Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/procgenerator.py @ 2:6af9afd405e9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -0400
parents 26e78fe6e8c4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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1 import copy
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2 from .process import Process, shortname
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3 from .load_tool import load_tool
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4 from schema_salad import validate
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5 from schema_salad.sourceline import indent
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6 from .errors import WorkflowException
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7 from .context import RuntimeContext, LoadingContext
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8 from typing import (Any, Callable, Dict, Generator, Iterable, List,
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9 Mapping, MutableMapping, MutableSequence,
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10 Optional, Tuple, Union, cast)
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11 from .loghandler import _logger
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12 from typing_extensions import Text # pylint: disable=unused-import
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13
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14 class ProcessGeneratorJob(object):
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15 def __init__(self, procgenerator):
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16 # type: (ProcessGenerator) -> None
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17 self.procgenerator = procgenerator
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18 self.jobout = None # type: Optional[Dict[Text, Any]]
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19 self.processStatus = None # type: Optional[Text]
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20
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21 def receive_output(self, jobout, processStatus):
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22 # type: (Dict[Text, Any], Text) -> None
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23 self.jobout = jobout
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24 self.processStatus = processStatus
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25
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26 def job(self,
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27 job_order, # type: Mapping[Text, Any]
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28 output_callbacks, # type: Callable[[Any, Any], Any]
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29 runtimeContext # type: RuntimeContext
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30 ): # type: (...) -> Generator[Any, None, None]
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31 # FIXME: Declare base type for what Generator yields
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32
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33 try:
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34 for tool in self.procgenerator.embedded_tool.job(
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35 job_order,
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36 self.receive_output,
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37 runtimeContext):
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38 yield tool
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39
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40 while self.processStatus is None:
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41 yield None
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42
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43 if self.processStatus != "success":
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44 output_callbacks(self.jobout, self.processStatus)
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45 return
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46
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47 if self.jobout is None:
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48 raise WorkflowException("jobout should not be None")
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49
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50 created_tool, runinputs = self.procgenerator.result(job_order, self.jobout, runtimeContext)
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51
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52 for tool in created_tool.job(
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53 runinputs,
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54 output_callbacks,
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55 runtimeContext):
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56 yield tool
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57
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58 except WorkflowException:
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59 raise
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60 except Exception as exc:
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61 _logger.exception("Unexpected exception")
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62 raise WorkflowException(Text(exc))
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63
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64
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65 class ProcessGenerator(Process):
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66 def __init__(self,
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67 toolpath_object, # type: MutableMapping[Text, Any]
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68 loadingContext # type: LoadingContext
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69 ): # type: (...) -> None
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70 super(ProcessGenerator, self).__init__(
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71 toolpath_object, loadingContext)
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72 self.loadingContext = loadingContext # type: LoadingContext
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73 try:
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74 if isinstance(toolpath_object["run"], MutableMapping):
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75 self.embedded_tool = loadingContext.construct_tool_object(
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76 toolpath_object["run"], loadingContext) # type: Process
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77 else:
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78 loadingContext.metadata = {}
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79 self.embedded_tool = load_tool(
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80 toolpath_object["run"], loadingContext)
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81 except validate.ValidationException as vexc:
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82 if loadingContext.debug:
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83 _logger.exception("Validation exception")
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84 raise WorkflowException(
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85 u"Tool definition %s failed validation:\n%s" %
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86 (toolpath_object["run"], indent(str(vexc))))
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87
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88 def job(self,
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89 job_order, # type: Mapping[Text, Text]
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90 output_callbacks, # type: Callable[[Any, Any], Any]
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91 runtimeContext # type: RuntimeContext
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92 ): # type: (...) -> Generator[Any, None, None]
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93 # FIXME: Declare base type for what Generator yields
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94 return ProcessGeneratorJob(self).job(job_order, output_callbacks, runtimeContext)
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95
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96 def result(self,
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97 job_order, # type: Mapping[Text, Any]
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98 jobout, # type: Mapping[Text, Any]
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99 runtimeContext # type: RuntimeContext
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100 ): # type: (...) -> Tuple[Process, MutableMapping[Text, Any]]
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101 try:
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102 loadingContext = self.loadingContext.copy()
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103 loadingContext.metadata = {}
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104 embedded_tool = load_tool(
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105 jobout["runProcess"]["location"], loadingContext)
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106 except validate.ValidationException as vexc:
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107 if runtimeContext.debug:
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108 _logger.exception("Validation exception")
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109 raise WorkflowException(
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110 u"Tool definition %s failed validation:\n%s" %
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111 (jobout["runProcess"], indent(str(vexc))))
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112
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113 if "runInputs" in jobout:
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114 runinputs = cast(MutableMapping[Text, Any], jobout["runInputs"])
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115 else:
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116 runinputs = cast(MutableMapping[Text, Any], copy.deepcopy(job_order))
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117 for i in self.embedded_tool.tool["inputs"]:
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118 if shortname(i["id"]) in runinputs:
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119 del runinputs[shortname(i["id"])]
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120 if "id" in runinputs:
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121 del runinputs["id"]
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122
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123 return embedded_tool, runinputs