Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/mutation.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 from __future__ import absolute_import
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2
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3 from collections import namedtuple
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4 from typing import Any, Dict
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5
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6 from typing_extensions import Text # pylint: disable=unused-import
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7 # move to a regular typing import when Python 3.3-3.6 is no longer supported
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8
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9 from .errors import WorkflowException
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10
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11
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12 MutationState = namedtuple("MutationTracker", ["generation", "readers", "stepname"])
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13
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14 _generation = "http://commonwl.org/cwltool#generation"
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15
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16 class MutationManager(object):
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17 """Lock manager for checking correctness of in-place update of files.
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18
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19 Used to validate that in-place file updates happen sequentially, and that a
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20 file which is registered for in-place update cannot be read or updated by
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21 any other steps.
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22
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23 """
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24
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25 def __init__(self): # type: () -> None
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26 """Initialize."""
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27 self.generations = {} # type: Dict[Text, MutationState]
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28
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29 def register_reader(self, stepname, obj):
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30 # type: (Text, Dict[Text, Any]) -> None
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31 loc = obj["location"]
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32 current = self.generations.get(loc, MutationState(0, [], ""))
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33 obj_generation = obj.get(_generation, 0)
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34
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35 if obj_generation != current.generation:
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36 raise WorkflowException(
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37 "[job {}] wants to read {} from generation {} but current "
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38 "generation is {}(last updated by {})".format(
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39 stepname, loc, obj_generation, current.generation, current.stepname))
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40
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41 current.readers.append(stepname)
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42 self.generations[loc] = current
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43
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44 def release_reader(self, stepname, obj):
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45 # type: (Text, Dict[Text, Any]) -> None
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46 loc = obj["location"]
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47 current = self.generations.get(loc, MutationState(0, [], ""))
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48 obj_generation = obj.get(_generation, 0)
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49
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50 if obj_generation != current.generation:
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51 raise WorkflowException(
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52 "[job {}] wants to release reader on {} from generation {}"
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53 " but current generation is {} (last updated by {})".format(
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54 stepname, loc, obj_generation, current.generation,
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55 current.stepname))
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56
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57 self.generations[loc].readers.remove(stepname)
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58
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59 def register_mutation(self, stepname, obj):
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60 # type: (Text, Dict[Text, Any]) -> None
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61 loc = obj["location"]
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62 current = self.generations.get(loc, MutationState(0, [], ""))
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63 obj_generation = obj.get(_generation, 0)
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64
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65 if len(current.readers) > 0:
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66 raise WorkflowException(
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67 "[job {}] wants to modify {} but has readers: {}".format(
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68 stepname, loc, current.readers))
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69
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70 if obj_generation != current.generation:
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71 raise WorkflowException(
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72 "[job {}] wants to modify {} from generation {} but current "
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73 "generation is {} (last updated by {})".format(
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74 stepname, loc, obj_generation, current.generation, current.stepname))
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75
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76 self.generations[loc] = MutationState(current.generation+1, current.readers, stepname)
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77
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78 def set_generation(self, obj): # type: (Dict[Text, Text]) -> None
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79 loc = obj["location"]
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80 current = self.generations.get(loc, MutationState(0, [], ""))
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81 obj[_generation] = current.generation
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82
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83 def unset_generation(self, obj): # type: (Dict[Text, Text]) -> None
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84 obj.pop(_generation, None)