Mercurial > repos > galaxyp > openms_openswathassaygenerator

annotate fill_ctd.py @ 13:de7a553552a6 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:07:50 +0000
parents df72ca515420
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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1 import collections
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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2 import json
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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3 import operator
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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4 import os
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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5 import re
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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6 import subprocess
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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7 import sys
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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8 from functools import reduce # forward compatibility for Python 3
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9
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10 from CTDopts.CTDopts import (
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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11 _Choices,
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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12 _InFile,
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13 _Null,
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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14 _NumericRange,
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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15 CTDModel
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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16 )
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19 def getFromDict(dataDict, mapList):
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20 return reduce(operator.getitem, mapList, dataDict)
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23 def setInDict(dataDict, mapList, value):
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24 getFromDict(dataDict, mapList[:-1])[mapList[-1]] = value
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27 def mergeDicts(d, e):
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28 """
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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29 insert values from the dict e into dict d
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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30 no values of d are overwritten
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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31 """
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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32 for k, v in e.items():
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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33 if (k in d and isinstance(d[k], dict) and isinstance(e[k], collections.abc.Mapping)):
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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34 mergeDicts(d[k], e[k])
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de7a553552a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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35 elif k not in d:
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36 d[k] = e[k]
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37 else:
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38 sys.stderr.write("fill_ctd.py: could not merge key %s for %s in %s" % (k, d, e))
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39 sys.exit(1)
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42 def _json_object_hook_noenvlookup(d):
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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43 return _json_object_hook(d, envlookup=False)
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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46 def _json_object_hook(d, envlookup=True):
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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47 """
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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48 wee helper to transform the json written by galaxy
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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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 -> []
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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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")
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77 d[k] = p.stdout.strip()
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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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82
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83
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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:
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
92 if p == "":
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
93 continue
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
94 if p.startswith('"') and p.endswith('"'):
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
95 lst.append(p[1:-1])
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
96 elif p.startswith('"'):
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
97 quoted = True
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
98 lst.append(p[1:] + " ")
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
99 elif p.endswith('"'):
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
100 quoted = False
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
101 lst[-1] += p[:-1]
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
102 else:
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
103 if quoted:
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
104 lst[-1] += p + " "
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
105 else:
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
106 lst.append(p)
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
107 return lst
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
108
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
109
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
110 def fix_underscores(args):
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
111 if type(args) is dict:
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
112 for k in list(args.keys()):
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
113 v = args[k]
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
114 if type(v) is dict:
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
115 fix_underscores(args[k])
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
116 if k.startswith("_"):
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
117 args[k[1:]] = v
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
118 del args[k]
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
119 elif type(args) is list:
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
120 for i, v in enumerate(args):
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
121 if type(v) is dict:
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
122 fix_underscores(args[i])
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
123
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
124
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
125 input_ctd = sys.argv[1]
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
126
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
127 # load user specified parameters from json
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
128 with open(sys.argv[2]) as fh:
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
129 args = json.load(fh, object_hook=_json_object_hook_noenvlookup)
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
130
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
131 # load hardcoded parameters from json
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
132 with open(sys.argv[3]) as fh:
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
133 hc_args = json.load(fh, object_hook=_json_object_hook)
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
134
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
135 # insert the hc_args into the args
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
136 mergeDicts(args, hc_args)
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
137
13
de7a553552a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 10
diff changeset
138 # put the contents of the advanced options section into the main dict
de7a553552a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 10
diff changeset
139 if "adv_opts" in args:
de7a553552a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 10
diff changeset
140 args.update(args["adv_opts"])
de7a553552a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 10
diff changeset
141 del args["adv_opts"]
9
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
142
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
143 # IDMapper has in and spectra:in params, in is used in out as format_source",
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
144 # which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493"
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
145 # therefore hardcoded params change the name of spectra:in to spectra:_in
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
146 # which is corrected here again
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
147 # TODO remove once PR is in and adapt profile accordingly
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
148 fix_underscores(args)
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
149
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
150 model = CTDModel(from_file=input_ctd)
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
151
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
152 # transform values from json that correspond to
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
153 # - old style booleans (string + restrictions) -> transformed to a str
10
df72ca515420 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e9568c650259d95b230d1a243e90f73a19564c2"
galaxyp
parents: 9
diff changeset
154 # - new style booleans that get a string (happens for hidden parameters [-test])
df72ca515420 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e9568c650259d95b230d1a243e90f73a19564c2"
galaxyp
parents: 9
diff changeset
155 # are transformed to a bool
9
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
156 # - unrestricted ITEMLIST which are represented as strings
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
157 # ("=quoted and space separated) in Galaxy -> transform to lists
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
158 # - optional data input parameters that have defaults and for which no
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
159 # value is given -> overwritte with the default
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
160 for p in model.get_parameters():
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
161
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
162 # check if the parameter is in the arguments from the galaxy tool
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
163 # (from the json file(s)), since advanced parameters are absent
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
164 # if the conditional is set to basic parameters
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
165 try:
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
166 getFromDict(args, p.get_lineage(name_only=True))
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
167 except KeyError:
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
168 # few tools use dashes in parameters which are automatically replaced
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
169 # by underscores by Galaxy. in these cases the dictionary needs to be
10
df72ca515420 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e9568c650259d95b230d1a243e90f73a19564c2"
galaxyp
parents: 9
diff changeset
170 # updated (better: then dash and the underscore variant are in the dict)
9
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
171 # TODO might be removed later https://github.com/OpenMS/OpenMS/pull/4529
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
172 try:
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
173 lineage = [_.replace("-", "_") for _ in p.get_lineage(name_only=True)]
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
174 val = getFromDict(args, lineage)
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
175 except KeyError:
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
176 continue
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
177 else:
10
df72ca515420 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e9568c650259d95b230d1a243e90f73a19564c2"
galaxyp
parents: 9
diff changeset
178 setInDict(args, p.get_lineage(name_only=True), val)
9
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
179
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
180 if p.type is str and type(p.restrictions) is _Choices and set(p.restrictions.choices) == set(["true", "false"]):
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
181 v = getFromDict(args, p.get_lineage(name_only=True))
5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
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)