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source: tags/svn.1.5.4/TOOLS/arb_test.cxx

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Last change on this file was 8268, checked in by westram, 14 years ago
removed unused(-but-set) variables/params
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 18.7 KB

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1	// =============================================================== //
2	// //
3	// File : arb_test.cxx //
4	// Purpose : unit tester for tools //
5	// //
6	// Coded by Ralf Westram (coder@reallysoft.de) in February 2011 //
7	// Institute of Microbiology (Technical University Munich) //
8	// http://www.arb-home.de/ //
9	// //
10	// =============================================================== //
11
12	#include <arbdbt.h>
13	#include <arb_defs.h>
14	#include <unistd.h>
15
16	int ARB_main(int , const char *[]) {
17	fputs("don't call us\n", stderr);
18	return EXIT_SUCCESS;
19	}
20
21	// --------------------------------------------------------------------------------
22
23	#ifdef UNIT_TESTS
24	#include <arb_file.h>
25	#include <test_unit.h>
26	#include <ut_valgrinded.h>
27
28	// --------------------------------------------------------------------------------
29
30
31	inline void make_valgrinded_call_from_pipe(char *&command) {
32	using namespace utvg;
33	static valgrind_info valgrind;
34	if (valgrind.wanted) {
35	char *pipeSym = strchr(command, '\|');
36	if (pipeSym) {
37	char *left = GB_strpartdup(command, pipeSym-1);
38	char *right = strdup(pipeSym+1);
39
40	make_valgrinded_call(left);
41	make_valgrinded_call_from_pipe(right);
42
43	freeset(command, GBS_global_string_copy("%s \| %s", left, right));
44
45	free(right);
46	free(left);
47	}
48	else {
49	make_valgrinded_call(command);
50	}
51	}
52	}
53
54	inline GB_ERROR valgrinded_system(const char *cmdline) {
55	char *cmddup = strdup(cmdline);
56	make_valgrinded_call_from_pipe(cmddup);
57
58	GB_ERROR error = GBK_system(cmddup);
59	free(cmddup);
60	return error;
61	}
62
63	#define RUN_TOOL(cmdline) valgrinded_system(cmdline)
64	#define RUN_TOOL_NEVER_VALGRIND(cmdline) GBK_system(cmdline)
65
66	#define TEST_RUN_TOOL(cmdline) TEST_ASSERT_NO_ERROR(RUN_TOOL(cmdline))
67	#define TEST_RUN_TOOL_NEVER_VALGRIND(cmdline) TEST_ASSERT_NO_ERROR(RUN_TOOL_NEVER_VALGRIND(cmdline))
68
69	void TEST_SLOW_ascii_2_bin_2_ascii() {
70	const char *ascii_ORG = "TEST_loadsave_ascii.arb";
71	const char *ascii = "bin2ascii.arb";
72	const char *binary = "ascii2bin.arb";
73	const char *binary_2ND = "ascii2bin2.arb";
74
75	// test conversion file -> file
76	TEST_RUN_TOOL(GBS_global_string("arb_2_bin %s %s", ascii_ORG, binary));
77	TEST_RUN_TOOL(GBS_global_string("arb_2_ascii %s %s", binary, ascii));
78
79	TEST_ASSERT_FILES_EQUAL(ascii, ascii_ORG);
80
81	// test conversion (bin->ascii->bin) via stream (this tests 'arb_repair')
82	TEST_RUN_TOOL(GBS_global_string("arb_2_ascii %s - \| arb_2_bin - %s", binary, binary_2ND));
83
84	// TEST_ASSERT_FILES_EQUAL(binary, binary_2ND); // can't compare binary files (they contain undefined bytes)
85
86	// instead convert back to ascii and compare result with original
87	TEST_ASSERT_ZERO_OR_SHOW_ERRNO(GB_unlink(ascii));
88	TEST_RUN_TOOL(GBS_global_string("arb_2_ascii %s %s", binary_2ND, ascii));
89	TEST_ASSERT_FILES_EQUAL(ascii, ascii_ORG);
90
91	TEST_ASSERT_ZERO_OR_SHOW_ERRNO(GB_unlink(ascii));
92	TEST_ASSERT_ZERO_OR_SHOW_ERRNO(GB_unlink(binary));
93	TEST_ASSERT_ZERO_OR_SHOW_ERRNO(GB_unlink(binary_2ND));
94	TEST_ASSERT_ZERO_OR_SHOW_ERRNO(GB_unlink("ascii2bin.ARF"));
95	TEST_ASSERT_ZERO_OR_SHOW_ERRNO(GB_unlink("ascii2bin2.ARF"));
96	}
97
98	void TEST_arb_primer() {
99	const char *primer_db = "TEST_nuc.arb";
100	const char *primer_stdin = "tools/arb_primer.in";
101	const char *primer_out = "tools/arb_primer.out";
102	const char *primer_expected = "tools/arb_primer_expected.out";
103
104	TEST_RUN_TOOL(GBS_global_string("arb_primer %s < %s", primer_db, primer_stdin));
105	TEST_ASSERT_FILES_EQUAL(primer_out, primer_expected);
106	TEST_ASSERT_ZERO_OR_SHOW_ERRNO(GB_unlink(primer_out));
107	}
108
109	static GB_ERROR removeVaryingDateFromTreeRemarks(const char *dbname) {
110	GB_ERROR error = NULL;
111	GB_shell shell;
112	GBDATA *gb_main = GB_open(dbname, "rw");
113	if (!gb_main) error = GB_await_error();
114	else {
115	{
116	GB_transaction ta(gb_main);
117	GBDATA *gb_tree_data = GB_entry(gb_main, "tree_data");
118	const char *truncate_after = "\nunittest-tree\n";
119	size_t truncate_offset = strlen(truncate_after);
120
121	if (!gb_tree_data) error = GB_await_error();
122	else {
123	for (GBDATA *gb_tree = GB_child(gb_tree_data);
124	gb_tree && !error;
125	gb_tree = GB_nextChild(gb_tree))
126	{
127	GBDATA *gb_remark = GB_entry(gb_tree, "remark");
128	if (!gb_remark) {
129	error = "could not find 'remark' entry";
130	}
131	else {
132	char *remark = GB_read_string(gb_remark);
133	char *found = strstr(remark, truncate_after);
134
135	if (found) {
136	strcpy(found+truncate_offset, "<date removed for testing>");
137	error = GB_write_string(gb_remark, remark);
138	}
139	free(remark);
140	}
141	}
142	}
143
144	ta.close(error);
145	}
146	if (!error) error = GB_save_as(gb_main, dbname, "a");
147	GB_close(gb_main);
148	}
149	return error;
150	}
151
152	void TEST_SLOW_arb_read_tree() {
153	struct {
154	const char *basename;
155	const char *extraArgs;
156	}
157	run[] = {
158	{ "newick", "" },
159	{ "newick_sq", "-commentFromFile general/text.input" },
160	{ "newick_dq", "-scale 0.5" },
161	{ "newick_group", "-scale 10 -consense 10" },
162	{ "newick_len", "" },
163	{ "newick_len_group", "" },
164	};
165
166	const char *dbin = "min_ascii.arb";
167	const char *dbout = "tools/read_tree_out.arb";
168	const char *dbexpected = "tools/read_tree_out_expected.arb";
169
170	for (size_t b = 0; b<ARRAY_ELEMS(run); ++b) {
171	const char *basename = run[b].basename;
172	const char *extraArgs = run[b].extraArgs;
173	char *treefile = GBS_global_string_copy("tools/%s.tree", basename);
174	char *treename = GBS_global_string_copy("tree_%s", basename);
175
176	TEST_RUN_TOOL(GBS_global_string("arb_read_tree -db %s %s %s %s \"test %s\" %s",
177	dbin, dbout, treename, treefile, basename, extraArgs));
178
179	dbin = dbout; // use out-db from previous loop ( = write all trees into one db)
180
181	free(treename);
182	free(treefile);
183	}
184
185	TEST_ASSERT_NO_ERROR(removeVaryingDateFromTreeRemarks(dbout));
186	TEST_ASSERT_TEXTFILES_EQUAL(dbout, dbexpected);
187	TEST_ASSERT_ZERO_OR_SHOW_ERRNO(GB_unlink(dbout));
188	}
189
190	#define TEST_ARB_REPLACE(infile,expected,args) do { \
191	char *tmpfile = GBS_global_string_copy("%s.tmp", expected); \
192	TEST_RUN_TOOL_NEVER_VALGRIND(GBS_global_string("cp %s %s", infile, tmpfile)); \
193	TEST_RUN_TOOL(GBS_global_string("arb_replace %s %s", args, tmpfile)); \
194	TEST_ASSERT_TEXTFILES_EQUAL(tmpfile, expected); \
195	TEST_ASSERT_ZERO_OR_SHOW_ERRNO(GB_unlink(tmpfile)); \
196	free(tmpfile); \
197	} while(0)
198
199	void TEST_arb_replace() {
200	const char *infile = "tools/arb_replace.in";
201	const char *file1 = "tools/arb_replace_1.out";
202	const char *file2 = "tools/arb_replace_2.out";
203
204	TEST_ARB_REPLACE(infile, "tools/arb_replace_1.out", "'gene=GONE'");
205	TEST_ARB_REPLACE(file1, infile, "-l 'GONE=gene'");
206	TEST_ARB_REPLACE(file1, file2, "-L 'GONE=gene:\"\"=( )'");
207	}
208
209	// --------------------------------------------------------------------------------
210
211	class CommandOutput : virtual Noncopyable {
212	char *stdoutput; // output from command
213	char *stderrput;
214	GB_ERROR error;
215
216	void appendError(GB_ERROR err) {
217	if (!error) error = err;
218	else error = GBS_global_string("%s\n%s", error, err);
219	}
220
221	char readAndUnlink(const char file) {
222	char *content = GB_read_file(file);
223	if (!content) appendError(GB_await_error());
224	int res = GB_unlink(file);
225	if (res == -1) appendError(GB_await_error());
226	return content;
227	}
228	public:
229	CommandOutput(const char *command, bool try_valgrind)
230	: stdoutput(NULL), stderrput(NULL), error(NULL)
231	{
232	char *escaped = GBS_string_eval(command, "'=\\\\'", NULL);
233	if (!escaped) {
234	appendError(GB_await_error());
235	}
236	else {
237	if (try_valgrind) make_valgrinded_call(escaped);
238
239	char *cmd = GBS_global_string_copy("bash -c '%s >stdout.log 2>stderr.log'", escaped);
240
241	appendError(GBK_system(cmd));
242	free(cmd);
243	free(escaped);
244
245	stdoutput = readAndUnlink("stdout.log");
246	stderrput = readAndUnlink("stderr.log");
247	}
248	if (error) {
249	printf("command '%s'\n"
250	"escaped command '%s'\n"
251	"stdout='%s'\n"
252	"stderr='%s'\n",
253	command, escaped, stdoutput, stderrput);
254	}
255	}
256	~CommandOutput() {
257	free(stderrput);
258	free(stdoutput);
259	}
260
261	GB_ERROR get_error() const { return error; }
262	const char *get_stdoutput() const { return stdoutput; }
263	const char *get_stderrput() const { return stderrput; }
264	};
265
266	// --------------------------------------------------------------------------------
267
268	#define TEST_OUTPUT_EQUALS(cmd, expected_std, expected_err) \
269	do { \
270	CommandOutput out(cmd, expected_err == NULL); \
271	TEST_ASSERT_NO_ERROR(out.get_error()); \
272	if (expected_std) { TEST_ASSERT_EQUAL(out.get_stdoutput(), expected_std); } \
273	if (expected_err) { TEST_ASSERT_EQUAL(out.get_stderrput(), expected_err); } \
274	} while(0)
275
276	#define TEST_OUTPUT_CONTAINS(cmd, expected_std, expected_err) \
277	do { \
278	CommandOutput out(cmd, expected_err == NULL); \
279	TEST_ASSERT_NO_ERROR(out.get_error()); \
280	if (expected_std) { TEST_ASSERT_CONTAINS(out.get_stdoutput(), expected_std); } \
281	if (expected_err) { TEST_ASSERT_CONTAINS(out.get_stderrput(), expected_err); } \
282	} while(0)
283
284	#define TEST_OUTPUT_HAS_CHECKSUM(cmd, checksum) \
285	do { \
286	CommandOutput out(cmd, false); \
287	TEST_ASSERT_NO_ERROR(out.get_error()); \
288	uint32_t css = GBS_checksum(out.get_stdoutput(), false, ""); \
289	uint32_t cse = GBS_checksum(out.get_stderrput(), false, ""); \
290	TEST_ASSERT_EQUAL(css^cse, uint32_t(checksum)); \
291	} while(0)
292
293	#define TEST_STDOUT_EQUALS(cmd, expected_std) TEST_OUTPUT_EQUALS(cmd, expected_std, (const char *)NULL)
294	#define TEST_STDERR_EQUALS(cmd, expected_err) TEST_OUTPUT_EQUALS(cmd, (const char *)NULL, expected_err)
295
296	#define TEST_STDOUT_CONTAINS(cmd, part) TEST_OUTPUT_CONTAINS(cmd, part, "")
297
298	// --------------------------------------------------------------------------------
299
300	void TEST_arb_message() {
301	TEST_STDERR_EQUALS("arb_message \"this is the test message\"",
302	"arb_message: this is the test message\n");
303	}
304
305	void TEST_SLOW_arb_probe() {
306	// test called here currently are duplicating the tests in
307	// arb_probe.cxx@TEST_SLOW_match_probe
308	// and arb_probe.cxx@TEST_SLOW_design_probe
309	//
310	// Here test of functionality is secondary.
311	// The primary goal here is to test calling the tools (i.e. arb_probe)
312
313	TEST_SETUP_GLOBAL_ENVIRONMENT("ptserver");
314	TEST_STDOUT_EQUALS("arb_probe"
315	" serverid=-666"
316	" matchsequence=UAUCGGAGAGUUUGA",
317
318	/* ---- */ " name---- fullname mis N_mis wmis pos ecoli rev 'UAUCGGAGAGUUUGA'\1"
319	"BcSSSS00\1" " BcSSSS00 0 0 0.0 3 2 0 .......UU-===============-UCAAGUCGA\1"
320	);
321
322	TEST_STDOUT_EQUALS("arb_probe"
323	" serverid=-666"
324	" designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr"
325	" designmintargets=100",
326
327	"Probe design Parameters:\n"
328	"Length of probe 18\n"
329	"Temperature [ 0.0 -400.0]\n"
330	"GC-Content [30.0 -80.0]\n"
331	"E.Coli Position [any]\n"
332	"Max Non Group Hits 0\n"
333	"Min Group Hits 100%\n"
334	"Target le apos ecol grps G+C 4GC+2AT Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
335	"CGAAAGGAAGAUUAAUAC 18 A= 94 82 4 33.3 48.0 GUAUUAAUCUUCCUUUCG \| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,\n"
336	"GAAAGGAAGAUUAAUACC 18 A+ 1 83 4 33.3 48.0 GGUAUUAAUCUUCCUUUC \| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,\n"
337	"UCAAGUCGAGCGAUGAAG 18 B= 18 17 4 50.0 54.0 CUUCAUCGCUCGACUUGA \| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,\n"
338	"AUCAAGUCGAGCGAUGAA 18 B- 1 16 4 44.4 52.0 UUCAUCGCUCGACUUGAU \| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 2, 3,\n"
339	);
340	}
341
342	#define IN_DB "tools/dnarates.arb"
343	#define OUT_DB "tools/dnarates_result.arb"
344	#define WANTED_DB "tools/dnarates_expected.arb"
345
346	void TEST_SLOW_arb_dna_rates() {
347	TEST_STDOUT_CONTAINS("arb_dnarates tools/dnarates.inp " IN_DB " " OUT_DB, "\nWriting 'POS_VAR_BY_ML_1'\n");
348	TEST_ASSERT_FILES_EQUAL(OUT_DB, WANTED_DB);
349	TEST_ASSERT_ZERO_OR_SHOW_ERRNO(GB_unlink(OUT_DB));
350	}
351
352	#define RATES_DB "tools/exportrates.arb"
353
354	void TEST_arb_export_rates() {
355	// Note: just testing against regression here.
356	// Since the output is quite longish, we just test the checksums of the results.
357	//
358	// If one of the checksums changes unexpectedly and you want to see more details about the change,
359	// - go back to a revision with a correct checksum,
360	// - add passing TEST_OUTPUT_EQUALS for broken command and
361	// - move that test to broken revision.
362
363	TEST_OUTPUT_HAS_CHECKSUM("arb_export_rates -d " RATES_DB " POS_VAR_BY_PARSIMONY", 0xc75a5fad);
364	TEST_OUTPUT_HAS_CHECKSUM("arb_export_rates -d " RATES_DB " -r POS_VAR_BY_PARSIMONY", 0xd69fb01e);
365	TEST_OUTPUT_HAS_CHECKSUM("arb_export_rates -d " RATES_DB " -r \"\"", 0xad0461ce);
366	}
367
368	#define TREE_DB "tools/tree.arb"
369
370	void TEST_arb_export_tree() {
371	TEST_STDOUT_EQUALS("arb_export_tree tree_mini " TREE_DB,
372	"((( 'VibFurni' :0.02952, 'VibVulni' :0.01880):0.04015, 'VibChole' :0.03760):1.00000,( 'AcnPleur' :0.12011, 'PrtVulga' :0.06756):1.00000, 'HlmHalod' :1.00000);\n");
373	TEST_STDOUT_EQUALS("arb_export_tree --bifurcated tree_mini " TREE_DB,
374	"(((( 'VibFurni' :0.02952, 'VibVulni' :0.01880):0.04015, 'VibChole' :0.03760):0.04610,( 'AcnPleur' :0.12011, 'PrtVulga' :0.06756):0.01732):0.07176, 'HlmHalod' :0.12399)'inner';\n");
375	TEST_STDOUT_EQUALS("arb_export_tree --doublequotes tree_mini " TREE_DB,
376	"((( \"VibFurni\" :0.02952, \"VibVulni\" :0.01880):0.04015, \"VibChole\" :0.03760):1.00000,( \"AcnPleur\" :0.12011, \"PrtVulga\" :0.06756):1.00000, \"HlmHalod\" :1.00000);\n");
377
378	TEST_STDOUT_EQUALS("arb_export_tree --nobranchlens tree_mini " TREE_DB,
379	"((( 'VibFurni' 'VibVulni' ) 'VibChole' ),( 'AcnPleur' 'PrtVulga' ), 'HlmHalod' );\n");
380	TEST_ASSERT__BROKEN(0); // the test above returns a wrong result (commas are missing)
381
382	TEST_OUTPUT_EQUALS("arb_export_tree \"\" " TREE_DB,
383	";\n", // shall export an empty newick tree
384	""); // without error!
385	TEST_OUTPUT_EQUALS("arb_export_tree tree_nosuch " TREE_DB,
386	";\n", // shall export an empty newick tree
387	"arb_export_tree: Tree 'tree_nosuch' does not exist in DB '" TREE_DB "'\n"); // with error!
388	}
389
390	static char *notification_result = NULL;
391	static void test_notification_cb(const char message, void cd) {
392	const char cds = (const char )cd;
393	notification_result = GBS_global_string_copy("message='%s' cd='%s'", message, cds);
394	}
395
396	#define INIT_NOTIFICATION \
397	GB_shell shell; \
398	GBDATA *gb_main = GBT_open("nosuch.arb", "crw"); \
399	const char *cd = "some argument"; \
400	char cmd = GB_generate_notification(gb_main, test_notification_cb, "the note", (void)cd)
401
402	#define EXIT_NOTIFICATION \
403	GB_close(gb_main); \
404	free(cmd)
405
406	#define TEST_DBSERVER_OPEN(gbmain) TEST_ASSERT_NO_ERROR(GBCMS_open(":", 0, gbmain))
407	#define TEST_DBSERVER_SERVE_UNTIL(gbmain, cond) do { \
408	bool success = GBCMS_accept_calls(gb_main, false); \
409	while (success) success = GBCMS_accept_calls(gb_main, true); \
410	GB_usleep(10000); \
411	} while(!(cond))
412
413	#define TEST_DBSERVER_CLOSE(gbmain) GBCMS_shutdown(gb_main)
414
415	void TEST_close_with_pending_notification() {
416	INIT_NOTIFICATION;
417	EXIT_NOTIFICATION;
418	}
419	void TEST_close_after_pending_notification_removed() {
420	INIT_NOTIFICATION;
421	TEST_ASSERT_NO_ERROR(GB_remove_last_notification(gb_main));
422	EXIT_NOTIFICATION;
423	}
424	void TEST_arb_notify() {
425	INIT_NOTIFICATION;
426
427	TEST_DBSERVER_OPEN(gb_main);
428
429	TEST_ASSERT_NULL(notification_result);
430	TEST_ASSERT_NO_ERROR(GBK_system(GBS_global_string("%s &", cmd))); // async call to arb_notify
431
432	TEST_DBSERVER_SERVE_UNTIL(gb_main, notification_result);
433	TEST_DBSERVER_CLOSE(gb_main);
434
435	TEST_ASSERT_EQUAL(notification_result, "message='the note' cd='some argument'");
436	freenull(notification_result);
437
438	EXIT_NOTIFICATION;
439	}
440
441	#endif // UNIT_TESTS
442

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