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