Mercurial > repos > galaxyp > openms_openmsinfo

annotate fill_ctd.py @ 0:5da903bcd4f1 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 21:41:52 +0000
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5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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1 import collections
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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2 import json
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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3 import operator
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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4 import os
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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5 import re
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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6 import subprocess
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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7 import sys
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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8 from functools import reduce # forward compatibility for Python 3
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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9
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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10 from CTDopts.CTDopts import (
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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11 _Choices,
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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12 _InFile,
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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13 _Null,
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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14 _NumericRange,
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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15 CTDModel
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16 )
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19 def getFromDict(dataDict, mapList):
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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20 return reduce(operator.getitem, mapList, dataDict)
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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23 def setInDict(dataDict, mapList, value):
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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24 getFromDict(dataDict, mapList[:-1])[mapList[-1]] = value
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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27 def mergeDicts(d, e):
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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28 """
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29 insert values from the dict e into dict d
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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30 no values of d are overwritten
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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31 """
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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32 for k, v in e.items():
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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33 if (k in d and isinstance(d[k], dict) and isinstance(e[k], collections.abc.Mapping)):
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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34 mergeDicts(d[k], e[k])
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35 elif k not in d:
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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36 d[k] = e[k]
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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37 else:
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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38 sys.stderr.write("fill_ctd.py: could not merge key %s for %s in %s" % (k, d, e))
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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39 sys.exit(1)
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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41
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42 def _json_object_hook_noenvlookup(d):
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43 return _json_object_hook(d, envlookup=False)
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44
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45
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46 def _json_object_hook(d, envlookup=True):
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47 """
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48 wee helper to transform the json written by galaxy
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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49 while loading
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50 - True/False (bool objects) -> "true"/"false" (lowercase string)
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51 - data inputs with multiple and optional true give [None] if no file is given -> []
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52 - None -> "" (empty string)
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53 - replace bash expressions (if envlookup is True):
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54 - environment variables (need to consist capital letters and _) by their value
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55 - expressions
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56 """
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57 for k in d.keys():
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58 # if type(d[k]) is bool:
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59 # d[k] = str(d[k]).lower()
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60 # else
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61 if type(d[k]) is list and len(d[k]) == 1 and d[k][0] is None:
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62 d[k] = []
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63 elif d[k] is None:
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64 d[k] = ""
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65 elif envlookup and type(d[k]) is str and d[k].startswith("$"):
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66 m = re.fullmatch(r"\$([A-Z_]+)", d[k])
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67 if m:
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68 d[k] = os.environ.get(m.group(1), "")
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69 continue
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70 m = re.fullmatch(r"\$(\{[A-Z_]+):-(.*)\}", d[k])
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71 if m:
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72 d[k] = os.environ.get(m.group(1), m.group(2))
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73 continue
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74
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75 try:
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76 p = subprocess.run("echo %s" % d[k], shell=True, check=True, stdout=subprocess.PIPE, encoding="utf8")
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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77 d[k] = p.stdout.strip()
5da903bcd4f1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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78 except subprocess.CalledProcessError:
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79 sys.stderr.write("fill_ctd error: Could not evaluate %s" % d[k])
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80 continue
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81 return d
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84 def qstring2list(qs):
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85 """
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86 transform a space separated string that is quoted by " into a list
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87 """
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88 lst = list()
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89 qs = qs.split(" ")
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90 quoted = False
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91 for p in qs:
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92 if p == "":
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93 continue
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94 if p.startswith('"') and p.endswith('"'):
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95 lst.append(p[1:-1])
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96 elif p.startswith('"'):
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97 quoted = True
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98 lst.append(p[1:] + " ")
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99 elif p.endswith('"'):
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100 quoted = False
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101 lst[-1] += p[:-1]
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102 else:
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103 if quoted:
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104 lst[-1] += p + " "
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105 else:
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106 lst.append(p)
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107 return lst
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108
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109
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110 def fix_underscores(args):
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111 if type(args) is dict:
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112 for k in list(args.keys()):
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113 v = args[k]
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114 if type(v) is dict:
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115 fix_underscores(args[k])
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116 if k.startswith("_"):
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117 args[k[1:]] = v
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118 del args[k]
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119 elif type(args) is list:
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120 for i, v in enumerate(args):
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121 if type(v) is dict:
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122 fix_underscores(args[i])
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123
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124
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125 input_ctd = sys.argv[1]
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126
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127 # load user specified parameters from json
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128 with open(sys.argv[2]) as fh:
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129 args = json.load(fh, object_hook=_json_object_hook_noenvlookup)
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130
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131 # load hardcoded parameters from json
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132 with open(sys.argv[3]) as fh:
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133 hc_args = json.load(fh, object_hook=_json_object_hook)
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134
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135 # insert the hc_args into the args
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136 mergeDicts(args, hc_args)
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137
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138 # put the contents of the advanced options section into the main dict
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139 if "adv_opts" in args:
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140 args.update(args["adv_opts"])
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141 del args["adv_opts"]
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142
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143 # IDMapper has in and spectra:in params, in is used in out as format_source",
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144 # which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493"
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145 # therefore hardcoded params change the name of spectra:in to spectra:_in
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146 # which is corrected here again
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147 # TODO remove once PR is in and adapt profile accordingly
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148 fix_underscores(args)
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149
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150 model = CTDModel(from_file=input_ctd)
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151
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152 # transform values from json that correspond to
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153 # - old style booleans (string + restrictions) -> transformed to a str
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154 # - new style booleans that get a string (happens for hidden parameters [-test])
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155 # are transformed to a bool
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156 # - unrestricted ITEMLIST which are represented as strings
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157 # ("=quoted and space separated) in Galaxy -> transform to lists
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158 # - optional data input parameters that have defaults and for which no
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159 # value is given -> overwritte with the default
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160 for p in model.get_parameters():
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161
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162 # check if the parameter is in the arguments from the galaxy tool
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163 # (from the json file(s)), since advanced parameters are absent
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164 # if the conditional is set to basic parameters
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165 try:
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166 getFromDict(args, p.get_lineage(name_only=True))
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167 except KeyError:
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168 # few tools use dashes in parameters which are automatically replaced
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169 # by underscores by Galaxy. in these cases the dictionary needs to be
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170 # updated (better: then dash and the underscore variant are in the dict)
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171 # TODO might be removed later https://github.com/OpenMS/OpenMS/pull/4529
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172 try:
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173 lineage = [_.replace("-", "_") for _ in p.get_lineage(name_only=True)]
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174 val = getFromDict(args, lineage)
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175 except KeyError:
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176 continue
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177 else:
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178 setInDict(args, p.get_lineage(name_only=True), val)
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179
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180 if p.type is str and type(p.restrictions) is _Choices and set(p.restrictions.choices) == set(["true", "false"]):
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181 v = getFromDict(args, p.get_lineage(name_only=True))
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182 setInDict(args, p.get_lineage(name_only=True), str(v).lower())
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183 elif p.type is bool:
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184 v = getFromDict(args, p.get_lineage(name_only=True))
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185 if isinstance(v, str):
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186 v = (v.lower() == "true")
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187 setInDict(args, p.get_lineage(name_only=True), v)
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188 elif p.is_list and (p.restrictions is None or type(p.restrictions) is _NumericRange):
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189 v = getFromDict(args, p.get_lineage(name_only=True))
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190 if type(v) is str:
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191 setInDict(args, p.get_lineage(name_only=True), qstring2list(v))
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192 elif p.type is _InFile and not (p.default is None or type(p.default) is _Null):
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193 v = getFromDict(args, p.get_lineage(name_only=True))
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194 if v in [[], ""]:
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195 setInDict(args, p.get_lineage(name_only=True), p.default)
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196
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197 model.write_ctd(input_ctd, arg_dict=args)