10)");
1344	TEST_CI_NOOP("1234567890", "head(20)");
1345
1346	TEST_CI ("1234567890", "tail(4)", "7890");
1347	TEST_CI ("1234567890", "tail(9)", "234567890");
1348	TEST_CI_NOOP("1234567890", "tail(10)");
1349	TEST_CI_NOOP("1234567890", "tail(20)");
1350
1351	TEST_CI("1234567890", "tail(0)", "");
1352	TEST_CI("1234567890", "head(0)", "");
1353	TEST_CI("1234567890", "tail(-2)", "");
1354	TEST_CI("1234567890", "head(-2)", "");
1355
1356	TEST_CI("1234567890", "mid(3,5)", "345");
1357	TEST_CI("1234567890", "mid(2,2)", "2");
1358
1359	TEST_CI("1234567890", "mid0(3,5)", "456");
1360
1361	TEST_CI("1234567890", "mid(9,20)", "90");
1362	TEST_CI("1234567890", "mid(20,20)", "");
1363
1364	TEST_CI("1234567890", "tail(3)", "890"); // example from ../HELP_SOURCE/oldhelp/commands.hlp@mid0
1365	TEST_CI("1234567890", "mid(-2,0)", "890");
1366	TEST_CI("1234567890", "mid0(-3,-1)", "890");
1367
1368	// tab + pretab
1369	TEST_CI("x,xx,xxx", WITH_SPLITTED("\|tab(2)"), "x ,xx,xxx");
1370	TEST_CI("x,xx,xxx", WITH_SPLITTED("\|tab(3)"), "x ,xx ,xxx");
1371	TEST_CI("x,xx,xxx", WITH_SPLITTED("\|tab(4)"), "x ,xx ,xxx ");
1372	TEST_CI("x,xx,xxx", WITH_SPLITTED("\|pretab(2)"), " x,xx,xxx");
1373	TEST_CI("x,xx,xxx", WITH_SPLITTED("\|pretab(3)"), " x, xx,xxx");
1374	TEST_CI("x,xx,xxx", WITH_SPLITTED("\|pretab(4)"), " x, xx, xxx");
1375
1376	// crop
1377	TEST_CI(" x x ", "crop(\" \")", "x x");
1378	TEST_CI("\n \t x x \n \t", "crop(\"\t\n \")", "x x");
1379
1380	// cut, drop, dropempty and dropzero
1381	TEST_CI("one,two,three,four,five,six", WITH_SPLITTED("\|cut(2,3,5)"), "two,three,five");
1382	TEST_CI("one,two,three,four,five,six", WITH_SPLITTED("\|drop(2,3,5)"), "one,four,six");
1383
1384	TEST_CI_ERROR_CONTAINS("a", "drop(2)", "Illegal stream number '2' (allowed [1..1])");
1385	TEST_CI_ERROR_CONTAINS("a", "drop(0)", "Illegal stream number '0' (allowed [1..1])");
1386	TEST_CI_ERROR_CONTAINS("a", "cut(2)", "Illegal stream number '2' (allowed [1..1])");
1387	TEST_CI_ERROR_CONTAINS("a", "cut(0)", "Illegal stream number '0' (allowed [1..1])");
1388
1389	TEST_CI("one,two,three,four,five,six", WITH_SPLITTED("\|dropempty\|streams"), "6");
1390	TEST_CI("one,two,,,five,six", WITH_SPLITTED("\|dropempty\|streams"), "4");
1391	TEST_CI(",,,,,", WITH_SPLITTED("\|dropempty"), "");
1392	TEST_CI(",,,,,", WITH_SPLITTED("\|dropempty\|streams"), "0");
1393
1394	TEST_CI("1,0,0,2,3,0", WITH_SPLITTED("\|dropzero"), "1,2,3");
1395	TEST_CI("0,0,0,0,0,0", WITH_SPLITTED("\|dropzero"), "");
1396	TEST_CI("0,0,0,0,0,0", WITH_SPLITTED("\|dropzero\|streams"), "0");
1397
1398	// swap
1399	TEST_CI("1,2,3,four,five,six", WITH_SPLITTED("\|swap"), "1,2,3,four,six,five");
1400	TEST_CI("1,2,3,four,five,six", WITH_SPLITTED("\|swap(2,3)"), "1,3,2,four,five,six");
1401	TEST_CI("1,2,3,four,five,six", WITH_SPLITTED("\|swap(2,3)\|swap(4,3)"), "1,3,four,2,five,six");
1402	TEST_CI_NOOP("1,2,3,four,five,six", WITH_SPLITTED("\|swap(3,3)"));
1403	TEST_CI_NOOP("1,2,3,four,five,six", WITH_SPLITTED("\|swap(3,2)\|swap(2,3)"));
1404	TEST_CI_NOOP("1,2,3,four,five,six", WITH_SPLITTED("\|swap(3,2)\|swap(3,1)\|swap(2,1)\|swap(1,3)"));
1405
1406	TEST_CI_ERROR_CONTAINS("a", "swap", "need at least two input streams");
1407	TEST_CI_ERROR_CONTAINS("a,b", WITH_SPLITTED("\|swap(2,3)"), "Illegal stream number '3' (allowed [1..2])");
1408	TEST_CI_ERROR_CONTAINS("a,b", WITH_SPLITTED("\|swap(3,2)"), "Illegal stream number '3' (allowed [1..2])");
1409
1410	// toback + tofront
1411	TEST_CI ("front,mid,back", WITH_SPLITTED("\|toback(2)"), "front,back,mid");
1412	TEST_CI ("front,mid,back", WITH_SPLITTED("\|tofront(2)"), "mid,front,back");
1413	TEST_CI_NOOP("front,mid,back", WITH_SPLITTED("\|toback(3)"));
1414	TEST_CI_NOOP("front,mid,back", WITH_SPLITTED("\|tofront(1)"));
1415	TEST_CI_NOOP("a", WITH_SPLITTED("\|tofront(1)"));
1416	TEST_CI_NOOP("a", WITH_SPLITTED("\|toback(1)"));
1417
1418	TEST_CI_ERROR_CONTAINS("a,b", WITH_SPLITTED("\|tofront(3)"), "Illegal stream number '3' (allowed [1..2])");
1419	TEST_CI_ERROR_CONTAINS("a,b", WITH_SPLITTED("\|toback(3)"), "Illegal stream number '3' (allowed [1..2])");
1420
1421	// split (default)
1422	TEST_CI("a\nb", "\|split" ACI_MERGE, "a,b");
1423
1424	// extract_words + extract_sequence
1425	TEST_CI("1,2,3,four,five,six", "extract_words(\"0123456789\",1)", "1 2 3");
1426	TEST_CI("1,2,3,four,five,six", "extract_words(\"abcdefghijklmnopqrstuvwxyz\", 3)", "five four six");
1427	TEST_CI("1,2,3,four,five,six", "extract_words(\"abcdefghijklmnopqrstuvwxyz\", 4)", "five four");
1428	TEST_CI("1,2,3,four,five,six", "extract_words(\"abcdefghijklmnopqrstuvwxyz\", 5)", "");
1429
1430	TEST_CI ("1,2,3,four,five,six", "extract_sequence(\"acgtu\", 1.0)", "");
1431	TEST_CI ("1,2,3,four,five,six", "extract_sequence(\"acgtu\", 0.5)", "");
1432	TEST_CI ("1,2,3,four,five,six", "extract_sequence(\"acgtu\", 0.0)", "four five six");
1433	TEST_CI ("..acg--ta-cgt...", "extract_sequence(\"acgtu\", 1.0)", "");
1434	TEST_CI_NOOP("..acg--ta-cgt...", "extract_sequence(\"acgtu-.\", 1.0)");
1435	TEST_CI_NOOP("..acg--ta-ygt...", "extract_sequence(\"acgtu-.\", 0.7)");
1436	TEST_CI ("70 ..acg--ta-cgt... 70", "extract_sequence(\"acgtu-.\", 1.0)", "..acg--ta-cgt...");
1437
1438	// checksum + gcgchecksum
1439	TEST_CI("", "sequence\|checksum", "4C549A5F");
1440	TEST_CI("", "sequence \| gcgchecksum", "4308");
1441
1442	// SRT
1443	TEST_CI( "The quick brown fox", "srt(\"quick=lazy:brown fox=dog\")", "The lazy dog");
1444	TEST_CI__BROKEN("The quick brown fox", "srt(quick=lazy:brown fox=dog)",
1445	"The lazy dog", // @@@ parsing problem ?
1446	"The lazy brown fox"); // document current (unwanted behavior)
1447	TEST_CI_ERROR_CONTAINS("x", "srt(x=y,z)", "SRT ERROR: no '=' found in command");
1448
1449	// REG
1450	TEST_CI("starstostripes", "/\\*/--/", "stars--to--stripes");
1451
1452	TEST_CI("sImILaRWIllBE,GonEEASIly", WITH_SPLITTED("\|command(/[A-Z]//)"), "small,only");
1453	TEST_CI("sthBIGinside,FATnotCAP", WITH_SPLITTED("\|command(/([A-Z])+/)"), "BIG,FAT");
1454
1455	// calculator
1456	TEST_CI("", "echo(9,3)\|plus", "12");
1457	TEST_CI("", "echo(9,3)\|minus", "6");
1458	TEST_CI("", "echo(9,3)\|mult", "27");
1459	TEST_CI("", "echo(9,3)\|div", "3");
1460	TEST_CI("", "echo(9,3)\|rest", "0");
1461	TEST_CI("", "echo(9,3)\|per_cent", "300");
1462
1463	TEST_CI("", "echo(1,2,3)\|plus(1)" ACI_MERGE, "2,3,4");
1464	TEST_CI("", "echo(1,2,3)\|minus(2)" ACI_MERGE, "-1,0,1");
1465	TEST_CI("", "echo(1,2,3)\|mult(42)" ACI_MERGE, "42,84,126");
1466	TEST_CI("", "echo(1,2,3)\|div(2)" ACI_MERGE, "0,1,1");
1467	TEST_CI("", "echo(1,2,3)\|rest(2)" ACI_MERGE, "1,0,1");
1468	TEST_CI("", "echo(1,2,3)\|per_cent(3)" ACI_MERGE, "33,66,100");
1469
1470	// readdb
1471	TEST_CI("", "readdb(name)", "LcbReu40");
1472	TEST_CI("", "readdb(acc)", "X76328");
1473
1474	// taxonomy
1475	TEST_CI("", "taxonomy(1)", "No default tree");
1476	TEST_CI("", "taxonomy(tree_nuc, 1)", "group1");
1477	TEST_CI("", "taxonomy(tree_nuc, 5)", "top/lower-red/group1");
1478	TEST_CI_ERROR_CONTAINS("", "taxonomy", "syntax: taxonomy([tree_name,]count)");
1479
1480	// diff, filter + change
1481	TEST_CI("..acg--ta-cgt..." ","
1482	"..acg--ta-cgt...", WITH_SPLITTED("\|diff(pairwise=1)"),
1483	"................");
1484	TEST_CI("..acg--ta-cgt..." ","
1485	"..cgt--ta-acg...", WITH_SPLITTED("\|diff(pairwise=1,equal==)"),
1486	"==cgt=====acg===");
1487	TEST_CI("..acg--ta-cgt..." ","
1488	"..cgt--ta-acg...", WITH_SPLITTED("\|diff(pairwise=1,differ=X)"),
1489	"..XXX.....XXX...");
1490	TEST_CI("", "sequence\|diff(species=LcbFruct)\|checksum", "645E3107");
1491
1492	TEST_CI("..XXX.....XXX..." ","
1493	"..acg--ta-cgt...", WITH_SPLITTED("\|filter(pairwise=1,exclude=X)"),
1494	"..--ta-...");
1495	TEST_CI("..XXX.....XXX..." ","
1496	"..acg--ta-cgt...", WITH_SPLITTED("\|filter(pairwise=1,include=X)"),
1497	"acgcgt");
1498	TEST_CI("", "sequence\|filter(species=LcbFruct,include=.-)", "-----------T----T-------G----------C-----T----T...");
1499
1500	TEST_CI("...XXX....XXX..." ","
1501	"..acg--ta-cgt...", WITH_SPLITTED("\|change(pairwise=1,include=X,to=C,change=100)"),
1502	"..aCC--ta-CCC...");
1503	TEST_CI("...XXXXXXXXX...." ","
1504	"..acg--ta-cgt...", WITH_SPLITTED("\|change(pairwise=1,include=X,to=-,change=100)"),
1505	"..a---------t...");
1506
1507
1508	// exec
1509	TEST_CI("c,b,c,b,a,a", WITH_SPLITTED("\|exec(\"(sort\|uniq)\")\|split\|dropempty"), "a,b,c");
1510	TEST_CI("a,aba,cac", WITH_SPLITTED("\|exec(\"perl\",-pe,s/([bc])/$1$1/g)\|split\|dropempty"), "a,abba,ccacc");
1511
1512	// error cases
1513	TEST_CI_ERROR_CONTAINS("", "nocmd", "Unknown command 'nocmd'");
1514	TEST_CI_ERROR_CONTAINS("", "\|nocmd", "Unknown command 'nocmd'");
1515	TEST_CI_ERROR_CONTAINS("", "caps(x)", "syntax: caps (no parameters)");
1516	TEST_CI_ERROR_CONTAINS("", "trace", "syntax: trace(0\|1)");
1517	TEST_CI_ERROR_CONTAINS("", "count", "syntax: count(\"characters to count\")");
1518	TEST_CI_ERROR_CONTAINS("", "count(a,b)", "syntax: count(\"characters to count\")");
1519	TEST_CI_ERROR_CONTAINS("", "len(a,b)", "syntax: len[(\"characters not to count\")]");
1520	TEST_CI_ERROR_CONTAINS("", "plus(a,b,c)", "syntax: plus[(Expr1[,Expr2])]");
1521	TEST_CI_ERROR_CONTAINS("", "count(a,b", "Reason: Missing ')'");
1522	TEST_CI_ERROR_CONTAINS("", "count(a,\"b)", "unbalanced '\"' in 'count(a,\"b)'");
1523	TEST_CI_ERROR_CONTAINS("", "count(a,\"b)\"", "Reason: Missing ')'");
1524	TEST_CI_ERROR_CONTAINS("", "dd;dd\|count", "syntax: count(\"characters to count\")");
1525	TEST_CI_ERROR_CONTAINS("", "\|count(\"a\"x)", "Reason: Missing '\"'");
1526	TEST_CI_ERROR_CONTAINS("", "\|count(\"a)", "unbalanced '\"' in '\|count(\"a)'");
1527
1528	TEST_CI_ERROR_CONTAINS("", "translate(a)", "syntax: translate(old,new[,other])");
1529	TEST_CI_ERROR_CONTAINS("", "translate(a,b,c,d)", "syntax: translate(old,new[,other])");
1530
1531	TEST_CI_ERROR_CONTAINS(NULL, "whatever", "ARB ERROR: Can't read this DB entry as string"); // here gb_data is the species container
1532
1533	gb_data = GB_entry(gb_data, "full_name"); // execute ACI on 'full_name' from here on ------------------------------
1534
1535	TEST_CI(NULL, "", "Lactobacillus reuteri"); // noop
1536	TEST_CI(NULL, "\|len", "21");
1537	TEST_CI(NULL, ":tobac=", "Lacillus reuteri");
1538	TEST_CI(NULL, "/ba.*us/B/", "LactoB reuteri");
1539
1540	TEST_CI(NULL, "\|taxonomy(1)", "No default tree");
1541	TEST_CI_ERROR_CONTAINS(NULL, "\|taxonomy(tree_nuc,2)", "Container has neither 'name' nor 'group_name' entry - can't detect container type");
1542
1543	gb_data = NULL;
1544	TEST_CI_ERROR_CONTAINS(NULL, "", "no input streams found");
1545	}
1546
1547	GB_set_ACISRT_trace(old_trace); // avoid side effect of TEST_GB_command_interpreter
1548	GB_close(gb_main);
1549	}
1550
1551	const char GBT_get_name(GBDATA gb_item);
1552
1553	struct TestDB : virtual Noncopyable {
1554	GB_shell shell;
1555	GBDATA *gb_main;
1556	GB_ERROR error;
1557
1558	GBDATA *gb_cont1;
1559	GBDATA *gb_cont2;
1560	GBDATA *gb_cont_empty;
1561	GBDATA *gb_cont_misc;
1562
1563	GB_ERROR create_many_items(GBDATA gb_parent, const char *item_key_list, int item_count) {
1564	int k = 0;
1565	for (int i = 0; i<item_count && !error; i++) {
1566	const char *item_key = item_key_list[k++];
1567	if (!item_key) { item_key = item_key_list[0]; k = 1; }
1568
1569	GBDATA *gb_child = GB_create_container(gb_parent, item_key);
1570	if (!gb_child) {
1571	error = GB_await_error();
1572	}
1573	else {
1574	if ((i%7) == 0) GB_write_flag(gb_child, 1); // mark some
1575
1576	GBDATA *gb_name = GB_create(gb_child, "name", GB_STRING);
1577	error = GB_write_string(gb_name, GBS_global_string("%s %i", item_key, i));
1578	}
1579	}
1580	return error;
1581	}
1582
1583	TestDB() {
1584	gb_main = GB_open("nosuch.arb", "c");
1585	error = gb_main ? NULL : GB_await_error();
1586
1587	if (!error) {
1588	GB_transaction ta(gb_main);
1589	gb_cont1 = GB_create_container(gb_main, "container1");
1590	gb_cont2 = GB_create_container(gb_main, "container2");
1591	gb_cont_empty = GB_create_container(gb_main, "empty");
1592	gb_cont_misc = GB_create_container(gb_main, "misc");
1593
1594	if (!gb_cont1 \|\| !gb_cont2) error = GB_await_error();
1595
1596	const char *single_key[] = { "entry", NULL };
1597	const char *mixed_keys[] = { "item", "other", NULL };
1598
1599	if (!error) error = create_many_items(gb_cont1, single_key, 100);
1600	if (!error) error = create_many_items(gb_cont2, mixed_keys, 20);
1601	}
1602	TEST_EXPECT_NO_ERROR(error);
1603	}
1604	~TestDB() {
1605	GB_close(gb_main);
1606	}
1607	};
1608
1609	void TEST_DB_search() {
1610	TestDB db;
1611	TEST_EXPECT_NO_ERROR(db.error);
1612
1613	{
1614	GB_transaction ta(db.gb_main);
1615
1616	TEST_EXPECT_EQUAL(GB_number_of_subentries(db.gb_cont1), 100);
1617	TEST_EXPECT_EQUAL(GB_number_of_subentries(db.gb_cont2), 20);
1618
1619	{
1620	GBDATA *gb_any_child = GB_child(db.gb_cont1);
1621	TEST_REJECT_NULL(gb_any_child);
1622	TEST_EXPECT_EQUAL(gb_any_child, GB_entry(db.gb_cont1, "entry"));
1623	TEST_EXPECT_EQUAL(gb_any_child, GB_search(db.gb_main, "container1/entry", GB_FIND));
1624
1625	TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(db.gb_main, "zic-zac", GB_FIND), "Invalid char '-' in key 'zic-zac'");
1626
1627	// check link-syntax
1628	TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(db.gb_main, "->entry", GB_FIND), "Missing linkname before '->' in '->entry'");
1629	TEST_EXPECT_NORESULT__NOERROREXPORTED(GB_search(db.gb_main, "entry->bla", GB_FIND));
1630	TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(db.gb_main, "container1/entry->nowhere", GB_FIND), "'entry' exists, but is not a link");
1631	TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(db.gb_main, "container1/nosuchentry->nowhere", GB_STRING), "Cannot create links on the fly in gb_search");
1632	TEST_EXPECT_NORESULT__NOERROREXPORTED(GB_search(db.gb_main, "entry->", GB_FIND)); // valid ? just deref link
1633
1634	// check ..
1635	TEST_EXPECT_EQUAL(GB_search(gb_any_child, "..", GB_FIND), db.gb_cont1);
1636	TEST_EXPECT_EQUAL(GB_search(gb_any_child, "../..", GB_FIND), db.gb_main);
1637	// above main entry
1638	TEST_EXPECT_NORESULT__NOERROREXPORTED(GB_search(gb_any_child, "../../..", GB_FIND));
1639	TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(gb_any_child, "../../../impossible", GB_STRING), "cannot use '..' at root node");
1640
1641	TEST_EXPECT_EQUAL(GB_search(gb_any_child, "", GB_FIND), gb_any_child); // return self
1642	TEST_EXPECT_EQUAL(GB_search(gb_any_child, "/container1/", GB_FIND), db.gb_cont1); // accept trailing slash for container ..
1643	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
1644
1645	TEST_EXPECT_EQUAL(GB_search(gb_any_child, "/", GB_FIND), db.gb_main);
1646	TEST_EXPECT_EQUAL(GB_search(gb_any_child, "/container1/..", GB_FIND), db.gb_main);
1647	TEST_EXPECT_NORESULT__NOERROREXPORTED(GB_search(gb_any_child, "/..", GB_FIND)); // main has no parent
1648	}
1649
1650	{
1651	GBDATA *gb_child1 = GB_child(db.gb_cont2); TEST_REJECT_NULL(gb_child1);
1652	GBDATA *gb_child2 = GB_nextChild(gb_child1); TEST_REJECT_NULL(gb_child2);
1653	GBDATA *gb_child3 = GB_nextChild(gb_child2); TEST_REJECT_NULL(gb_child3);
1654	GBDATA *gb_child4 = GB_nextChild(gb_child3); TEST_REJECT_NULL(gb_child4);
1655
1656	TEST_EXPECT_EQUAL(GB_read_key_pntr(gb_child1), "item");
1657	TEST_EXPECT_EQUAL(GB_read_key_pntr(gb_child2), "other");
1658	TEST_EXPECT_EQUAL(GB_read_key_pntr(gb_child3), "item");
1659	TEST_EXPECT_EQUAL(GB_read_key_pntr(gb_child4), "other");
1660
1661	TEST_EXPECT_NORESULT__NOERROREXPORTED(GB_entry(db.gb_cont2, "entry"));
1662	TEST_EXPECT_EQUAL(GB_entry(db.gb_cont2, "item"), gb_child1);
1663	TEST_EXPECT_EQUAL(GB_entry(db.gb_cont2, "other"), gb_child2);
1664
1665	TEST_EXPECT_EQUAL(GB_nextEntry(gb_child1), gb_child3);
1666	TEST_EXPECT_EQUAL(GB_nextEntry(gb_child2), gb_child4);
1667
1668	// check ..
1669	TEST_EXPECT_EQUAL(GB_search(gb_child3, "../item", GB_FIND), gb_child1);
1670	TEST_EXPECT_EQUAL(GB_search(gb_child3, "../other", GB_FIND), gb_child2);
1671	TEST_EXPECT_EQUAL(GB_search(gb_child3, "../other/../item", GB_FIND), gb_child1);
1672	}
1673
1674	// ------------------------
1675	// single entries
1676
1677	{
1678	GBDATA *gb_str = GB_searchOrCreate_string(db.gb_cont_misc, "str", "bla"); TEST_REJECT_NULL(gb_str);
1679	GBDATA *gb_str_same = GB_searchOrCreate_string(db.gb_cont_misc, "str", "blub");
1680
1681	TEST_EXPECT_EQUAL(gb_str, gb_str_same);
1682	TEST_EXPECT_EQUAL(GB_read_char_pntr(gb_str), "bla");
1683
1684	GBDATA *gb_int = GB_searchOrCreate_int(db.gb_cont_misc, "int", 4711); TEST_REJECT_NULL(gb_int);
1685	GBDATA *gb_int_same = GB_searchOrCreate_int(db.gb_cont_misc, "int", 2012);
1686
1687	TEST_EXPECT_EQUAL(gb_int, gb_int_same);
1688	TEST_EXPECT_EQUAL(GB_read_int(gb_int), 4711);
1689
1690	GBDATA *gb_float = GB_searchOrCreate_float(db.gb_cont_misc, "float", 0.815); TEST_REJECT_NULL(gb_float);
1691	GBDATA *gb_float_same = GB_searchOrCreate_float(db.gb_cont_misc, "float", 3.1415);
1692
1693	TEST_EXPECT_EQUAL(gb_float, gb_float_same);
1694	TEST_EXPECT_SIMILAR(GB_read_float(gb_float), 0.815, 0.0001);
1695
1696	TEST_EXPECT_EQUAL (GB_read_char_pntr(GB_searchOrCreate_string(db.gb_cont_misc, "sub1/str", "blub")), "blub");
1697	TEST_EXPECT_EQUAL (GB_read_int (GB_searchOrCreate_int (db.gb_cont_misc, "sub2/int", 2012)), 2012);
1698	TEST_EXPECT_SIMILAR(GB_read_float (GB_searchOrCreate_float (db.gb_cont_misc, "sub3/float", 3.1415)), 3.1415, 0.00001);
1699
1700	TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_searchOrCreate_float (db.gb_cont_misc, "int", 0.815), "has wrong type");
1701	TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_searchOrCreate_float (db.gb_cont_misc, "str", 0.815), "has wrong type");
1702	TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_searchOrCreate_int (db.gb_cont_misc, "float", 4711), "has wrong type");
1703	TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_searchOrCreate_int (db.gb_cont_misc, "str", 4711), "has wrong type");
1704	TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_searchOrCreate_string(db.gb_cont_misc, "float", "bla"), "has wrong type");
1705	TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_searchOrCreate_string(db.gb_cont_misc, "int", "bla"), "has wrong type");
1706
1707	TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_searchOrCreate_string(db.gb_cont_misc, "", "bla"), "Invalid char '' in key '*'");
1708	TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_searchOrCreate_string(db.gb_cont_misc, "int", "bla"), "Invalid char '' in key 'int*'");
1709	TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_searchOrCreate_string(db.gb_cont_misc, "sth_else", "bla"), "Invalid char '' in key 'sth_else*'");
1710
1711	GBDATA *gb_entry;
1712	TEST_EXPECT_NORESULT__NOERROREXPORTED(GB_search(db.gb_cont_misc, "subcont/entry", GB_FIND));
1713	TEST_EXPECT_RESULT__NOERROREXPORTED(gb_entry = GB_search(db.gb_cont_misc, "subcont/entry", GB_INT));
1714	TEST_EXPECT_EQUAL(GB_read_int(gb_entry), 0);
1715
1716	GBDATA *gb_cont1;
1717	TEST_EXPECT_RESULT__NOERROREXPORTED(gb_cont1 = GB_search(db.gb_cont_misc, "subcont", GB_CREATE_CONTAINER));
1718	TEST_EXPECT_EQUAL(GB_child(gb_cont1), gb_entry); // test GB_search found the container created implicitely above
1719
1720	GBDATA *gb_cont2;
1721	TEST_EXPECT_RESULT__NOERROREXPORTED(gb_cont2 = GB_search(db.gb_cont_misc, "subcont2", GB_CREATE_CONTAINER)); // create new container
1722
1723	// -----------------------
1724	// search values
1725
1726	GBDATA *gb_4711;
1727	TEST_EXPECT_RESULT__NOERROREXPORTED(gb_4711 = GB_find_int(db.gb_cont_misc, "int", 4711, SEARCH_CHILD));
1728	TEST_EXPECT_EQUAL(gb_4711, gb_int);
1729
1730	TEST_EXPECT_NULL(GB_find_int(db.gb_cont_misc, "int", 2012, SEARCH_CHILD));
1731
1732	GBDATA *gb_bla;
1733	TEST_EXPECT_RESULT__NOERROREXPORTED(gb_bla = GB_find_string(db.gb_cont_misc, "str", "bla", GB_MIND_CASE, SEARCH_CHILD));
1734	TEST_EXPECT_EQUAL(gb_bla, gb_str);
1735	TEST_EXPECT_RESULT__NOERROREXPORTED(gb_bla = GB_find_string(gb_4711, "str", "bla", GB_MIND_CASE, SEARCH_BROTHER));
1736	TEST_EXPECT_EQUAL(gb_bla, gb_str);
1737
1738	TEST_EXPECT_NULL(GB_find_string(db.gb_cont_misc, "str", "blub", GB_MIND_CASE, SEARCH_CHILD));
1739
1740	GBDATA *gb_name;
1741	TEST_REJECT_NULL (GB_find_string (db.gb_cont1, "name", "entry 77", GB_MIND_CASE, SEARCH_GRANDCHILD));
1742	TEST_REJECT_NULL (GB_find_string (db.gb_cont1, "name", "entry 99", GB_MIND_CASE, SEARCH_GRANDCHILD));
1743	TEST_EXPECT_NORESULT__NOERROREXPORTED(GB_find_string (db.gb_cont1, "name", "entry 100", GB_MIND_CASE, SEARCH_GRANDCHILD));
1744	TEST_EXPECT_NORESULT__NOERROREXPORTED(GB_find_string (db.gb_cont1, "name", "ENTRY 13", GB_MIND_CASE, SEARCH_GRANDCHILD));
1745	TEST_REJECT_NULL (gb_name = GB_find_string(db.gb_cont1, "name", "ENTRY 13", GB_IGNORE_CASE, SEARCH_GRANDCHILD));
1746
1747	GBDATA *gb_sub;
1748	TEST_REJECT_NULL(gb_sub = GB_get_father(gb_name)); TEST_EXPECT_EQUAL(GBT_get_name(gb_sub), "entry 13");
1749	TEST_REJECT_NULL(gb_sub = GB_followingEntry(gb_sub, 0)); TEST_EXPECT_EQUAL(GBT_get_name(gb_sub), "entry 14");
1750	TEST_REJECT_NULL(gb_sub = GB_followingEntry(gb_sub, 1)); TEST_EXPECT_EQUAL(GBT_get_name(gb_sub), "entry 16");
1751	TEST_REJECT_NULL(gb_sub = GB_followingEntry(gb_sub, 10)); TEST_EXPECT_EQUAL(GBT_get_name(gb_sub), "entry 27");
1752	TEST_EXPECT_NORESULT__NOERROREXPORTED(GB_followingEntry(gb_sub, -1U));
1753	TEST_REJECT_NULL(gb_sub = GB_brother(gb_sub, "entry")); TEST_EXPECT_EQUAL(GBT_get_name(gb_sub), "entry 0");
1754
1755	TEST_EXPECT_EQUAL(gb_bla = GB_search(gb_cont1, "/misc/str", GB_FIND), gb_str); // fullpath (ignores passed GBDATA)
1756
1757	// keyless search
1758	TEST_EXPECT_NORESULT__NOERROREXPORTED(GB_search(db.gb_cont_misc, NULL, GB_FIND));
1759
1760	// ----------------------------
1761	// GB_get_GBDATA_path
1762
1763	TEST_EXPECT_EQUAL(GB_get_GBDATA_path(gb_int), "/main/misc/int");
1764	TEST_EXPECT_EQUAL(GB_get_GBDATA_path(gb_str), "/main/misc/str");
1765	TEST_EXPECT_EQUAL(GB_get_GBDATA_path(gb_entry), "/main/misc/subcont/entry");
1766	TEST_EXPECT_EQUAL(GB_get_GBDATA_path(gb_cont2), "/main/misc/subcont2");
1767
1768	// -----------------------------------------
1769	// search/create with changed type
1770
1771	TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(db.gb_cont_misc, "str", GB_INT), "Inconsistent type for field");
1772	TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(db.gb_cont_misc, "subcont", GB_STRING), "Inconsistent type for field");
1773
1774	// ---------------------------------------------
1775	// search containers with trailing '/'
1776
1777	GBDATA *gb_cont2_slash;
1778	TEST_EXPECT_RESULT__NOERROREXPORTED(gb_cont2_slash = GB_search(db.gb_cont_misc, "subcont2/", GB_FIND));
1779	TEST_EXPECT_EQUAL(gb_cont2_slash, gb_cont2);
1780
1781	GBDATA *gb_rootcont;
1782	GBDATA *gb_rootcont_slash;
1783	TEST_EXPECT_RESULT__NOERROREXPORTED(gb_rootcont = GB_search(db.gb_main, "/container1", GB_FIND));
1784	TEST_EXPECT_RESULT__NOERROREXPORTED(gb_rootcont_slash = GB_search(db.gb_main, "/container1/", GB_FIND));
1785	TEST_EXPECT_EQUAL(gb_rootcont_slash, gb_rootcont);
1786	}
1787
1788	{
1789	// check invalid searches
1790	TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(db.gb_cont_misc, "sub/invalid", GB_INT), "Invalid char '' in key 'inva*lid'");
1791	TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(db.gb_cont_misc, "sub/1 3", GB_INT), "Invalid char ' ' in key '1 3'");
1792	TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(db.gb_cont_misc, "sub//sub", GB_INT), "Invalid '//' in key 'sub//sub'");
1793	TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(db.gb_cont_misc, "subcont2//", GB_FIND), "Invalid '//' in key 'subcont2//'");
1794	TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(db.gb_cont_misc, "sub/..sub", GB_INT), "Expected '/' after '..' in key '..sub'");
1795	TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GB_search(db.gb_cont_misc, "subcont/entry/", GB_FIND), "terminal entry 'entry' cannot be used as container");
1796	}
1797
1798	// ---------------
1799	// marks
1800
1801	TEST_EXPECT_EQUAL(GB_number_of_marked_subentries(db.gb_cont1), 15);
1802	TEST_EXPECT_EQUAL(GB_number_of_marked_subentries(db.gb_cont2), 3);
1803
1804	TEST_EXPECT_NORESULT__NOERROREXPORTED(GB_first_marked(db.gb_cont2, "entry"));
1805
1806	GBDATA *gb_marked;
1807	TEST_REJECT_NULL(gb_marked = GB_first_marked(db.gb_cont2, "item"));
1808	TEST_EXPECT_EQUAL(GBT_get_name(gb_marked), "item 0");
1809
1810	TEST_EXPECT_NORESULT__NOERROREXPORTED(GB_following_marked(gb_marked, "item", 1)); // skip over last
1811
1812	TEST_REJECT_NULL(gb_marked = GB_next_marked(gb_marked, "item")); // find last
1813	TEST_EXPECT_EQUAL(GBT_get_name(gb_marked), "item 14");
1814	}
1815
1816	// @@@ delete some species, then search again
1817
1818	TEST_EXPECT_NO_ERROR(db.error);
1819	}
1820
1821
1822	#endif // UNIT_TESTS

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