ARB
arb_test.cxx
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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 <arb_sleep.h>
15 #include <arb_diff.h>
16 #include <unistd.h>
17 
18 int ARB_main(int , char *[]) {
19  fputs("don't call us\n", stderr);
20  return EXIT_SUCCESS;
21 }
22 
23 // --------------------------------------------------------------------------------
24 
25 #ifdef UNIT_TESTS
26 #include <arb_file.h>
27 #include <test_unit.h>
28 #include <test_runtool.h>
29 
30 // --------------------------------------------------------------------------------
31 
32 
33 void TEST_AFTER_SLOW_ascii_2_bin_2_ascii() { // run after TEST_SLOW_loadsave
34  const char *ascii_ORG = "TEST_loadsave_ascii.arb";
35  const char *ascii = "bin2ascii.arb";
36  const char *binary = "ascii2bin.arb";
37  const char *binary_2ND = "ascii2bin2.arb";
38  const char *binary_3RD = "ascii2bin3.arb";
39 
40  // test that errors from _each_ part of a piped command propagate correctly:
41  const char *failing_piped_cmds[] = {
42  "arb_weirdo | wc -l", // first command fails
43  "echo hello | arb_weirdo", // second command fails
44  "arb_weirdo | arb_weirdo", // both commands fail
45 
46  "arb_weirdo | wc -l | sort", // first command fails
47  "echo hello | arb_weirdo | sort", // second command fails
48  "echo hello | wc -l | arb_weirdo", // third command fails
49  };
50  for (unsigned c = 0; c<ARRAY_ELEMS(failing_piped_cmds); ++c) {
51  TEST_EXPECT_ERROR_CONTAINS(RUN_TOOL(failing_piped_cmds[c]), "System call failed");
52  }
53 
54  TEST_RUN_TOOL("arb_2_ascii --help"); // checks proper documentation of available compression flags (in GB_get_supported_compression_flags)
55 
56  // test conversion file -> file
57  TEST_RUN_TOOL(GBS_global_string("arb_2_bin %s %s", ascii_ORG, binary));
58  TEST_RUN_TOOL(GBS_global_string("arb_2_ascii %s %s", binary, ascii));
59 
60  TEST_EXPECT_TEXTFILES_EQUAL(ascii, ascii_ORG);
61 
62  // test conversion (bin->ascii->bin) via stream (this tests 'arb_repair')
63  TEST_RUN_TOOL(GBS_global_string("arb_2_ascii %s - | arb_2_bin - %s", binary, binary_2ND));
64  // TEST_EXPECT_FILES_EQUAL(binary, binary_2ND); // can't compare binary files (binary_2ND differs (keys?))
65  // instead convert back to ascii and compare result with original
66  TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(ascii));
67  TEST_RUN_TOOL(GBS_global_string("arb_2_ascii %s %s", binary_2ND, ascii));
68  TEST_EXPECT_FILES_EQUAL(ascii, ascii_ORG);
69 
70 
71  // test same using compression (gzip and bzip2)
72  TEST_RUN_TOOL(GBS_global_string("arb_2_ascii -Cz %s - | arb_2_bin -CB - %s", binary, binary_3RD));
73  // TEST_EXPECT_FILES_EQUAL(binary, binary_2ND); // can't compare binary files (binary_3RD differs (keys?))
74  // instead convert back to ascii and compare result with original
75  TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(ascii));
76  TEST_RUN_TOOL(GBS_global_string("arb_2_ascii %s %s", binary_3RD, ascii));
77  TEST_EXPECT_FILES_EQUAL(ascii, ascii_ORG);
78 
79  TEST_EXPECT_ERROR_CONTAINS(RUN_TOOL("arb_2_ascii -Cq -"), "System call failed"); // "Unknown compression flag 'q'"
80 
81  TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(ascii));
82  TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(binary));
83  TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(binary_2ND));
84  TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(binary_3RD));
85  TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink("ascii2bin.ARF"));
86  TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink("ascii2bin2.ARF"));
87  TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink("ascii2bin3.ARF"));
88 }
89 
90 void TEST_arb_primer() {
91  const char *primer_db = "TEST_nuc.arb";
92  const char *primer_stdin = "tools/arb_primer.in";
93  const char *primer_out = "tools/arb_primer.out";
94  const char *primer_expected = "tools/arb_primer_expected.out";
95 
96  TEST_RUN_TOOL(GBS_global_string("arb_primer %s < %s", primer_db, primer_stdin));
97  TEST_EXPECT_FILES_EQUAL(primer_out, primer_expected);
98  TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(primer_out));
99 }
100 
101 static GB_ERROR removeVaryingDateFromTreeRemarks(const char *dbname) {
102  GB_ERROR error = NULp;
103  GB_shell shell;
104  GBDATA *gb_main = GB_open(dbname, "rw");
105  if (!gb_main) error = GB_await_error();
106  else {
107  {
108  GB_transaction ta(gb_main);
109 
110  GBDATA *gb_tree_data = GBT_get_tree_data(gb_main);
111  const char *truncate_after = "\nunittest-tree\n";
112  size_t truncate_offset = strlen(truncate_after);
113 
114  if (!gb_tree_data) error = GB_await_error();
115  else {
116  for (GBDATA *gb_tree = GB_child(gb_tree_data);
117  gb_tree && !error;
118  gb_tree = GB_nextChild(gb_tree))
119  {
120  GBDATA *gb_remark = GB_entry(gb_tree, "remark");
121  if (!gb_remark) {
122  error = "could not find 'remark' entry";
123  }
124  else {
125  char *remark = GB_read_string(gb_remark);
126  char *found = strstr(remark, truncate_after);
127 
128  if (found) {
129  strcpy(found+truncate_offset, "<date removed for testing>");
130  error = GB_write_string(gb_remark, remark);
131  }
132  free(remark);
133  }
134  }
135  }
136 
137  ta.close(error);
138  }
139  if (!error) error = GB_save_as(gb_main, dbname, "a");
140  GB_close(gb_main);
141  }
142  return error;
143 }
144 
145 // #define TEST_AUTO_UPDATE_TREE // uncomment to auto-update expected tree
146 
147 void TEST_SLOW_arb_read_tree() {
148  struct {
149  const char *basename;
150  const char *extraArgs;
151  }
152  run[] = {
153  { "newick", "" },
154  { "newick_sq", "-commentFromFile general/text.input" },
155  { "newick_dq", "-scale 0.5" },
156  { "newick_group", "-scale 10 -consense 10" },
157  { "newick_len", "" },
158  { "newick_len_group", "" },
159  };
160 
161  const char *dbin = "min_ascii.arb";
162  const char *dbout = "tools/read_tree_out.arb";
163  const char *dbexpected = "tools/read_tree_out_expected.arb";
164 
165  for (size_t b = 0; b<ARRAY_ELEMS(run); ++b) {
166  const char *basename = run[b].basename;
167  const char *extraArgs = run[b].extraArgs;
168  char *treefile = GBS_global_string_copy("tools/%s.tree", basename);
169  char *treename = GBS_global_string_copy("tree_%s", basename);
170 
171  TEST_RUN_TOOL(GBS_global_string("arb_read_tree -db %s %s %s %s \"test %s\" %s",
172  dbin, dbout, treename, treefile, basename, extraArgs));
173 
174  dbin = dbout; // use out-db from previous loop ( = write all trees into one db)
175 
176  free(treename);
177  free(treefile);
178  }
179 
180  TEST_EXPECT_NO_ERROR(removeVaryingDateFromTreeRemarks(dbout));
181 #if defined(TEST_AUTO_UPDATE_TREE)
182  TEST_COPY_FILE(dbout, dbexpected);
183 #else // !defined(TEST_AUTO_UPDATE_TREE)
184  TEST_EXPECT_TEXTFILES_EQUAL(dbexpected, dbout);
185 #endif
186  TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(dbout));
187 }
188 
189 #define TEST_ARB_REPLACE(infile,expected,args) do { \
190  char *tmpfile = GBS_global_string_copy("%s.tmp", expected); \
191  TEST_RUN_TOOL_NEVER_VALGRIND(GBS_global_string("cp %s %s", infile, tmpfile)); \
192  TEST_RUN_TOOL(GBS_global_string("arb_replace %s %s", args, tmpfile)); \
193  TEST_EXPECT_TEXTFILES_EQUAL(tmpfile, expected); \
194  TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(tmpfile)); \
195  free(tmpfile); \
196  } while(0)
197 
198 void TEST_arb_replace() {
199  const char *infile = "tools/arb_replace.in";
200  const char *file1 = "tools/arb_replace_1.out";
201  const char *file2 = "tools/arb_replace_2.out";
202 
203  TEST_ARB_REPLACE(infile, "tools/arb_replace_1.out", "'gene=GONE'");
204  TEST_ARB_REPLACE(file1, infile, "-l 'GONE=gene'");
205  TEST_ARB_REPLACE(file1, file2, "-L 'GONE=gene:\"*\"=( * )'");
206 }
207 
208 // --------------------------------------------------------------------------------
209 
210 #include "command_output.h"
211 
212 void TEST_arb_message() {
213  TEST_STDERR_CONTAINS("arb_message \"this is the test message\"",
214  "arb_message: this is the test message\n");
215 }
216 
217 void TEST_SLOW_arb_probe() {
218  // test called here currently are duplicating the tests in
219  // arb_probe.cxx@TEST_SLOW_match_probe
220  // and arb_probe.cxx@TEST_SLOW_design_probe
221  //
222  // Here test of functionality is secondary.
223  // The primary goal here is to test calling the tools (i.e. arb_probe)
224 
225  TEST_SETUP_GLOBAL_ENVIRONMENT("ptserver");
226  TEST_STDOUT_EQUALS("arb_probe"
227  " serverid=-666"
228  " matchsequence=UAUCGGAGAGUUUGA",
229 
230  /* ---- */ " name---- fullname mis N_mis wmis pos ecoli rev 'UAUCGGAGAGUUUGA'\1"
231  "BcSSSS00\1" " BcSSSS00 0 0 0.0 3 2 0 .......UU-===============-UCAAGUCGA\1"
232  );
233 
234  TEST_STDOUT_EQUALS("arb_probe"
235  " serverid=-666"
236  " designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr"
237  " designmintargets=100",
238 
239  "Probe design parameters:\n"
240  "Length of probe 18\n"
241  "Temperature [ 0.0 -400.0]\n"
242  "GC-content [30.0 - 80.0]\n"
243  "E.Coli position [any]\n"
244  "Max. nongroup hits 0\n"
245  "Min. group hits 100% (max. rejected coverage: 75%)\n"
246  "Target le apos ecol qual grps G+C temp Probe sequence | Decrease T by n*.3C -> probe matches n non group species\n"
247  "CGAAAGGAAGAUUAAUAC 18 A=94 82 77 4 33.3 48.0 GUAUUAAUCUUCCUUUCG | - - - - - - - - - - - - - - - - - - - -\n"
248  "GAAAGGAAGAUUAAUACC 18 A+ 1 83 77 4 33.3 48.0 GGUAUUAAUCUUCCUUUC | - - - - - - - - - - - - - - - - - - - -\n"
249  "UCAAGUCGAGCGAUGAAG 18 B=18 17 61 4 50.0 54.0 CUUCAUCGCUCGACUUGA | - - - - - - - - - - - - - - - 2 2 2 2 2\n"
250  "AUCAAGUCGAGCGAUGAA 18 B- 1 16 45 4 44.4 52.0 UUCAUCGCUCGACUUGAU | - - - - - - - - - - - 2 2 2 2 2 2 2 2 2\n"
251  );
252 }
253 
254 void TEST_SLOW_arb_probe_match() {
255  TEST_SETUP_GLOBAL_ENVIRONMENT("ptserver");
256 
257  // this probe-match is also tested with 'arb_probe'. see arb_probe.cxx@TEST_arb_probe_match
258  TEST_STDOUT_EQUALS("arb_probe_match"
259  " --port :../sok/pt.socket"
260  " --n-matches 0"
261  " --n-match-bound 4"
262  " --mismatches 3"
263  " --sequence GAGCGGUCAG",
264 
265  "acc \t" "start\t" "stop\t" "pos\t" "mis\t" "wmis\t" "nmis\t" "dt\t" "rev\t" "seq\n"
266  "ARB_2CA9F764\t" "0\t" "0\t" "24\t" "1\t" "1.1\t" "0\t" "0\t" "0\t" "GAUCAAGUC-======A===-AUGGGAGCU\t" "\n"
267  "ARB_6B04C30A\t" "10\t" "20\t" "24\t" "2\t" "2.2\t" "0\t" "0\t" "0\t" "GAUCAAGUC-======A=C=-ACGGGAGCU\t" "\n"
268  "ARB_4C6C9E8C\t" "20\t" "170\t" "67\t" "3\t" "2.4\t" "0\t" "0\t" "0\t" "GGAUUUGUU-=g====CG==-CGGCGGACG\t" "\n"
269  "ARB_948948A3\t" "0\t" "0\t" "81\t" "3\t" "2.8\t" "0\t" "0\t" "0\t" "ACGAGUGGC-=gA===C===-UUGGAAACG\t" "\n"
270  "ARB_5BEE4C92\t" "0\t" "0\t" "85\t" "3\t" "3.2\t" "0\t" "0\t" "0\t" "CGGCGGGAC-=g==CU====-AACCUGCGG\t" "\n"
271  "ARB_2180C521\t" "0\t" "0\t" "24\t" "3\t" "3.6\t" "0\t" "0\t" "0\t" "GAUCAAGUC-======Aa=C-GAUGGAAGC\t" "\n"
272  "ARB_815E94DB\t" "0\t" "0\t" "94\t" "3\t" "3.6\t" "0\t" "0\t" "0\t" "GGACUGCCC-==Aa==A===-CUAAUACCG\t" "\n"
273  "ARB_948948A3\t" "0\t" "0\t" "24\t" "3\t" "4\t" "0\t" "0\t" "0\t" "GAUCAAGUC-==A====a=C-AGGUCUUCG\t" "\n"
274  "ARB_9E1D1B16\t" "0\t" "0\t" "28\t" "3\t" "4\t" "0\t" "0\t" "0\t" "GAUCAAGUC-==A====a=C-GGGAAGGGA\t" "\n"
275  "ARB_CEB24FD3\t" "0\t" "0\t" "24\t" "3\t" "4.1\t" "0\t" "0\t" "0\t" "GAUCAAGUC-=====A=G=A-GUUCCUUCG\t" "\n"
276  "ARB_4FCDD74F\t" "0\t" "0\t" "24\t" "3\t" "4.1\t" "0\t" "0\t" "0\t" ".AUCAAGUC-=====A=G=A-GCUUCUUCG\t" "\n"
277  "ARB_CF69AC5C\t" "0\t" "0\t" "24\t" "3\t" "4.1\t" "0\t" "0\t" "0\t" "GAUCAAGUC-=====A=G=A-GUUCCUUCG\t" "\n"
278  "ARB_5BEE4C92\t" "0\t" "0\t" "24\t" "3\t" "4.1\t" "0\t" "0\t" "0\t" "GAUCAAGUC-=====A=G=A-GUUUCCUUC\t" "\n"
279  "ARB_815E94DB\t" "0\t" "0\t" "156\t" "3\t" "4.1\t" "0\t" "0\t" "0\t" "GUAGCCGUU-===GAA====-CGGCUGGAU\t" "\n"
280  "ARB_1763CF6\t" "0\t" "0\t" "24\t" "3\t" "2.4\t" "3\t" "0\t" "0\t" "GAUCAAGUC-=======...-<more>\t" "\n"
281  "ARB_ED8B86F\t" "0\t" "0\t" "28\t" "3\t" "2.4\t" "3\t" "0\t" "0\t" "GAUCAAGUC-=======...-<more>\t" "\n"
282  );
283 }
284 
285 #define IN_DB "tools/dnarates.arb"
286 #define OUT_DB "tools/dnarates_result.arb"
287 #define WANTED_DB "tools/dnarates_expected.arb"
288 
289 // #define TEST_AUTO_UPDATE_SAI // uncomment to auto-update expected SAI
290 
291 void TEST_SLOW_arb_dna_rates() {
292  TEST_STDOUT_CONTAINS("arb_dnarates tools/dnarates.inp " IN_DB " " OUT_DB, "\nWriting 'POS_VAR_BY_ML_1'\n");
293 
294 #if defined(TEST_AUTO_UPDATE_SAI)
295  TEST_COPY_FILE(OUT_DB, WANTED_DB);
296 #else // !defined(TEST_AUTO_UPDATE_SAI)
297  TEST_EXPECT_TEXTFILES_EQUAL(WANTED_DB, OUT_DB);
298 #endif
299  TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(OUT_DB));
300 }
301 
302 #define RATES_DB "tools/exportrates.arb"
303 
304 void TEST_arb_export_rates() {
305  // Note: just testing against regression here.
306  // Since the output is quite longish, we just test the checksums of the results.
307  //
308  // If one of the checksums changes unexpectedly and you want to see more details about the change,
309  // - go back to a revision with a correct checksum,
310  // - add passing TEST_OUTPUT_EQUALS for broken command and
311  // - move that test to broken revision.
312 
313  TEST_OUTPUT_HAS_CHECKSUM("arb_export_rates -d " RATES_DB " POS_VAR_BY_PARSIMONY", 0xc75a5fad);
314  TEST_OUTPUT_HAS_CHECKSUM("arb_export_rates -d " RATES_DB " -r POS_VAR_BY_PARSIMONY", 0xd69fb01e);
315  TEST_OUTPUT_HAS_CHECKSUM("arb_export_rates -d " RATES_DB " -r \"\"", 0xad0461ce);
316 }
317 
318 #define TREE_DB "tools/tree.arb"
319 
320 void TEST_arb_export_tree() {
321  TEST_STDOUT_EQUALS("arb_export_tree tree_mini " TREE_DB,
322  "((( '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");
323  TEST_STDOUT_EQUALS("arb_export_tree --bifurcated tree_mini " TREE_DB,
324  "(((( '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);\n");
325  TEST_STDOUT_EQUALS("arb_export_tree --doublequotes tree_mini " TREE_DB,
326  "((( \"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");
327 
328  TEST_STDOUT_EQUALS("arb_export_tree --nobranchlens tree_mini " TREE_DB,
329  "((( 'VibFurni' 'VibVulni' ) 'VibChole' ),( 'AcnPleur' 'PrtVulga' ), 'HlmHalod' );\n");
330  TEST_EXPECT__BROKEN(0); // the test above returns a wrong result (commas are missing)
331 
332  TEST_OUTPUT_EQUALS("arb_export_tree \"\" " TREE_DB,
333  ";\n", // shall export an empty newick tree
334  ""); // without error!
335  TEST_OUTPUT_EQUALS("arb_export_tree tree_nosuch " TREE_DB,
336  ";\n", // shall export an empty newick tree
337  "arb_export_tree from '" TREE_DB "': ARB ERROR: Failed to read tree 'tree_nosuch' (Reason: tree not found)\n"); // with error!
338 }
339 TEST_PUBLISH(TEST_arb_export_tree);
340 
341 // --------------------------------------------------------------------------------
342 
343 // #define TEST_AUTO_UPDATE_EXP_SEQ // uncomment to auto-update expected sequence exports
344 
345 #define EXPECTED(file) file ".expected"
346 #if defined(TEST_AUTO_UPDATE_EXP_SEQ)
347 #define UPDATE_OR_COMPARE(outfile) TEST_COPY_FILE(outfile, EXPECTED(outfile))
348 #else // !defined(TEST_AUTO_UPDATE_EXP_SEQ)
349 #define UPDATE_OR_COMPARE(outfile) TEST_EXPECT_TEXTFILES_EQUAL(outfile, EXPECTED(outfile))
350 #endif
351 #define TEST_OUTFILE_EXPECTED(outfile) do{ \
352  UPDATE_OR_COMPARE(outfile); \
353  TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(outfile)); \
354  }while(0)
355 
356 #define TEST_OUTFILE_EXPECTED__BROKEN(outfile) do{ \
357  TEST_EXPECT_TEXTFILES_EQUAL__BROKEN(outfile, EXPECTED(outfile)); \
358  TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(outfile)); \
359  }while(0)
360 
361 #define SEQ_DB "TEST_loadsave.arb"
362 #define TEMPLATE_DB "tools/min_template.arb"
363 #define EFT "../../lib/export/fasta_wide.eft" // ../lib/export/fasta_wide.eft
364 #define EXSEQ_EFT "tools/exseq_via_eft.fasta"
365 #define EXSEQ_FASTA "tools/exseq.fasta"
366 #define EXSEQ_ARB "tools/exseq.arb"
367 #define EXSEQ_ARB_ASCII "tools/exseq_ascii.arb"
368 #define EXSEQ_RESTRICT "tools/acc.list"
369 
370 void TEST_arb_export_sequences() {
371  TEST_RUN_TOOL("arb_export_sequences --source " SEQ_DB " --format FASTA --dest " EXSEQ_FASTA);
372  TEST_OUTFILE_EXPECTED(EXSEQ_FASTA);
373 
374  TEST_RUN_TOOL("arb_export_sequences --source " SEQ_DB " --format " EFT " --dest " EXSEQ_EFT " --accs " EXSEQ_RESTRICT);
375  TEST_OUTFILE_EXPECTED(EXSEQ_EFT);
376 
377  TEST_RUN_TOOL("arb_export_sequences --source " SEQ_DB " --format ARB --dest " EXSEQ_ARB " --arb-template " TEMPLATE_DB
378  " && "
379  "arb_2_ascii " EXSEQ_ARB " " EXSEQ_ARB_ASCII
380  );
381  TEST_OUTFILE_EXPECTED(EXSEQ_ARB_ASCII);
382  TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(EXSEQ_ARB));
383 }
384 
385 #define FILTSEQ_DB "TEST_prot_tiny.arb" // ../UNIT_TESTER/run/TEST_prot_tiny.arb
386 #define EXFLT_DNA_UNFILTERED "tools/exflt_DNA_unfiltered.fasta" // ../UNIT_TESTER/run/tools/
387 #define EXFLT_AMI_UNFILTERED "tools/exflt_AMI_unfiltered.fasta"
388 #define EXFLT_DNA_PARTIAL_ALI "tools/exflt_DNA_partial.fasta"
389 #define EXFLT_AMI_SKIP_SHORT "tools/exflt_AMI_skipShort.fasta"
390 #define EXFLT_DNA_PVP_FILT_GAPS "tools/exflt_DNA_pvp_gaps.fasta"
391 #define EXFLT_DNA_PVP_FILT_G03 "tools/exflt_DNA_pvp.fasta"
392 #define EXFLT_DNA_PVP_FILT_G05 "tools/exflt_DNA_pvp_g05.fasta"
393 #define EXFLT_DNA_MF_FILT "tools/exflt_DNA_mf.fasta"
394 #define EXFLT_DNA_MFPVP_FILT "tools/exflt_DNA_mfpvp.fasta"
395 #define EXFLT_AMI_MF_FILT "tools/exflt_AMI_mf.fasta"
396 #define EXFLT_EMPTY "tools/exflt_empty.fasta"
397 #define EXFLT_NOTSAVED "tools/exflt_notSaved.fasta"
398 
399 void TEST_arb_filtered_sequence_export() {
400  // see also ../SL/FILTSEQEXP/FilteredExport.cxx@SAI_FILTERED_EXPORT_TESTS
401  // ./arb_export_seq_filtered.cxx@show_help
402 
403 #define EXPORT_FILTERED_TO "arb_export_seq_filtered --db " FILTSEQ_DB " --fasta "
404 
405  // fail to export from missing database:
406  TEST_FAILURE_OUTPUT_CONTAINS("arb_export_seq_filtered --db " FILTSEQ_DB "xxx --fasta " EXFLT_NOTSAVED,
407  NULp,
408  "Database 'TEST_prot_tiny.arbxxx' not found");
409 
410  // export default alignment ('ali_dna'):
411  TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_DNA_UNFILTERED " --id \"readdb(name);\\\" \\\";readdb(acc)\"");
412  TEST_OUTFILE_EXPECTED(EXFLT_DNA_UNFILTERED);
413 
414  // export 'ali_prot':
415  TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_AMI_UNFILTERED " --ali ali_prot");
416  TEST_OUTFILE_EXPECTED(EXFLT_AMI_UNFILTERED);
417 
418  // fail to export unknown alignment:
419  TEST_FAILURE_OUTPUT_CONTAINS(EXPORT_FILTERED_TO EXFLT_NOTSAVED " --ali ali_nosuch",
420  NULp,
421  "alignment 'ali_nosuch' not found");
422 
423  // fail if not all species contain data
424  TEST_FAILURE_OUTPUT_CONTAINS(EXPORT_FILTERED_TO EXFLT_NOTSAVED " --ali ali_dna_incomplete",
425  NULp,
426  "species 'TaxOcell' has no data in 'ali_dna_incomplete'");
427 
428  // fail if ACI is broken
429  TEST_FAILURE_OUTPUT_CONTAINS(EXPORT_FILTERED_TO EXFLT_NOTSAVED " --id \"readdb(name)|invalid\"",
430  NULp,
431  "Command 'readdb(name)|invalid' failed:\nReason: Unknown command 'invalid'");
432 
433  // export 'ali_dna_incomplete' (where only 1 species has data):
434  TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_DNA_PARTIAL_ALI " --ali ali_dna_incomplete --accept-missing-data");
435  TEST_EXPECTATION(CommandOutput(EXPORT_FILTERED_TO EXFLT_DNA_PARTIAL_ALI " --ali ali_dna_incomplete --accept-missing-data", true).Contains(NULp, "Skipped species 'StrCoel9' (Reason: has no data)"));
436  TEST_OUTFILE_EXPECTED(EXFLT_DNA_PARTIAL_ALI);
437 
438  // skip "short" species:
439  TEST_EXPECTATION(CommandOutput(EXPORT_FILTERED_TO EXFLT_AMI_SKIP_SHORT " --ali ali_prot --min-bases 62", true).Contains(NULp, "Skipped species 'BctFra12' (Reason: not enough base-characters left)")); // below 62 less species are filtered
440  TEST_OUTFILE_EXPECTED(EXFLT_AMI_SKIP_SHORT);
441  TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_AMI_UNFILTERED " --ali ali_prot --min-bases 57"); // all sequences contain 57 AA
442  TEST_OUTFILE_EXPECTED(EXFLT_AMI_UNFILTERED);
443  TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_EMPTY " --ali ali_prot --min-bases 94"); // no sequence contains 94 AA
444  TEST_OUTFILE_EXPECTED(EXFLT_EMPTY);
445 
446  // pass custom bases to count
447  TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_AMI_SKIP_SHORT " --ali ali_prot --min-bases 62 --count-bases \"AC-IK-NP-TV-Y\"");
448  TEST_OUTFILE_EXPECTED(EXFLT_AMI_SKIP_SHORT);
449  TEST_EXPECTATION(CommandOutput(EXPORT_FILTERED_TO EXFLT_EMPTY " --count-bases \"x-z\" --min-bases 1", true).Contains(NULp, "warning: generated empty file")); // no data contains 'xyz' -> skips all
450  TEST_OUTFILE_EXPECTED(EXFLT_EMPTY);
451 
452  // apply SAI filters:
453  TEST_FAILURE_OUTPUT_CONTAINS(EXPORT_FILTERED_TO EXFLT_NOTSAVED " --ali ali_prot --filterby \"POS_VAR_BY_PARSIMONY\" --block \"-.=012345\"",
454  NULp,
455  "SAI 'POS_VAR_BY_PARSIMONY' has no data in alignment 'ali_prot'");
456 
457  TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_DNA_PVP_FILT_G03 " --filterby POS_VAR_BY_PARSIMONY --block \"-.=0123\"");
458  TEST_OUTFILE_EXPECTED(EXFLT_DNA_PVP_FILT_G03);
459 
460  TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_DNA_PVP_FILT_GAPS " --filterby POS_VAR_BY_PARSIMONY --pass allbut \"-.=\"");
461  TEST_OUTFILE_EXPECTED(EXFLT_DNA_PVP_FILT_GAPS);
462 
463  TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_DNA_PVP_FILT_G03 " --filterby POS_VAR_BY_PARSIMONY --pass allbut \"-.=0123\"");
464  TEST_OUTFILE_EXPECTED(EXFLT_DNA_PVP_FILT_G03);
465 
466  TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_DNA_PVP_FILT_G03 " --filterby POS_VAR_BY_PARSIMONY --pass allbut \".-=0123\""); // ".-=" no longer interpreted as range
467  TEST_OUTFILE_EXPECTED(EXFLT_DNA_PVP_FILT_G03);
468 
469  TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_DNA_PVP_FILT_G05 " --filterby POS_VAR_BY_PARSIMONY --pass allbut \"-.=012345\"");
470  TEST_OUTFILE_EXPECTED(EXFLT_DNA_PVP_FILT_G05);
471 
472  TEST_FAILURE_OUTPUT_CONTAINS(EXPORT_FILTERED_TO EXFLT_NOTSAVED " --filterby POS_VAR_BY_PARSIMONY --pass allbut \"-.=0123456789\"",
473  NULp,
474  "Sequence completely filtered out");
475 
476  TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_DNA_MF_FILT " --filterby MAX_FREQUENCY --pass \"789\"");
477  TEST_OUTFILE_EXPECTED(EXFLT_DNA_MF_FILT);
478 
479  TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_DNA_MF_FILT " --filterby MAX_FREQUENCY --pass \"7-9\""); // use char-range
480  TEST_OUTFILE_EXPECTED(EXFLT_DNA_MF_FILT);
481 
482  TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_AMI_MF_FILT " --ali ali_prot --filterby MAX_FREQUENCY --block allbut 5-9");
483  TEST_OUTFILE_EXPECTED(EXFLT_AMI_MF_FILT);
484 
485  TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_AMI_MF_FILT " --ali ali_prot --filterby MAX_FREQUENCY --pass \"5-9\"");
486  TEST_OUTFILE_EXPECTED(EXFLT_AMI_MF_FILT);
487 
488  // test failure of block/pass w/o filterby:
489  TEST_FAILURE_OUTPUT_CONTAINS(EXPORT_FILTERED_TO EXFLT_NOTSAVED " --block \"-.=012345\"",
490  NULp,
491  "--pass and --block have to be preceeded by --filterby");
492  // test failure of filterby w/o block/pass:
493  TEST_FAILURE_OUTPUT_CONTAINS(EXPORT_FILTERED_TO EXFLT_NOTSAVED " --filterby \"POS_VAR_BY_PARSIMONY\"",
494  NULp,
495  "--filterby has to be followed by --pass or --block");
496 
497  // apply combined filters:
498  TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_DNA_MF_FILT
499  " --filterby MAX_FREQUENCY --pass 0-9"
500  " --filterby MAX_FREQUENCY --block allbut 987");
501  TEST_OUTFILE_EXPECTED(EXFLT_DNA_MF_FILT);
502 
503  TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_DNA_MFPVP_FILT
504  " --seqpp :.=-"
505  " --filterby MAX_FREQUENCY --pass 7-9"
506  " --filterby POS_VAR_BY_PARSIMONY --pass 4-7");
507  TEST_OUTFILE_EXPECTED(EXFLT_DNA_MFPVP_FILT);
508 
509 }
510 
511 // --------------------------------------------------------------------------------
512 
513 #undef UPDATE_OR_COMPARE
514 
515 // #define TEST_AUTO_UPDATE_EXP_PVP // uncomment to auto-update expected pvp data
516 
517 #if defined(TEST_AUTO_UPDATE_EXP_PVP)
518 #define UPDATE_OR_COMPARE(outfile) TEST_COPY_FILE(outfile, EXPECTED(outfile))
519 #else // !defined(TEST_AUTO_UPDATE_EXP_SEQ)
520 #define UPDATE_OR_COMPARE(outfile) TEST_EXPECT_TEXTFILES_EQUAL(outfile, EXPECTED(outfile))
521 #endif
522 
523 #define TEST_DBPART_EQUALS(sub,saveName) \
524  TEST_RUN_TOOL("arb_sub2ascii pvp/calc.arb " sub " pvp/" saveName ".dump"); \
525  TEST_OUTFILE_EXPECTED("pvp/" saveName ".dump")
526 
527 #define TEST_CALC_PVP(treeName,addArgs,sub,saveName) \
528  TEST_RUN_TOOL("arb_calc_pvp TEST_nuc.arb --savename pvp/calc.arb " treeName " ali_16s " addArgs); \
529  TEST_DBPART_EQUALS(sub,saveName)
530 
531 void TEST_arb_calc_pvp() {
532  // see also ../SL/PVP/pvp.cxx@TEST_pvp
533  // ./arb_calc_pvp.cxx@show_help
534 
535  TEST_FAILURE_OUTPUT_CONTAINS("arb_calc_pvp", NULp, "argument <database> has not been provided");
536  TEST_FAILURE_OUTPUT_CONTAINS("arb_calc_pvp db", NULp, "argument <treename>");
537  TEST_FAILURE_OUTPUT_CONTAINS("arb_calc_pvp db tree", NULp, "argument <aliname>");
538 
539  TEST_FAILURE_OUTPUT_CONTAINS("arb_calc_pvp db tree_bla ali_123 xtra", NULp, "too many arguments");
540  TEST_FAILURE_OUTPUT_CONTAINS("arb_calc_pvp db tree_bla ali_123", NULp, "Database 'db' not found");
541  TEST_FAILURE_OUTPUT_CONTAINS("arb_calc_pvp TEST_nuc.arb tree_bla ali_123", NULp, "alignment 'ali_123' not found");
542  TEST_FAILURE_OUTPUT_CONTAINS("arb_calc_pvp TEST_nuc.arb tree_bla ali_16s", NULp, "Failed to read tree 'tree_bla'");
543 
544  // expected results in ../UNIT_TESTER/run/pvp
545 
546  TEST_CALC_PVP("tree_nuc", "", "extended_data", "standard"); // use tree in DB
547  TEST_CALC_PVP("tree_import", "--tree-import trees/nuc_flipped.tree", "extended_data", "flippedTreeImported"); // load tree from file
548  TEST_DBPART_EQUALS("tree_data/tree_import/node", "gottree"); // test imported tree was saved to DB (just a hacked test, otherwise problems with date in remark)
549  TEST_CALC_PVP("tree_nuc", "--tree-import trees/nuc_flipped.tree", "extended_data", "standard"); // load + overwrite tree
550  TEST_CALC_PVP("tree_nuc", "--tree-delete", "tree_data", "notree"); // use tree in DB + delete tree
551  TEST_CALC_PVP("tree_nuc", "--sainame custPVP", "extended_data", "custom"); // test alternate SAI-name
552 
553  TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink("pvp/calc.arb"));
554  TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink("pvp/calc.ARF"));
555 }
556 
557 // --------------------------------------------------------------------------------
558 
559 #define ARB_EXPORT_NEWICK_CMD "arb_export_newick --tree tree_test --newick-file /dev/stdout --db tools/export_newick.arb "
560 #define ARB_EXPORT_NEWICK_CMD2 "arb_export_newick --tree tree_test --newick-file test.tree "
561 
562 
563 void TEST_arb_export_newick() {
564  // using contains instead of equals - did not find a way to suppress the
565  // tree comment or at least the date in it
566  TEST_STDOUT_CONTAINS(ARB_EXPORT_NEWICK_CMD,
567  "((((((((((LacViri2,\nLacVirid\n),\nLacBulga\n),\nLacPlant\n),\nLacBrevi\n),\nEntFaeca\n),\n((StaAureu,\nStaEpide\n),\nAnaAbact\n)\n),\n(((CloTyro3,\nCloTyro4\n),\nCloTyro2\n),\nCloTyrob\n)\n),\n(BacMegat,\nBacPaste\n)\n),\n(PlaCitre,\nPlaKocur\n)\n),\n((BacSpec2,\nBacSubt2\n),\nBacLich2\n)\n);\n");
568  TEST_STDOUT_CONTAINS(ARB_EXPORT_NEWICK_CMD "--quoting none",
569  "((((((((((LacViri2,\nLacVirid\n),\nLacBulga\n),\nLacPlant\n),\nLacBrevi\n),\nEntFaeca\n),\n((StaAureu,\nStaEpide\n),\nAnaAbact\n)\n),\n(((CloTyro3,\nCloTyro4\n),\nCloTyro2\n),\nCloTyrob\n)\n),\n(BacMegat,\nBacPaste\n)\n),\n(PlaCitre,\nPlaKocur\n)\n),\n((BacSpec2,\nBacSubt2\n),\nBacLich2\n)\n);\n");
570  TEST_STDOUT_CONTAINS(ARB_EXPORT_NEWICK_CMD "--quoting single",
571  "(((((((((('LacViri2',\n'LacVirid'\n),\n'LacBulga'\n),\n'LacPlant'\n),\n'LacBrevi'\n),\n'EntFaeca'\n),\n(('StaAureu',\n'StaEpide'\n),\n'AnaAbact'\n)\n),\n((('CloTyro3',\n'CloTyro4'\n),\n'CloTyro2'\n),\n'CloTyrob'\n)\n),\n('BacMegat',\n'BacPaste'\n)\n),\n('PlaCitre',\n'PlaKocur'\n)\n),\n(('BacSpec2',\n'BacSubt2'\n),\n'BacLich2'\n)\n);\n");
572  TEST_STDOUT_CONTAINS(ARB_EXPORT_NEWICK_CMD "--quoting double",
573  "((((((((((\"LacViri2\",\n\"LacVirid\"\n),\n\"LacBulga\"\n),\n\"LacPlant\"\n),\n\"LacBrevi\"\n),\n\"EntFaeca\"\n),\n((\"StaAureu\",\n\"StaEpide\"\n),\n\"AnaAbact\"\n)\n),\n(((\"CloTyro3\",\n\"CloTyro4\"\n),\n\"CloTyro2\"\n),\n\"CloTyrob\"\n)\n),\n(\"BacMegat\",\n\"BacPaste\"\n)\n),\n(\"PlaCitre\",\n\"PlaKocur\"\n)\n),\n((\"BacSpec2\",\n\"BacSubt2\"\n),\n\"BacLich2\"\n)\n);\n");
574  TEST_STDOUT_CONTAINS(ARB_EXPORT_NEWICK_CMD "--quoting single --add-branch-lengths --add-bootstraps --add-group-names",
575  "(((((((((('LacViri2':0.01905,\n'LacVirid':0.01905\n):0.17308,\n'LacBulga':0.14286\n)'19':0.03261,\n'LacPlant':0.05714\n)'36':0.00990,\n'LacBrevi':0.06667\n)'19':0.02985,\n'EntFaeca':0.09524\n):1.35323,\n(('StaAureu':0.06087,\n'StaEpide':0.04348\n)'99':0.08929,\n'AnaAbact':0.15044\n)'21:xx':0.01923\n)'35':0.01163,\n((('CloTyro3':1.04569,\n'CloTyro4':0.06061\n)'40':0.02581,\n'CloTyro2':0.01732\n)'0':0.01717,\n'CloTyrob':0.00866\n)'97:test':0.06639\n)'0':0.00000,\n('BacMegat':0.04386,\n'BacPaste':0.04348\n)'53':0.02667\n)'outer':0.14592,\n('PlaCitre':0.00862,\n'PlaKocur':0.01724\n):0.13913\n)'0':0.00889,\n(('BacSpec2':0.05714,\n'BacSubt2':0.25743\n):1.21875,\n'BacLich2':0.15652\n)'0':0.04571\n);\n");
576  TEST_STDOUT_CONTAINS(ARB_EXPORT_NEWICK_CMD "--pretty",
577  "(\n (\n (\n (\n (\n (\n (\n (\n (\n (\n LacViri2,\n LacVirid\n ),\n LacBulga\n ),\n LacPlant\n ),\n LacBrevi\n ),\n EntFaeca\n ),\n (\n (\n StaAureu,\n StaEpide\n ),\n AnaAbact\n )\n ),\n (\n (\n (\n CloTyro3,\n CloTyro4\n ),\n CloTyro2\n ),\n CloTyrob\n )\n ),\n (\n BacMegat,\n BacPaste\n )\n ),\n (\n PlaCitre,\n PlaKocur\n )\n ),\n (\n (\n BacSpec2,\n BacSubt2\n ),\n BacLich2\n )\n);\n");
578  TEST_STDOUT_CONTAINS(ARB_EXPORT_NEWICK_CMD "--replace-problem-chars --leaf-aci \"readdb(\\\"ber_tax\\\")\"",
579  "((((((((((PROKARYOTA__EUBACTERIA__GRAMPOSITIVES__CLOSTRIDIOBACTERIA.,\nPROKARYOTA__EUBACTERIA__GRAMPOSITIVES__CLOSTRIDIOBACTERIA.\n),\nPROKARYOTA__EUBACTERIA__GRAMPOSITIVES__CLOSTRIDIOBACTERIA.\n),\nPROKARYOTA__EUBACTERIA__GRAMPOSITIVES__CLOSTRIDIOBACTERIA.\n),\nPROKARYOTA__EUBACTERIA__GRAMPOSITIVES__CLOSTRIDIOBACTERIA.\n),\nPROKARYOTA__EUBACTERIA__GRAMPOSITIVES__CLOSTRIDIOBACTERIA.\n),\n((PROKARYOTA__EUBACTERIA__GRAMPOSITIVES__CLOSTRIDIOBACTERIA.,\nPROKARYOTA__EUBACTERIA__GRAMPOSITIVES__CLOSTRIDIOBACTERIA.\n),\nPROKARYOTA__EUBACTERIA__GRAMPOSITIVES__CLOSTRIDIOBACTERIA_|MOLLICUTES__ACHOLEPLASMATALES__ANAEROPLASMATACEAE.\n)\n),\n(((PROKARYOTA__EUBACTERIA__GRAMPOSITIVES__CLOSTRIDIOBACTERIA.,\nPROKARYOTA__EUBACTERIA__GRAMPOSITIVES__CLOSTRIDIOBACTERIA.\n),\nPROKARYOTA__EUBACTERIA__GRAMPOSITIVES__CLOSTRIDIOBACTERIA.\n),\nPROKARYOTA__EUBACTERIA__GRAMPOSITIVES__CLOSTRIDIOBACTERIA.\n)\n),\n(PROKARYOTA__EUBACTERIA__GRAMPOSITIVES__CLOSTRIDIOBACTERIA.,\nPROKARYOTA__EUBACTERIA__GRAMPOSITIVES__CLOSTRIDIOBACTERIA.\n)\n),\n(PROKARYOTA__EUBACTERIA__GRAMPOSITIVES__CLOSTRIDIOBACTERIA.,\nPROKARYOTA__EUBACTERIA__GRAMPOSITIVES__CLOSTRIDIOBACTERIA.\n)\n),\n((PROKARYOTA__EUBACTERIA__GRAMPOSITIVES__CLOSTRIDIOBACTERIA.,\nPROKARYOTA__EUBACTERIA__GRAMPOSITIVES__CLOSTRIDIOBACTERIA.\n),\nPROKARYOTA__EUBACTERIA__GRAMPOSITIVES__CLOSTRIDIOBACTERIA.\n)\n);\n");
580 
581  // The following format is required by the SILVA pipeline.
582  TEST_STDOUT_CONTAINS(ARB_EXPORT_NEWICK_CMD "--quoting single --add-branch-lengths --leaf-aci \"readdb(\\\"acc\\\");\\\".\\\";readdb(\\\"start\\\");\\\".\\\";readdb(\\\"stop\\\");merge\"",
583  "(((((((((('ARB_3951DE2B.1.117':0.01905,\n'ARB_C57D21E1.1.117':0.01905\n):0.17308,\n'ARB_9B3FAE39.1.117':0.14286\n):0.03261,\n'ARB_F2164787.1.117':0.05714\n):0.00990,\n'ARB_8C51921E.1.117':0.06667\n):0.02985,\n'ARB_831183A2.1.117':0.09524\n):1.35323,\n(('ARB_9F013D16.1.115':0.06087,\n'ARB_E5492501.1.115':0.04348\n):0.08929,\n'ARB_30492909.1.113':0.15044\n):0.01923\n):0.01163,\n((('ARB_D9683416.1.117':1.04569,\n'ARB_3A0C4A19.1.117':0.06061\n):0.02581,\n'ARB_44CFBEF7.1.116':0.01732\n):0.01717,\n'ARB_9B15850C.1.116':0.00866\n):0.06639\n):0.00000,\n('ARB_2F6EC950.1.116':0.04386,\n'ARB_1E14162F.1.117':0.04348\n):0.02667\n):0.14592,\n('ARB_FDEBCF58.1.116':0.00862,\n'ARB_CE41B26E.1.116':0.01724\n):0.13913\n):0.00889,\n(('ARB_B9CB66D2.1.116':0.05714,\n'ARB_914AF372.1.116':0.25743\n):1.21875,\n'ARB_15DC3437.1.116':0.15652\n):0.04571\n);\n");
584 
585  // very briefly test if help is supported
586  TEST_FAILURE_OUTPUT_CONTAINS(ARB_EXPORT_NEWICK_CMD "--help", (const char *)NULp, "Usage: arb_export_newick");
587 
588  // missing mandatory arguments
589  TEST_FAILURE_OUTPUT_CONTAINS("arb_export_newick ", (const char *)NULp, "Error: no input database specified\n");
590  TEST_FAILURE_OUTPUT_CONTAINS("arb_export_newick --db DUMMY_DB", (const char *)NULp, "Error: no tree name specified\n");
591  TEST_FAILURE_OUTPUT_CONTAINS("arb_export_newick --db DUMMY_DB --tree tree_test", (const char *)NULp, "Error: no output file specified\n");
592 
593  // illegal arguments
594  TEST_FAILURE_OUTPUT_CONTAINS(ARB_EXPORT_NEWICK_CMD2 "--db DUMMY_DB --quoting n0N€", (const char *)NULp, "unknown quoting mode 'n0N€'");
595  TEST_FAILURE_OUTPUT_CONTAINS(ARB_EXPORT_NEWICK_CMD2 "--db DUMMY_DB --illegal-command", (const char *)NULp, "unexpected argument '--illegal-command'");
596  TEST_FAILURE_OUTPUT_CONTAINS(ARB_EXPORT_NEWICK_CMD2 "--db DUMMY_DB --leaf-aci \"illegal-command\"", (const char *)NULp, "Database 'DUMMY_DB' not found (While opening 'DUMMY_DB': No such file or directory)");
597  TEST_FAILURE_OUTPUT_CONTAINS(ARB_EXPORT_NEWICK_CMD2 "--db tools/export_newick.arb --leaf-aci \"illegal-command\"", (const char *)NULp, "Command 'illegal-command' failed:\nReason: Unknown command 'illegal-command'");
598 
599  TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink("test.tree"));
600 }
601 TEST_PUBLISH(TEST_arb_export_newick);
602 
603 #endif // UNIT_TESTS
604 
GB_ERROR
const char * GB_ERROR
Definition: arb_core.h:25
TEST_STDOUT_EQUALS
#define TEST_STDOUT_EQUALS(cmd, expected_std)
Definition: command_output.h:174
test_unit.h
GB_open
GBDATA * GB_open(const char *path, const char *opent)
Definition: ad_load.cxx:1363
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GB_child
GBDATA * GB_child(GBDATA *father)
Definition: adquery.cxx:322
GB_write_string
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Definition: arbdb.cxx:1387
TEST_SETUP_GLOBAL_ENVIRONMENT
#define TEST_SETUP_GLOBAL_ENVIRONMENT(modulename)
Definition: test_unit.h:1491
TEST_OUTPUT_HAS_CHECKSUM
#define TEST_OUTPUT_HAS_CHECKSUM(cmd, checksum)
Definition: command_output.h:171
TEST_STDOUT_CONTAINS
#define TEST_STDOUT_CONTAINS(cmd, part)
Definition: command_output.h:177
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const char * GBS_global_string(const char *templat,...)
Definition: arb_msg.cxx:203
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#define RUN_TOOL(cmdline)
Definition: test_runtool.h:104
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Definition: adtree.cxx:27
EXIT_SUCCESS
#define EXIT_SUCCESS
Definition: arb_a2ps.c:154
TEST_STDERR_CONTAINS
#define TEST_STDERR_CONTAINS(cmd, part)
Definition: command_output.h:178
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int GB_unlink(const char *path)
Definition: arb_file.cxx:188
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#define ARRAY_ELEMS(array)
Definition: arb_defs.h:19
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#define TEST_PUBLISH(testfunction)
Definition: test_unit.h:1517
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GB_ERROR GB_await_error()
Definition: arb_msg.cxx:342
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#define TEST_OUTPUT_EQUALS(cmd, expected_std, expected_err)
Definition: command_output.h:136
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Definition: arb_test.cxx:18
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Definition: test_runtool.h:109
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Definition: ad_save_load.cxx:1371
error
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Definition: mkptypes.cxx:96
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Definition: command_output.h:160
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Definition: test_unit.h:1090
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TEST_EXPECTATION
#define TEST_EXPECTATION(EXPCTN)
Definition: test_unit.h:1048
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Definition: arbdb.h:171
fputs
fputs(TRACE_PREFIX, stderr)
GB_transaction::close
GB_ERROR close(GB_ERROR error)
Definition: arbdbpp.cxx:35
arb_file.h
TEST_EXPECT_FILES_EQUAL
#define TEST_EXPECT_FILES_EQUAL(f1, f2)
Definition: test_unit.h:1422
GB_read_string
char * GB_read_string(GBDATA *gbd)
Definition: arbdb.cxx:909
TEST_EXPECT_NO_ERROR
#define TEST_EXPECT_NO_ERROR(call)
Definition: test_unit.h:1118
NULp
#define NULp
Definition: cxxforward.h:116
TEST_EXPECT_ERROR_CONTAINS
#define TEST_EXPECT_ERROR_CONTAINS(call, part)
Definition: test_unit.h:1114
GB_transaction
Definition: arbdb.h:143
GB_nextChild
GBDATA * GB_nextChild(GBDATA *child)
Definition: adquery.cxx:326
command_output.h
ta
GB_transaction ta(gb_var)
gb_main
GBDATA * gb_main
Definition: adname.cxx:32
TEST_EXPECT_TEXTFILES_EQUAL
#define TEST_EXPECT_TEXTFILES_EQUAL(fgot, fwant)
Definition: test_unit.h:1424
GB_entry
GBDATA * GB_entry(GBDATA *father, const char *key)
Definition: adquery.cxx:334
TEST_EXPECT__BROKEN
#define TEST_EXPECT__BROKEN(cond)
Definition: test_unit.h:1329
GBS_global_string_copy
char * GBS_global_string_copy(const char *templat,...)
Definition: arb_msg.cxx:194
GB_close
void GB_close(GBDATA *gbd)
Definition: arbdb.cxx:655
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