Mercurial > repos > galaxyp > openms_tofcalibration

annotate fill_ctd.py @ 11:57905fb0008f draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f5fcdd54599554099fb00b1973cc91a766ad246a"
author galaxyp
date Wed, 23 Sep 2020 13:16:22 +0000
parents bfc2c3b46325
children
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rev   line source
10
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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diff changeset
1 import collections
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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2 import json
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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3 import operator
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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4 import os
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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5 import re
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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6 import subprocess
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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7 import sys
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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8 from functools import reduce # forward compatibility for Python 3
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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9
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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10 from CTDopts.CTDopts import (
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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11 _Choices,
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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12 _InFile,
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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13 _Null,
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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14 _NumericRange,
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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15 CTDModel
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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16 )
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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17
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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19 def getFromDict(dataDict, mapList):
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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20 return reduce(operator.getitem, mapList, dataDict)
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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21
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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23 def setInDict(dataDict, mapList, value):
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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24 getFromDict(dataDict, mapList[:-1])[mapList[-1]] = value
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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27 def mergeDicts(d, e):
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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28 """
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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29 insert values from the dict e into dict d
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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30 no values of d are overwritten
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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31 """
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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32 for k, v in e.items():
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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33 if (k in d and isinstance(d[k], dict) and isinstance(e[k], collections.abc.Mapping)):
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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34 mergeDicts(d[k], e[k])
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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35 elif k not in d and not isinstance(e[k], collections.abc.Mapping):
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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36 d[k] = e[k]
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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37 else:
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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38 sys.stderr.write("fill_ctd.py: could not merge key %s for %s in %s" % (k, d, e))
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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39 sys.exit(1)
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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41
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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42 def _json_object_hook_noenvlookup(d):
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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43 return _json_object_hook(d, envlookup=False)
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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44
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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45
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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46 def _json_object_hook(d, envlookup=True):
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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47 """
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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48 wee helper to transform the json written by galaxy
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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49 while loading
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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50 - True/False (bool objects) -> "true"/"false" (lowercase string)
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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51 - data inputs with multiple and optional true give [None] if no file is given -> []
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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52 - None -> "" (empty string)
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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53 - replace bash expressions (if envlookup is True):
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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54 - environment variables (need to consist capital letters and _) by their value
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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55 - expressions
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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56 """
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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57 for k in d.keys():
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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58 # if type(d[k]) is bool:
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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59 # d[k] = str(d[k]).lower()
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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60 # else
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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61 if type(d[k]) is list and len(d[k]) == 1 and d[k][0] is None:
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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62 d[k] = []
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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63 elif d[k] is None:
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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64 d[k] = ""
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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65 elif envlookup and type(d[k]) is str and d[k].startswith("$"):
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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66 m = re.fullmatch(r"\$([A-Z_]+)", d[k])
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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67 if m:
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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68 d[k] = os.environ.get(m.group(1), "")
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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69 continue
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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70 m = re.fullmatch(r"\$(\{[A-Z_]+):-(.*)\}", d[k])
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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71 if m:
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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72 d[k] = os.environ.get(m.group(1), m.group(2))
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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73 continue
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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74
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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75 try:
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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76 p = subprocess.run("echo %s" % d[k], shell=True, check=True, stdout=subprocess.PIPE, encoding="utf8")
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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77 d[k] = p.stdout.strip()
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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78 except subprocess.CalledProcessError:
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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79 sys.stderr.write("fill_ctd error: Could not evaluate %s" % d[k])
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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80 continue
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81 return d
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82
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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83
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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84 def qstring2list(qs):
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85 """
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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parents:
diff changeset
86 transform a space separated string that is quoted by " into a list
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
87 """
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
88 lst = list()
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
89 qs = qs.split(" ")
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
90 quoted = False
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
91 for p in qs:
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
92 if p == "":
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
93 continue
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
94 if p.startswith('"') and p.endswith('"'):
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
95 lst.append(p[1:-1])
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
96 elif p.startswith('"'):
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
97 quoted = True
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
98 lst.append(p[1:] + " ")
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
99 elif p.endswith('"'):
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
100 quoted = False
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
101 lst[-1] += p[:-1]
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
102 else:
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
103 if quoted:
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
104 lst[-1] += p + " "
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
105 else:
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
106 lst.append(p)
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
107 return lst
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
108
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
109
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
110 def fix_underscores(args):
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
111 if type(args) is dict:
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
112 for k in list(args.keys()):
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
113 v = args[k]
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
114 if type(v) is dict:
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
115 fix_underscores(args[k])
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
116 if k.startswith("_"):
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
117 args[k[1:]] = v
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
118 del args[k]
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
119 elif type(args) is list:
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
120 for i, v in enumerate(args):
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
121 if type(v) is dict:
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
122 fix_underscores(args[i])
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
123
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
124
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
125 input_ctd = sys.argv[1]
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
126
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
127 # load user specified parameters from json
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
128 with open(sys.argv[2]) as fh:
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
129 args = json.load(fh, object_hook=_json_object_hook_noenvlookup)
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
130
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
131 # load hardcoded parameters from json
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
132 with open(sys.argv[3]) as fh:
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
133 hc_args = json.load(fh, object_hook=_json_object_hook)
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
134
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
135 # insert the hc_args into the args
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
136 mergeDicts(args, hc_args)
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
137
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
138 if "adv_opts_cond" in args:
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
139 args.update(args["adv_opts_cond"])
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
140 del args["adv_opts_cond"]
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
141
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
142 # IDMapper has in and spectra:in params, in is used in out as format_source",
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
143 # which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493"
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
144 # therefore hardcoded params change the name of spectra:in to spectra:_in
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
145 # which is corrected here again
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
146 # TODO remove once PR is in and adapt profile accordingly
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
147 fix_underscores(args)
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
148
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
149 model = CTDModel(from_file=input_ctd)
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
150
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
151 # transform values from json that correspond to
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
152 # - old style booleans (string + restrictions) -> transformed to a str
11
57905fb0008f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f5fcdd54599554099fb00b1973cc91a766ad246a"
galaxyp
parents: 10
diff changeset
153 # - new style booleans that get a string (happens for hidden parameters [-test])
57905fb0008f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f5fcdd54599554099fb00b1973cc91a766ad246a"
galaxyp
parents: 10
diff changeset
154 # are transformed to a bool
10
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
155 # - unrestricted ITEMLIST which are represented as strings
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
156 # ("=quoted and space separated) in Galaxy -> transform to lists
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
157 # - optional data input parameters that have defaults and for which no
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
158 # value is given -> overwritte with the default
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
159 for p in model.get_parameters():
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
160
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
161 # check if the parameter is in the arguments from the galaxy tool
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
162 # (from the json file(s)), since advanced parameters are absent
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
163 # if the conditional is set to basic parameters
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
164 try:
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
165 getFromDict(args, p.get_lineage(name_only=True))
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
166 except KeyError:
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
167 # few tools use dashes in parameters which are automatically replaced
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
168 # by underscores by Galaxy. in these cases the dictionary needs to be
11
57905fb0008f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f5fcdd54599554099fb00b1973cc91a766ad246a"
galaxyp
parents: 10
diff changeset
169 # updated (better: then dash and the underscore variant are in the dict)
10
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
170 # TODO might be removed later https://github.com/OpenMS/OpenMS/pull/4529
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
171 try:
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
172 lineage = [_.replace("-", "_") for _ in p.get_lineage(name_only=True)]
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
173 val = getFromDict(args, lineage)
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174 except KeyError:
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175 continue
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176 else:
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177 setInDict(args, p.get_lineage(name_only=True), val)
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178
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179 if p.type is str and type(p.restrictions) is _Choices and set(p.restrictions.choices) == set(["true", "false"]):
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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180 v = getFromDict(args, p.get_lineage(name_only=True))
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181 setInDict(args, p.get_lineage(name_only=True), str(v).lower())
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182 elif p.type is bool:
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183 v = getFromDict(args, p.get_lineage(name_only=True))
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184 if isinstance(v, str):
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185 v = (v.lower() == "true")
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186 setInDict(args, p.get_lineage(name_only=True), v)
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187 elif p.is_list and (p.restrictions is None or type(p.restrictions) is _NumericRange):
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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188 v = getFromDict(args, p.get_lineage(name_only=True))
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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189 if type(v) is str:
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190 setInDict(args, p.get_lineage(name_only=True), qstring2list(v))
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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191 elif p.type is _InFile and not (p.default is None or type(p.default) is _Null):
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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192 v = getFromDict(args, p.get_lineage(name_only=True))
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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193 if v in [[], ""]:
bfc2c3b46325 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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194 setInDict(args, p.get_lineage(name_only=True), p.default)
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195
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196 model.write_ctd(input_ctd, arg_dict=args)