source: branches/stable/TOOLS/arb_test.cxx

Last change on this file was 18437, checked in by westram, 6 years ago
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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
18int 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
33void 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
90void 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
101static 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
147void 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
198void 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
212void 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
217void 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
254void 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
291void 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
304void 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
320void 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}
339TEST_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
370void 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
399void 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
531void 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
563void 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}
601TEST_PUBLISH(TEST_arb_export_newick);
602
603#endif // UNIT_TESTS
604
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