Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/procgenerator.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 import copy |
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2 from typing import Dict, Optional, Tuple, cast |
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3 |
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4 from ruamel.yaml.comments import CommentedMap |
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5 from schema_salad.exceptions import ValidationException |
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6 from schema_salad.sourceline import indent |
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7 |
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8 from .context import LoadingContext, RuntimeContext |
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9 from .errors import WorkflowException |
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10 from .load_tool import load_tool |
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11 from .loghandler import _logger |
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12 from .process import Process, shortname |
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13 from .utils import CWLObjectType, JobsGeneratorType, OutputCallbackType |
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14 |
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15 |
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16 class ProcessGeneratorJob: |
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17 """Result of ProcessGenerator.job().""" |
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18 |
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19 def __init__(self, procgenerator: "ProcessGenerator") -> None: |
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20 """Create a ProccessGenerator Job.""" |
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21 self.procgenerator = procgenerator |
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22 self.jobout = None # type: Optional[CWLObjectType] |
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23 self.processStatus = None # type: Optional[str] |
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24 |
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25 def receive_output( |
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26 self, jobout: Optional[CWLObjectType], processStatus: str |
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27 ) -> None: |
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28 self.jobout = jobout |
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29 self.processStatus = processStatus |
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30 |
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31 def job( |
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32 self, |
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33 job_order: CWLObjectType, |
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34 output_callbacks: Optional[OutputCallbackType], |
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35 runtimeContext: RuntimeContext, |
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36 ) -> JobsGeneratorType: |
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37 |
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38 try: |
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39 yield from self.procgenerator.embedded_tool.job( |
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40 job_order, self.receive_output, runtimeContext |
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41 ) |
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42 |
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43 while self.processStatus is None: |
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44 yield None |
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45 |
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46 if self.processStatus != "success" and output_callbacks: |
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47 output_callbacks(self.jobout, self.processStatus) |
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48 return |
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49 |
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50 if self.jobout is None: |
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51 raise WorkflowException("jobout should not be None") |
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52 |
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53 created_tool, runinputs = self.procgenerator.result( |
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54 job_order, self.jobout, runtimeContext |
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55 ) |
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56 |
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57 yield from created_tool.job(runinputs, output_callbacks, runtimeContext) |
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58 |
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59 except WorkflowException: |
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60 raise |
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61 except Exception as exc: |
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62 _logger.exception("Unexpected exception") |
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63 raise WorkflowException(str(exc)) |
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64 |
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65 |
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66 class ProcessGenerator(Process): |
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67 def __init__( |
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68 self, |
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69 toolpath_object: CommentedMap, |
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70 loadingContext: LoadingContext, |
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71 ) -> None: |
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72 """Create a ProcessGenerator from the given dictionary and context.""" |
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73 super().__init__(toolpath_object, loadingContext) |
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74 self.loadingContext = loadingContext # type: LoadingContext |
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75 try: |
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76 if isinstance(toolpath_object["run"], CommentedMap): |
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77 self.embedded_tool = loadingContext.construct_tool_object( |
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78 toolpath_object["run"], loadingContext |
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79 ) # type: Process |
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80 else: |
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81 loadingContext.metadata = {} |
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82 self.embedded_tool = load_tool(toolpath_object["run"], loadingContext) |
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83 except ValidationException as vexc: |
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84 if loadingContext.debug: |
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85 _logger.exception("Validation exception") |
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86 raise WorkflowException( |
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87 "Tool definition %s failed validation:\n%s" |
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88 % (toolpath_object["run"], indent(str(vexc))) |
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89 ) |
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90 |
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91 def job( |
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92 self, |
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93 job_order: CWLObjectType, |
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94 output_callbacks: Optional[OutputCallbackType], |
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95 runtimeContext: RuntimeContext, |
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96 ) -> JobsGeneratorType: |
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97 return ProcessGeneratorJob(self).job( |
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98 job_order, output_callbacks, runtimeContext |
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99 ) |
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100 |
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101 def result( |
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102 self, |
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103 job_order: CWLObjectType, |
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104 jobout: CWLObjectType, |
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105 runtimeContext: RuntimeContext, |
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106 ) -> Tuple[Process, CWLObjectType]: |
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107 try: |
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108 loadingContext = self.loadingContext.copy() |
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109 loadingContext.metadata = {} |
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110 embedded_tool = load_tool( |
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111 cast(Dict[str, str], jobout["runProcess"])["location"], loadingContext |
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112 ) |
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113 except ValidationException as vexc: |
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114 if runtimeContext.debug: |
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115 _logger.exception("Validation exception") |
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116 raise WorkflowException( |
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117 "Tool definition %s failed validation:\n%s" |
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118 % (jobout["runProcess"], indent(str(vexc))) |
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119 ) |
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120 |
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121 if "runInputs" in jobout: |
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122 runinputs = cast(CWLObjectType, jobout["runInputs"]) |
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123 else: |
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124 runinputs = copy.deepcopy(job_order) |
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125 for i in self.embedded_tool.tool["inputs"]: |
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126 if shortname(i["id"]) in runinputs: |
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127 del runinputs[shortname(i["id"])] |
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128 if "id" in runinputs: |
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129 del runinputs["id"] |
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130 |
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131 return embedded_tool, runinputs |