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source: branches/stable/MERGE/MG_checkfield.cxx

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Last change on this file was 18159, checked in by westram, 5 years ago
full update from child 'fix' into 'trunk' fix item name accessors (`GBT_get_name` + `GBT_get_name_or_description`) add `null2empty` adds: log:branches/fix@18140:18158
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 13.1 KB

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1	// =============================================================== //
2	// //
3	// File : MG_checkfield.cxx //
4	// Purpose : //
5	// //
6	// Institute of Microbiology (Technical University Munich) //
7	// http://www.arb-home.de/ //
8	// //
9	// =============================================================== //
10
11	#include "merge.hxx"
12
13	#include <item_sel_list.h>
14
15	#include <aw_awar.hxx>
16	#include <aw_root.hxx>
17	#include <aw_msg.hxx>
18	#include <arb_progress.h>
19
20	#include <arbdbt.h>
21	#include <arb_strbuf.h>
22	#include <arb_global_defs.h>
23
24	#include <cctype>
25
26	#define AWAR_CHECK AWAR_MERGE_TMP "chk/"
27
28	#define AWAR_COMPARE_FIELD AWAR_CHECK "compare"
29	#define AWAR_REPORT_FIELD AWAR_CHECK "report"
30	#define AWAR_TOUPPER AWAR_CHECK "ToUpper"
31	#define AWAR_EXCLUDE AWAR_CHECK "exclude"
32	#define AWAR_CORRECT AWAR_CHECK "correct"
33	#define AWAR_ETAG AWAR_CHECK "tag"
34
35
36	static int gbs_cmp_strings(char str1, char str2, int *tab) { // returns 0 if strings are equal
37	char s1, s2;
38	int c1, c2;
39	s1 = str1;
40	s2 = str2;
41	int count = 10;
42	do {
43	do { c1 = *(s1++); } while (tab[c1] < 0);
44	do { c2 = *(s2++); } while (tab[c2] < 0);
45	if (tab[c1] != tab[c2]) { // difference found
46	return 1;
47	}
48	count --;
49	} while (count && c1 && c2);
50	return 0;
51	}
52
53
54	static char MG_diff_strings(char str1, char * &str2, char *exclude, bool ToUpper, bool correct,
55	char res1, char res2, bool& corrrected) {
56
57	char buffer1[256];
58	char buffer2[256];
59	char *dest1 = buffer1;
60	char *dest2 = buffer2;
61	char s1, s2;
62	int c1, c2;
63	int count = 3;
64	int tab[256];
65	int i;
66
67	s1 = str1;
68	s2 = str2;
69	*dest1 = 0;
70	*dest2 = 0;
71	tab[0] = 0;
72	char gapchar = '#';
73	if (strlen(exclude)) gapchar = exclude[0];
74	else exclude = NULp;
75
76	for (i=1; i<256; i++) { // LOOP_VECTORIZED[!<6.0,!>=8.0]
77	tab[i] = i;
78	if (exclude && strchr(exclude, i)) {
79	tab[i] = -1;
80	continue;
81	}
82	if (ToUpper && i >= 'a' && i <= 'z') {
83	tab[i] = i-'a'+'A';
84	}
85	}
86
87	do {
88	do { c1 = *(s1++); } while (tab[c1] < 0);
89	do { c2 = *(s2++); } while (tab[c2] < 0);
90	if (tab[c1] != tab[c2]) { // difference found
91	if (correct) {
92	// check substitution
93	{
94	int c = s2[-1];
95	s2[-1] = s1[-1];
96	if (toupper(c1) == toupper(c2) \|\| !gbs_cmp_strings(s1, s2, &tab[0])) {
97	corrrected = true;
98	continue;
99	}
100	s2[-1] = c;
101	}
102
103	// check insertion in s2
104	if (!gbs_cmp_strings(s1-1, s2, &tab[0])) {
105	s2[-1] = gapchar;
106	do { c2 = *(s2++); } while (tab[c2] < 0); // eat s2
107	corrrected = true;
108	continue;
109	}
110	// check deletion in s2
111	if (!gbs_cmp_strings(s1, s2-1, &tab[0])) {
112	int toins = c1;
113	char *toinspos = s2-1;
114	if (toinspos > str2) toinspos--;
115	if (tab[(unsigned char)toinspos[0]]> 0) { // real insertion
116	GBS_strstruct *str = GBS_stropen(strlen(str2+10));
117	int pos = s2-str2-1;
118	GBS_strncat(str, str2, pos);
119	GBS_chrcat(str, toins);
120	GBS_strcat(str, str2+pos);
121	delete str2;
122	str2 = GBS_strclose(str);
123	s2 = str2+pos+1;
124	corrrected = true;
125	continue;
126	}
127	int side=1; // 0 = left 1= right
128	if (tab[(unsigned char)s1[0]]<0) side = 0;
129	if (! side) {
130	while (toinspos > str2 &&
131	tab[(unsigned char)toinspos[-1]] < 0) toinspos--;
132	}
133	toinspos[0] = toins;
134	corrrected = true;
135	do { c1 = *(s1++); } while (tab[c1] < 0); // eat s1
136	continue;
137	}
138
139	// one correction rejected -> don't try further
140	corrrected = false;
141	correct = false;
142	}
143	if (count >= 0) {
144	sprintf(dest1, "%ti ", s1-str1-1);
145	sprintf(dest2, "%ti ", s2-str2-1);
146	dest1 += strlen(dest1);
147	dest2 += strlen(dest2);
148	}
149	count --;
150	}
151	} while (c1 && c2);
152
153	if (c1 \|\| c2) {
154	sprintf(dest1, "... %ti ", s1-str1-1);
155	sprintf(dest2, "... %ti ", s2-str2-1);
156	dest1 += strlen(dest1);
157	dest2 += strlen(dest2);
158	}
159	if (count<0) {
160	sprintf(dest1, "and %i more", 1-count);
161	sprintf(dest2, "and %i more", 1-count);
162	dest1 += strlen(dest1);
163	dest2 += strlen(dest2);
164	}
165	if (strlen(buffer1)) {
166	*res1 = ARB_strdup(buffer1);
167	*res2 = ARB_strdup(buffer2);
168	}
169	else {
170	*res1 = NULp;
171	*res2 = NULp;
172	}
173	return NULp;
174	}
175
176	long mg_count_queried(GBDATA *gb_main) {
177	long queried = 0;
178	for (GBDATA *gb_spec = GBT_first_species(gb_main);
179	gb_spec;
180	gb_spec = GBT_next_species(gb_spec))
181	{
182	if (IS_QUERIED_SPECIES(gb_spec)) queried++;
183	}
184	return queried;
185	}
186
187	static void mg_check_field_cb(AW_window *aww) {
188	AW_root *root = aww->get_root();
189	GB_ERROR error = NULp;
190	char *compareField = root->awar(AWAR_COMPARE_FIELD)->read_string();
191	char *exclude = root->awar(AWAR_EXCLUDE)->read_string();
192	bool ToUpper = root->awar(AWAR_TOUPPER)->read_int();
193	bool correct = root->awar(AWAR_CORRECT)->read_int();
194	char *tag = root->awar(AWAR_ETAG)->read_string();
195	int correctCount = 0;
196
197	if (strcmp(compareField, NO_FIELD_SELECTED) == 0) {
198	error = "Please select a field to compare";
199	}
200
201	if (!error) error = GB_begin_transaction(GLOBAL_gb_src);
202	if (!error) error = GB_begin_transaction(GLOBAL_gb_dst);
203
204	const char *reportField = NULp;
205	if (!error) {
206	reportField = prepare_and_get_selected_itemfield(root, AWAR_REPORT_FIELD, GLOBAL_gb_src, SPECIES_get_selector());
207	if (!reportField) {
208	error = GB_await_error();
209	}
210	else {
211	const char *otherdb_reportField = prepare_and_get_selected_itemfield(root, AWAR_REPORT_FIELD, GLOBAL_gb_dst, SPECIES_get_selector());
212	if (!otherdb_reportField) {
213	error = GB_await_error();
214	}
215	else {
216	mg_assert(strcmp(reportField, otherdb_reportField) == 0);
217	}
218	}
219	}
220
221	if (!error) {
222	GBDATA *gb_src_species_data = GBT_get_species_data(GLOBAL_gb_src);
223	GBDATA *gb_dst_species_data = GBT_get_species_data(GLOBAL_gb_dst);
224
225	GBDATA *gb_src_species;
226	GBDATA *gb_dst_species;
227
228	// First step: count selected species
229	arb_progress progress("Checking fields", mg_count_queried(GLOBAL_gb_src));
230
231	// Delete all 'report' fields in target database
232	for (gb_dst_species = GBT_first_species_rel_species_data(gb_dst_species_data);
233	gb_dst_species && !error;
234	gb_dst_species = GBT_next_species(gb_dst_species))
235	{
236	GBDATA *gbd = GB_search(gb_dst_species, reportField, GB_FIND);
237	if (gbd) error = GB_delete(gbd);
238	}
239
240	bool seenQueried = false;
241	for (gb_src_species = GBT_first_species_rel_species_data(gb_src_species_data);
242	gb_src_species && !error;
243	gb_src_species = GBT_next_species(gb_src_species))
244	{
245	{ // Delete all 'report' fields in source database
246	GBDATA *gbd = GB_search(gb_src_species, reportField, GB_FIND);
247	if (gbd) error = GB_delete(gbd);
248	}
249
250	if (!error) {
251	if (IS_QUERIED_SPECIES(gb_src_species)) {
252	seenQueried = true;
253	const char *src_name = GBT_get_name_or_description(gb_src_species);
254	gb_dst_species = GB_find_string(gb_dst_species_data, "name", src_name, GB_IGNORE_CASE, SEARCH_GRANDCHILD);
255	if (!gb_dst_species) {
256	aw_message(GBS_global_string("WARNING: Species %s not found in target DB", src_name));
257	}
258	else {
259	gb_dst_species = GB_get_father(gb_dst_species);
260
261	GBDATA *gb_src_field = GB_search(gb_src_species, compareField, GB_FIND);
262	GBDATA *gb_dst_field = GB_search(gb_dst_species, compareField, GB_FIND);
263
264	char *src_val = gb_src_field ? GB_read_as_tagged_string(gb_src_field, tag) : NULp;
265	char *dst_val = gb_dst_field ? GB_read_as_tagged_string(gb_dst_field, tag) : NULp;
266
267	if (src_val \|\| dst_val) {
268	char *src_positions = NULp;
269	char *dst_positions = NULp;
270
271	if (src_val && dst_val) {
272	bool corrected = false;
273	MG_diff_strings(src_val, dst_val, exclude, ToUpper, correct, &src_positions, &dst_positions, corrected);
274	if (corrected) {
275	error = GB_write_autoconv_string(gb_dst_field, dst_val);
276	if (!error) {
277	GB_write_flag(gb_dst_species, 1);
278	correctCount++;
279	}
280	}
281	}
282	else {
283	src_positions = GBS_global_string_copy("field missing in %s DB", src_val ? "other" : "this");
284	dst_positions = GBS_global_string_copy("field missing in %s DB", dst_val ? "other" : "this");
285	}
286
287	if (src_positions && !error) {
288	error = GBT_write_string(gb_dst_species, reportField, dst_positions);
289	if (!error) error = GBT_write_string(gb_src_species, reportField, src_positions);
290	}
291
292	free(dst_positions);
293	free(src_positions);
294	}
295
296	free(dst_val);
297	free(src_val);
298	}
299	progress.inc_and_check_user_abort(error);
300	}
301	}
302	}
303
304	if (!seenQueried && !error) {
305	error = "Empty hitlist in source database (nothing to do)";
306	}
307	}
308
309	error = GB_end_transaction(GLOBAL_gb_src, error);
310	error = GB_end_transaction(GLOBAL_gb_dst, error);
311
312	if (error) {
313	aw_message(error);
314	}
315	else if (correctCount) {
316	aw_message(GBS_global_string("Corrected field content of %i species\n"
317	"(species %s been marked in target database).",
318	correctCount, correctCount == 1 ? "has" : "have"));
319	}
320
321	free(tag);
322	free(exclude);
323	free(compareField);
324	}
325
326
327	AW_window create_mg_check_fields_window(AW_root aw_root) {
328	aw_root->awar_string(AWAR_COMPARE_FIELD, NO_FIELD_SELECTED);
329	aw_root->awar_string(AWAR_REPORT_FIELD, "tmp", AW_ROOT_DEFAULT);
330	aw_root->awar_string(AWAR_EXCLUDE, ".-", AW_ROOT_DEFAULT);
331	aw_root->awar_string(AWAR_ETAG, "");
332	aw_root->awar_int(AWAR_TOUPPER);
333	aw_root->awar_int(AWAR_CORRECT);
334
335	AW_window_simple *aws = new AW_window_simple;
336	aws->init(aw_root, "MERGE_COMPARE_FIELD", "COMPARE DATABASE FIELD");
337	aws->load_xfig("merge/seqcheck.fig");
338
339	aws->callback(AW_POPDOWN);
340	aws->create_button("CLOSE", "CLOSE", "C");
341
342	aws->at("help");
343	aws->callback(makeHelpCallback("checkfield.hlp"));
344	aws->create_button("HELP", "HELP", "H");
345
346
347	aws->at("exclude");
348	aws->create_input_field(AWAR_EXCLUDE);
349
350	aws->at("toupper");
351	aws->create_toggle(AWAR_TOUPPER);
352
353	aws->at("correct");
354	aws->create_toggle(AWAR_CORRECT);
355
356	aws->at("tag");
357	aws->create_input_field(AWAR_ETAG, 6);
358
359	create_itemfield_selection_button(aws, FieldSelDef(AWAR_COMPARE_FIELD, GLOBAL_gb_dst, SPECIES_get_selector(), FIELD_FILTER_STRING_READABLE), "source");
360	create_itemfield_selection_button(aws, FieldSelDef(AWAR_REPORT_FIELD, GLOBAL_gb_dst, SPECIES_get_selector(), FIELD_FILTER_STRING_WRITEABLE, "report-field", SF_ALLOW_NEW), "dest");
361
362	aws->at("go");
363	aws->highlight();
364	aws->callback(mg_check_field_cb);
365	aws->create_button("GO", "GO");
366
367	return aws;
368	}

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