ARB
db_query.cxx
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1 // ============================================================ //
2 // //
3 // File : db_query.cxx //
4 // Purpose : Database queries //
5 // //
6 // Institute of Microbiology (Technical University Munich) //
7 // http://www.arb-home.de/ //
8 // //
9 // ============================================================ //
10 
11 #include "db_query.h"
12 #include "db_query_local.h"
13 #include "query_expr.h"
14 
15 #include <dbui.h>
16 #include <item_sel_list.h>
17 #include <awt_config_manager.hxx>
18 #include <awt_sel_boxes.hxx>
19 
20 #include <aw_advice.hxx>
21 #include <aw_color_groups.hxx>
22 #include <aw_file.hxx>
23 #include <aw_msg.hxx>
24 #include <aw_awar.hxx>
25 #include <arb_progress.h>
26 #include <aw_root.hxx>
27 #include <aw_question.hxx>
28 #include <rootAsWin.h>
29 
30 #include <ad_cb.h>
31 
32 #include <arb_strbuf.h>
33 #include <arb_sort.h>
34 #include <arb_global_defs.h>
35 #include <Keeper.h>
36 
37 #include <list>
38 #include <stack>
39 
40 using namespace std;
41 using namespace QUERY;
42 
43 #define MAX_QUERY_LIST_LEN 100000
44 
45 #define AWAR_COLORIZE "tmp/dbquery_all/colorize"
46 
47 static void free_hit_description(long info) {
48  free(reinterpret_cast<char*>(info));
49 }
50 
51 inline void SET_QUERIED(GBDATA *gb_species, DbQuery *query, const char *hitInfo, size_t hitInfoLen = 0) {
52  dbq_assert(hitInfo);
53 
54  GB_raise_user_flag(gb_species, query->select_bit);
55 
56  char *name = query->selector.generate_item_id(query->gb_main, gb_species);
57  char *info;
58 
59  if (hitInfoLen == 0) hitInfoLen = strlen(hitInfo);
60  if (hitInfoLen>MAX_SHOWN_DATA_SIZE) {
61  char *dupInfo = strdup(hitInfo);
62  hitInfoLen = GBS_shorten_repeated_data(dupInfo);
63  if (hitInfoLen>MAX_SHOWN_DATA_SIZE) {
64  strcpy(dupInfo+hitInfoLen-5, "[...]");
65  }
66  info = strdup(dupInfo);
67  free(dupInfo);
68  }
69  else {
70  info = strdup(hitInfo);
71  }
72 
73  GBS_write_hash(query->hit_description, name, reinterpret_cast<long>(info)); // overwrite hit info (also deallocates)
74  free(name);
75 }
76 
77 inline void CLEAR_QUERIED(GBDATA *gb_species, DbQuery *query) {
78  GB_clear_user_flag(gb_species, query->select_bit);
79 
80  char *name = query->selector.generate_item_id(query->gb_main, gb_species);
81  GBS_write_hash(query->hit_description, name, 0); // delete hit info (also deallocates)
82  free(name);
83 }
84 
85 inline const char *getHitInfo(const char *item_id, DbQuery *query) {
86  long info = GBS_read_hash(query->hit_description, item_id);
87  return reinterpret_cast<const char*>(info);
88 }
89 inline const char *getHitInfo(GBDATA *gb_species, DbQuery *query) {
90  char *name = query->selector.generate_item_id(query->gb_main, gb_species);
91  const char *result = getHitInfo(name, query);
92  free(name);
93  return result;
94 }
95 inline string keptHitReason(const string& currentHitReason, GBDATA *gb_item, DbQuery *query) {
96  string reason = string("kept because ")+currentHitReason;
97  const char *hitinfo = getHitInfo(gb_item, query);
98  if (hitinfo) reason = string(hitinfo)+" ("+reason+')';
99  return reason;
100 }
101 
102 static void create_query_independent_awars(AW_root *aw_root, AW_default aw_def) {
103  aw_root->awar_int(AWAR_COLORIZE, 0, aw_def);
104 }
105 
106 GBDATA *QUERY::query_get_gb_main(DbQuery *query) {
107  return query->gb_main;
108 }
109 
110 const ItemSelector& QUERY::get_queried_itemtype(DbQuery *query) {
111  return query->selector;
112 }
113 
114 enum EXT_QUERY_TYPES {
115  EXT_QUERY_NONE,
116  EXT_QUERY_COMPARE_LINES,
117  EXT_QUERY_COMPARE_WORDS
118 };
119 
120 query_spec::query_spec(ItemSelector& selector_)
121  : selector(selector_),
122  gb_main(NULp),
123  gb_ref(NULp),
124  expect_hit_in_ref_list(false),
125  species_name(NULp),
126  tree_name(NULp),
127  select_bit(GB_USERFLAG_QUERY), // always == GB_USERFLAG_QUERY atm (nevertheless DO NOT hardcode)
128  use_menu(0),
129  ere_pos_fig(NULp),
130  where_pos_fig(NULp),
131  by_pos_fig(NULp),
132  qbox_pos_fig(NULp),
133  key_pos_fig(NULp),
134  query_pos_fig(NULp),
135  result_pos_fig(NULp),
136  count_pos_fig(NULp),
137  do_query_pos_fig(NULp),
138  config_pos_fig(NULp),
139  do_mark_pos_fig(NULp),
140  do_unmark_pos_fig(NULp),
141  do_mark_nt_pos_fig(NULp),
142  do_unmark_nt_pos_fig(NULp),
143  do_delete_pos_fig(NULp),
144  do_set_pos_fig(NULp),
145  open_parser_pos_fig(NULp),
146  do_refresh_pos_fig(NULp),
147  popup_info_window(NULp),
148  info_box_pos_fig(NULp)
149 {
150  dbq_assert(&selector);
151 }
152 
153 bool query_spec::is_queried(GBDATA *gb_item) const {
154  return GB_user_flag(gb_item, select_bit);
155 }
156 
157 bool QUERY::IS_QUERIED(GBDATA *gb_item, const DbQuery *query) {
158  return query->is_queried(gb_item);
159 }
160 
161 long QUERY::count_queried_items(DbQuery *query, QUERY_RANGE range) {
162  GBDATA *gb_main = query->gb_main;
163  ItemSelector& selector = query->selector;
164 
165  long count = 0;
166 
167  for (GBDATA *gb_item_container = selector.get_first_item_container(gb_main, query->aws->get_root(), range);
168  gb_item_container;
169  gb_item_container = selector.get_next_item_container(gb_item_container, range))
170  {
171  for (GBDATA *gb_item = selector.get_first_item(gb_item_container, QUERY_ALL_ITEMS);
172  gb_item;
173  gb_item = selector.get_next_item(gb_item, QUERY_ALL_ITEMS))
174  {
175  if (IS_QUERIED(gb_item, query)) count++;
176  }
177  }
178  return count;
179 }
180 
181 // @@@ replace query_count_items by "method" of selector
182 static int query_count_items(DbQuery *query, QUERY_RANGE range, QUERY_MODES mode) {
183  int count = 0;
184  GBDATA *gb_main = query->gb_main;
185  ItemSelector& selector = query->selector;
186  GB_transaction ta(gb_main);
187 
188  for (GBDATA *gb_item_container = selector.get_first_item_container(gb_main, query->aws->get_root(), range);
189  gb_item_container;
190  gb_item_container = selector.get_next_item_container(gb_item_container, range))
191  {
192  for (GBDATA *gb_item = selector.get_first_item(gb_item_container, QUERY_ALL_ITEMS);
193  gb_item;
194  gb_item = selector.get_next_item(gb_item, QUERY_ALL_ITEMS))
195  {
196  switch (mode) {
197  case QUERY_GENERATE: ++count; break;
198  case QUERY_ENLARGE: count += !IS_QUERIED(gb_item, query); break;
199  case QUERY_REDUCE: count += IS_QUERIED(gb_item, query); break;
200  }
201  }
202  }
203  return count;
204 }
205 
206 const int MAX_CRITERIA = int(sizeof(unsigned long)*8/QUERY_SORT_CRITERIA_BITS);
207 
208 static void split_sort_mask(unsigned long sort_mask, QUERY_RESULT_ORDER *order) {
209  // splits the sort order bit mask 'sort_mask' into single sort criteria and write these into 'order'
210  // (order[0] will contain the primary sort criteria, order[1] the secondary, ...)
211 
212  for (int o = 0; o<MAX_CRITERIA; ++o) {
213  order[o] = QUERY_RESULT_ORDER(sort_mask&QUERY_SORT_CRITERIA_MASK);
214  dbq_assert(order[o] == (order[o]&QUERY_SORT_CRITERIA_MASK));
215  sort_mask = sort_mask>>QUERY_SORT_CRITERIA_BITS;
216  }
217 }
218 
219 static QUERY_RESULT_ORDER find_display_determining_sort_order(QUERY_RESULT_ORDER *order) {
220  // Returns the first criteria in 'order' (which has to have MAX_CRITERIA elements)
221  // that matches
222  // - QUERY_SORT_BY_1STFIELD_CONTENT or
223  // - QUERY_SORT_NUM_BY_1STFIELD_CONTENT or
224  // - QUERY_SORT_BY_HIT_DESCRIPTION
225  // (or QUERY_SORT_NONE if none of the above is used)
226 
227  QUERY_RESULT_ORDER first = QUERY_SORT_NONE;
228  for (int o = 0; o<MAX_CRITERIA && first == QUERY_SORT_NONE; ++o) {
229  if (order[o] & (QUERY_SORT_BY_1STFIELD_CONTENT|QUERY_SORT_NUM_BY_1STFIELD_CONTENT|QUERY_SORT_BY_HIT_DESCRIPTION)) {
230  first = order[o];
231  }
232  }
233  return first;
234 }
235 
236 static void remove_keydependent_sort_criteria(QUERY_RESULT_ORDER *order) {
237  // removes all sort-criteria from order which would use the order of the currently selected primary key
238 
239  int n = 0;
240  for (int o = 0; o<MAX_CRITERIA; ++o) {
241  if (order[o] != QUERY_SORT_BY_1STFIELD_CONTENT && order[o] != QUERY_SORT_NUM_BY_1STFIELD_CONTENT) {
242  order[n++] = order[o];
243  }
244  }
245  for (; n<MAX_CRITERIA; ++n) {
246  order[n] = QUERY_SORT_NONE;
247  }
248 }
249 
250 static void first_searchkey_changed_cb(AW_root *, DbQuery *query) {
251  QUERY_RESULT_ORDER order[MAX_CRITERIA];
252  split_sort_mask(query->sort_mask, order);
253 
254  QUERY_RESULT_ORDER usedOrder = find_display_determining_sort_order(order);
255  if (usedOrder != QUERY_SORT_BY_HIT_DESCRIPTION && usedOrder != QUERY_SORT_NONE) { // do we display values?
256  DbQuery_update_list(query);
257  }
258 }
259 
260 inline bool keep_criteria(QUERY_RESULT_ORDER old_criteria, QUERY_RESULT_ORDER new_criteria) {
261  return
262  old_criteria != QUERY_SORT_NONE && // do not keep 'unsorted' (it is no real criteria)
263  (old_criteria != new_criteria || // do not keep new criteria (added later)
264  old_criteria == QUERY_SORT_REVERSE); // reverse may occur several times -> always keep
265 }
266 
267 static void result_sort_order_changed_cb(AW_root *aw_root, DbQuery *query) {
268  // adds the new selected sort order to the sort order mask
269  // (added order removes itself, if it previously existed in sort order mask)
270  //
271  // if 'unsorted' is selected -> delete sort order
272 
273  QUERY_RESULT_ORDER new_criteria = (QUERY_RESULT_ORDER)aw_root->awar(query->awar_sort)->read_int();
274  if (new_criteria == QUERY_SORT_NONE) {
275  query->sort_mask = QUERY_SORT_NONE; // clear sort_mask
276  }
277  else {
278  QUERY_RESULT_ORDER order[MAX_CRITERIA];
279  split_sort_mask(query->sort_mask, order);
280 
281  int empty_or_same = 0;
282  for (int o = 0; o<MAX_CRITERIA; o++) {
283  if (!keep_criteria(order[o], new_criteria)) {
284  empty_or_same++; // these criteria will be skipped below
285  }
286  }
287 
288  unsigned long new_sort_mask = 0;
289  for (int o = MAX_CRITERIA-(empty_or_same>0 ? 1 : 2); o >= 0; o--) {
290  if (keep_criteria(order[o], new_criteria)) {
291  new_sort_mask = (new_sort_mask<<QUERY_SORT_CRITERIA_BITS)|order[o];
292  }
293  }
294  query->sort_mask = (new_sort_mask<<QUERY_SORT_CRITERIA_BITS)|new_criteria; // add new primary key
295  }
296  DbQuery_update_list(query);
297 }
298 
299 struct hits_sort_params : virtual Noncopyable {
300  DbQuery *query;
301  char *first_key;
302  GB_TYPES first_type;
303  QUERY_RESULT_ORDER order[MAX_CRITERIA];
304 
305  hits_sort_params(DbQuery *q, const char *fk)
306  : query(q),
307  first_key(strdup(fk))
308  {
309  first_type = GBT_get_type_of_changekey(query->gb_main, first_key, query->selector.change_key_path);
310  }
311 
312  ~hits_sort_params() {
313  free(first_key);
314  }
315 };
316 
317 inline int numeric_string_cmp(const char *str1, const char *str2) {
318  const char *end1;
319  const char *end2;
320 
321  double double1 = strtod(str1, const_cast<char**>(&end1));
322  double double2 = strtod(str2, const_cast<char**>(&end2));
323 
324  bool conv1 = !end1[0] && str1[0];
325  bool conv2 = !end2[0] && str2[0];
326 
327  bool both_converted = conv1 && conv2;
328 
329  int cmp;
330  if (both_converted) {
331  cmp = double_cmp(double1, double2);
332  }
333  else {
334  bool conv_partial1 = end1>str1;
335  bool conv_partial2 = end2>str2;
336 
337  if (conv_partial1 && conv_partial2) {
338  cmp = double_cmp(double1, double2);
339  if (!cmp) {
340  cmp = numeric_string_cmp(end1, end2);
341  }
342  }
343  else cmp = strcmp(str1, str2);
344  }
345  return cmp;
346 }
347 
348 static int compare_hits(const void *cl_item1, const void *cl_item2, void *cl_param) {
349  const hits_sort_params *param = static_cast<const hits_sort_params*>(cl_param);
350 
351  GBDATA *gb_item1 = (GBDATA*)cl_item1;
352  GBDATA *gb_item2 = (GBDATA*)cl_item2;
353 
354  DbQuery *query = param->query;
355  ItemSelector& selector = query->selector;
356 
357  int cmp = 0;
358 
359  for (int o = 0; o<MAX_CRITERIA && cmp == 0; o++) {
360  QUERY_RESULT_ORDER criteria = param->order[o];
361 
362  switch (criteria) {
363  case QUERY_SORT_NONE:
364  o = MAX_CRITERIA; // don't sort further
365  break;
366 
367  case QUERY_SORT_BY_1STFIELD_CONTENT: {
368  char *field1 = GBT_read_as_string(gb_item1, param->first_key);
369  char *field2 = GBT_read_as_string(gb_item2, param->first_key);
370 
371  cmp = ARB_strNULLcmp(field1, field2);
372 
373  free(field2);
374  free(field1);
375  break;
376  }
377  case QUERY_SORT_NUM_BY_1STFIELD_CONTENT: {
378  switch (param->first_type) {
379  case GB_INT: {
380  long *have1 = GBT_read_int(gb_item1, param->first_key);
381  long L1 = have1 ? *have1 : 0;
382  long *have2 = GBT_read_int(gb_item2, param->first_key);
383  long L2 = have2 ? *have2 : 0;
384 
385  cmp = have1 // use same logic as ARB_strNULLcmp
386  ? (have2 ? long_cmp(L1,L2) : -1)
387  : (have2 ? 1 : 0);
388  break;
389  }
390  case GB_FLOAT: {
391  float *have1 = GBT_read_float(gb_item1, param->first_key);
392  float f1 = have1 ? *have1 : 0;
393  float *have2 = GBT_read_float(gb_item2, param->first_key);
394  float f2 = have2 ? *have2 : 0;
395 
396  cmp = have1
397  ? (have2 ? float_cmp(f1,f2) : -1)
398  : (have2 ? 1 : 0);
399  break;
400  }
401  default: {
402  char *field1 = GBT_read_as_string(gb_item1, param->first_key);
403  char *field2 = GBT_read_as_string(gb_item2, param->first_key);
404 
405  cmp = (field1 && field2)
406  ? numeric_string_cmp(field1, field2)
407  : ARB_strNULLcmp(field1, field2);
408 
409  free(field2);
410  free(field1);
411  }
412  }
413  break;
414  }
415  case QUERY_SORT_BY_NESTED_PID: {
416  if (selector.parent_selector) {
417  GBDATA *gb_parent1 = selector.get_parent(gb_item1);
418  GBDATA *gb_parent2 = selector.get_parent(gb_item2);
419 
420  char *pid1 = selector.generate_item_id(query->gb_main, gb_parent1);
421  char *pid2 = selector.generate_item_id(query->gb_main, gb_parent2);
422 
423  cmp = ARB_strNULLcmp(pid1, pid2);
424 
425  free(pid2);
426  free(pid1);
427  }
428  break;
429  }
430  case QUERY_SORT_BY_ID: {
431  const char *id1 = GBT_read_char_pntr(gb_item1, selector.id_field);
432  const char *id2 = GBT_read_char_pntr(gb_item2, selector.id_field);
433 
434  cmp = strcmp(id1, id2);
435  break;
436  }
437  case QUERY_SORT_BY_MARKED:
438  cmp = GB_read_flag(gb_item2)-GB_read_flag(gb_item1);
439  break;
440 
441  case QUERY_SORT_BY_HIT_DESCRIPTION: {
442  const char *id1 = GBT_read_char_pntr(gb_item1, selector.id_field);
443  const char *id2 = GBT_read_char_pntr(gb_item2, selector.id_field);
444  const char *info1 = reinterpret_cast<const char *>(GBS_read_hash(query->hit_description, id1));
445  const char *info2 = reinterpret_cast<const char *>(GBS_read_hash(query->hit_description, id2));
446  cmp = ARB_strNULLcmp(info1, info2);
447  break;
448  }
449  case QUERY_SORT_REVERSE: {
450  GBDATA *tmp = gb_item1; // swap items for following compares (this is a prefix revert!)
451  gb_item1 = gb_item2;
452  gb_item2 = tmp;
453  break;
454  }
455  }
456  }
457 
458  return cmp;
459 }
460 
461 static void detectMaxNameLength(const char *key, long /*val*/, void *cl_len) {
462  int *len = (int*)cl_len;
463  int klen = strlen(key);
464 
465  if (klen>*len) *len = klen;
466 }
467 
468 #if defined(ASSERTION_USED)
469 inline bool SLOW_is_pseudo_key(const char *key) {
470  return
471  strcmp(key, PSEUDO_FIELD_ANY_FIELD) == 0 ||
472  strcmp(key, PSEUDO_FIELD_ALL_FIELDS) == 0 ||
473  strcmp(key, PSEUDO_FIELD_ANY_FIELD_REC) == 0 ||
474  strcmp(key, PSEUDO_FIELD_ALL_FIELDS_REC) == 0;
475 }
476 #endif
477 inline bool is_pseudo_key(const char *key) {
478  // returns true, if 'key' is a pseudo-key
479  bool is_pseudo = key[0] == '[';
480  dbq_assert(is_pseudo == SLOW_is_pseudo_key(key));
481  return is_pseudo;
482 }
483 
484 void QUERY::DbQuery_update_list(DbQuery *query) {
485  GB_push_transaction(query->gb_main);
486 
487  dbq_assert(query->hitlist);
488  query->hitlist->clear();
489 
490  AW_window *aww = query->aws;
491  AW_root *aw_root = aww->get_root();
492  QUERY_RANGE range = (QUERY_RANGE)aw_root->awar(query->awar_where)->read_int();
493  ItemSelector& selector = query->selector;
494 
495  // create array of hits
496  long count = count_queried_items(query, range);
497  GBDATA **sorted = ARB_alloc<GBDATA*>(count);
498  {
499  long s = 0;
500 
501  for (GBDATA *gb_item_container = selector.get_first_item_container(query->gb_main, aw_root, range);
502  gb_item_container;
503  gb_item_container = selector.get_next_item_container(gb_item_container, range))
504  {
505  for (GBDATA *gb_item = selector.get_first_item(gb_item_container, QUERY_ALL_ITEMS);
506  gb_item;
507  gb_item = selector.get_next_item(gb_item, QUERY_ALL_ITEMS))
508  {
509  if (IS_QUERIED(gb_item, query)) sorted[s++] = gb_item;
510  }
511  }
512  }
513 
514  // sort hits
515 
516  hits_sort_params param(query, aww->get_root()->awar(query->awar_keys[0])->read_char_pntr());
517 
518  bool is_pseudo = is_pseudo_key(param.first_key);
519  bool show_value = !is_pseudo; // cannot refer to key-value of pseudo key
520 
521  if (query->sort_mask != QUERY_SORT_NONE) { // unsorted -> don't sort
522  split_sort_mask(query->sort_mask, param.order);
523  if (is_pseudo) {
524  remove_keydependent_sort_criteria(param.order);
525  }
526  if (show_value && find_display_determining_sort_order(param.order) == QUERY_SORT_BY_HIT_DESCRIPTION) {
527  show_value = false;
528  }
529  GB_sort((void**)sorted, 0, count, compare_hits, &param);
530  }
531 
532  // display hits
533 
534  int name_len = selector.item_name_length;
535  if (name_len == -1) { // if name_len is unknown -> detect
536  GBS_hash_do_const_loop(query->hit_description, detectMaxNameLength, &name_len);
537  }
538 
539  long i;
540  for (i = 0; i<count && i<MAX_QUERY_LIST_LEN; i++) {
541  char *name = selector.generate_item_id(query->gb_main, sorted[i]);
542  if (name) {
543  char *toFree = NULp;
544  const char *info;
545 
546  if (show_value) {
547  toFree = GBT_read_as_string(sorted[i], param.first_key);
548  if (toFree) {
549  if (strlen(toFree)>MAX_SHOWN_DATA_SIZE) {
550  size_t shortened_len = GBS_shorten_repeated_data(toFree);
551  if (shortened_len>MAX_SHOWN_DATA_SIZE) {
552  strcpy(toFree+MAX_SHOWN_DATA_SIZE-5, "[...]");
553  }
554  }
555  }
556  else {
557  toFree = GBS_global_string_copy("<%s has no data>", param.first_key);
558  }
559  info = toFree;
560  }
561  else {
562  info = getHitInfo(name, query);
563  if (!info) info = "<no hit info>";
564  }
565 
566  dbq_assert(info);
567  const char *line = GBS_global_string("%c %-*s :%s",
568  GB_read_flag(sorted[i]) ? '*' : ' ',
569  name_len, name,
570  info);
571 
572  query->hitlist->insert(line, name);
573  free(toFree);
574  free(name);
575  }
576  }
577 
578  if (count>MAX_QUERY_LIST_LEN) {
579  query->hitlist->insert("***** List truncated *****", "");
580  }
581 
582  free(sorted);
583 
584  query->hitlist->insert_default("End of list", "");
585  query->hitlist->update();
586  aww->get_root()->awar(query->awar_count)->write_int((long)count);
587  GB_pop_transaction(query->gb_main);
588 }
589 
590 static void mark_queried_cb(AW_window*, DbQuery *query, int mark) {
591  // Mark listed species
592  // mark = 1 -> mark listed
593  // mark | 8 -> don't change rest
594 
595  ItemSelector& selector = query->selector;
596  GB_push_transaction(query->gb_main);
597 
598  for (GBDATA *gb_item_container = selector.get_first_item_container(query->gb_main, query->aws->get_root(), QUERY_ALL_ITEMS);
599  gb_item_container;
600  gb_item_container = selector.get_next_item_container(gb_item_container, QUERY_ALL_ITEMS))
601  {
602  for (GBDATA *gb_item = selector.get_first_item(gb_item_container, QUERY_ALL_ITEMS);
603  gb_item;
604  gb_item = selector.get_next_item(gb_item, QUERY_ALL_ITEMS))
605  {
606  if (IS_QUERIED(gb_item, query)) {
607  GB_write_flag(gb_item, mark&1);
608  }
609  else if ((mark&8) == 0) {
610  GB_write_flag(gb_item, 1-(mark&1));
611  }
612  }
613  }
614 
615  DbQuery_update_list(query);
616  GB_pop_transaction(query->gb_main);
617 }
618 
619 void QUERY::unquery_all(void *, DbQuery *query) {
620  GB_push_transaction(query->gb_main);
621  GBDATA *gb_species;
622  for (gb_species = GBT_first_species(query->gb_main);
623  gb_species;
624  gb_species = GBT_next_species(gb_species)) {
625  CLEAR_QUERIED(gb_species, query);
626  }
627  DbQuery_update_list(query);
628  GB_pop_transaction(query->gb_main);
629 }
630 
631 static void delete_queried_species_cb(AW_window*, DbQuery *query) {
632  ItemSelector& selector = query->selector;
633  GB_begin_transaction(query->gb_main);
634 
635  long cnt = 0;
636  for (GBDATA *gb_item_container = selector.get_first_item_container(query->gb_main, query->aws->get_root(), QUERY_ALL_ITEMS);
637  gb_item_container;
638  gb_item_container = selector.get_next_item_container(gb_item_container, QUERY_ALL_ITEMS))
639  {
640  for (GBDATA *gb_item = selector.get_first_item(gb_item_container, QUERY_ALL_ITEMS);
641  gb_item;
642  gb_item = selector.get_next_item(gb_item, QUERY_ALL_ITEMS))
643  {
644  if (IS_QUERIED(gb_item, query)) cnt++;
645  }
646  }
647 
648  if (!cnt || !aw_ask_sure("delete_queried_species", GBS_global_string("Are you sure to delete %li %s", cnt, selector.items_name))) {
649  GB_abort_transaction(query->gb_main);
650  return;
651  }
652 
653  GB_ERROR error = NULp;
654 
655  for (GBDATA *gb_item_container = selector.get_first_item_container(query->gb_main, query->aws->get_root(), QUERY_ALL_ITEMS);
656  !error && gb_item_container;
657  gb_item_container = selector.get_next_item_container(gb_item_container, QUERY_ALL_ITEMS))
658  {
659  for (GBDATA *gb_item = selector.get_first_item(gb_item_container, QUERY_ALL_ITEMS);
660  !error && gb_item;
661  gb_item = selector.get_next_item(gb_item, QUERY_ALL_ITEMS))
662  {
663  if (IS_QUERIED(gb_item, query)) {
664  error = GB_delete(gb_item);
665  }
666  }
667  }
668 
669  if (error) {
670  GB_abort_transaction(query->gb_main);
671  aw_message(error);
672  }
673  else {
674  DbQuery_update_list(query);
675  GB_commit_transaction(query->gb_main);
676  }
677 }
678 
679 static GB_HASH *create_ref_hash(const DbQuery *query, const char *key, bool split_words) {
680  GBDATA *gb_ref = query->gb_ref;
681  bool queried_only = query->expect_hit_in_ref_list;
682  GB_HASH *hash = GBS_create_hash(GBT_get_species_count(gb_ref), GB_IGNORE_CASE);
683 
684  for (GBDATA *gb_species = GBT_first_species(gb_ref);
685  gb_species;
686  gb_species = GBT_next_species(gb_species))
687  {
688  if (!queried_only || IS_QUERIED(gb_species, query)) {
689  GBDATA *gb_name = GB_search(gb_species, key, GB_FIND);
690  if (gb_name) {
691  char *keyas = GB_read_as_string(gb_name);
692  if (keyas && strlen(keyas)) {
693  if (split_words) {
694  char *t;
695  for (t = strtok(keyas, " "); t; t = strtok(NULp, " ")) {
696  if (t[0]) GBS_write_hash(hash, t, (long)gb_species);
697  }
698  }
699  else {
700  GBS_write_hash(hash, keyas, (long)gb_species);
701  }
702  }
703  free(keyas);
704  }
705  }
706  }
707  return hash;
708 }
709 
710 class TargetItem : public QueryTarget {
711  RefPtr<GBDATA> gb_item;
712 public:
713  TargetItem(const DbQuery& query) :
714  QueryTarget(query.gb_main, query.get_tree_name()),
715  gb_item(NULp)
716  {}
717 
718  void aimTo(GBDATA *gb_next_item) {
719  dbq_assert(gb_next_item); // @@@ maybe allow? (to invalidate target)
720  gb_item = gb_next_item;
721  }
722  GBDATA *get_item() const {
723  dbq_assert(gb_item); // you have to call aimTo before!
724  return gb_item;
725  }
726 
727  // QueryTarget interface:
728  GBDATA *get_ACI_item() const OVERRIDE { return get_item(); }
729 };
730 
731 class ItemQueryKey FINAL_TYPE : public QueryKey, virtual Noncopyable {
732  char *key; // search key (=name of DB field or pseudo-field)
733  bool hierarchical; // is 'key' hierarchical?
734  GBQUARK keyquark; // valid only if get_type() == QKEY_EXPLICIT!
735 
736  typedef std::stack<GBDATA*> ParentStack;
737 
738  mutable GBDATA *gb_key; // last read key-entry
739  mutable ParentStack parent; // container(s) descended
740 
741  static query_key_type detect_key_type(const char *field_name) {
742  if (is_pseudo_key(field_name)) {
743  if (strcmp(field_name, PSEUDO_FIELD_ANY_FIELD) == 0) return QKEY_ANY;
744  if (strcmp(field_name, PSEUDO_FIELD_ANY_FIELD_REC) == 0) return QKEY_ANY_REC;
745  if (strcmp(field_name, PSEUDO_FIELD_ALL_FIELDS) == 0) return QKEY_ALL;
746  if (strcmp(field_name, PSEUDO_FIELD_ALL_FIELDS_REC) == 0) return QKEY_ALL_REC;
747  dbq_assert(0);
748  }
749  return QKEY_EXPLICIT;
750  }
751 
752 public:
753  ItemQueryKey(GBDATA *gb_main, const char *field_name) :
754  QueryKey(detect_key_type(field_name)),
755  key(strdup(field_name)),
756  hierarchical(false),
757  keyquark(0), // invalid quark
758  gb_key(NULp)
759  {
760  if (get_type() == QKEY_EXPLICIT) {
761  if (GB_first_non_key_char(key)) {
762  hierarchical = true;
763  }
764  else {
765  keyquark = GB_find_or_create_quark(gb_main, key);
766  }
767  }
768  }
769  ~ItemQueryKey() {
770  free(key);
771  }
772 
773  // QueryKey interface:
774  char *get_target_data(const QueryTarget& target, GB_ERROR& error) const OVERRIDE {
775  // retrieve content of target key
776  if (!gb_key) {
777  const TargetItem& target_item = DOWNCAST_REFERENCE(const TargetItem, target);
778  gb_key = get_first_field(target_item.get_item());
779  }
780 
781  char *data;
782  if (gb_key) {
783  data = GB_read_as_string(gb_key);
784  if (!data) {
785  if (GB_readable_as_string(gb_key)) {
786  error = GB_await_error();
787  }
788  else {
789  gb_assert(!GB_have_error());
790  error = GBS_global_string("field '%s' has wrong type", GB_read_key_pntr(gb_key));
791  }
792  }
793  }
794  else {
795  data = strdup(""); // non-existing field -> assume "" as default value
796  // (needed to search for missing fields using '!=*' ?)
797  }
798  return data;
799  }
800  const char *get_name() const OVERRIDE {
801  // name of target (e.g. for reports)
802  // - for explicit keys, it simply returns the specified key name
803  // - for iterating keys, it returns the name of the DB field at current iteration position,
804  // showing path to key relative to item (e.g. 'ali_16s/data')
805  // If not yet iterating, it returns the name of the pseudo-field.
806 
807  if (get_type() != QKEY_EXPLICIT && gb_key) {
808  const char *keyname = GB_read_key_pntr(gb_key);
809  if (!parent.empty()) {
810  const char *parent_path = GB_get_db_path(parent.top());
811  dbq_assert(parent.top() == GB_get_father(gb_key));
812  const char *rslash = strrchr(parent_path, '/');
813  for (int nest = parent.size()-1; rslash && nest; --nest) {
814  rslash = strrchr(rslash-1, '/');
815  }
816  return GBS_global_string("%s/%s", rslash ? rslash+1 : "<unknown>", keyname);
817  }
818  return keyname;
819  }
820  return key;
821  }
822 
823 private:
824  bool accept_or_iterate() const {
825  dbq_assert(get_type() != QKEY_EXPLICIT);
826  if (gb_key) {
827  GB_TYPES ktype = GB_read_type(gb_key);
828  if (ktype == GB_DB) {
829  switch (get_type()) {
830  case QKEY_ALL:
831  case QKEY_ANY:
832  return iterate(); // = skip over containers
833 
834  case QKEY_ALL_REC:
835  case QKEY_ANY_REC:
836  parent.push(gb_key); // remember position ..
837  gb_key = GB_child(gb_key); // .. and descend into container
838  break;
839 
840  case QKEY_EXPLICIT:
841  dbq_assert(0);
842  }
843  return accept_or_iterate();
844  }
845  if (!GB_TYPE_readable_as_string(ktype)) {
846  return iterate();
847  }
848  return true;
849  }
850  if (!parent.empty()) {
851  gb_key = parent.top();
852  parent.pop();
853  return iterate();
854  }
855  return false;
856  }
857 public:
858 
859  bool iterate() const OVERRIDE { // iterate key to next item
860  dbq_assert(get_type() != QKEY_EXPLICIT);
861  if (gb_key) gb_key = GB_nextChild(gb_key);
862  return accept_or_iterate();
863  }
864  void reset() const OVERRIDE {
865  // restart multi-key iteration
866  gb_key = NULp;
867  parent = ParentStack();
868  }
869  // ----------
870 
871 
872  GBDATA *get_first_field(GBDATA *gb_item) const {
873  GBDATA *gb_field = NULp;
874 
875  if (hierarchical) {
876  gb_field = GB_search(gb_item, key, GB_FIND);
877  }
878  else if (get_type() != QKEY_EXPLICIT) {
879  gb_field = GB_child(gb_item);
880  // no need to use same method as normal search (we just need any key here)
881  while (gb_field && GB_read_type(gb_field) == GB_DB) {
882  gb_field = GB_nextChild(gb_field);
883  }
884  }
885  else {
886  gb_field = GB_find_sub_by_quark(gb_item, keyquark, NULp, 0);
887  }
888 
889  return gb_field;
890  }
891 };
892 
893 inline query_operator awarvalue2query_operator(const char *awarvalue) {
894  if (strcmp(awarvalue, "and") == 0) return AND;
895  if (strcmp(awarvalue, "or") == 0) return OR;
896  return ILLEGAL;
897 }
898 
899 SmartPtr<QueryExpr> DbQuery::buildQueryExpr() {
900  AW_root *aw_root = aws->get_root();
901  QueryExpr *first_qe = NULp;
902 
903  for (int idx = 0; idx<QUERY_EXPRESSIONS; ++idx) {
904  query_operator aqo = idx
905  ? awarvalue2query_operator(aw_root->awar(awar_operator[idx])->read_char_pntr())
906  : OR; // initial value is false, (false OR QUERY1) == QUERY1
907 
908  if (aqo != ILLEGAL) {
909  bool not_equal = aw_root->awar(awar_not[idx])->read_int() != 0;
910  const char *expression = aw_root->awar(awar_queries[idx])->read_char_pntr();
911  const char *field_name = aw_root->awar(awar_keys[idx])->read_char_pntr();
912  QueryKeyPtr qkey = new ItemQueryKey(gb_main, field_name);
913 
914  QueryExpr *qe = new QueryExpr(aqo, qkey, not_equal, expression);
915 
916  if (!field_name[0] || strcmp(field_name, NO_FIELD_SELECTED) == 0) {
917  qe->setError("No field selected");
918  }
919 
920  if (!first_qe) first_qe = qe;
921  else first_qe->append(qe);
922  }
923  }
924 
925  return first_qe;
926 }
927 
928 static void perform_query_cb(AW_window*, DbQuery *query, EXT_QUERY_TYPES ext_query) {
929  ItemSelector& selector = query->selector;
930 
931  GB_push_transaction(query->gb_main);
932 
933  AW_root *aw_root = query->aws->get_root();
934  SmartPtr<QueryExpr> qexpr = query->buildQueryExpr();
935 
936  QUERY_MODES mode = (QUERY_MODES)aw_root->awar(query->awar_ere)->read_int();
937  QUERY_RANGE range = (QUERY_RANGE)aw_root->awar(query->awar_where)->read_int();
938  QUERY_TYPES type = (QUERY_TYPES)aw_root->awar(query->awar_by)->read_int();
939 
940  if (query->gb_ref && type != QUERY_MARKED) { // special for merge tool!
941  char *first_query = aw_root->awar(query->awar_queries[0])->read_string();
942  if (strlen(first_query) == 0) {
943  if (!ext_query) ext_query = EXT_QUERY_COMPARE_LINES;
944  }
945  free(first_query);
946  }
947 
948  GB_ERROR error = qexpr->getError();
949 
950  if (!error) {
951  size_t item_count = query_count_items(query, range, mode);
952  if (item_count) {
953  arb_progress progress("Searching", item_count);
954 
955  if (query->gb_ref && // merge tool only
956  (ext_query == EXT_QUERY_COMPARE_LINES || ext_query == EXT_QUERY_COMPARE_WORDS))
957  {
958  if (qexpr->get_key_type() != QKEY_EXPLICIT) {
959  error = "Please select an explicit field or specify a search string (for first expression)";
960  }
961  else {
962  GB_push_transaction(query->gb_ref);
963 
964  char *first_keyname = aw_root->awar(query->awar_keys[0])->read_string();
965  GB_HASH *ref_hash = create_ref_hash(query, first_keyname, ext_query == EXT_QUERY_COMPARE_WORDS);
966 
967  if (GBS_hash_elements(ref_hash) == 0) {
968  error = GBS_global_string("No data found in field '%s'", first_keyname);
969  }
970 
971 #if defined(DEBUG)
972  printf("query: search identical %s in field %s%s\n",
973  (ext_query == EXT_QUERY_COMPARE_WORDS ? "words" : "values"),
974  first_keyname,
975  query->expect_hit_in_ref_list ? " of species listed in other hitlist" : "");
976 #endif // DEBUG
977 
978  for (GBDATA *gb_item_container = selector.get_first_item_container(query->gb_main, aw_root, range);
979  gb_item_container && !error;
980  gb_item_container = selector.get_next_item_container(gb_item_container, range))
981  {
982  for (GBDATA *gb_item = selector.get_first_item(gb_item_container, QUERY_ALL_ITEMS);
983  gb_item && !error;
984  gb_item = selector.get_next_item(gb_item, QUERY_ALL_ITEMS))
985  {
986  switch (mode) {
987  case QUERY_GENERATE: CLEAR_QUERIED(gb_item, query); break;
988  case QUERY_ENLARGE: if (IS_QUERIED(gb_item, query)) continue; break;
989  case QUERY_REDUCE: if (!IS_QUERIED(gb_item, query)) continue; break;
990  }
991 
992  // Note: here only the first query is used (special case in merge tool only)
993 
994  ItemQueryKey& query_key = DOWNCAST_REFERENCE(ItemQueryKey, qexpr->get_key());
995  GBDATA *gb_key = query_key.get_first_field(gb_item);
996  if (gb_key) {
997  char *data = GB_read_as_string(gb_key);
998 
999  if (data && data[0]) {
1000  string hit_reason;
1001  bool this_hit = false;
1002 
1003  if (ext_query == EXT_QUERY_COMPARE_WORDS) {
1004  for (char *t = strtok(data, " "); t; t = strtok(NULp, " ")) {
1005  GBDATA *gb_ref_pntr = (GBDATA *)GBS_read_hash(ref_hash, t);
1006  if (gb_ref_pntr) { // found item in other DB, with 'first_keyname' containing word from 'gb_key'
1007  this_hit = true;
1008  hit_reason = GBS_global_string("%s%s has word '%s' in %s",
1009  query->expect_hit_in_ref_list ? "Hit " : "",
1010  selector.generate_item_id(query->gb_ref, gb_ref_pntr),
1011  t, first_keyname);
1012  }
1013  }
1014  }
1015  else {
1016  GBDATA *gb_ref_pntr = (GBDATA *)GBS_read_hash(ref_hash, data);
1017  if (gb_ref_pntr) { // found item in other DB, with identical 'first_keyname'
1018  this_hit = true;
1019  hit_reason = GBS_global_string("%s%s matches %s",
1020  query->expect_hit_in_ref_list ? "Hit " : "",
1021  selector.generate_item_id(query->gb_ref, gb_ref_pntr),
1022  first_keyname);
1023  }
1024  }
1025 
1026  if (type == QUERY_DONT_MATCH) {
1027  this_hit = !this_hit;
1028  if (this_hit) hit_reason = "<no matching entry>";
1029  }
1030 
1031  if (this_hit) {
1032  dbq_assert(!hit_reason.empty());
1033  SET_QUERIED(gb_item, query, hit_reason.c_str(), hit_reason.length());
1034  }
1035  else CLEAR_QUERIED(gb_item, query);
1036  }
1037  free(data);
1038  }
1039 
1040  progress.inc_and_check_user_abort(error);
1041  }
1042  }
1043 
1044  GBS_free_hash(ref_hash);
1045  GB_pop_transaction(query->gb_ref);
1046  }
1047  }
1048  else { // "normal" query
1049  if (type == QUERY_DONT_MATCH) {
1050 #if defined(DEBUG)
1051  fputs("query: !(", stdout); qexpr->dump();
1052 #endif // DEBUG
1053 
1054  qexpr->negate();
1055  type = QUERY_MATCH;
1056 
1057 #if defined(DEBUG)
1058  fputs(") => query: ", stdout); qexpr->dump(); fputc('\n', stdout);
1059 #endif // DEBUG
1060  }
1061 #if defined(DEBUG)
1062  else { fputs("query: ", stdout); qexpr->dump(); fputc('\n', stdout); }
1063 #endif // DEBUG
1064 
1065  TargetItem target_item(*query);
1066 
1067  for (GBDATA *gb_item_container = selector.get_first_item_container(query->gb_main, aw_root, range);
1068  gb_item_container && !error;
1069  gb_item_container = selector.get_next_item_container(gb_item_container, range))
1070  {
1071  for (GBDATA *gb_item = selector.get_first_item(gb_item_container, QUERY_ALL_ITEMS);
1072  gb_item && !error;
1073  gb_item = selector.get_next_item(gb_item, QUERY_ALL_ITEMS))
1074  {
1075  switch (mode) {
1076  case QUERY_GENERATE: CLEAR_QUERIED(gb_item, query); break;
1077  case QUERY_ENLARGE: if (IS_QUERIED(gb_item, query)) continue; break;
1078  case QUERY_REDUCE: if (!IS_QUERIED(gb_item, query)) continue; break;
1079  }
1080 
1081  bool hit = false;
1082  string hit_reason;
1083 
1084  switch (type) {
1085  case QUERY_MARKED:
1086  hit = GB_read_flag(gb_item);
1087  hit_reason = "<marked>";
1088  break;
1089 
1090  case QUERY_MATCH:
1091  dbq_assert(ext_query == EXT_QUERY_NONE);
1092  target_item.aimTo(gb_item);
1093  hit = qexpr->matches(target_item, hit_reason);
1094  break;
1095 
1096  default: dbq_assert(0); break;
1097  }
1098 
1099  if (hit) {
1100  dbq_assert(!hit_reason.empty());
1101 
1102  if (mode == QUERY_REDUCE) hit_reason = keptHitReason(hit_reason, gb_item, query);
1103  SET_QUERIED(gb_item, query, hit_reason.c_str(), hit_reason.length());
1104  }
1105  else CLEAR_QUERIED(gb_item, query);
1106 
1107  if (error) {
1108  error = GB_failedTo_error("query", GBT_get_name_or_description(gb_item), error);
1109  }
1110  else {
1111  progress.inc_and_check_user_abort(error);
1112  }
1113  }
1114  }
1115  }
1116 
1117  if (error) progress.done();
1118  }
1119  }
1120 
1121  if (!error) error = qexpr->getError(); // check for query error
1122 
1123  if (error) aw_message(error);
1124  else DbQuery_update_list(query);
1125 
1126  GB_pop_transaction(query->gb_main);
1127 }
1128 
1129 void QUERY::copy_selection_list_2_query_box(DbQuery *query, AW_selection_list *srclist, const char *hit_description) {
1130  GB_transaction ta(query->gb_main);
1131 
1132  dbq_assert(strstr(hit_description, "%s")); // hit_description needs '%s' (which is replaced by visible content of 'id')
1133 
1134  GB_ERROR error = NULp;
1135  AW_window *aww = query->aws;
1136  AW_root *aw_root = aww->get_root();
1137  GB_HASH *list_hash = srclist->to_hash(false);
1138  QUERY_MODES mode = (QUERY_MODES)aw_root->awar(query->awar_ere)->read_int();
1139  QUERY_TYPES type = (QUERY_TYPES)aw_root->awar(query->awar_by)->read_int();
1140 
1141  if (type == QUERY_MARKED) {
1142  error = "Query mode 'that are marked' does not apply here.\nEither select 'that match the query' or 'that don't match the q.'";
1143  }
1144 
1145  if (type != QUERY_MATCH || mode != QUERY_GENERATE) { // different behavior as in the past -> advice
1146  AW_advice("'Move to hitlist' now depends on the values selected for\n"
1147  " * 'Search/Add/Keep species' and\n"
1148  " * 'that match/don't match the query'\n"
1149  "in the search tool.",
1150  AW_ADVICE_TOGGLE_AND_HELP,
1151  "Behavior changed",
1152  "next_neighbours.hlp");
1153  }
1154 
1155  long inHitlist = GBS_hash_elements(list_hash);
1156  long seenInDB = 0;
1157 
1158  for (GBDATA *gb_species = GBT_first_species(query->gb_main);
1159  gb_species && !error;
1160  gb_species = GBT_next_species(gb_species))
1161  {
1162  switch (mode) {
1163  case QUERY_GENERATE: CLEAR_QUERIED(gb_species, query); break;
1164  case QUERY_ENLARGE: if (IS_QUERIED(gb_species, query)) continue; break;
1165  case QUERY_REDUCE: if (!IS_QUERIED(gb_species, query)) continue; break;
1166  }
1167 
1168  const char *displayed = reinterpret_cast<const char*>(GBS_read_hash(list_hash, GBT_get_name_or_description(gb_species)));
1169 
1170  if (displayed) seenInDB++;
1171 
1172  if (contradicted(displayed, type == QUERY_DONT_MATCH)) {
1173  string hit_reason = GBS_global_string(hit_description, displayed ? displayed : "<no near neighbour>");
1174 
1175  if (mode == QUERY_REDUCE) hit_reason = keptHitReason(hit_reason, gb_species, query);
1176  SET_QUERIED(gb_species, query, hit_reason.c_str(), hit_reason.length());
1177  }
1178  else {
1179  CLEAR_QUERIED(gb_species, query);
1180  }
1181  }
1182 
1183  if (seenInDB < inHitlist) {
1184  aw_message(GBS_global_string("%li of %li hits were found in database", seenInDB, inHitlist));
1185  }
1186 
1187  GBS_free_hash(list_hash);
1188  if (error) aw_message(error);
1189  DbQuery_update_list(query);
1190 }
1191 
1192 
1193 void QUERY::search_duplicated_field_content(AW_window *, DbQuery *query, bool tokenize) {
1194  AW_root *aw_root = query->aws->get_root();
1195  char *key = aw_root->awar(query->awar_keys[0])->read_string();
1196  GB_ERROR error = NULp;
1197 
1198  if (strlen(key) == 0) {
1199  error = "Please select a key (in the first query expression)";
1200  }
1201  else if (is_pseudo_key(key)) {
1202  error = "You have to select an explicit key (in the first query expression)";
1203  }
1204  else {
1205  GB_transaction dumy(query->gb_main);
1206  ItemSelector& selector = query->selector;
1207 
1208  GBDATA *gb_species_data = GBT_get_species_data(query->gb_main);
1209  long hashsize;
1210  QUERY_RANGE range = QUERY_ALL_ITEMS;
1211  QUERY_TYPES type = (QUERY_TYPES)aw_root->awar(query->awar_by)->read_int();
1212 
1213  switch (selector.type) {
1214  case QUERY_ITEM_SPECIES:
1215  case QUERY_ITEM_ORGANISM: {
1216  hashsize = GB_number_of_subentries(gb_species_data);
1217  break;
1218  }
1219  case QUERY_ITEM_EXPERIMENTS:
1220  case QUERY_ITEM_GENES: {
1221  // handle species sub-items
1222  hashsize = 0;
1223 
1224  for (GBDATA *gb_item_container = selector.get_first_item_container(query->gb_main, aw_root, range);
1225  gb_item_container;
1226  gb_item_container = selector.get_next_item_container(gb_item_container, range))
1227  {
1228  hashsize += GB_number_of_subentries(gb_item_container);
1229  }
1230 
1231  break;
1232  }
1233  default: {
1234  dbq_assert(0);
1235  hashsize = 0;
1236  break;
1237  }
1238  }
1239 
1240  if (!hashsize) {
1241  error = "No items exist";
1242  }
1243  else if (type == QUERY_MARKED) {
1244  error = "'that are marked' is not applicable here";
1245  }
1246 
1247  if (!error) {
1248  GB_HASH *hash = GBS_create_hash(hashsize, GB_IGNORE_CASE);
1249 
1250  for (GBDATA *gb_item_container = selector.get_first_item_container(query->gb_main, aw_root, range);
1251  gb_item_container;
1252  gb_item_container = selector.get_next_item_container(gb_item_container, range))
1253  {
1254  for (GBDATA *gb_item = selector.get_first_item(gb_item_container, QUERY_ALL_ITEMS);
1255  gb_item;
1256  gb_item = selector.get_next_item(gb_item, QUERY_ALL_ITEMS))
1257  {
1258  CLEAR_QUERIED(gb_item, query);
1259  GB_write_flag(gb_item, 0);
1260 
1261  GBDATA *gb_key = GB_search(gb_item, key, GB_FIND); if (!gb_key) continue;
1262  char *data = GB_read_as_string(gb_key); if (!data) continue;
1263 
1264  if (tokenize) {
1265  char *s;
1266  for (s=strtok(data, ",; \t."); s; s = strtok(NULp, ",; \t.")) {
1267  GBDATA *gb_old = (GBDATA *)GBS_read_hash(hash, s);
1268  if (gb_old) {
1269  const char *oldInfo = NULp;
1270  char *firstInfo = GBS_global_string_copy("1st=%s", s);
1271 
1272  if (IS_QUERIED(gb_old, query)) {
1273  const char *prevInfo = getHitInfo(gb_old, query);
1274  if (!prevInfo) {
1275  oldInfo = firstInfo;
1276  }
1277  else if (!strstr(prevInfo, firstInfo)) { // not already have 1st-entry here
1278  oldInfo = GBS_global_string("%s %s", prevInfo, firstInfo);
1279  }
1280  }
1281  else {
1282  oldInfo = firstInfo;
1283  }
1284 
1285  if (oldInfo) SET_QUERIED(gb_old, query, oldInfo);
1286  SET_QUERIED(gb_item, query, GBS_global_string("dup=%s", s));
1287  GB_write_flag(gb_item, 1);
1288 
1289  free(firstInfo);
1290  }
1291  else {
1292  GBS_write_hash(hash, s, (long)gb_item);
1293  }
1294  }
1295  }
1296  else {
1297  GBDATA *gb_old = (GBDATA *)GBS_read_hash(hash, data);
1298  if (gb_old) {
1299  if (!IS_QUERIED(gb_old, query)) {
1300  SET_QUERIED(gb_old, query, GBS_global_string("%s (1st)", data));
1301  }
1302  SET_QUERIED(gb_item, query, GBS_global_string("%s (duplicate)", data));
1303  GB_write_flag(gb_item, 1);
1304  }
1305  else {
1306  GBS_write_hash(hash, data, (long)gb_item);
1307  }
1308  }
1309 
1310  free(data);
1311  }
1312 
1313  if (type == QUERY_DONT_MATCH) {
1314  for (GBDATA *gb_item = selector.get_first_item(gb_item_container, QUERY_ALL_ITEMS);
1315  gb_item;
1316  gb_item = selector.get_next_item(gb_item, QUERY_ALL_ITEMS))
1317  {
1318  if (IS_QUERIED(gb_item, query)) {
1319  CLEAR_QUERIED(gb_item, query);
1320  GB_write_flag(gb_item, 0); // unmark
1321  }
1322  else {
1323  SET_QUERIED(gb_item, query, tokenize ? "<entry with unique words>" : "<unique entry>");
1324  }
1325  }
1326  }
1327  }
1328 
1329  GBS_free_hash(hash);
1330  }
1331 
1332  if (type != QUERY_MATCH) {
1333  AW_advice("'Find equal entries' now depends on the values selected for\n"
1334  " * 'that match/don't match the query'\n"
1335  "in the search tool.",
1336  AW_ADVICE_TOGGLE_AND_HELP,
1337  "Behavior changed",
1338  "search_duplicates.hlp");
1339  }
1340  }
1341 
1342  free(key);
1343 
1344  if (error) aw_message(error);
1345  DbQuery_update_list(query);
1346 }
1347 
1348 static void modify_fields_of_queried_cb(AW_window*, DbQuery *query) {
1349  ItemSelector& selector = query->selector;
1350  AW_root *aw_root = query->aws->get_root();
1351  GB_ERROR error = GB_begin_transaction(query->gb_main);
1352 
1353  const char *key;
1354  if (!error) {
1355  bool acceptIdMod = aw_root->awar(query->awar_acceptIdMod)->read_int();
1356  FailIfField failMode = acceptIdMod ? FIF_ALLOW_ID_CHANGE : FIF_STANDARD;
1357  key = prepare_and_get_selected_itemfield(aw_root, query->awar_parskey, query->gb_main, selector, failMode);
1358  if (!key) error = GB_await_error();
1359  }
1360 
1361  if (!error) {
1362  GB_TYPES key_type = GBT_get_type_of_changekey(query->gb_main, key, selector.change_key_path);
1363  bool safe_conversion = (key_type != GB_STRING) && !aw_root->awar(query->awar_acceptConvError)->read_int();
1364  char *command = aw_root->awar(query->awar_parsvalue)->read_string();
1365 
1366  if (!strlen(command)) error = "Please enter a command";
1367 
1368  if (!error) {
1369  long ncount = aw_root->awar(query->awar_count)->read_int();
1370  char *deftag = aw_root->awar(query->awar_deftag)->read_string();
1371  char *tag = aw_root->awar(query->awar_tag)->read_string();
1372 
1373  {
1374  long use_tag = aw_root->awar(query->awar_use_tag)->read_int();
1375  if (!use_tag || !strlen(tag)) {
1376  freenull(tag);
1377  }
1378  }
1379  int double_pars = aw_root->awar(query->awar_double_pars)->read_int();
1380 
1381  arb_progress progress("Parse fields", ncount);
1382  QUERY_RANGE range = (QUERY_RANGE)aw_root->awar(query->awar_where)->read_int();
1383  GBL_env env(query->gb_main, query->get_tree_name());
1384 
1385  for (GBDATA *gb_item_container = selector.get_first_item_container(query->gb_main, aw_root, range);
1386  !error && gb_item_container;
1387  gb_item_container = selector.get_next_item_container(gb_item_container, range))
1388  {
1389  for (GBDATA *gb_item = selector.get_first_item(gb_item_container, QUERY_ALL_ITEMS);
1390  !error && gb_item;
1391  gb_item = selector.get_next_item(gb_item, QUERY_ALL_ITEMS))
1392  {
1393  if (IS_QUERIED(gb_item, query)) {
1394  GBDATA *gb_new = GB_search(gb_item, key, GB_FIND);
1395  error = GB_incur_error_if(!gb_new);
1396 
1397  if (!error) {
1398  GBL_call_env callEnv(gb_item, env);
1399 
1400  char *str = gb_new ? GB_read_as_string(gb_new) : strdup("");
1401  char *parsed = NULp;
1402 
1403  if (double_pars) {
1404  char *com2 = GB_command_interpreter_in_env(str, command, callEnv);
1405  if (com2) {
1406  if (tag) parsed = GBS_modify_tagged_string_with_ACI("", deftag, tag, com2, callEnv);
1407  else parsed = GB_command_interpreter_in_env ("", com2, callEnv);
1408 
1409  free(com2);
1410  }
1411  }
1412  else {
1413  if (tag) parsed = GBS_modify_tagged_string_with_ACI(str, deftag, tag, command, callEnv);
1414  else parsed = GB_command_interpreter_in_env (str, command, callEnv);
1415  }
1416 
1417  if (!parsed) error = GB_await_error();
1418  else {
1419  if (strcmp(parsed, str) != 0) { // any change?
1420  if (gb_new && parsed[0] == 0) { // empty result -> delete field
1421  error = GB_delete(gb_new);
1422  }
1423  else {
1424  if (!gb_new) {
1425  gb_new = GB_search(gb_item, key, key_type);
1426  if (!gb_new) error = GB_await_error();
1427  }
1428  if (!error) {
1429  error = GB_write_autoconv_string(gb_new, parsed); // <- field is actually written HERE
1430  if (!error && safe_conversion) {
1431  dbq_assert(key_type != GB_STRING);
1432  char *resulting = GB_read_as_string(gb_new);
1433  if (!resulting) {
1434  error = GB_await_error();
1435  }
1436  else {
1437  if (strcmp(resulting, parsed) != 0) {
1438  error = GBS_global_string("Conversion error: writing '%s'\n"
1439  "resulted in '%s'\n"
1440  "(mark checkbox to accept conversion errors)",
1441  parsed, resulting);
1442  }
1443  }
1444  }
1445  }
1446  }
1447  }
1448  free(parsed);
1449  }
1450  free(str);
1451  }
1452 
1453  if (error) {
1454  char *errCopy = strdup(error);
1455  char *itemId = selector.generate_item_id(query->gb_main, gb_item);
1456 
1457  error = GBS_global_string("While modifying field of %s '%s':\n%s",
1458  selector.item_name, itemId, errCopy);
1459 
1460  free(itemId);
1461  free(errCopy);
1462  }
1463 
1464  progress.inc_and_check_user_abort(error);
1465  }
1466  }
1467  }
1468 
1469  delete tag;
1470  free(deftag);
1471 
1472  if (error) progress.done();
1473  }
1474 
1475  free(command);
1476  }
1477 
1478  error = GB_end_transaction(query->gb_main, error);
1479  aw_message_if(error);
1480 }
1481 
1482 static void predef_prg(AW_root *aw_root, DbQuery *query) {
1483  char *str = aw_root->awar(query->awar_parspredefined)->read_string();
1484  char *brk = strchr(str, '#');
1485  if (brk) {
1486  *(brk++) = 0;
1487  char *kv = str;
1488  if (!strcmp(str, "ali_*/data")) { // when the target field contains this string -> replace it with current alignment
1489  GB_transaction ta(query->gb_main);
1490  char *use = GBT_get_default_alignment(query->gb_main);
1491  if (!use) {
1492  aw_message(GB_await_error());
1493  }
1494  else {
1495  kv = GBS_global_string_copy("%s/data", use);
1496  free(use);
1497  }
1498  }
1499  aw_root->awar(query->awar_parskey)->write_string(kv);
1500  if (kv != str) free(kv);
1501  aw_root->awar(query->awar_parsvalue)->write_string(brk);
1502  }
1503  else {
1504  aw_root->awar(query->awar_parsvalue)->write_string(str);
1505  }
1506  free(str);
1507 }
1508 
1509 static void colorize_queried_cb(AW_window *, DbQuery *query) {
1510  ItemSelector& selector = query->selector;
1511  GB_transaction ta(query->gb_main);
1512  GB_ERROR error = NULp;
1513  AW_root *aw_root = query->aws->get_root();
1514  int color_group = aw_root->awar(AWAR_COLORIZE)->read_int();
1515  QUERY_RANGE range = (QUERY_RANGE)aw_root->awar(query->awar_where)->read_int();
1516  bool changed = false;
1517 
1518  for (GBDATA *gb_item_container = selector.get_first_item_container(query->gb_main, aw_root, range);
1519  !error && gb_item_container;
1520  gb_item_container = selector.get_next_item_container(gb_item_container, range))
1521  {
1522  for (GBDATA *gb_item = selector.get_first_item(gb_item_container, QUERY_ALL_ITEMS);
1523  !error && gb_item;
1524  gb_item = selector.get_next_item(gb_item, QUERY_ALL_ITEMS))
1525  {
1526  if (IS_QUERIED(gb_item, query)) {
1527  error = GBT_set_color_group(gb_item, color_group);
1528  if (!error) changed = true;
1529  }
1530  }
1531  }
1532 
1533  if (error) GB_export_error(error);
1534  else if (changed) selector.trigger_display_refresh();
1535 }
1536 
1537 static void colorize_marked_cb(AW_window *aww, BoundItemSel *cmd) {
1538  ItemSelector& sel = cmd->selector;
1539  GB_transaction ta(cmd->gb_main);
1540  GB_ERROR error = NULp;
1541  AW_root *aw_root = aww->get_root();
1542  int color_group = aw_root->awar(AWAR_COLORIZE)->read_int();
1543  QUERY_RANGE range = QUERY_ALL_ITEMS; // @@@ FIXME: make customizable
1544 
1545  for (GBDATA *gb_item_container = sel.get_first_item_container(cmd->gb_main, aw_root, range);
1546  !error && gb_item_container;
1547  gb_item_container = sel.get_next_item_container(gb_item_container, range))
1548  {
1549  for (GBDATA *gb_item = sel.get_first_item(gb_item_container, QUERY_ALL_ITEMS);
1550  !error && gb_item;
1551  gb_item = sel.get_next_item(gb_item, QUERY_ALL_ITEMS))
1552  {
1553  if (GB_read_flag(gb_item)) {
1554  error = GBT_set_color_group(gb_item, color_group);
1555  }
1556  }
1557  }
1558 
1559  if (error) GB_export_error(error);
1560 }
1561 
1562 enum mark_mode {
1563  UNMARK,
1564  MARK,
1565  INVERT,
1566 };
1567 
1568 static void mark_colored_cb(AW_window *aww, BoundItemSel *cmd, mark_mode mode) {
1569  // @@@ mark_colored_cb is obsolete! (will be replaced by dynamic coloring in the future)
1570  ItemSelector& sel = cmd->selector;
1571  AW_root *aw_root = aww->get_root();
1572  int color_group = aw_root->awar(AWAR_COLORIZE)->read_int();
1573  QUERY_RANGE range = QUERY_ALL_ITEMS; // @@@ FIXME: make customizable
1574 
1575  GB_transaction ta(cmd->gb_main);
1576 
1577  for (GBDATA *gb_item_container = sel.get_first_item_container(cmd->gb_main, aw_root, range);
1578  gb_item_container;
1579  gb_item_container = sel.get_next_item_container(gb_item_container, range))
1580  {
1581  for (GBDATA *gb_item = sel.get_first_item(gb_item_container, QUERY_ALL_ITEMS);
1582  gb_item;
1583  gb_item = sel.get_next_item(gb_item, QUERY_ALL_ITEMS))
1584  {
1585  int my_color = GBT_get_color_group(gb_item);
1586  if (my_color == color_group) {
1587  bool marked = GB_read_flag(gb_item);
1588 
1589  switch (mode) {
1590  case UNMARK: marked = 0; break;
1591  case MARK: marked = 1; break;
1592  case INVERT: marked = !marked; break;
1593 
1594  default: dbq_assert(0); break;
1595  }
1596 
1597  GB_write_flag(gb_item, marked);
1598  }
1599  }
1600  }
1601 
1602 }
1603 
1604 // --------------------------------------------------------------------------------
1605 // color sets
1606 
1607 struct color_save_data {
1608  BoundItemSel *bsel;
1609  AW_selection_list *colorsets;
1610 
1611  const char *get_items_name() const {
1612  return bsel->selector.items_name;
1613  }
1614 };
1615 
1616 #define AWAR_COLOR_LOADSAVE_NAME "tmp/colorset/name"
1617 
1618 inline GBDATA *get_colorset_root(BoundItemSel *bsel) {
1619  return GBT_colorset_root(bsel->gb_main, bsel->selector.items_name);
1620 }
1621 
1622 static void update_colorset_selection_list(const color_save_data *csd) {
1623  ConstStrArray foundSets;
1624  {
1625  GB_transaction ta(csd->bsel->gb_main);
1626  GBT_get_colorset_names(foundSets, get_colorset_root(csd->bsel));
1627  }
1628 
1629  AW_selection_list *sel = csd->colorsets;
1630  sel->clear();
1631  sel->insert_default("<new colorset>", "");
1632  for (size_t i = 0; i<foundSets.size(); ++i) {
1633  sel->insert(foundSets[i], foundSets[i]);
1634  }
1635  sel->update();
1636 }
1637 
1638 static void colorset_changed_cb(GBDATA*, const color_save_data *csd, GB_CB_TYPE cbt) {
1639  if (cbt&GB_CB_CHANGED) {
1640  update_colorset_selection_list(csd);
1641  }
1642 }
1643 
1644 static void create_colorset_representation(BoundItemSel *bsel, AW_root *aw_root, StrArray& colordefs, GB_ERROR& error) {
1645  ItemSelector& sel = bsel->selector;
1646  GBDATA *gb_main = bsel->gb_main;
1647 
1648  dbq_assert(!error);
1649 
1650  for (GBDATA *gb_item_container = sel.get_first_item_container(gb_main, aw_root, QUERY_ALL_ITEMS);
1651  gb_item_container;
1652  gb_item_container = sel.get_next_item_container(gb_item_container, QUERY_ALL_ITEMS))
1653  {
1654  for (GBDATA *gb_item = sel.get_first_item(gb_item_container, QUERY_ALL_ITEMS);
1655  gb_item;
1656  gb_item = sel.get_next_item(gb_item, QUERY_ALL_ITEMS))
1657  {
1658  int color = GBT_get_color_group(gb_item);
1659  if (color>0) {
1660  char *id = sel.generate_item_id(gb_main, gb_item);
1661  char *color_def = GBS_global_string_copy("%s=%i", id, color);
1662 
1663  colordefs.put(color_def);
1664  free(id);
1665  }
1666  }
1667  }
1668 
1669  if (colordefs.empty()) {
1670  error = GBS_global_string("Could not find any colored %s", sel.items_name);
1671  }
1672 }
1673 
1674 static GB_ERROR clear_all_colors(BoundItemSel *bsel, AW_root *aw_root) {
1675  ItemSelector& sel = bsel->selector;
1676  GB_ERROR error = NULp;
1677  bool changed = false;
1678 
1679  for (GBDATA *gb_item_container = sel.get_first_item_container(bsel->gb_main, aw_root, QUERY_ALL_ITEMS);
1680  !error && gb_item_container;
1681  gb_item_container = sel.get_next_item_container(gb_item_container, QUERY_ALL_ITEMS))
1682  {
1683  for (GBDATA *gb_item = sel.get_first_item(gb_item_container, QUERY_ALL_ITEMS);
1684  !error && gb_item;
1685  gb_item = sel.get_next_item(gb_item, QUERY_ALL_ITEMS))
1686  {
1687  error = GBT_set_color_group(gb_item, 0); // clear colors
1688  if (!error) changed = true;
1689  }
1690  }
1691 
1692  if (changed && !error) sel.trigger_display_refresh();
1693  return error;
1694 }
1695 
1696 static void clear_all_colors_cb(AW_window *aww, BoundItemSel *bsel) {
1697  GB_transaction ta(bsel->gb_main);
1698  GB_ERROR error = clear_all_colors(bsel, aww->get_root());
1699 
1700  if (error) {
1701  error = ta.close(error);
1702  aw_message(error);
1703  }
1704 }
1705 
1706 static GB_ERROR restore_colorset_representation(BoundItemSel *bsel, CharPtrArray& colordefs) {
1707  ItemSelector& sel = bsel->selector;
1708  GBDATA *gb_main = bsel->gb_main;
1709  bool changed = false;
1710  GB_ERROR error = NULp;
1711  int ignores = 0;
1712 
1713  for (size_t d = 0; d<colordefs.size() && !error; ++d) {
1714  const char *def = colordefs[d];
1715  const char *equal = strchr(def, '=');
1716 
1717  if (equal) {
1718  LocallyModify<char> tempSplit(const_cast<char*>(equal)[0], 0);
1719 
1720  const char *id = def;
1721  GBDATA *gb_item = sel.find_item_by_id(gb_main, id);
1722  if (!gb_item) {
1723  aw_message(GBS_global_string("No such %s: '%s' (ignored)", sel.item_name, id)); // only warn
1724  ++ignores;
1725  }
1726  else {
1727  int color_group = atoi(equal+1);
1728  if (color_group>0) { // bugfix: saved color groups contained zero (which means "no color") by mistake; ignore
1729  error = GBT_set_color_group(gb_item, color_group);
1730  if (!error) changed = true;
1731  }
1732  }
1733  }
1734  else {
1735  aw_message(GBS_global_string("Invalid colordef '%s' (ignored)", def));
1736  ++ignores;
1737  }
1738  }
1739  if (changed && !error) sel.trigger_display_refresh();
1740  if (ignores>0 && !error) {
1741  aw_message(GBS_global_string("Warning: failed to restore color assignment for %i %s", ignores, sel.items_name));
1742  }
1743 
1744  return error;
1745 }
1746 
1747 enum loadsave_mode {
1748  SAVE,
1749  LOAD,
1750  OVERLAY,
1751  DELETE,
1752 };
1753 
1754 static void loadsave_colorset_cb(AW_window *aws, BoundItemSel *bsel, loadsave_mode mode) {
1755  AW_root *aw_root = aws->get_root();
1756  char *name = aw_root->awar(AWAR_COLOR_LOADSAVE_NAME)->read_string();
1757  GB_ERROR error = NULp;
1758 
1759  if (name[0] == 0) error = "Please enter a name for the colorset.";
1760  else {
1761  GB_transaction ta(bsel->gb_main);
1762 
1763  GBDATA *gb_colorset_root = get_colorset_root(bsel);
1764  GBDATA *gb_colorset = gb_colorset_root ? GBT_find_colorset(gb_colorset_root, name) : NULp;
1765 
1766  error = GB_incur_error();
1767  if (!error) {
1768  if (mode == SAVE) {
1769  if (!gb_colorset) { // create new colorset
1770  gb_colorset = GBT_find_or_create_colorset(gb_colorset_root, name);
1771  if (!gb_colorset) error = GB_await_error();
1772  }
1773  dbq_assert(gb_colorset || error);
1774 
1775  if (!error) {
1776  StrArray colordefs;
1777  create_colorset_representation(bsel, aw_root, colordefs, error);
1778  if (!error) error = GBT_save_colorset(gb_colorset, colordefs);
1779  }
1780  }
1781  else {
1782  if (!gb_colorset) error = GBS_global_string("Colorset '%s' not found", name);
1783  else {
1784  if (mode == LOAD || mode == OVERLAY) {
1785  ConstStrArray colordefs;
1786  error = GBT_load_colorset(gb_colorset, colordefs);
1787 
1788  if (!error && colordefs.empty()) error = "oops.. empty colorset";
1789  if (!error && mode == LOAD) error = clear_all_colors(bsel, aw_root);
1790  if (!error) error = restore_colorset_representation(bsel, colordefs);
1791  }
1792  else {
1793  dbq_assert(mode == DELETE);
1794  error = GB_delete(gb_colorset);
1795  }
1796  }
1797  }
1798  }
1799  error = ta.close(error);
1800  }
1801  free(name);
1802 
1803  if (error) aw_message(error);
1804 }
1805 
1806 static AW_window *create_loadsave_colored_window(AW_root *aw_root, color_save_data *csd) {
1807  static AW_window **aw_loadsave = NULp;
1808  if (!aw_loadsave) {
1809  // init data
1810  aw_root->awar_string(AWAR_COLOR_LOADSAVE_NAME, "", AW_ROOT_DEFAULT);
1811  ARB_calloc(aw_loadsave, QUERY_ITEM_TYPES); // contains loadsave windows for each item type
1812  }
1813 
1814  QUERY_ITEM_TYPE type = csd->bsel->selector.type;
1815 
1816  dbq_assert(type<QUERY_ITEM_TYPES);
1817 
1818  if (!aw_loadsave[type]) {
1819  // init window
1820  AW_window_simple *aws = new AW_window_simple;
1821  {
1822  char *window_id = GBS_global_string_copy("colorset_loadsave_%s", csd->get_items_name());
1823  aws->init(aw_root, window_id, GBS_global_string("Load/Save %s colorset", csd->get_items_name()));
1824  free(window_id);
1825  }
1826 
1827  aws->load_xfig("query/color_loadsave.fig");
1828 
1829  aws->at("close");
1830  aws->callback(AW_POPDOWN);
1831  aws->create_button("CLOSE", "CLOSE", "C");
1832 
1833  aws->at("help");
1834  aws->callback(makeHelpCallback("color_loadsave.hlp"));
1835  aws->create_button("HELP", "HELP", "H");
1836 
1837  dbq_assert(!csd->colorsets);
1838  csd->colorsets = awt_create_selection_list_with_input_field(aws, AWAR_COLOR_LOADSAVE_NAME, "list", "name");
1839 
1840  update_colorset_selection_list(csd);
1841 
1842  aws->at("save"); aws->callback(makeWindowCallback(loadsave_colorset_cb, csd->bsel, SAVE)); aws->create_button("save", "Save", "S");
1843  aws->at("load"); aws->callback(makeWindowCallback(loadsave_colorset_cb, csd->bsel, LOAD)); aws->create_button("load", "Load", "L");
1844  aws->at("overlay"); aws->callback(makeWindowCallback(loadsave_colorset_cb, csd->bsel, OVERLAY)); aws->create_button("overlay", "Overlay", "O");
1845  aws->at("delete"); aws->callback(makeWindowCallback(loadsave_colorset_cb, csd->bsel, DELETE)); aws->create_button("delete", "Delete", "D");
1846 
1847  aws->at("reset");
1848  aws->callback(makeWindowCallback(clear_all_colors_cb, csd->bsel));
1849  aws->create_button("reset", "Reset", "R");
1850 
1851  // callbacks
1852  {
1853  GB_transaction ta(csd->bsel->gb_main);
1854  GBDATA *gb_colorset = get_colorset_root(csd->bsel);
1855  GB_add_callback(gb_colorset, GB_CB_CHANGED, makeDatabaseCallback(colorset_changed_cb, csd));
1856  }
1857 
1858  aw_loadsave[type] = aws;
1859  }
1860 
1861  return aw_loadsave[type];
1862 }
1863 
1864 static AW_window *create_colorize_window(AW_root *aw_root, GBDATA *gb_main, DbQuery *query, ItemSelector *sel) {
1865  // invoked by 'colorize listed' (sel != 0)
1866  // and 'colorize marked/mark colored' (query != 0)
1867 
1868  enum { COLORIZE_INVALID, COLORIZE_LISTED, COLORIZE_MARKED } mode = COLORIZE_INVALID;
1869 
1870  create_query_independent_awars(aw_root, AW_ROOT_DEFAULT);
1871 
1872  AW_window_simple *aws = new AW_window_simple;
1873 
1874  dbq_assert(contradicted(query, sel));
1875 
1876  if (query) {
1877  dbq_assert(mode == COLORIZE_INVALID);
1878  mode = COLORIZE_LISTED;
1879  }
1880  if (sel) {
1881  dbq_assert(mode == COLORIZE_INVALID);
1882  mode = COLORIZE_MARKED;
1883  }
1884  dbq_assert(!(mode == COLORIZE_INVALID));
1885 
1886  ItemSelector& Sel = mode == COLORIZE_LISTED ? query->selector : *sel;
1887  const char *what = mode == COLORIZE_LISTED ? "listed" : "marked";
1888 
1889  {
1890  char *macro_name = GBS_global_string_copy("COLORIZE_%s_%s", what, Sel.items_name);
1891  char *window_name = GBS_global_string_copy("Colorize %s %s", what, Sel.items_name);
1892 
1893  aws->init(aw_root, macro_name, window_name);
1894 
1895  free(window_name);
1896  free(macro_name);
1897  }
1898 
1899  aws->load_xfig("query/colorize.fig");
1900 
1901  aws->auto_space(10, 10);
1902 
1903  aws->at("close");
1904  aws->callback(AW_POPDOWN);
1905  aws->create_button("CLOSE", "CLOSE", "C");
1906 
1907  aws->at("help");
1908  aws->callback(makeHelpCallback(mode == COLORIZE_LISTED ? "set_color_of_listed.hlp" : "colorize.hlp"));
1909  aws->create_button("HELP", "HELP", "H");
1910 
1911  aws->at("colorize");
1912 
1913  BoundItemSel *bsel = new BoundItemSel(gb_main, ((mode == COLORIZE_MARKED) ? *sel : query->selector)); // do not free, bound to CB
1914 
1915  if (mode == COLORIZE_LISTED) aws->callback(makeWindowCallback(colorize_queried_cb, query));
1916  else aws->callback(makeWindowCallback(colorize_marked_cb, bsel));
1917 
1918  aws->create_autosize_button("COLORIZE", GBS_global_string_copy("Set color of %s %s to ...", what, Sel.items_name), "S", 2);
1919 
1920  {
1921  int color_group;
1922 
1923  aws->create_option_menu(AWAR_COLORIZE);
1924  aws->insert_default_option("No color group", "none", 0);
1925  for (color_group = 1; color_group <= AW_COLOR_GROUPS; ++color_group) {
1926  char *name = AW_get_color_group_name(aw_root, color_group);
1927  aws->insert_option(name, "", color_group);
1928  free(name);
1929  }
1930  aws->update_option_menu();
1931  }
1932 
1933  color_save_data *csd = new color_save_data; // do not free, bound to CB
1934  csd->bsel = bsel;
1935  csd->colorsets = NULp;
1936 
1937  aws->at("loadsave");
1938  aws->callback(makeCreateWindowCallback(create_loadsave_colored_window, csd));
1939  aws->create_autosize_button("LOADSAVE_COLORED", "Load/Save", "L");
1940 
1941  if (mode == COLORIZE_MARKED) {
1942  aws->at("mark");
1943  aws->callback(makeWindowCallback(mark_colored_cb, bsel, MARK));
1944  aws->create_autosize_button("MARK_COLORED", GBS_global_string_copy("Mark all %s of ...", Sel.items_name), "M", 2);
1945 
1946  aws->at("unmark");
1947  aws->callback(makeWindowCallback(mark_colored_cb, bsel, UNMARK));
1948  aws->create_autosize_button("UNMARK_COLORED", GBS_global_string_copy("Unmark all %s of ...", Sel.items_name), "U", 2);
1949 
1950  aws->at("invert");
1951  aws->callback(makeWindowCallback(mark_colored_cb, bsel, INVERT));
1952  aws->create_autosize_button("INVERT_COLORED", GBS_global_string_copy("Invert all %s of ...", Sel.items_name), "I", 2);
1953  }
1954 
1955  aws->at_newline();
1956  aws->window_fit();
1957 
1958  return aws;
1959 }
1960 
1961 static AW_window *create_colorize_queried_window(AW_root *aw_root, DbQuery *query) {
1962  return create_colorize_window(aw_root, query->gb_main, query, NULp);
1963 }
1964 
1965 AW_window *QUERY::create_colorize_items_window(AW_root *aw_root, GBDATA *gb_main, ItemSelector& sel) {
1966  return create_colorize_window(aw_root, gb_main, NULp, &sel);
1967 }
1968 
1969 static void setup_modify_fields_config(AWT_config_definition& cdef, const DbQuery *query) {
1970  const char *typeawar = get_itemfield_type_awarname(query->awar_parskey);
1971  dbq_assert(typeawar);
1972 
1973  cdef.add(query->awar_parskey, "key");
1974  cdef.add(typeawar, "type");
1975  cdef.add(query->awar_use_tag, "usetag");
1976  cdef.add(query->awar_deftag, "deftag");
1977  cdef.add(query->awar_tag, "modtag");
1978  cdef.add(query->awar_double_pars, "doubleparse");
1979  cdef.add(query->awar_acceptConvError, "acceptconv");
1980  cdef.add(query->awar_acceptIdMod, "acceptidmod");
1981  cdef.add(query->awar_parsvalue, "aci");
1982 }
1983 
1984 static AW_window *create_modify_fields_window(AW_root *aw_root, DbQuery *query) {
1985  AW_window_simple *aws = new AW_window_simple;
1986 
1987  {
1988  char *macro_name = GBS_global_string_copy("MODIFY_DATABASE_FIELD_%s", query->selector.items_name);
1989  char *window_name = GBS_global_string_copy("MODIFY DATABASE FIELD of listed %s", query->selector.items_name);
1990 
1991  aws->init(aw_root, macro_name, window_name);
1992 
1993  free(window_name);
1994  free(macro_name);
1995  }
1996 
1997  aws->load_xfig("query/modify_fields.fig");
1998 
1999  aws->at("close");
2000  aws->callback(AW_POPDOWN);
2001  aws->create_button("CLOSE", "CLOSE", "C");
2002 
2003  aws->at("help");
2004  aws->callback(makeHelpCallback("mod_field_list.hlp"));
2005  aws->create_button("HELP", "HELP", "H");
2006 
2007  aws->at("helptags");
2008  aws->callback(makeHelpCallback("tags.hlp"));
2009  aws->create_button("HELP_TAGS", "Help tags", "H");
2010 
2011  create_itemfield_selection_button(aws, FieldSelDef(query->awar_parskey, query->gb_main, query->selector, FIELD_FILTER_STRING_READABLE, "target field", SF_ALLOW_NEW), "field");
2012  aws->at("acceptErr"); aws->create_toggle(query->awar_acceptConvError);
2013 
2014  // ------------------------
2015  // expert section
2016  aws->at("usetag"); aws->create_toggle (query->awar_use_tag);
2017  aws->at("deftag"); aws->create_input_field(query->awar_deftag);
2018  aws->at("tag"); aws->create_input_field(query->awar_tag);
2019  aws->at("double"); aws->create_toggle (query->awar_double_pars);
2020  aws->at("acceptID"); aws->create_toggle (query->awar_acceptIdMod);
2021  // ------------------------
2022 
2023  aws->at("parser");
2024  aws->create_text_field(query->awar_parsvalue);
2025 
2026  aws->at("go");
2027  aws->callback(makeWindowCallback(modify_fields_of_queried_cb, query));
2028  aws->create_button("GO", "GO", "G");
2029 
2030  aws->at("pre");
2031  AW_selection_list *programs = aws->create_selection_list(query->awar_parspredefined);
2032 
2033  const char *sellst = NULp;
2034  switch (query->selector.type) {
2035  case QUERY_ITEM_SPECIES:
2036  case QUERY_ITEM_ORGANISM: sellst = "mod_fields*.sellst"; break;
2037  case QUERY_ITEM_GENES: sellst = "mod_gene_fields*.sellst"; break;
2038  case QUERY_ITEM_EXPERIMENTS: sellst = "mod_experiment_fields*.sellst"; break;
2039  default: dbq_assert(0); break;
2040  }
2041 
2042  GB_ERROR error;
2043  if (sellst) {
2044  StorableSelectionList storable_sellist(TypedSelectionList("sellst", programs, "field modification scripts", "mod_fields"));
2045  error = storable_sellist.load(GB_concat_path_in_ARBLIB("sellists", sellst), false);
2046  }
2047  else {
2048  error = "No default selection list for query-type";
2049  }
2050 
2051  if (error) {
2052  aw_message(error);
2053  }
2054  else {
2055  aws->get_root()->awar(query->awar_parspredefined)->add_callback(makeRootCallback(predef_prg, query));
2056  }
2057 
2058  aws->at("config");
2059  AWT_insert_config_manager(aws, AW_ROOT_DEFAULT,
2060  GBS_global_string("mod_%s_fields", query->selector.item_name),
2061  makeConfigSetupCallback(setup_modify_fields_config, query));
2062 
2063  return aws;
2064 }
2065 
2066 static void set_field_of_queried_cb(AW_window*, DbQuery *query, bool append) {
2067  // set fields of listed items
2068  ItemSelector& selector = query->selector;
2069  GB_ERROR error = NULp;
2070  AW_root *aw_root = query->aws->get_root();
2071  bool allow_loss = aw_root->awar(query->awar_writelossy)->read_int();
2072 
2073  char *value = aw_root->awar(query->awar_setvalue)->read_string();
2074  if (value[0] == 0) freenull(value);
2075 
2076  size_t value_len = value ? strlen(value) : 0;
2077 
2078  GB_begin_transaction(query->gb_main);
2079 
2080  const char *key = prepare_and_get_selected_itemfield(aw_root, query->awar_writekey, query->gb_main, selector);
2081  if (!key) error = GB_await_error();
2082 
2083  for (GBDATA *gb_item_container = selector.get_first_item_container(query->gb_main, aw_root, QUERY_ALL_ITEMS);
2084  !error && gb_item_container;
2085  gb_item_container = selector.get_next_item_container(gb_item_container, QUERY_ALL_ITEMS))
2086  {
2087  for (GBDATA *gb_item = selector.get_first_item(gb_item_container, QUERY_ALL_ITEMS);
2088  !error && gb_item;
2089  gb_item = selector.get_next_item(gb_item, QUERY_ALL_ITEMS))
2090  {
2091  if (IS_QUERIED(gb_item, query)) {
2092  if (!value) { // empty value -> delete field
2093  if (!append) {
2094  GBDATA *gb_field = GB_search(gb_item, key, GB_FIND);
2095  if (gb_field) error = GB_delete(gb_field);
2096  }
2097  // otherwise "nothing" is appended (=noop)
2098  }
2099  else {
2100  GBDATA *gb_field = GBT_searchOrCreate_itemfield_according_to_changekey(gb_item, key, selector.change_key_path);
2101  if (!gb_field) error = GB_await_error();
2102  else {
2103  const char *new_content = value;
2104  SmartCharPtr content;
2105 
2106  if (append) {
2107  char *old = GB_read_as_string(gb_field);
2108  if (!old) error = "field has incompatible type";
2109  else {
2110  size_t old_len = strlen(old);
2111  GBS_strstruct buf(old_len+value_len+2);
2112 
2113  buf.ncat(old, old_len);
2114  buf.ncat(value, value_len);
2115 
2116  content = buf.release();
2117  new_content = &*content;
2118  }
2119  }
2120 
2121  error = GB_write_autoconv_string(gb_field, new_content);
2122 
2123  if (!allow_loss && !error) {
2124  char *result = GB_read_as_string(gb_field);
2125  dbq_assert(result);
2126 
2127  if (strcmp(new_content, result) != 0) {
2128  error = GBS_global_string("value modified by type conversion\n('%s' -> '%s')", new_content, result);
2129  }
2130  free(result);
2131  }
2132  }
2133  }
2134 
2135  if (error) { // add name of current item to error
2136  const char *name = GBT_read_char_pntr(gb_item, "name");
2137  error = GBS_global_string("Error while writing to %s '%s':\n%s", selector.item_name, name, error);
2138  }
2139  }
2140  }
2141  }
2142 
2143  GB_end_transaction_show_error(query->gb_main, error, aw_message);
2144 
2145  free(value);
2146 }
2147 
2148 static AW_window *create_writeFieldOfListed_window(AW_root *aw_root, DbQuery *query) {
2149  AW_window_simple *aws = new AW_window_simple;
2150  init_itemType_specific_window(aw_root, aws, query->selector, "WRITE_DB_FIELD_OF_LISTED", "Write field of listed %s", true);
2151  aws->load_xfig("query/write_fields.fig");
2152 
2153  aws->at("close");
2154  aws->callback(AW_POPDOWN);
2155  aws->create_button("CLOSE", "CLOSE", "C");
2156 
2157  aws->at("help");
2158  aws->callback(makeHelpCallback("write_field_list.hlp"));
2159  aws->create_button("HELP", "HELP", "H");
2160 
2161  create_itemfield_selection_button(aws, FieldSelDef(query->awar_writekey, query->gb_main, query->selector, FIELD_FILTER_STRING_READABLE, "target field", SF_ALLOW_NEW), "field");
2162 
2163  aws->at("val");
2164  aws->create_text_field(query->awar_setvalue, 2, 2);
2165 
2166  aws->at("lossy");
2167  aws->label("Allow lossy conversion?");
2168  aws->create_toggle(query->awar_writelossy);
2169 
2170  aws->at("create");
2171  aws->callback(makeWindowCallback(set_field_of_queried_cb, query, false));
2172  aws->create_button("SET_SINGLE_FIELD_OF_LISTED", "WRITE");
2173 
2174  aws->at("do");
2175  aws->callback(makeWindowCallback(set_field_of_queried_cb, query, true));
2176  aws->create_button("APPEND_SINGLE_FIELD_OF_LISTED", "APPEND");
2177 
2178  return aws;
2179 }
2180 
2181 static void set_protection_of_queried_cb(AW_window*, DbQuery *query) {
2182  // set protection of listed items
2183  ItemSelector& selector = query->selector;
2184  AW_root *aw_root = query->aws->get_root();
2185  char *key = aw_root->awar(query->awar_protectkey)->read_string();
2186 
2187  if (strcmp(key, NO_FIELD_SELECTED) == 0) {
2188  aw_message("Please select a field for which you want to set the protection");
2189  }
2190  else {
2191  GB_begin_transaction(query->gb_main);
2192 
2193  GB_ERROR error = NULp;
2194  GBDATA *gb_key_data = GB_search(query->gb_main, selector.change_key_path, GB_CREATE_CONTAINER);
2195  GBDATA *gb_key_name = GB_find_string(gb_key_data, CHANGEKEY_NAME, key, GB_IGNORE_CASE, SEARCH_GRANDCHILD);
2196 
2197  if (!gb_key_name) {
2198  error = GBS_global_string("The destination field '%s' does not exists", key);
2199  }
2200  else {
2201  int level = aw_root->awar(query->awar_setprotection)->read_int();
2202  QUERY_RANGE range = (QUERY_RANGE)aw_root->awar(query->awar_where)->read_int();
2203 
2204  for (GBDATA *gb_item_container = selector.get_first_item_container(query->gb_main, aw_root, range);
2205  !error && gb_item_container;
2206  gb_item_container = selector.get_next_item_container(gb_item_container, range))
2207  {
2208  for (GBDATA *gb_item = selector.get_first_item(gb_item_container, QUERY_ALL_ITEMS);
2209  !error && gb_item;
2210  gb_item = selector.get_next_item(gb_item, QUERY_ALL_ITEMS))
2211  {
2212  if (IS_QUERIED(gb_item, query)) {
2213  GBDATA *gb_new = GB_search(gb_item, key, GB_FIND);
2214  if (gb_new) {
2215  error = GB_write_security_delete(gb_new, level);
2216  if (!error) error = GB_write_security_write(gb_new, level);
2217  }
2218  }
2219  }
2220  }
2221  }
2222  GB_end_transaction_show_error(query->gb_main, error, aw_message);
2223  }
2224 
2225  free(key);
2226 }
2227 
2228 static AW_window *create_set_protection_window(AW_root *aw_root, DbQuery *query) {
2229  AW_window_simple *aws = new AW_window_simple;
2230  init_itemType_specific_window(aw_root, aws, query->selector, "SET_PROTECTION_OF_FIELD_OF_LISTED", "Protect field of listed %s", true);
2231  aws->load_xfig("query/set_protection.fig");
2232 
2233  aws->at("close");
2234  aws->callback(AW_POPDOWN);
2235  aws->create_button("CLOSE", "CLOSE", "C");
2236 
2237  aws->at("help");
2238  aws->callback(makeHelpCallback("set_protection.hlp"));
2239  aws->create_button("HELP", "HELP", "H");
2240 
2241 
2242  aws->at("prot");
2243  aws->create_toggle_field(query->awar_setprotection, AW_VERTICAL);
2244  aws->insert_toggle("0 temporary", "0", 0);
2245  aws->insert_toggle("1 checked", "1", 1);
2246  aws->insert_toggle("2", "2", 2);
2247  aws->insert_toggle("3", "3", 3);
2248  aws->insert_toggle("4 normal", "4", 4);
2249  aws->insert_toggle("5 ", "5", 5);
2250  aws->insert_toggle("6 the truth", "5", 6);
2251  aws->update_toggle_field();
2252 
2253  create_itemfield_selection_list(aws, FieldSelDef(query->awar_protectkey, query->gb_main, query->selector, FIELD_UNFILTERED, "field to protect"), "list");
2254 
2255  aws->at("go");
2256  aws->callback(makeWindowCallback(set_protection_of_queried_cb, query));
2257  aws->create_autosize_button("SET_PROTECTION_OF_FIELD_OF_LISTED", "Assign\nprotection\nto field\nof listed");
2258 
2259  return aws;
2260 }
2261 
2262 static void toggle_flag_cb(AW_window *aww, DbQuery *query) {
2263  GB_transaction ta(query->gb_main);
2264  GBDATA *gb_item = query->selector.get_selected_item(query->gb_main, aww->get_root());
2265  if (gb_item) {
2266  long flag = GB_read_flag(gb_item);
2267  GB_write_flag(gb_item, 1-flag);
2268  }
2269  DbQuery_update_list(query);
2270 }
2271 
2272 static void new_selection_made_cb(AW_root *aw_root, const char *awar_selection, DbQuery *query) {
2273  char *item_name = aw_root->awar(awar_selection)->read_as_string();
2274  query->selector.update_item_awars(query->gb_main, aw_root, item_name);
2275  free(item_name);
2276 }
2277 
2278 static void query_box_setup_config(AWT_config_definition& cdef, DbQuery *query) {
2279  // this defines what is saved/restored to/from configs
2280  for (int key_id = 0; key_id<QUERY_EXPRESSIONS; ++key_id) {
2281  cdef.add(query->awar_keys[key_id], "key", key_id);
2282  cdef.add(query->awar_queries[key_id], "query", key_id);
2283  cdef.add(query->awar_not[key_id], "not", key_id);
2284  cdef.add(query->awar_operator[key_id], "operator", key_id);
2285  }
2286 }
2287 
2288 template<typename CB>
2289 static void query_rel_menu_entry(AW_window *aws, const char *id, const char *query_id, const char* label, const char *mnemonic, const char *helpText, AW_active Mask, const CB& cb) {
2290  char *rel_id = GBS_global_string_copy("%s_%s", query_id, id);
2291  aws->insert_menu_topic(rel_id, label, mnemonic, helpText, Mask, cb);
2292  free(rel_id);
2293 }
2294 
2295 const char *DbQuery::get_tree_name() const {
2296  if (!awar_tree_name)
2297  return NULp;
2298  else
2299  return aws->get_root()->awar(awar_tree_name)->read_char_pntr();
2300 }
2301 
2302 DbQuery::~DbQuery() {
2303  for (int s = 0; s<QUERY_EXPRESSIONS; ++s) {
2304  free(awar_keys[s]);
2305  free(awar_queries[s]);
2306  free(awar_not[s]);
2307  free(awar_operator[s]);
2308  }
2309 
2310  free(species_name);
2311 
2312  free(awar_writekey);
2313  free(awar_writelossy);
2314  free(awar_protectkey);
2315  free(awar_setprotection);
2316  free(awar_setvalue);
2317 
2318  free(awar_parskey);
2319  free(awar_parsvalue);
2320  free(awar_parspredefined);
2321  free(awar_acceptConvError);
2322  free(awar_acceptIdMod);
2323 
2324  free(awar_ere);
2325  free(awar_where);
2326  free(awar_by);
2327  free(awar_use_tag);
2328  free(awar_double_pars);
2329  free(awar_deftag);
2330  free(awar_tag);
2331  free(awar_count);
2332  free(awar_sort);
2333 
2334  GBS_free_hash(hit_description);
2335 }
2336 
2337 // ----------------------------------------
2338 // store query data until DB close
2339 
2340 typedef Keeper<DbQuery*> QueryKeeper;
2341 template<> void Keeper<DbQuery*>::destroy(DbQuery *q) { delete q; }
2342 static SmartPtr<QueryKeeper> queryKeeper;
2343 static void destroyKeptQueries() {
2344  queryKeeper.setNull();
2345 }
2346 static void keepQuery(GBDATA *gbmain, DbQuery *q) {
2347  if (queryKeeper.isNull()) {
2348  queryKeeper = new QueryKeeper;
2349  GB_atclose_callback(gbmain, makeDatabaseCallback(destroyKeptQueries));
2350  }
2351  queryKeeper->keep(q);
2352 }
2353 
2354 // ----------------------------------------
2355 
2356 DbQuery *QUERY::create_query_box(AW_window *aws, query_spec *awtqs, const char *query_id) {
2357  char buffer[256];
2358  AW_root *aw_root = aws->get_root();
2359  GBDATA *gb_main = awtqs->gb_main;
2360  DbQuery *query = new DbQuery(awtqs->get_queried_itemtype());
2361 
2362  keepQuery(gb_main, query); // transfers ownership of query
2363 
2364  // @@@ set all the things below via ctor!
2365  // @@@ create a copyable object containing everything query_spec and DbQuery have in common -> pass that object to DbQuery-ctor
2366 
2367  query->gb_main = awtqs->gb_main;
2368  query->aws = aws;
2369  query->gb_ref = awtqs->gb_ref;
2370  query->expect_hit_in_ref_list = awtqs->expect_hit_in_ref_list;
2371  query->select_bit = awtqs->select_bit;
2372  query->species_name = strdup(awtqs->species_name);
2373 
2374  query->set_tree_awar_name(awtqs->tree_name);
2375  query->hit_description = GBS_create_dynaval_hash(query_count_items(query, QUERY_ALL_ITEMS, QUERY_GENERATE), GB_IGNORE_CASE, free_hit_description);
2376 
2377  GB_push_transaction(gb_main);
2378 
2379  // Create query box AWARS
2380  create_query_independent_awars(aw_root, AW_ROOT_DEFAULT);
2381 
2382  {
2383  const char *default_key[QUERY_EXPRESSIONS+1] = { "name", "name", "name", NULp };
2384 
2385  for (int key_id = 0; key_id<QUERY_EXPRESSIONS; ++key_id) {
2386  sprintf(buffer, "tmp/dbquery_%s/key_%i", query_id, key_id);
2387  query->awar_keys[key_id] = strdup(buffer);
2388  dbq_assert(default_key[key_id]);
2389  aw_root->awar_string(query->awar_keys[key_id], default_key[key_id], AW_ROOT_DEFAULT);
2390 
2391  sprintf(buffer, "tmp/dbquery_%s/query_%i", query_id, key_id);
2392  query->awar_queries[key_id] = strdup(buffer);
2393  aw_root->awar_string(query->awar_queries[key_id], "*", AW_ROOT_DEFAULT);
2394 
2395  sprintf(buffer, "tmp/dbquery_%s/not_%i", query_id, key_id);
2396  query->awar_not[key_id] = strdup(buffer);
2397  aw_root->awar_int(query->awar_not[key_id], 0, AW_ROOT_DEFAULT);
2398 
2399  sprintf(buffer, "tmp/dbquery_%s/operator_%i", query_id, key_id);
2400  query->awar_operator[key_id] = strdup(buffer);
2401  aw_root->awar_string(query->awar_operator[key_id], "ign", AW_ROOT_DEFAULT);
2402  }
2403  aw_root->awar(query->awar_keys[0])->add_callback(makeRootCallback(first_searchkey_changed_cb, query));
2404  }
2405 
2406  sprintf(buffer, "tmp/dbquery_%s/ere", query_id);
2407  query->awar_ere = strdup(buffer);
2408  aw_root->awar_int(query->awar_ere, QUERY_GENERATE);
2409 
2410  sprintf(buffer, "tmp/dbquery_%s/where", query_id);
2411  query->awar_where = strdup(buffer);
2412  aw_root->awar_int(query->awar_where, QUERY_ALL_ITEMS);
2413 
2414  sprintf(buffer, "tmp/dbquery_%s/count", query_id);
2415  query->awar_count = strdup(buffer);
2416  aw_root->awar_int(query->awar_count, 0);
2417 
2418  sprintf(buffer, "tmp/dbquery_%s/sort", query_id);
2419  query->awar_sort = strdup(buffer);
2420  aw_root->awar_int(query->awar_sort, QUERY_SORT_NONE)->add_callback(makeRootCallback(result_sort_order_changed_cb, query));
2421  query->sort_mask = QUERY_SORT_NONE; // default to unsorted
2422 
2423  sprintf(buffer, "tmp/dbquery_%s/by", query_id);
2424  query->awar_by = strdup(buffer);
2425  aw_root->awar_int(query->awar_by, QUERY_MATCH);
2426 
2427  if (awtqs->ere_pos_fig) {
2428  aws->at(awtqs->ere_pos_fig);
2429  aws->create_toggle_field(query->awar_ere);
2430 
2431  aws->insert_toggle(GBS_global_string("Search %s", query->selector.items_name), "G", (int)QUERY_GENERATE);
2432  aws->insert_toggle(GBS_global_string("Add %s", query->selector.items_name), "E", (int)QUERY_ENLARGE);
2433  aws->insert_toggle(GBS_global_string("Keep %s", query->selector.items_name), "R", (int)QUERY_REDUCE);
2434 
2435  aws->update_toggle_field();
2436  }
2437  if (awtqs->where_pos_fig) {
2438  aws->at(awtqs->where_pos_fig);
2439  aws->create_toggle_field(query->awar_where);
2440  aws->insert_toggle("of current organism", "C", (int)QUERY_CURRENT_ITEM);
2441  aws->insert_toggle("of marked organisms", "M", (int)QUERY_MARKED_ITEMS);
2442  aws->insert_toggle("of all organisms", "A", (int)QUERY_ALL_ITEMS);
2443  aws->update_toggle_field();
2444 
2445  }
2446  if (awtqs->by_pos_fig) {
2447  aws->at(awtqs->by_pos_fig);
2448  aws->create_toggle_field(query->awar_by);
2449  aws->insert_toggle("that match the query", "M", (int)QUERY_MATCH);
2450  aws->insert_toggle("that don't match the q.", "D", (int)QUERY_DONT_MATCH);
2451  aws->insert_toggle("that are marked", "A", (int)QUERY_MARKED);
2452  aws->update_toggle_field();
2453  }
2454 
2455  // distances for multiple queries :
2456 
2457 #define KEY_Y_OFFSET 32
2458 
2459  int xpos_calc[3] = { -1, -1, -1 }; // X-positions for elements in search expressions
2460 
2461  if (awtqs->qbox_pos_fig) {
2462  aws->auto_space(1, 1);
2463  aws->at(awtqs->qbox_pos_fig);
2464 
2465  SmartPtr<AW_at_storage> at_size(AW_at_storage::make(aws, AW_AT_SIZE_AND_ATTACH));
2466 
2467  int xpos, ypos;
2468  aws->get_at_position(&xpos, &ypos);
2469 
2470  int ypos_dummy;
2471 
2472  for (int key = QUERY_EXPRESSIONS-1; key >= 0; --key) {
2473  if (key) {
2474  aws->at(xpos, ypos+key*KEY_Y_OFFSET);
2475  aws->create_option_menu(query->awar_operator[key]);
2476  aws->insert_option("and", "", "and");
2477  aws->insert_option("or", "", "or");
2478  aws->insert_option("ign", "", "ign");
2479  aws->update_option_menu();
2480 
2481  if (xpos_calc[0] == -1) aws->get_at_position(&xpos_calc[0], &ypos_dummy);
2482  }
2483 
2484  aws->at(xpos_calc[0], ypos+key*KEY_Y_OFFSET);
2485  aws->restore_at_from(*at_size);
2486 
2487  create_itemfield_selection_button(aws, FieldSelDef(query->awar_keys[key], gb_main, awtqs->get_queried_itemtype(), FIELD_FILTER_STRING_READABLE, "source field", SF_PSEUDO), NULp);
2488 
2489  if (xpos_calc[1] == -1) aws->get_at_position(&xpos_calc[1], &ypos_dummy);
2490 
2491  aws->at(xpos_calc[1], ypos+key*KEY_Y_OFFSET);
2492  aws->create_toggle(query->awar_not[key], "#equal.xpm", "#notEqual.xpm");
2493 
2494  if (xpos_calc[2] == -1) aws->get_at_position(&xpos_calc[2], &ypos_dummy);
2495  }
2496  }
2497  if (awtqs->key_pos_fig) {
2498  aws->at(awtqs->key_pos_fig);
2499  aws->create_input_field(query->awar_keys[0], 12);
2500  }
2501 
2502  if (awtqs->query_pos_fig) {
2503  aws->at(awtqs->query_pos_fig);
2504 
2505  SmartPtr<AW_at_storage> at_size(AW_at_storage::make(aws, AW_AT_SIZE_AND_ATTACH));
2506 
2507  int xpos, ypos;
2508  aws->get_at_position(&xpos, &ypos);
2509 
2510  for (int key = 0; key<QUERY_EXPRESSIONS; ++key) {
2511  aws->at(xpos_calc[2], ypos+key*KEY_Y_OFFSET);
2512  aws->restore_at_from(*at_size);
2513  aws->d_callback(makeWindowCallback(perform_query_cb, query, EXT_QUERY_NONE)); // enable ENTER in searchfield to start search
2514  aws->create_input_field(query->awar_queries[key], 12);
2515  }
2516  }
2517 
2518  if (awtqs->result_pos_fig) {
2519  aws->at(awtqs->result_pos_fig);
2520  aws->d_callback(makeWindowCallback(toggle_flag_cb, query));
2521 
2522  {
2523  const char *this_awar_name = ARB_keep_string(GBS_global_string_copy("tmp/dbquery_%s/select", query_id)); // do not free this cause it's passed to new_selection_made_cb
2524  AW_awar *awar = aw_root->awar_string(this_awar_name, "", AW_ROOT_DEFAULT);
2525 
2526  query->hitlist = aws->create_selection_list(this_awar_name, 5, 5);
2527  awar->add_callback(makeRootCallback(new_selection_made_cb, this_awar_name, query));
2528  }
2529  query->hitlist->insert_default("end of list", "");
2530  query->hitlist->update();
2531  }
2532 
2533  if (awtqs->count_pos_fig) {
2534  aws->button_length(13);
2535  aws->at(awtqs->count_pos_fig);
2536  aws->label("Hits:");
2537  aws->create_button(NULp, query->awar_count, NULp, "+");
2538 
2539  if (awtqs->popup_info_window) {
2540  aws->callback(RootAsWindowCallback::simple(awtqs->popup_info_window, query->gb_main));
2541  aws->create_button("popinfo", "Info");
2542  }
2543  }
2544  else {
2545  dbq_assert(!awtqs->popup_info_window); // dont know where to display
2546  }
2547 
2548  if (awtqs->config_pos_fig) {
2549  aws->button_length(0);
2550  aws->at(awtqs->config_pos_fig);
2551  char *macro_id = GBS_global_string_copy("SAVELOAD_CONFIG_%s", query_id);
2552  AWT_insert_config_manager(aws, AW_ROOT_DEFAULT, "query_box", makeConfigSetupCallback(query_box_setup_config, query), macro_id);
2553  free(macro_id);
2554  }
2555 
2556  aws->button_length(18);
2557 
2558  if (awtqs->do_query_pos_fig) {
2559  aws->at(awtqs->do_query_pos_fig);
2560  aws->callback(makeWindowCallback(perform_query_cb, query, EXT_QUERY_NONE));
2561  char *macro_id = GBS_global_string_copy("SEARCH_%s", query_id);
2562  aws->create_button(macro_id, "Search", "S", "+");
2563  free(macro_id);
2564  }
2565  if (awtqs->do_refresh_pos_fig) {
2566  aws->at(awtqs->do_refresh_pos_fig);
2567  aws->create_option_menu(query->awar_sort);
2568  aws->insert_default_option("unsorted", "u", QUERY_SORT_NONE);
2569  aws->insert_option ("by value", "v", QUERY_SORT_BY_1STFIELD_CONTENT);
2570  aws->insert_option ("by number", "n", QUERY_SORT_NUM_BY_1STFIELD_CONTENT);
2571  aws->insert_option ("by id", "i", QUERY_SORT_BY_ID);
2572  if (query->selector.parent_selector) {
2573  aws->insert_option ("by parent", "p", QUERY_SORT_BY_NESTED_PID);
2574  }
2575  aws->insert_option ("by marked", "m", QUERY_SORT_BY_MARKED);
2576  aws->insert_option ("by hit", "h", QUERY_SORT_BY_HIT_DESCRIPTION);
2577  aws->insert_option ("reverse", "r", QUERY_SORT_REVERSE);
2578  aws->update_option_menu();
2579  }
2580  else {
2581  dbq_assert(0); // hmm - no sort button here. -> tell ralf where this happens
2582  }
2583 
2584  if (awtqs->do_mark_pos_fig) {
2585  aws->at(awtqs->do_mark_pos_fig);
2586  aws->help_text("mark_list.hlp");
2587  aws->callback(makeWindowCallback(mark_queried_cb, query, 1));
2588  aws->create_button("MARK_LISTED_UNMARK_REST", "Mark Listed\nUnmark Rest", "M");
2589  }
2590  if (awtqs->do_unmark_pos_fig) {
2591  aws->at(awtqs->do_unmark_pos_fig);
2592  aws->help_text("unmark_list.hlp");
2593  aws->callback(makeWindowCallback(mark_queried_cb, query, 0));
2594  aws->create_button("UNMARK_LISTED_MARK_REST", "Unmark Listed\nMark Rest", "U");
2595  }
2596 
2597  if (awtqs->do_mark_nt_pos_fig) {
2598  aws->at(awtqs->do_mark_nt_pos_fig);
2599  aws->help_text("mark_list.hlp");
2600  aws->callback(makeWindowCallback(mark_queried_cb, query, 9));
2601  aws->create_button("MARK_LISTED_KEEP_REST", "Mark Listed", "M");
2602  }
2603  if (awtqs->do_unmark_nt_pos_fig) {
2604  aws->at(awtqs->do_unmark_nt_pos_fig);
2605  aws->help_text("unmark_list.hlp");
2606  aws->callback(makeWindowCallback(mark_queried_cb, query, 8));
2607  aws->create_button("UNMARK_LISTED_KEEP_REST", "Unmark Listed", "U");
2608  }
2609 
2610  if (awtqs->do_delete_pos_fig) {
2611  aws->at(awtqs->do_delete_pos_fig);
2612  aws->help_text("del_list.hlp");
2613  aws->callback(makeWindowCallback(delete_queried_species_cb, query));
2614  char *macro_id = GBS_global_string_copy("DELETE_LISTED_%s", query_id);
2615  aws->create_button(macro_id, "Delete Listed", "D");
2616  free(macro_id);
2617  }
2618  if (awtqs->do_set_pos_fig) {
2619  query->awar_writekey = GBS_global_string_copy("tmp/dbquery_%s/write_key", query_id); aw_root->awar_string(query->awar_writekey);
2620  query->awar_writelossy = GBS_global_string_copy("tmp/dbquery_%s/write_lossy", query_id); aw_root->awar_int (query->awar_writelossy);
2621  query->awar_protectkey = GBS_global_string_copy("tmp/dbquery_%s/protect_key", query_id); aw_root->awar_string(query->awar_protectkey);
2622  query->awar_setprotection = GBS_global_string_copy("tmp/dbquery_%s/set_protection", query_id); aw_root->awar_int (query->awar_setprotection, 4);
2623  query->awar_setvalue = GBS_global_string_copy("tmp/dbquery_%s/set_value", query_id); aw_root->awar_string(query->awar_setvalue);
2624 
2625  aws->at(awtqs->do_set_pos_fig);
2626  aws->help_text("mod_field_list.hlp");
2627  aws->callback(makeCreateWindowCallback(create_writeFieldOfListed_window, query));
2628  char *macro_id = GBS_global_string_copy("WRITE_TO_FIELDS_OF_LISTED_%s", query_id);
2629  aws->create_button(macro_id, "Write to Fields\nof Listed", "S");
2630  free(macro_id);
2631  }
2632 
2633  char *Items = strdup(query->selector.items_name);
2634  Items[0] = toupper(Items[0]);
2635 
2636  if ((awtqs->use_menu || awtqs->open_parser_pos_fig)) {
2637  sprintf(buffer, "tmp/dbquery_%s/tag", query_id); query->awar_tag = strdup(buffer); aw_root->awar_string(query->awar_tag);
2638  sprintf(buffer, "tmp/dbquery_%s/use_tag", query_id); query->awar_use_tag = strdup(buffer); aw_root->awar_int (query->awar_use_tag);
2639  sprintf(buffer, "tmp/dbquery_%s/deftag", query_id); query->awar_deftag = strdup(buffer); aw_root->awar_string(query->awar_deftag);
2640  sprintf(buffer, "tmp/dbquery_%s/double_pars", query_id); query->awar_double_pars = strdup(buffer); aw_root->awar_int (query->awar_double_pars);
2641  sprintf(buffer, "tmp/dbquery_%s/parskey", query_id); query->awar_parskey = strdup(buffer); aw_root->awar_string(query->awar_parskey);
2642  sprintf(buffer, "tmp/dbquery_%s/parsvalue", query_id); query->awar_parsvalue = strdup(buffer); aw_root->awar_string(query->awar_parsvalue);
2643  sprintf(buffer, "tmp/dbquery_%s/awar_parspredefined", query_id); query->awar_parspredefined = strdup(buffer); aw_root->awar_string(query->awar_parspredefined);
2644  sprintf(buffer, "tmp/dbquery_%s/acceptConvError", query_id); query->awar_acceptConvError = strdup(buffer); aw_root->awar_int (query->awar_acceptConvError);
2645  sprintf(buffer, "tmp/dbquery_%s/acceptNameMod", query_id); query->awar_acceptIdMod = strdup(buffer); aw_root->awar_int (query->awar_acceptIdMod);
2646 
2647  if (awtqs->use_menu) {
2648  sprintf(buffer, "Modify Fields of Listed %s", Items); query_rel_menu_entry(aws, "mod_fields_of_listed", query_id, buffer, "F", "mod_field_list.hlp", AWM_ALL, makeCreateWindowCallback(create_modify_fields_window, query));
2649  }
2650  else {
2651  aws->at(awtqs->open_parser_pos_fig);
2652  aws->callback(makeCreateWindowCallback(create_modify_fields_window, query));
2653  aws->create_button("MODIFY_FIELDS_OF_LISTED", "MODIFY FIELDS\nOF LISTED", "F");
2654  }
2655  }
2656  if (awtqs->use_menu) {
2657  sprintf(buffer, "Set Protection of Fields of Listed %s", Items); query_rel_menu_entry(aws, "s_prot_of_listed", query_id, buffer, "P", "set_protection.hlp", AWM_ALL, makeCreateWindowCallback(create_set_protection_window, query));
2658  aws->sep______________();
2659  sprintf(buffer, "Mark Listed %s, don't Change Rest", Items); query_rel_menu_entry(aws, "mark_listed", query_id, buffer, "M", "mark.hlp", AWM_ALL, makeWindowCallback(mark_queried_cb, query, 1|8));
2660  sprintf(buffer, "Mark Listed %s, Unmark Rest", Items); query_rel_menu_entry(aws, "mark_listed_unmark_rest", query_id, buffer, "L", "mark.hlp", AWM_ALL, makeWindowCallback(mark_queried_cb, query, 1 ));
2661  sprintf(buffer, "Unmark Listed %s, don't Change Rest", Items); query_rel_menu_entry(aws, "unmark_listed", query_id, buffer, "U", "mark.hlp", AWM_ALL, makeWindowCallback(mark_queried_cb, query, 0|8));
2662  sprintf(buffer, "Unmark Listed %s, Mark Rest", Items); query_rel_menu_entry(aws, "unmark_listed_mark_rest", query_id, buffer, "R", "mark.hlp", AWM_ALL, makeWindowCallback(mark_queried_cb, query, 0 ));
2663  aws->sep______________();
2664 
2665 
2666  sprintf(buffer, "Set Color of Listed %s", Items); query_rel_menu_entry(aws, "set_color_of_listed", query_id, buffer, "C", "set_color_of_listed.hlp", AWM_ALL, makeCreateWindowCallback(create_colorize_queried_window, query));
2667 
2668  if (query->gb_ref) {
2669  dbq_assert(speciesOrOrganism(query->selector.type)); // stuff below works only for species/organisms
2670  aws->sep______________();
2671  if (query->expect_hit_in_ref_list) {
2672  aws->insert_menu_topic("search_equal_fields_and_listed_in_I", "Search entries existing in both DBs and listed in the source DB hitlist", "S",
2673  "search_equal_fields.hlp", AWM_ALL, makeWindowCallback(perform_query_cb, query, EXT_QUERY_COMPARE_LINES));
2674  aws->insert_menu_topic("search_equal_words_and_listed_in_I", "Search words existing in entries of both DBs and listed in the source DB hitlist", "w",
2675  "search_equal_fields.hlp", AWM_ALL, makeWindowCallback(perform_query_cb, query, EXT_QUERY_COMPARE_WORDS));
2676  }
2677  else {
2678  aws->insert_menu_topic("search_equal_field_in_both_db", "Search entries existing in both DBs", "S",
2679  "search_equal_fields.hlp", AWM_ALL, makeWindowCallback(perform_query_cb, query, EXT_QUERY_COMPARE_LINES));
2680  aws->insert_menu_topic("search_equal_word_in_both_db", "Search words existing in entries of both DBs", "w",
2681  "search_equal_fields.hlp", AWM_ALL, makeWindowCallback(perform_query_cb, query, EXT_QUERY_COMPARE_WORDS));
2682  }
2683  }
2684  }
2685 
2686  free(Items);
2687 
2688  GB_pop_transaction(gb_main);
2689  return query;
2690 }
2691 
2692 // --------------------------------------------------------------------------------
2693 
2694 #ifdef UNIT_TESTS
2695 #ifndef TEST_UNIT_H
2696 #include <test_unit.h>
2697 #endif
2698 
2699 void TEST_nullcmp() {
2700  const char *whatever = "bla";
2701  TEST_EXPECT_EQUAL(ARB_strNULLcmp(NULp, NULp), 0);
2702  TEST_EXPECT_EQUAL(ARB_strNULLcmp(whatever, whatever), 0);
2703  TEST_EXPECT_EQUAL(ARB_strNULLcmp("a", "b"), -1);
2704 
2705  // document uncommon behavior: NULp is bigger than any other text!
2706  TEST_EXPECT_EQUAL(ARB_strNULLcmp(whatever, NULp), -1);
2707  TEST_EXPECT_EQUAL(ARB_strNULLcmp(NULp, whatever), 1);
2708 }
2709 
2710 #endif // UNIT_TESTS
2711 
2712 // --------------------------------------------------------------------------------
2713 
GB_begin_transaction
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Definition: arbdb.cxx:2528
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makeHelpCallback
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Definition: aw_window.hxx:106
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Definition: AW_select.cxx:190
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Definition: arbdb.cxx:1643
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Definition: db_query.cxx:1961
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FINAL_TYPE::~ItemQueryKey
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const char * do_unmark_pos_fig
Definition: db_query.h:64
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Definition: arb_msg.cxx:194
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const char * do_refresh_pos_fig
Definition: db_query.h:71
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QUERY_ITEM_TYPE type
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Definition: item_sel_list.h:49
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const char * label
Definition: item_sel_list.cxx:118
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Definition: adhash.cxx:253
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Definition: AW_button.cxx:448
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Definition: aditem.cxx:105
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Definition: AW_awar.cxx:154
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