Context Navigation

source: branches/profile/ARBDB/adname.cxx

Visit:

Last change on this file was 12438, checked in by westram, 10 years ago
activate errors on missing test-source location publish all missing tests missing location apparently only occurs in dynamic libraries and for last test of a module Note: the reverse is not true!
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 12.6 KB

Line
1	// =============================================================== //
2	// //
3	// File : adname.cxx //
4	// Purpose : species names //
5	// //
6	// Institute of Microbiology (Technical University Munich) //
7	// http://www.arb-home.de/ //
8	// //
9	// =============================================================== //
10
11	#include "gb_local.h"
12
13	#include <ad_config.h>
14	#include <arbdbt.h>
15
16	#include <arb_progress.h>
17	#include <arb_strbuf.h>
18	#include <arb_strarray.h>
19	#include <arb_file.h>
20	#include <arb_diff.h>
21
22	#include <cctype>
23
24	struct gbt_renamed {
25	int used_by;
26	char data[1];
27	};
28
29	static struct {
30	GB_HASH *renamed_hash;
31	GB_HASH *old_species_hash;
32	GBDATA *gb_main;
33	GBDATA *gb_species_data;
34	int all_flag;
35	} NameSession;
36
37	#if defined(WARN_TODO)
38	#warning change all_flag into estimated number of renames ( == 0 shall mean all)
39	#endif
40
41	GB_ERROR GBT_begin_rename_session(GBDATA *gb_main, int all_flag) {
42	/* Starts a rename session (to rename one or many species)
43	* all_flag == 1 -> rename all species in DB
44	* Call GBT_abort_rename_session() or GBT_commit_rename_session() to close the session.
45	*/
46
47	GB_ERROR error = GB_push_transaction(gb_main);
48	if (!error) {
49	NameSession.gb_main = gb_main;
50	NameSession.gb_species_data = GBT_get_species_data(gb_main);
51
52	if (!all_flag) { // this is meant to be used for single or few species
53	int hash_size = 128;
54
55	NameSession.renamed_hash = GBS_create_dynaval_hash(hash_size, GB_MIND_CASE, GBS_dynaval_free);
56	NameSession.old_species_hash = 0;
57	}
58	else {
59	NameSession.renamed_hash = GBS_create_dynaval_hash(GBT_get_species_count(gb_main), GB_MIND_CASE, GBS_dynaval_free);
60	NameSession.old_species_hash = GBT_create_species_hash(gb_main);
61	}
62	NameSession.all_flag = all_flag;
63	}
64	return error;
65	}
66
67	GB_ERROR GBT_rename_species(const char oldname, const char newname, bool ignore_protection)
68	{
69	GBDATA *gb_species;
70	GBDATA *gb_name;
71	GB_ERROR error;
72
73	if (strcmp(oldname, newname) == 0)
74	return 0;
75
76	#if defined(DEBUG) && 1
77	if (isdigit(oldname[0])) {
78	printf("oldname='%s' newname='%s'\n", oldname, newname);
79	}
80	#endif
81
82	if (NameSession.all_flag) {
83	gb_assert(NameSession.old_species_hash);
84	gb_species = (GBDATA *)GBS_read_hash(NameSession.old_species_hash, oldname);
85	}
86	else {
87	GBDATA *gb_found_species;
88
89	gb_assert(NameSession.old_species_hash == 0);
90	gb_found_species = GBT_find_species_rel_species_data(NameSession.gb_species_data, newname);
91	gb_species = GBT_find_species_rel_species_data(NameSession.gb_species_data, oldname);
92
93	if (gb_found_species && gb_species != gb_found_species) {
94	return GB_export_errorf("A species named '%s' already exists.", newname);
95	}
96	}
97
98	if (!gb_species) {
99	return GB_export_errorf("Expected that a species named '%s' exists (maybe there are duplicate species, database might be corrupt)", oldname);
100	}
101
102	gb_name = GB_entry(gb_species, "name");
103	if (ignore_protection) GB_push_my_security(NameSession.gb_main);
104	error = GB_write_string(gb_name, newname);
105	if (ignore_protection) GB_pop_my_security(NameSession.gb_main);
106
107	if (!error) {
108	if (NameSession.old_species_hash) {
109	GBS_write_hash(NameSession.old_species_hash, oldname, 0);
110	}
111	gbt_renamed rns = (gbt_renamed )GB_calloc(strlen(newname) + sizeof (gbt_renamed), sizeof(char));
112	strcpy(&rns->data[0], newname);
113	GBS_write_hash(NameSession.renamed_hash, oldname, (long)rns);
114	}
115	return error;
116	}
117
118	static void gbt_free_rename_session_data() {
119	if (NameSession.renamed_hash) {
120	GBS_free_hash(NameSession.renamed_hash);
121	NameSession.renamed_hash = 0;
122	}
123	if (NameSession.old_species_hash) {
124	GBS_free_hash(NameSession.old_species_hash);
125	NameSession.old_species_hash = 0;
126	}
127	}
128
129	GB_ERROR GBT_abort_rename_session() {
130	gbt_free_rename_session_data();
131	return GB_abort_transaction(NameSession.gb_main);
132	}
133
134	static const char *currentTreeName = 0;
135
136	static GB_ERROR gbt_rename_tree_rek(GBT_TREE *tree, int tree_index) {
137	if (tree) {
138	if (tree->is_leaf) {
139	if (tree->name) {
140	gbt_renamed rns = (gbt_renamed )GBS_read_hash(NameSession.renamed_hash, tree->name);
141	if (rns) {
142	char *newname;
143	if (rns->used_by == tree_index) { // species more than once in the tree
144	static int counter = 0;
145	char buffer[256];
146
147	sprintf(buffer, "%s_%i", rns->data, counter++);
148	GB_warningf("Species '%s' more than once in '%s', creating zombie '%s'",
149	tree->name, currentTreeName, buffer);
150	newname = buffer;
151	}
152	else {
153	newname = &rns->data[0];
154	}
155	freedup(tree->name, newname);
156	rns->used_by = tree_index;
157	}
158	}
159	}
160	else {
161	gbt_rename_tree_rek(tree->leftson, tree_index);
162	gbt_rename_tree_rek(tree->rightson, tree_index);
163	}
164	}
165	return NULL;
166	}
167
168	GB_ERROR GBT_commit_rename_session() { // goes to header: __ATTR__USERESULT
169	arb_progress commit_progress("Renaming name references", 3);
170	commit_progress.allow_title_reuse();
171
172	GB_ERROR error = 0;
173
174	// rename species in trees
175	{
176	ConstStrArray tree_names;
177	GBT_get_tree_names(tree_names, NameSession.gb_main, false);
178
179	if (!tree_names.empty()) {
180	int tree_count = tree_names.size();
181	arb_progress progress(GBS_global_string("Renaming species in %i tree%c", tree_count, "s"[tree_count<2]),
182	tree_count*3);
183
184	for (int count = 0; count<tree_count && !error; ++count) {
185	const char *tname = tree_names[count];
186	GBT_TREE *tree = GBT_read_tree(NameSession.gb_main, tname, GBT_TREE_NodeFactory());
187	++progress;
188
189	if (tree) {
190	currentTreeName = tname; // provide tree name (used for error message)
191	gbt_rename_tree_rek(tree, count+1);
192	currentTreeName = 0;
193
194	++progress;
195
196	GBT_write_tree(NameSession.gb_main, tname, tree);
197	delete tree;
198
199	progress.inc_and_check_user_abort(error);
200	}
201	else {
202	GBT_message(NameSession.gb_main, GBS_global_string("Warning: failed to read '%s' (Reason: %s)", tname, GB_await_error()));
203	++progress;
204	++progress;
205	}
206	}
207	}
208	commit_progress.inc_and_check_user_abort(error);
209	}
210	// rename configurations
211	if (!error) {
212	ConstStrArray config_names;
213	GBT_get_configuration_names(config_names, NameSession.gb_main);
214
215	if (!config_names.empty()) {
216	int config_count = config_names.size();
217	arb_progress progress(GBS_global_string("Renaming species in %i config%c", config_count, "s"[config_count<2]), config_count);
218
219	for (int count = 0; !error && count<config_count; ++count) {
220	GBT_config *config = GBT_load_configuration_data(NameSession.gb_main, config_names[count], &error);
221	if (!error) {
222	int need_save = 0;
223	int mode;
224
225	for (mode = 0; !error && mode<2; ++mode) {
226	char **configStrPtr = (mode == 0 ? &config->top_area : &config->middle_area);
227	GBT_config_parser parser = GBT_start_config_parser(configStrPtr);
228	GBT_config_item *item = GBT_create_config_item();
229	GBS_strstruct *strstruct = GBS_stropen(1000);
230
231	error = GBT_parse_next_config_item(parser, item);
232	while (!error && item->type != CI_END_OF_CONFIG) {
233	if (item->type == CI_SPECIES) {
234	gbt_renamed rns = (gbt_renamed )GBS_read_hash(NameSession.renamed_hash, item->name);
235	if (rns) { // species was renamed
236	freedup(item->name, rns->data);
237	need_save = 1;
238	}
239	}
240	GBT_append_to_config_string(item, strstruct);
241	error = GBT_parse_next_config_item(parser, item);
242	}
243
244	if (!error) freeset(*configStrPtr, GBS_strclose(strstruct));
245	else {
246	error = GBS_global_string("Failed to parse configuration '%s' (Reason: %s)", config_names[count], error);
247	}
248
249	GBT_free_config_item(item);
250	GBT_free_config_parser(parser);
251	}
252
253	if (!error && need_save) {
254	error = GBT_save_configuration_data(config, NameSession.gb_main, config_names[count]);
255	}
256	GBT_free_configuration_data(config);
257	}
258	progress.inc_and_check_user_abort(error);
259	}
260	}
261	}
262	commit_progress.inc_and_check_user_abort(error);
263
264	// rename links in pseudo-species
265	if (!error && GEN_is_genome_db(NameSession.gb_main, -1)) {
266	GBDATA *gb_pseudo;
267	for (gb_pseudo = GEN_first_pseudo_species(NameSession.gb_main);
268	gb_pseudo && !error;
269	gb_pseudo = GEN_next_pseudo_species(gb_pseudo))
270	{
271	GBDATA *gb_origin_organism = GB_entry(gb_pseudo, "ARB_origin_species");
272	if (gb_origin_organism) {
273	const char *origin = GB_read_char_pntr(gb_origin_organism);
274	gbt_renamed rns = (gbt_renamed )GBS_read_hash(NameSession.renamed_hash, origin);
275	if (rns) { // species was renamed
276	const char *newname = &rns->data[0];
277	error = GB_write_string(gb_origin_organism, newname);
278	}
279	}
280	}
281	}
282	commit_progress.inc_and_check_user_abort(error);
283
284	gbt_free_rename_session_data();
285
286	error = GB_end_transaction(NameSession.gb_main, error);
287	return error;
288	}
289
290	// --------------------------------------------------------------------------------
291
292	#ifdef UNIT_TESTS
293	#ifndef TEST_UNIT_H
294	#include <test_unit.h>
295	#endif
296
297	// #define TEST_AUTO_UPDATE // uncomment to auto-update test result db
298
299	void TEST_SLOW_rename_session() {
300	const char *inputname = "TEST_opti_ascii_in.arb";
301	const char *outputname = "TEST_opti_ascii_renamed.arb";
302	const char *expectedname = "TEST_opti_ascii_renamed_expected.arb";
303
304	{
305	GB_shell shell;
306	GBDATA *gb_main;
307	TEST_EXPECT_RESULT__NOERROREXPORTED(gb_main = GB_open(inputname, "rw"));
308
309	for (int session = 1; session <= 2; ++session) {
310	TEST_ANNOTATE(GBS_global_string("session=%i", session));
311
312	TEST_EXPECT_NO_ERROR(GBT_begin_rename_session(gb_main, 0));
313	if (session == 2) { // session 1 tests renaming nothing
314	// only in config 'some':
315	TEST_EXPECT_NO_ERROR(GBT_rename_species("FrnPhilo", "olihPnrF", true));
316	TEST_EXPECT_NO_ERROR(GBT_rename_species("DsfDesul", "luseDfsD", true));
317	// also in config 'other':
318	TEST_EXPECT_NO_ERROR(GBT_rename_species("CalSacch", "hccaSlaC", true));
319	TEST_EXPECT_NO_ERROR(GBT_rename_species("LacReute", "etueRcaL", true));
320	}
321	TEST_EXPECT_NO_ERROR(GBT_commit_rename_session());
322	}
323
324	TEST_EXPECT_NO_ERROR(GB_save_as(gb_main, outputname, "a"));
325	GB_close(gb_main);
326	}
327
328	#if defined(TEST_AUTO_UPDATE)
329	TEST_COPY_FILE(outputname, expectedname);
330	#endif
331	TEST_EXPECT_TEXTFILE_DIFFLINES(outputname, expectedname, 0);
332	TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(outputname));
333	}
334	TEST_PUBLISH(TEST_SLOW_rename_session);
335
336	#endif // UNIT_TESTS
337
338	// --------------------------------------------------------------------------------

Note: See TracBrowser for help on using the repository browser.

Download in other formats: