Mercurial > repos > galaxyp > openms_dtaextractor

annotate get_tests.py @ 18:78024781d209 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:43:05 +0000
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18
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1 #!/usr/bin/env python
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2
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3 import argparse
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4 import os.path
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5 import re
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6 import shlex
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7 import sys
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8 import tempfile
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9 from typing import (
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10 Dict,
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11 List,
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12 Optional,
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13 TextIO,
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14 Tuple,
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15 )
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16
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17 from ctdconverter.common.utils import (
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18 ParameterHardcoder,
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19 parse_hardcoded_parameters,
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20 parse_input_ctds,
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21 )
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22 from ctdconverter.galaxy.converter import convert_models
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23 from CTDopts.CTDopts import (
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24 CTDModel,
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25 ModelTypeError,
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26 Parameters,
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27 )
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28
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29 SKIP_LIST = [
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30 r"_prepare\"",
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31 r"_convert",
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32 r"WRITEINI",
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33 r"WRITECTD",
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34 r"INVALIDVALUE",
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35 r"\.ini\.json",
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36 r"OpenSwathMzMLFileCacher .*-convert_back", # - OpenSwathMzMLFileCacher with -convert_back argument https://github.com/OpenMS/OpenMS/issues/4399
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37 r"MaRaClusterAdapter.*-consensus_out", # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456)
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38 r"FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta ", # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed)
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39 r'^(TOPP_OpenSwathAnalyzer_test_3|TOPP_OpenSwathAnalyzer_test_4)$', # no suppert for cached mzML
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40 r'TOPP_SiriusAdapter_[0-9]+$', # Do not test SiriusAdapter https://github.com/OpenMS/OpenMS/issues/7000 .. will be removed anyway
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41 r'TOPP_AssayGeneratorMetabo_(7|8|9|10|11|12|13|14|15|16|17|18)$' # Skip AssayGeneratorMetabo tests using Sirius https://github.com/OpenMS/OpenMS/issues/7150 (will be replaced by two tools)
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42 ]
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43
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44
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45 def get_failing_tests(cmake: List[str]) -> List[str]:
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46 failing_tests = []
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47 re_fail = re.compile(r"set_tests_properties\(\"([^\"]+)\" PROPERTIES WILL_FAIL 1\)")
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48
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49 for cmake in args.cmake:
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50 with open(cmake) as cmake_fh:
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51 for line in cmake_fh:
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52 match = re_fail.search(line)
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53 if match:
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54 failing_tests.append(match.group(1))
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55 return failing_tests
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56
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57
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58 def fix_tmp_files(line: str, diff_pairs: Dict[str, str]) -> str:
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59 """
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60 OpenMS tests output to tmp files and compare with FuzzyDiff to the expected file.
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61 problem: the extension of the tmp files is unusable for test generation.
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62 unfortunately the extensions used in the DIFF lines are not always usable for the CLI
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63 (e.g. for prepare_test_data, e.g. CLI expects csv but test file is txt)
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64 this function replaces the tmp file by the expected file.
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65 """
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66 cmd = shlex.split(line)
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67 for i, e in enumerate(cmd):
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68 if e in diff_pairs:
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69 dst = os.path.join("test-data", diff_pairs[e])
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70 if os.path.exists(dst):
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71 os.unlink(dst)
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72 sys.stderr.write(f"symlink {e} {dst}\n")
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73 os.symlink(e, dst)
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74 cmd[i] = diff_pairs[e]
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75 return shlex.join(cmd)
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76
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77
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78 def get_ini(line: str, tool_id: str) -> Tuple[str, str]:
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79 """
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80 if there is an ini file then we use this to generate the test
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81 otherwise the ctd file is used
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82 other command line parameters are inserted later into this xml
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83 """
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84 cmd = shlex.split(line)
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85 ini = None
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86 for i, e in enumerate(cmd):
78024781d209 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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87 if e == "-ini":
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88 ini = cmd[i + 1]
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89 cmd = cmd[:i] + cmd[i + 2:]
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90 if ini:
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91 return os.path.join("test-data", ini), shlex.join(cmd)
78024781d209 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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92 else:
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93 return os.path.join("ctd", f"{tool_id}.ctd"), line
78024781d209 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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94
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95
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96 def unique_files(line: str):
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97 """
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98 some tests use the same file twice which does not work in planemo tests
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99 hence we create symlinks for each file used twice
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100 """
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101 cmd = shlex.split(line)
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102 # print(f"{cmd}")
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103 files = {}
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104 # determine the list of indexes where each file argument (anything appearing in test-data/) appears
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105 for idx, e in enumerate(cmd):
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106 p = os.path.join("test-data", e)
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107 if not os.path.exists(p) and not os.path.islink(p):
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108 continue
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109 try:
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110 files[e].append(idx)
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111 except KeyError:
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112 files[e] = [idx]
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113 # print(f"{files=}")
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114 for f in files:
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115 if len(files[f]) < 2:
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116 continue
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117 for i, idx in enumerate(files[f]):
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118 f_parts = f.split(".")
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119 f_parts[0] = f"{f_parts[0]}_{i}"
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120 new_f = ".".join(f_parts)
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121 # if os.path.exists(os.path.join("test-data", new_f)):
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122 # os.unlink(os.path.join("test-data", new_f))
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123 sys.stderr.write(
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124 f'\tsymlink {os.path.join("test-data", new_f)} {f}\n'
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125 )
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126 try:
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127 os.symlink(f, os.path.join("test-data", new_f))
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128 except FileExistsError:
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129 pass
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130 cmd[idx] = new_f
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131 return shlex.join(cmd)
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132
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133
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134 def fill_ctd_clargs(ini: str, line: str, ctd_tmp: TextIO) -> None:
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135 cmd = shlex.split(line)
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136
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137 # load CTDModel
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138 ini_model = None
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139 try:
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140 ini_model = CTDModel(from_file=ini)
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141 except ModelTypeError:
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142 pass
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143 try:
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144 ini_model = Parameters(from_file=ini)
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145 except ModelTypeError:
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146 pass
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147 assert ini_model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (
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148 args.ini_file
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149 )
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150
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151 # get a dictionary of the ctd arguments where the values of the parameters
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152 # given on the command line are overwritten
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153 ini_values = ini_model.parse_cl_args(cl_args=cmd, ignore_required=True)
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154 ini_model.write_ctd(ctd_tmp, ini_values)
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155
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156
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157 def process_test_line(
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158 id: str,
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159 line: str,
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160 failing_tests: List[str],
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161 skip_list: List[str],
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162 diff_pairs: Dict[str, str],
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163 ) -> Optional[str]:
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164
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165 re_test_id = re.compile(r"add_test\(\"([^\"]+)\" ([^ ]+) (.*)")
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166 re_id_out_test = re.compile(r"_out_?[0-9]?")
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167
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168 # TODO auto extract from set(OLD_OSW_PARAM ... lin
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169 line = line.replace(
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170 "${OLD_OSW_PARAM}",
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171 " -test -mz_extraction_window 0.05 -mz_extraction_window_unit Th -ms1_isotopes 0 -Scoring:TransitionGroupPicker:compute_peak_quality -Scoring:Scores:use_ms1_mi false -Scoring:Scores:use_mi_score false",
78024781d209 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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172 )
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173
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174 line = line.replace("${TOPP_BIN_PATH}/", "")
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175 line = line.replace("${DATA_DIR_TOPP}/", "")
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176 line = line.replace("THIRDPARTY/", "")
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177 line = line.replace("${DATA_DIR_SHARE}/", "")
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178 # IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differently
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179 line = line.replace("${TMP_RIP_PATH}/", "")
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180 # some input files are originally in a subdir (degenerated cases/), but not in test-data
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181 line = line.replace("degenerate_cases/", "")
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182 # determine the test and tool ids and remove the 1) add_test("TESTID" 2) trailing )
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183 match = re_test_id.match(line)
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184 if not match:
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185 sys.exit(f"Ill formated test line {line}\n")
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186 test_id = match.group(1)
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187 tool_id = match.group(2)
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188
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189 line = f"{match.group(2)} {match.group(3)}"
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190
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191 if test_id in failing_tests:
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192 sys.stderr.write(f" skip failing {test_id} {line}\n")
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193 return
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194
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195 if id != tool_id:
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196 sys.stderr.write(f" skip {test_id} ({id} != {tool_id}) {line}\n")
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197 return
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198
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199 if re_id_out_test.search(test_id):
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200 sys.stderr.write(f" skip {test_id} {line}\n")
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201 return
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202
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203 for skip in skip_list:
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204 if re.search(skip, line):
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205 return
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206 if re.search(skip, test_id):
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207 return
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208
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209 line = fix_tmp_files(line, diff_pairs)
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210 # print(f"fix {line=}")
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211 line = unique_files(line)
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212 # print(f"unq {line=}")
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213 ini, line = get_ini(line, tool_id)
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214
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215 from dataclasses import dataclass, field
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216
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217 @dataclass
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218 class CTDConverterArgs:
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219 input_files: list
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220 output_destination: str
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221 default_executable_path: Optional[str] = None
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222 hardcoded_parameters: Optional[str] = None
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223 parameter_hardcoder: Optional[ParameterHardcoder] = None
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224 xsd_location: Optional[str] = None
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225 formats_file: Optional[str] = None
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226 add_to_command_line: str = ""
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227 required_tools_file: Optional[str] = None
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228 skip_tools_file: Optional[str] = None
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229 macros_files: Optional[List[str]] = field(default_factory=list)
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230 test_macros_files: Optional[List[str]] = field(default_factory=list)
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231 test_macros_prefix: Optional[List[str]] = field(default_factory=list)
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232 test_test: bool = False
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233 test_only: bool = False
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234 test_unsniffable: Optional[List[str]] = field(default_factory=list)
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235 test_condition: Optional[List[str]] = ("compare=sim_size", "delta_frac=0.05")
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236 tool_version: str = None
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237 tool_profile: str = None
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238 bump_file: str = None
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239
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240 # create an ini/ctd file where the values are equal to the arguments from the command line
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241 # and transform it to xml
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242 test = [f"<!-- {test_id} -->\n"]
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243 with tempfile.NamedTemporaryFile(
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244 mode="w+", delete_on_close=False
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245 ) as ctd_tmp, tempfile.NamedTemporaryFile(
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246 mode="w+", delete_on_close=False
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247 ) as xml_tmp:
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248 fill_ctd_clargs(ini, line, ctd_tmp)
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249 ctd_tmp.close()
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250 xml_tmp.close()
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251 parsed_ctd = parse_input_ctds(None, [ctd_tmp.name], xml_tmp.name, "xml")
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252 ctd_args = CTDConverterArgs(
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253 input_files=[ctd_tmp.name],
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254 output_destination=xml_tmp.name,
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255 macros_files=["macros.xml"],
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256 skip_tools_file="aux/tools_blacklist.txt",
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257 formats_file="aux/filetypes.txt",
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258 # tool_conf_destination = "tool.conf",
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259 hardcoded_parameters="aux/hardcoded_params.json",
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260 tool_version="3.1",
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261 test_only=True,
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262 test_unsniffable=[
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263 "csv",
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264 "tsv",
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265 "txt",
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266 "dta",
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267 "dta2d",
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268 "edta",
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269 "mrm",
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270 "splib",
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271 ],
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272 test_condition=["compare=sim_size", "delta_frac=0.7"],
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273 )
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274 ctd_args.parameter_hardcoder = parse_hardcoded_parameters(
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275 ctd_args.hardcoded_parameters
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276 )
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277 convert_models(ctd_args, parsed_ctd)
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278 xml_tmp = open(xml_tmp.name, "r")
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279 for l in xml_tmp:
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280 test.append(l)
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281
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282 return "".join(test)
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283
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284
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285 parser = argparse.ArgumentParser(description="Create Galaxy tests for a OpenMS tools")
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286 parser.add_argument("--id", dest="id", help="tool id")
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287 parser.add_argument("--cmake", nargs="+", help="OpenMS test CMake files")
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288 args = parser.parse_args()
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289 sys.stderr.write(f"generate tests for {args.id}\n")
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290
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291 re_comment = re.compile("#.*")
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292 re_empty_prefix = re.compile(r"^\s*")
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293 re_empty_suffix = re.compile(r"\s*$")
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294 re_add_test = re.compile(r"add_test\(\"(TOPP|UTILS)_.*/" + args.id)
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295 re_diff = re.compile(r"\$\{DIFF\}.* -in1 ([^ ]+) -in2 ([^ ]+)")
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296 failing_tests = get_failing_tests(args.cmake)
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297 tests = []
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298
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299 # process the given CMake files and compile lists of
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300 # - test lines .. essentially add_test(...)
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301 # - and pairs of files that are diffed
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302 jline = ""
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303 test_lines = []
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304 diff_pairs = {}
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305 for cmake in args.cmake:
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306 with open(cmake) as cmake_fh:
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307 for line in cmake_fh:
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308 # remove comments, empty prefixes and suffixes
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309 line = re_comment.sub("", line)
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310 line = re_empty_prefix.sub("", line)
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311 line = re_empty_suffix.sub("", line)
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312 # skip empty lines
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313 if line == "":
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314 continue
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315
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316 # join test statements that are split over multiple lines
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317 if line.endswith(")"):
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318 jline += " " + line[:-1]
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diff changeset
319 else:
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320 jline = line
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321 continue
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322 line, jline = jline.strip(), ""
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galaxyp
parents:
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323 match = re_diff.search(line)
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324 if match:
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325 in1 = match.group(1).split("/")[-1]
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326 in2 = match.group(2).split("/")[-1]
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327 if in1 != in2:
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galaxyp
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328 diff_pairs[in1] = in2
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galaxyp
parents:
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329 elif re_add_test.match(line):
78024781d209 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
diff changeset
330 test_lines.append(line)
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parents:
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331
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galaxyp
parents:
diff changeset
332 for line in test_lines:
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galaxyp
parents:
diff changeset
333 test = process_test_line(args.id, line, failing_tests, SKIP_LIST, diff_pairs)
78024781d209 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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diff changeset
334 if test:
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galaxyp
parents:
diff changeset
335 tests.append(test)
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parents:
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336
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galaxyp
parents:
diff changeset
337 tests = "\n".join(tests)
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galaxyp
parents:
diff changeset
338 print(
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galaxyp
parents:
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339 f"""
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galaxyp
parents:
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340 <xml name="autotest_{args.id}">
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parents:
diff changeset
341 {tests}
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diff changeset
342 </xml>
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galaxyp
parents:
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343 """
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344 )