Mercurial > repos > galaxyp > openms_spectrafilternormalizer
annotate get_tests.py @ 14:4ba7fb47318c draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author | galaxyp |
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date | Fri, 14 Jun 2024 21:30:31 +0000 |
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14
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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1 #!/usr/bin/env python |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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2 |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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3 import argparse |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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4 import os.path |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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5 import re |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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6 import shlex |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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7 import sys |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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8 import tempfile |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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9 from typing import ( |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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10 Dict, |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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11 List, |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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12 Optional, |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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13 TextIO, |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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14 Tuple, |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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15 ) |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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16 |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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17 from ctdconverter.common.utils import ( |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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18 ParameterHardcoder, |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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19 parse_hardcoded_parameters, |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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20 parse_input_ctds, |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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21 ) |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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22 from ctdconverter.galaxy.converter import convert_models |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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23 from CTDopts.CTDopts import ( |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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24 CTDModel, |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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25 ModelTypeError, |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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26 Parameters, |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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27 ) |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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28 |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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29 SKIP_LIST = [ |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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30 r"_prepare\"", |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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31 r"_convert", |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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32 r"WRITEINI", |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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33 r"WRITECTD", |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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34 r"INVALIDVALUE", |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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35 r"\.ini\.json", |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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36 r"OpenSwathMzMLFileCacher .*-convert_back", # - OpenSwathMzMLFileCacher with -convert_back argument https://github.com/OpenMS/OpenMS/issues/4399 |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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37 r"MaRaClusterAdapter.*-consensus_out", # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456) |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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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) |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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39 r'^(TOPP_OpenSwathAnalyzer_test_3|TOPP_OpenSwathAnalyzer_test_4)$', # no suppert for cached mzML |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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40 r'TOPP_SiriusAdapter_[0-9]+$', # Do not test SiriusAdapter https://github.com/OpenMS/OpenMS/issues/7000 .. will be removed anyway |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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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) |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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42 ] |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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43 |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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44 |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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45 def get_failing_tests(cmake: List[str]) -> List[str]: |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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46 failing_tests = [] |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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47 re_fail = re.compile(r"set_tests_properties\(\"([^\"]+)\" PROPERTIES WILL_FAIL 1\)") |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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48 |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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49 for cmake in args.cmake: |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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50 with open(cmake) as cmake_fh: |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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51 for line in cmake_fh: |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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52 match = re_fail.search(line) |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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53 if match: |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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54 failing_tests.append(match.group(1)) |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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55 return failing_tests |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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56 |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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57 |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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58 def fix_tmp_files(line: str, diff_pairs: Dict[str, str]) -> str: |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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59 """ |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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60 OpenMS tests output to tmp files and compare with FuzzyDiff to the expected file. |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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61 problem: the extension of the tmp files is unusable for test generation. |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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62 unfortunately the extensions used in the DIFF lines are not always usable for the CLI |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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63 (e.g. for prepare_test_data, e.g. CLI expects csv but test file is txt) |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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64 this function replaces the tmp file by the expected file. |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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65 """ |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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66 cmd = shlex.split(line) |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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67 for i, e in enumerate(cmd): |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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68 if e in diff_pairs: |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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69 dst = os.path.join("test-data", diff_pairs[e]) |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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70 if os.path.exists(dst): |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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71 os.unlink(dst) |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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72 sys.stderr.write(f"symlink {e} {dst}\n") |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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73 os.symlink(e, dst) |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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74 cmd[i] = diff_pairs[e] |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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75 return shlex.join(cmd) |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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76 |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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77 |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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78 def get_ini(line: str, tool_id: str) -> Tuple[str, str]: |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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79 """ |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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80 if there is an ini file then we use this to generate the test |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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81 otherwise the ctd file is used |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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82 other command line parameters are inserted later into this xml |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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83 """ |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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84 cmd = shlex.split(line) |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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85 ini = None |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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86 for i, e in enumerate(cmd): |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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87 if e == "-ini": |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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88 ini = cmd[i + 1] |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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89 cmd = cmd[:i] + cmd[i + 2:] |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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90 if ini: |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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91 return os.path.join("test-data", ini), shlex.join(cmd) |
4ba7fb47318c
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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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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93 return os.path.join("ctd", f"{tool_id}.ctd"), line |
4ba7fb47318c
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94 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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95 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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96 def unique_files(line: str): |
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97 """ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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98 some tests use the same file twice which does not work in planemo tests |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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99 hence we create symlinks for each file used twice |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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100 """ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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101 cmd = shlex.split(line) |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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102 # print(f"{cmd}") |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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103 files = {} |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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104 # determine the list of indexes where each file argument (anything appearing in test-data/) appears |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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105 for idx, e in enumerate(cmd): |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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106 p = os.path.join("test-data", e) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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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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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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109 try: |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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110 files[e].append(idx) |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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111 except KeyError: |
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112 files[e] = [idx] |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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113 # print(f"{files=}") |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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114 for f in files: |
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115 if len(files[f]) < 2: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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116 continue |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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117 for i, idx in enumerate(files[f]): |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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118 f_parts = f.split(".") |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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119 f_parts[0] = f"{f_parts[0]}_{i}" |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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120 new_f = ".".join(f_parts) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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121 # if os.path.exists(os.path.join("test-data", new_f)): |
4ba7fb47318c
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122 # os.unlink(os.path.join("test-data", new_f)) |
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123 sys.stderr.write( |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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124 f'\tsymlink {os.path.join("test-data", new_f)} {f}\n' |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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125 ) |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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126 try: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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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 |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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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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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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136 |
4ba7fb47318c
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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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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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141 except ModelTypeError: |
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142 pass |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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143 try: |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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144 ini_model = Parameters(from_file=ini) |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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145 except ModelTypeError: |
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146 pass |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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147 assert ini_model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % ( |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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148 args.ini_file |
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149 ) |
4ba7fb47318c
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150 |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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151 # get a dictionary of the ctd arguments where the values of the parameters |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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152 # given on the command line are overwritten |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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153 ini_values = ini_model.parse_cl_args(cl_args=cmd, ignore_required=True) |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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154 ini_model.write_ctd(ctd_tmp, ini_values) |
4ba7fb47318c
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155 |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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156 |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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157 def process_test_line( |
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158 id: str, |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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159 line: str, |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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160 failing_tests: List[str], |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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161 skip_list: List[str], |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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162 diff_pairs: Dict[str, str], |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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163 ) -> Optional[str]: |
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164 |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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165 re_test_id = re.compile(r"add_test\(\"([^\"]+)\" ([^ ]+) (.*)") |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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166 re_id_out_test = re.compile(r"_out_?[0-9]?") |
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167 |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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168 # TODO auto extract from set(OLD_OSW_PARAM ... lin |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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169 line = line.replace( |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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170 "${OLD_OSW_PARAM}", |
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171 " -test -mz_extraction_window 0.05 -mz_extraction_window_unit Th -ms1_isotopes 0 -Scoring:TransitionGroupPicker:compute_peak_quality -Scoring:Scores:use_ms1_mi false -Scoring:Scores:use_mi_score false", |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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172 ) |
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173 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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174 line = line.replace("${TOPP_BIN_PATH}/", "") |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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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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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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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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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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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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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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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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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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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 |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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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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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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194 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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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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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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198 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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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") |
4ba7fb47318c
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201 return |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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202 |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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203 for skip in skip_list: |
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204 if re.search(skip, line): |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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205 return |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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206 if re.search(skip, test_id): |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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207 return |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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208 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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209 line = fix_tmp_files(line, diff_pairs) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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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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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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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) |
4ba7fb47318c
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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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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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313 if line == "": |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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314 continue |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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315 |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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316 # join test statements that are split over multiple lines |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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317 if line.endswith(")"): |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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318 jline += " " + line[:-1] |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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319 else: |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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320 jline = line |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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321 continue |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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322 line, jline = jline.strip(), "" |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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323 match = re_diff.search(line) |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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324 if match: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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325 in1 = match.group(1).split("/")[-1] |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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326 in2 = match.group(2).split("/")[-1] |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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327 if in1 != in2: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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328 diff_pairs[in1] = in2 |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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329 elif re_add_test.match(line): |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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330 test_lines.append(line) |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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331 |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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332 for line in test_lines: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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333 test = process_test_line(args.id, line, failing_tests, SKIP_LIST, diff_pairs) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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334 if test: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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335 tests.append(test) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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336 |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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337 tests = "\n".join(tests) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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338 print( |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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339 f""" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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340 <xml name="autotest_{args.id}"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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341 {tests} |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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342 </xml> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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343 """ |
4ba7fb47318c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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344 ) |