| 1 | // =============================================================== // |
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| 2 | // // |
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| 3 | // File : arb_test.cxx // |
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| 4 | // Purpose : unit tester for tools // |
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| 5 | // // |
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| 6 | // Coded by Ralf Westram (coder@reallysoft.de) in February 2011 // |
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| 7 | // Institute of Microbiology (Technical University Munich) // |
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| 8 | // http://www.arb-home.de/ // |
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| 9 | // // |
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| 10 | // =============================================================== // |
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| 11 | |
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| 12 | #include <arbdbt.h> |
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| 13 | #include <arb_defs.h> |
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| 14 | #include <arb_sleep.h> |
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| 15 | #include <arb_diff.h> |
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| 16 | #include <unistd.h> |
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| 17 | |
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| 18 | int ARB_main(int , char *[]) { |
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| 19 | fputs("don't call us\n", stderr); |
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| 20 | return EXIT_SUCCESS; |
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| 21 | } |
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| 22 | |
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| 23 | // -------------------------------------------------------------------------------- |
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| 24 | |
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| 25 | #ifdef UNIT_TESTS |
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| 26 | #include <arb_file.h> |
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| 27 | #include <test_unit.h> |
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| 28 | #include <test_runtool.h> |
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| 29 | |
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| 30 | // -------------------------------------------------------------------------------- |
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| 31 | |
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| 32 | |
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| 33 | void TEST_SLOW_ascii_2_bin_2_ascii() { |
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| 34 | const char *ascii_ORG = "TEST_loadsave_ascii.arb"; |
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| 35 | const char *ascii = "bin2ascii.arb"; |
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| 36 | const char *binary = "ascii2bin.arb"; |
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| 37 | const char *binary_2ND = "ascii2bin2.arb"; |
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| 38 | const char *binary_3RD = "ascii2bin3.arb"; |
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| 39 | |
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| 40 | // test that errors from _each_ part of a piped command propagate correctly: |
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| 41 | const char *failing_piped_cmds[] = { |
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| 42 | "arb_weirdo | wc -l", // first command fails |
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| 43 | "echo hello | arb_weirdo", // second command fails |
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| 44 | "arb_weirdo | arb_weirdo", // both commands fail |
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| 45 | |
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| 46 | "arb_weirdo | wc -l | sort", // first command fails |
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| 47 | "echo hello | arb_weirdo | sort", // second command fails |
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| 48 | "echo hello | wc -l | arb_weirdo", // third command fails |
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| 49 | }; |
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| 50 | for (unsigned c = 0; c<ARRAY_ELEMS(failing_piped_cmds); ++c) { |
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| 51 | TEST_EXPECT_ERROR_CONTAINS(RUN_TOOL(failing_piped_cmds[c]), "System call failed"); |
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| 52 | } |
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| 53 | |
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| 54 | TEST_RUN_TOOL("arb_2_ascii --help"); // checks proper documentation of available compression flags (in GB_get_supported_compression_flags) |
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| 55 | |
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| 56 | // test conversion file -> file |
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| 57 | TEST_RUN_TOOL(GBS_global_string("arb_2_bin %s %s", ascii_ORG, binary)); |
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| 58 | TEST_RUN_TOOL(GBS_global_string("arb_2_ascii %s %s", binary, ascii)); |
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| 59 | |
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| 60 | TEST_EXPECT_TEXTFILES_EQUAL(ascii, ascii_ORG); |
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| 61 | |
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| 62 | // test conversion (bin->ascii->bin) via stream (this tests 'arb_repair') |
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| 63 | TEST_RUN_TOOL(GBS_global_string("arb_2_ascii %s - | arb_2_bin - %s", binary, binary_2ND)); |
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| 64 | // TEST_EXPECT_FILES_EQUAL(binary, binary_2ND); // can't compare binary files (binary_2ND differs (keys?)) |
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| 65 | // instead convert back to ascii and compare result with original |
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| 66 | TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(ascii)); |
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| 67 | TEST_RUN_TOOL(GBS_global_string("arb_2_ascii %s %s", binary_2ND, ascii)); |
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| 68 | TEST_EXPECT_FILES_EQUAL(ascii, ascii_ORG); |
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| 69 | |
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| 70 | |
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| 71 | // test same using compression (gzip and bzip2) |
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| 72 | TEST_RUN_TOOL(GBS_global_string("arb_2_ascii -Cz %s - | arb_2_bin -CB - %s", binary, binary_3RD)); |
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| 73 | // TEST_EXPECT_FILES_EQUAL(binary, binary_2ND); // can't compare binary files (binary_3RD differs (keys?)) |
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| 74 | // instead convert back to ascii and compare result with original |
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| 75 | TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(ascii)); |
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| 76 | TEST_RUN_TOOL(GBS_global_string("arb_2_ascii %s %s", binary_3RD, ascii)); |
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| 77 | TEST_EXPECT_FILES_EQUAL(ascii, ascii_ORG); |
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| 78 | |
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| 79 | TEST_EXPECT_ERROR_CONTAINS(RUN_TOOL("arb_2_ascii -Cq -"), "System call failed"); // "Unknown compression flag 'q'" |
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| 80 | |
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| 81 | TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(ascii)); |
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| 82 | TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(binary)); |
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| 83 | TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(binary_2ND)); |
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| 84 | TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(binary_3RD)); |
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| 85 | TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink("ascii2bin.ARF")); |
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| 86 | TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink("ascii2bin2.ARF")); |
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| 87 | TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink("ascii2bin3.ARF")); |
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| 88 | } |
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| 89 | |
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| 90 | void TEST_arb_primer() { |
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| 91 | const char *primer_db = "TEST_nuc.arb"; |
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| 92 | const char *primer_stdin = "tools/arb_primer.in"; |
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| 93 | const char *primer_out = "tools/arb_primer.out"; |
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| 94 | const char *primer_expected = "tools/arb_primer_expected.out"; |
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| 95 | |
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| 96 | TEST_RUN_TOOL(GBS_global_string("arb_primer %s < %s", primer_db, primer_stdin)); |
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| 97 | TEST_EXPECT_FILES_EQUAL(primer_out, primer_expected); |
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| 98 | TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(primer_out)); |
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| 99 | } |
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| 100 | |
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| 101 | static GB_ERROR removeVaryingDateFromTreeRemarks(const char *dbname) { |
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| 102 | GB_ERROR error = NULp; |
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| 103 | GB_shell shell; |
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| 104 | GBDATA *gb_main = GB_open(dbname, "rw"); |
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| 105 | if (!gb_main) error = GB_await_error(); |
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| 106 | else { |
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| 107 | { |
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| 108 | GB_transaction ta(gb_main); |
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| 109 | |
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| 110 | GBDATA *gb_tree_data = GBT_get_tree_data(gb_main); |
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| 111 | const char *truncate_after = "\nunittest-tree\n"; |
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| 112 | size_t truncate_offset = strlen(truncate_after); |
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| 113 | |
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| 114 | if (!gb_tree_data) error = GB_await_error(); |
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| 115 | else { |
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| 116 | for (GBDATA *gb_tree = GB_child(gb_tree_data); |
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| 117 | gb_tree && !error; |
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| 118 | gb_tree = GB_nextChild(gb_tree)) |
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| 119 | { |
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| 120 | GBDATA *gb_remark = GB_entry(gb_tree, "remark"); |
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| 121 | if (!gb_remark) { |
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| 122 | error = "could not find 'remark' entry"; |
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| 123 | } |
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| 124 | else { |
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| 125 | char *remark = GB_read_string(gb_remark); |
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| 126 | char *found = strstr(remark, truncate_after); |
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| 127 | |
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| 128 | if (found) { |
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| 129 | strcpy(found+truncate_offset, "<date removed for testing>"); |
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| 130 | error = GB_write_string(gb_remark, remark); |
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| 131 | } |
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| 132 | free(remark); |
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| 133 | } |
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| 134 | } |
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| 135 | } |
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| 136 | |
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| 137 | ta.close(error); |
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| 138 | } |
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| 139 | if (!error) error = GB_save_as(gb_main, dbname, "a"); |
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| 140 | GB_close(gb_main); |
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| 141 | } |
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| 142 | return error; |
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| 143 | } |
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| 144 | |
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| 145 | // #define TEST_AUTO_UPDATE_TREE // uncomment to auto-update expected tree |
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| 146 | |
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| 147 | void TEST_SLOW_arb_read_tree() { |
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| 148 | struct { |
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| 149 | const char *basename; |
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| 150 | const char *extraArgs; |
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| 151 | } |
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| 152 | run[] = { |
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| 153 | { "newick", "" }, |
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| 154 | { "newick_sq", "-commentFromFile general/text.input" }, |
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| 155 | { "newick_dq", "-scale 0.5" }, |
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| 156 | { "newick_group", "-scale 10 -consense 10" }, |
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| 157 | { "newick_len", "" }, |
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| 158 | { "newick_len_group", "" }, |
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| 159 | }; |
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| 160 | |
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| 161 | const char *dbin = "min_ascii.arb"; |
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| 162 | const char *dbout = "tools/read_tree_out.arb"; |
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| 163 | const char *dbexpected = "tools/read_tree_out_expected.arb"; |
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| 164 | |
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| 165 | for (size_t b = 0; b<ARRAY_ELEMS(run); ++b) { |
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| 166 | const char *basename = run[b].basename; |
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| 167 | const char *extraArgs = run[b].extraArgs; |
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| 168 | char *treefile = GBS_global_string_copy("tools/%s.tree", basename); |
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| 169 | char *treename = GBS_global_string_copy("tree_%s", basename); |
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| 170 | |
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| 171 | TEST_RUN_TOOL(GBS_global_string("arb_read_tree -db %s %s %s %s \"test %s\" %s", |
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| 172 | dbin, dbout, treename, treefile, basename, extraArgs)); |
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| 173 | |
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| 174 | dbin = dbout; // use out-db from previous loop ( = write all trees into one db) |
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| 175 | |
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| 176 | free(treename); |
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| 177 | free(treefile); |
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| 178 | } |
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| 179 | |
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| 180 | TEST_EXPECT_NO_ERROR(removeVaryingDateFromTreeRemarks(dbout)); |
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| 181 | #if defined(TEST_AUTO_UPDATE_TREE) |
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| 182 | TEST_COPY_FILE(dbout, dbexpected); |
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| 183 | #else // !defined(TEST_AUTO_UPDATE_TREE) |
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| 184 | TEST_EXPECT_TEXTFILES_EQUAL(dbexpected, dbout); |
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| 185 | #endif |
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| 186 | TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(dbout)); |
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| 187 | } |
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| 188 | |
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| 189 | #define TEST_ARB_REPLACE(infile,expected,args) do { \ |
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| 190 | char *tmpfile = GBS_global_string_copy("%s.tmp", expected); \ |
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| 191 | TEST_RUN_TOOL_NEVER_VALGRIND(GBS_global_string("cp %s %s", infile, tmpfile)); \ |
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| 192 | TEST_RUN_TOOL(GBS_global_string("arb_replace %s %s", args, tmpfile)); \ |
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| 193 | TEST_EXPECT_TEXTFILES_EQUAL(tmpfile, expected); \ |
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| 194 | TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(tmpfile)); \ |
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| 195 | free(tmpfile); \ |
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| 196 | } while(0) |
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| 197 | |
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| 198 | void TEST_arb_replace() { |
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| 199 | const char *infile = "tools/arb_replace.in"; |
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| 200 | const char *file1 = "tools/arb_replace_1.out"; |
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| 201 | const char *file2 = "tools/arb_replace_2.out"; |
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| 202 | |
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| 203 | TEST_ARB_REPLACE(infile, "tools/arb_replace_1.out", "'gene=GONE'"); |
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| 204 | TEST_ARB_REPLACE(file1, infile, "-l 'GONE=gene'"); |
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| 205 | TEST_ARB_REPLACE(file1, file2, "-L 'GONE=gene:\"*\"=( * )'"); |
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| 206 | } |
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| 207 | |
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| 208 | // -------------------------------------------------------------------------------- |
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| 209 | |
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| 210 | #include "command_output.h" |
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| 211 | |
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| 212 | void TEST_arb_message() { |
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| 213 | TEST_STDERR_CONTAINS("arb_message \"this is the test message\"", |
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| 214 | "arb_message: this is the test message\n"); |
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| 215 | } |
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| 216 | |
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| 217 | void TEST_SLOW_arb_probe() { |
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| 218 | // test called here currently are duplicating the tests in |
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| 219 | // arb_probe.cxx@TEST_SLOW_match_probe |
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| 220 | // and arb_probe.cxx@TEST_SLOW_design_probe |
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| 221 | // |
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| 222 | // Here test of functionality is secondary. |
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| 223 | // The primary goal here is to test calling the tools (i.e. arb_probe) |
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| 224 | |
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| 225 | TEST_SETUP_GLOBAL_ENVIRONMENT("ptserver"); |
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| 226 | TEST_STDOUT_EQUALS("arb_probe" |
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| 227 | " serverid=-666" |
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| 228 | " matchsequence=UAUCGGAGAGUUUGA", |
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| 229 | |
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| 230 | /* ---- */ " name---- fullname mis N_mis wmis pos ecoli rev 'UAUCGGAGAGUUUGA'\1" |
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| 231 | "BcSSSS00\1" " BcSSSS00 0 0 0.0 3 2 0 .......UU-===============-UCAAGUCGA\1" |
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| 232 | ); |
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| 233 | |
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| 234 | TEST_STDOUT_EQUALS("arb_probe" |
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| 235 | " serverid=-666" |
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| 236 | " designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr" |
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| 237 | " designmintargets=100", |
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| 238 | |
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| 239 | "Probe design parameters:\n" |
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| 240 | "Length of probe 18\n" |
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| 241 | "Temperature [ 0.0 -400.0]\n" |
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| 242 | "GC-content [30.0 - 80.0]\n" |
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| 243 | "E.Coli position [any]\n" |
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| 244 | "Max. nongroup hits 0\n" |
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| 245 | "Min. group hits 100% (max. rejected coverage: 75%)\n" |
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| 246 | "Target le apos ecol qual grps G+C temp Probe sequence | Decrease T by n*.3C -> probe matches n non group species\n" |
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| 247 | "CGAAAGGAAGAUUAAUAC 18 A=94 82 77 4 33.3 48.0 GUAUUAAUCUUCCUUUCG | - - - - - - - - - - - - - - - - - - - -\n" |
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| 248 | "GAAAGGAAGAUUAAUACC 18 A+ 1 83 77 4 33.3 48.0 GGUAUUAAUCUUCCUUUC | - - - - - - - - - - - - - - - - - - - -\n" |
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| 249 | "UCAAGUCGAGCGAUGAAG 18 B=18 17 61 4 50.0 54.0 CUUCAUCGCUCGACUUGA | - - - - - - - - - - - - - - - 2 2 2 2 2\n" |
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| 250 | "AUCAAGUCGAGCGAUGAA 18 B- 1 16 45 4 44.4 52.0 UUCAUCGCUCGACUUGAU | - - - - - - - - - - - 2 2 2 2 2 2 2 2 2\n" |
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| 251 | ); |
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| 252 | } |
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| 253 | |
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| 254 | void TEST_SLOW_arb_probe_match() { |
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| 255 | TEST_SETUP_GLOBAL_ENVIRONMENT("ptserver"); |
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| 256 | |
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| 257 | // this probe-match is also tested with 'arb_probe'. see arb_probe.cxx@TEST_arb_probe_match |
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| 258 | TEST_STDOUT_EQUALS("arb_probe_match" |
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| 259 | " --port :../sok/pt.socket" |
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| 260 | " --n-matches 0" |
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| 261 | " --n-match-bound 4" |
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| 262 | " --mismatches 3" |
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| 263 | " --sequence GAGCGGUCAG", |
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| 264 | |
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| 265 | "acc \t" "start\t" "stop\t" "pos\t" "mis\t" "wmis\t" "nmis\t" "dt\t" "rev\t" "seq\n" |
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| 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" |
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| 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" |
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| 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" |
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| 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" |
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| 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" |
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| 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" |
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| 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" |
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| 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" |
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| 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" |
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| 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" |
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| 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" |
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| 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" |
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| 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" |
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| 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" |
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| 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" |
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| 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" |
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| 282 | ); |
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| 283 | } |
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| 284 | |
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| 285 | #define IN_DB "tools/dnarates.arb" |
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| 286 | #define OUT_DB "tools/dnarates_result.arb" |
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| 287 | #define WANTED_DB "tools/dnarates_expected.arb" |
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| 288 | |
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| 289 | // #define TEST_AUTO_UPDATE_SAI // uncomment to auto-update expected SAI |
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| 290 | |
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| 291 | void TEST_SLOW_arb_dna_rates() { |
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| 292 | TEST_STDOUT_CONTAINS("arb_dnarates tools/dnarates.inp " IN_DB " " OUT_DB, "\nWriting 'POS_VAR_BY_ML_1'\n"); |
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| 293 | |
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| 294 | #if defined(TEST_AUTO_UPDATE_SAI) |
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| 295 | TEST_COPY_FILE(OUT_DB, WANTED_DB); |
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| 296 | #else // !defined(TEST_AUTO_UPDATE_SAI) |
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| 297 | TEST_EXPECT_TEXTFILES_EQUAL(WANTED_DB, OUT_DB); |
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| 298 | #endif |
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| 299 | TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(OUT_DB)); |
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| 300 | } |
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| 301 | |
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| 302 | #define RATES_DB "tools/exportrates.arb" |
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| 303 | |
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| 304 | void TEST_arb_export_rates() { |
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| 305 | // Note: just testing against regression here. |
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| 306 | // Since the output is quite longish, we just test the checksums of the results. |
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| 307 | // |
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| 308 | // If one of the checksums changes unexpectedly and you want to see more details about the change, |
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| 309 | // - go back to a revision with a correct checksum, |
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| 310 | // - add passing TEST_OUTPUT_EQUALS for broken command and |
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| 311 | // - move that test to broken revision. |
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| 312 | |
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| 313 | TEST_OUTPUT_HAS_CHECKSUM("arb_export_rates -d " RATES_DB " POS_VAR_BY_PARSIMONY", 0xc75a5fad); |
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| 314 | TEST_OUTPUT_HAS_CHECKSUM("arb_export_rates -d " RATES_DB " -r POS_VAR_BY_PARSIMONY", 0xd69fb01e); |
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| 315 | TEST_OUTPUT_HAS_CHECKSUM("arb_export_rates -d " RATES_DB " -r \"\"", 0xad0461ce); |
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| 316 | } |
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| 317 | |
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| 318 | #define TREE_DB "tools/tree.arb" |
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| 319 | |
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| 320 | void TEST_arb_export_tree() { |
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| 321 | TEST_STDOUT_EQUALS("arb_export_tree tree_mini " TREE_DB, |
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| 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"); |
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| 323 | TEST_STDOUT_EQUALS("arb_export_tree --bifurcated tree_mini " TREE_DB, |
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| 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"); |
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| 325 | TEST_STDOUT_EQUALS("arb_export_tree --doublequotes tree_mini " TREE_DB, |
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| 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"); |
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| 327 | |
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| 328 | TEST_STDOUT_EQUALS("arb_export_tree --nobranchlens tree_mini " TREE_DB, |
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| 329 | "((( 'VibFurni' 'VibVulni' ) 'VibChole' ),( 'AcnPleur' 'PrtVulga' ), 'HlmHalod' );\n"); |
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| 330 | TEST_EXPECT__BROKEN(0); // the test above returns a wrong result (commas are missing) |
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| 331 | |
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| 332 | TEST_OUTPUT_EQUALS("arb_export_tree \"\" " TREE_DB, |
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| 333 | ";\n", // shall export an empty newick tree |
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| 334 | ""); // without error! |
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| 335 | TEST_OUTPUT_EQUALS("arb_export_tree tree_nosuch " TREE_DB, |
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| 336 | ";\n", // shall export an empty newick tree |
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| 337 | "arb_export_tree from '" TREE_DB "': ARB ERROR: Failed to read tree 'tree_nosuch' (Reason: tree not found)\n"); // with error! |
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| 338 | } |
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| 339 | TEST_PUBLISH(TEST_arb_export_tree); |
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| 340 | |
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| 341 | // -------------------------------------------------------------------------------- |
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| 342 | |
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| 343 | // #define TEST_AUTO_UPDATE_EXP_SEQ // uncomment to auto-update expected sequence exports |
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| 344 | |
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| 345 | #define EXPECTED(file) file ".expected" |
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| 346 | #if defined(TEST_AUTO_UPDATE_EXP_SEQ) |
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| 347 | #define UPDATE_OR_COMPARE(outfile) TEST_COPY_FILE(outfile, EXPECTED(outfile)) |
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| 348 | #else // !defined(TEST_AUTO_UPDATE_EXP_SEQ) |
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| 349 | #define UPDATE_OR_COMPARE(outfile) TEST_EXPECT_TEXTFILES_EQUAL(outfile, EXPECTED(outfile)) |
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| 350 | #endif |
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| 351 | #define TEST_OUTFILE_EXPECTED(outfile) do{ \ |
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| 352 | UPDATE_OR_COMPARE(outfile); \ |
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| 353 | TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(outfile)); \ |
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| 354 | }while(0) |
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| 355 | |
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| 356 | #define TEST_OUTFILE_EXPECTED__BROKEN(outfile) do{ \ |
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| 357 | TEST_EXPECT_TEXTFILES_EQUAL__BROKEN(outfile, EXPECTED(outfile)); \ |
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| 358 | TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(outfile)); \ |
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| 359 | }while(0) |
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| 360 | |
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| 361 | #define SEQ_DB "TEST_loadsave.arb" |
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| 362 | #define TEMPLATE_DB "tools/min_template.arb" |
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| 363 | #define EFT "../../lib/export/fasta_wide.eft" // ../lib/export/fasta_wide.eft |
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| 364 | #define EXSEQ_EFT "tools/exseq_via_eft.fasta" |
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| 365 | #define EXSEQ_FASTA "tools/exseq.fasta" |
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| 366 | #define EXSEQ_ARB "tools/exseq.arb" |
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| 367 | #define EXSEQ_ARB_ASCII "tools/exseq_ascii.arb" |
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| 368 | #define EXSEQ_RESTRICT "tools/acc.list" |
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| 369 | |
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| 370 | void TEST_arb_export_sequences() { |
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| 371 | TEST_RUN_TOOL("arb_export_sequences --source " SEQ_DB " --format FASTA --dest " EXSEQ_FASTA); |
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| 372 | TEST_OUTFILE_EXPECTED(EXSEQ_FASTA); |
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| 373 | |
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| 374 | TEST_RUN_TOOL("arb_export_sequences --source " SEQ_DB " --format " EFT " --dest " EXSEQ_EFT " --accs " EXSEQ_RESTRICT); |
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| 375 | TEST_OUTFILE_EXPECTED(EXSEQ_EFT); |
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| 376 | |
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| 377 | TEST_RUN_TOOL("arb_export_sequences --source " SEQ_DB " --format ARB --dest " EXSEQ_ARB " --arb-template " TEMPLATE_DB |
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| 378 | " && " |
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| 379 | "arb_2_ascii " EXSEQ_ARB " " EXSEQ_ARB_ASCII |
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| 380 | ); |
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| 381 | TEST_OUTFILE_EXPECTED(EXSEQ_ARB_ASCII); |
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| 382 | TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(EXSEQ_ARB)); |
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| 383 | } |
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| 384 | |
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| 385 | #define FILTSEQ_DB "TEST_prot_tiny.arb" // ../UNIT_TESTER/run/TEST_prot_tiny.arb |
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| 386 | #define EXFLT_DNA_UNFILTERED "tools/exflt_DNA_unfiltered.fasta" |
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| 387 | #define EXFLT_AMI_UNFILTERED "tools/exflt_AMI_unfiltered.fasta" |
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| 388 | #define EXFLT_DNA_PARTIAL_ALI "tools/exflt_DNA_partial.fasta" |
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| 389 | #define EXFLT_AMI_SKIP_SHORT "tools/exflt_AMI_skipShort.fasta" |
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| 390 | #define EXFLT_DNA_PVP_FILT "tools/exflt_DNA_pvp.fasta" |
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| 391 | #define EXFLT_DNA_MF_FILT "tools/exflt_DNA_mf.fasta" |
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| 392 | #define EXFLT_DNA_MFPVP_FILT "tools/exflt_DNA_mfpvp.fasta" |
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| 393 | #define EXFLT_AMI_MF_FILT "tools/exflt_AMI_mf.fasta" |
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| 394 | #define EXFLT_EMPTY "tools/exflt_empty.fasta" |
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| 395 | #define EXFLT_NOTSAVED "tools/exflt_notSaved.fasta" |
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| 396 | |
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| 397 | void TEST_arb_filtered_sequence_export() { |
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| 398 | // see also ../SL/FILTSEQEXP/FilteredExport.cxx@SAI_FILTERED_EXPORT_TESTS |
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| 399 | // ./arb_export_seq_filtered.cxx@show_help |
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| 400 | |
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| 401 | #define EXPORT_FILTERED_TO "arb_export_seq_filtered --db " FILTSEQ_DB " --fasta " |
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| 402 | |
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| 403 | // fail to export from missing database: |
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| 404 | TEST_FAILURE_OUTPUT_CONTAINS("arb_export_seq_filtered --db " FILTSEQ_DB "xxx --fasta " EXFLT_NOTSAVED, |
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| 405 | NULp, |
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| 406 | "Database 'TEST_prot_tiny.arbxxx' not found"); |
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| 407 | |
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| 408 | // export default alignment ('ali_dna'): |
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| 409 | TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_DNA_UNFILTERED " --id \"readdb(name);\\\" \\\";readdb(acc)\""); |
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| 410 | TEST_OUTFILE_EXPECTED(EXFLT_DNA_UNFILTERED); |
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| 411 | |
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| 412 | // export 'ali_prot': |
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| 413 | TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_AMI_UNFILTERED " --ali ali_prot"); |
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| 414 | TEST_OUTFILE_EXPECTED(EXFLT_AMI_UNFILTERED); |
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| 415 | |
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| 416 | // fail to export unknown alignment: |
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| 417 | TEST_FAILURE_OUTPUT_CONTAINS(EXPORT_FILTERED_TO EXFLT_NOTSAVED " --ali ali_nosuch", |
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| 418 | NULp, |
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| 419 | "alignment 'ali_nosuch' not found"); |
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| 420 | |
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| 421 | // fail if not all species contain data |
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| 422 | TEST_FAILURE_OUTPUT_CONTAINS(EXPORT_FILTERED_TO EXFLT_NOTSAVED " --ali ali_dna_incomplete", |
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| 423 | NULp, |
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| 424 | "species 'TaxOcell' has no data in 'ali_dna_incomplete'"); |
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| 425 | |
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| 426 | // fail if ACI is broken |
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| 427 | TEST_FAILURE_OUTPUT_CONTAINS(EXPORT_FILTERED_TO EXFLT_NOTSAVED " --id \"readdb(name)|invalid\"", |
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| 428 | NULp, |
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| 429 | "Command 'readdb(name)|invalid' failed:\nReason: Unknown command 'invalid'"); |
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| 430 | |
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| 431 | // export 'ali_dna_incomplete' (where only 1 species has data): |
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| 432 | TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_DNA_PARTIAL_ALI " --ali ali_dna_incomplete --accept-missing-data"); |
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| 433 | 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)")); |
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| 434 | TEST_OUTFILE_EXPECTED(EXFLT_DNA_PARTIAL_ALI); |
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| 435 | |
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| 436 | // skip "short" species: |
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| 437 | 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 |
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| 438 | TEST_OUTFILE_EXPECTED(EXFLT_AMI_SKIP_SHORT); |
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| 439 | TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_AMI_UNFILTERED " --ali ali_prot --min-bases 57"); // all sequences contain 57 AA |
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| 440 | TEST_OUTFILE_EXPECTED(EXFLT_AMI_UNFILTERED); |
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| 441 | TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_EMPTY " --ali ali_prot --min-bases 94"); // no sequence contains 94 AA |
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| 442 | TEST_OUTFILE_EXPECTED(EXFLT_EMPTY); |
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| 443 | |
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| 444 | // pass custom bases to count |
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| 445 | TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_AMI_SKIP_SHORT " --ali ali_prot --min-bases 62 --count-bases \"AC-IN-KP-TY-V\""); |
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| 446 | TEST_OUTFILE_EXPECTED(EXFLT_AMI_SKIP_SHORT); |
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| 447 | TEST_EXPECTATION(CommandOutput(EXPORT_FILTERED_TO EXFLT_EMPTY " --count-bases \"z-x\" --min-bases 1", true).Contains(NULp, "warning: generated empty file")); // no data contains 'xyz' -> skips all |
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| 448 | TEST_OUTFILE_EXPECTED(EXFLT_EMPTY); |
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| 449 | |
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| 450 | // apply SAI filters: |
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| 451 | TEST_FAILURE_OUTPUT_CONTAINS(EXPORT_FILTERED_TO EXFLT_NOTSAVED " --ali ali_prot --filterby \"POS_VAR_BY_PARSIMONY\" --block \"-.=012345\"", |
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| 452 | NULp, |
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| 453 | "SAI 'POS_VAR_BY_PARSIMONY' has no data in alignment 'ali_prot'"); |
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| 454 | |
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| 455 | TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_DNA_PVP_FILT " --filterby POS_VAR_BY_PARSIMONY --block \"-.=0123\""); |
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| 456 | TEST_OUTFILE_EXPECTED(EXFLT_DNA_PVP_FILT); |
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| 457 | |
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| 458 | TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_DNA_PVP_FILT " --filterby POS_VAR_BY_PARSIMONY --pass allbut \"-.=0123\""); |
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| 459 | TEST_OUTFILE_EXPECTED(EXFLT_DNA_PVP_FILT); |
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| 460 | |
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| 461 | TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_DNA_MF_FILT " --filterby MAX_FREQUENCY --pass \"789\""); |
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| 462 | TEST_OUTFILE_EXPECTED(EXFLT_DNA_MF_FILT); |
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| 463 | |
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| 464 | TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_DNA_MF_FILT " --filterby MAX_FREQUENCY --pass \"7-9\""); // use char-range |
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| 465 | TEST_OUTFILE_EXPECTED(EXFLT_DNA_MF_FILT); |
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| 466 | |
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| 467 | TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_AMI_MF_FILT " --ali ali_prot --filterby MAX_FREQUENCY --block allbut 9-5"); |
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| 468 | TEST_OUTFILE_EXPECTED(EXFLT_AMI_MF_FILT); |
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| 469 | |
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| 470 | TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_AMI_MF_FILT " --ali ali_prot --filterby MAX_FREQUENCY --pass \"5-9\""); |
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| 471 | TEST_OUTFILE_EXPECTED(EXFLT_AMI_MF_FILT); |
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| 472 | |
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| 473 | // test failure of block/pass w/o filterby: |
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| 474 | TEST_FAILURE_OUTPUT_CONTAINS(EXPORT_FILTERED_TO EXFLT_NOTSAVED " --block \"-.=012345\"", |
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| 475 | NULp, |
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| 476 | "--pass and --block have to be preceeded by --filterby"); |
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| 477 | // test failure of filterby w/o block/pass: |
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| 478 | TEST_FAILURE_OUTPUT_CONTAINS(EXPORT_FILTERED_TO EXFLT_NOTSAVED " --filterby \"POS_VAR_BY_PARSIMONY\"", |
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| 479 | NULp, |
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| 480 | "--filterby has to be followed by --pass or --block"); |
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| 481 | |
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| 482 | // apply combined filters: |
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| 483 | TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_DNA_MF_FILT |
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| 484 | " --filterby MAX_FREQUENCY --pass 0-9" |
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| 485 | " --filterby MAX_FREQUENCY --block allbut 987"); |
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| 486 | TEST_OUTFILE_EXPECTED(EXFLT_DNA_MF_FILT); |
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| 487 | |
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| 488 | TEST_RUN_TOOL(EXPORT_FILTERED_TO EXFLT_DNA_MFPVP_FILT |
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| 489 | " --seqpp :.=-" |
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| 490 | " --filterby MAX_FREQUENCY --pass 7-9" |
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| 491 | " --filterby POS_VAR_BY_PARSIMONY --pass 4-7"); |
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| 492 | TEST_OUTFILE_EXPECTED(EXFLT_DNA_MFPVP_FILT); |
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| 493 | |
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| 494 | } |
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| 495 | |
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| 496 | // -------------------------------------------------------------------------------- |
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| 497 | |
|---|
| 498 | #undef UPDATE_OR_COMPARE |
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| 499 | |
|---|
| 500 | // #define TEST_AUTO_UPDATE_EXP_PVP // uncomment to auto-update expected pvp data |
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| 501 | |
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| 502 | #if defined(TEST_AUTO_UPDATE_EXP_PVP) |
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| 503 | #define UPDATE_OR_COMPARE(outfile) TEST_COPY_FILE(outfile, EXPECTED(outfile)) |
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| 504 | #else // !defined(TEST_AUTO_UPDATE_EXP_SEQ) |
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| 505 | #define UPDATE_OR_COMPARE(outfile) TEST_EXPECT_TEXTFILES_EQUAL(outfile, EXPECTED(outfile)) |
|---|
| 506 | #endif |
|---|
| 507 | |
|---|
| 508 | #define TEST_DBPART_EQUALS(sub,saveName) \ |
|---|
| 509 | TEST_RUN_TOOL("arb_sub2ascii pvp/calc.arb " sub " pvp/" saveName ".dump"); \ |
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| 510 | TEST_OUTFILE_EXPECTED("pvp/" saveName ".dump") |
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| 511 | |
|---|
| 512 | #define TEST_CALC_PVP(treeName,addArgs,sub,saveName) \ |
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| 513 | TEST_RUN_TOOL("arb_calc_pvp TEST_nuc.arb --savename pvp/calc.arb " treeName " ali_16s " addArgs); \ |
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| 514 | TEST_DBPART_EQUALS(sub,saveName) |
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| 515 | |
|---|
| 516 | void TEST_arb_calc_pvp() { |
|---|
| 517 | // see also ../SL/PVP/pvp.cxx@TEST_pvp |
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| 518 | // ./arb_calc_pvp.cxx@show_help |
|---|
| 519 | |
|---|
| 520 | TEST_FAILURE_OUTPUT_CONTAINS("arb_calc_pvp", NULp, "argument <database> has not been provided"); |
|---|
| 521 | TEST_FAILURE_OUTPUT_CONTAINS("arb_calc_pvp db", NULp, "argument <treename>"); |
|---|
| 522 | TEST_FAILURE_OUTPUT_CONTAINS("arb_calc_pvp db tree", NULp, "argument <aliname>"); |
|---|
| 523 | |
|---|
| 524 | TEST_FAILURE_OUTPUT_CONTAINS("arb_calc_pvp db tree_bla ali_123 xtra", NULp, "too many arguments"); |
|---|
| 525 | TEST_FAILURE_OUTPUT_CONTAINS("arb_calc_pvp db tree_bla ali_123", NULp, "Database 'db' not found"); |
|---|
| 526 | TEST_FAILURE_OUTPUT_CONTAINS("arb_calc_pvp TEST_nuc.arb tree_bla ali_123", NULp, "alignment 'ali_123' not found"); |
|---|
| 527 | TEST_FAILURE_OUTPUT_CONTAINS("arb_calc_pvp TEST_nuc.arb tree_bla ali_16s", NULp, "Failed to read tree 'tree_bla'"); |
|---|
| 528 | |
|---|
| 529 | // expected results in ../UNIT_TESTER/run/pvp |
|---|
| 530 | |
|---|
| 531 | TEST_CALC_PVP("tree_nuc", "", "extended_data", "standard"); // use tree in DB |
|---|
| 532 | TEST_CALC_PVP("tree_import", "--tree-import trees/nuc_flipped.tree", "extended_data", "flippedTreeImported"); // load tree from file |
|---|
| 533 | 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) |
|---|
| 534 | TEST_CALC_PVP("tree_nuc", "--tree-import trees/nuc_flipped.tree", "extended_data", "standard"); // load + overwrite tree |
|---|
| 535 | TEST_CALC_PVP("tree_nuc", "--tree-delete", "tree_data", "notree"); // use tree in DB + delete tree |
|---|
| 536 | TEST_CALC_PVP("tree_nuc", "--sainame custPVP", "extended_data", "custom"); // test alternate SAI-name |
|---|
| 537 | |
|---|
| 538 | TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink("pvp/calc.arb")); |
|---|
| 539 | TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink("pvp/calc.ARF")); |
|---|
| 540 | } |
|---|
| 541 | |
|---|
| 542 | #endif // UNIT_TESTS |
|---|
| 543 | |
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