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annotate env/lib/python3.9/site-packages/cwltool/factory.py @ 0:4f3585e2f14b draft default tip

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000 (2021-03-22)
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1 import os
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2 from typing import Any, Dict, Optional, Union
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3
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4 from . import load_tool
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5 from .context import LoadingContext, RuntimeContext
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6 from .errors import WorkflowException
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7 from .executors import JobExecutor, SingleJobExecutor
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8 from .process import Process
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9 from .utils import CWLObjectType
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10
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11
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12 class WorkflowStatus(Exception):
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13 def __init__(self, out: Optional[CWLObjectType], status: str) -> None:
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14 """Signaling exception for the status of a Workflow."""
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15 super().__init__("Completed %s" % status)
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16 self.out = out
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17 self.status = status
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18
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19
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20 class Callable:
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21 """Result of Factory.make()."""
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22
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23 def __init__(self, t: Process, factory: "Factory") -> None:
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24 """Initialize."""
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25 self.t = t
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26 self.factory = factory
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27
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28 def __call__(self, **kwargs):
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29 # type: (**Any) -> Union[str, Optional[CWLObjectType]]
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30 runtime_context = self.factory.runtime_context.copy()
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31 runtime_context.basedir = os.getcwd()
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32 out, status = self.factory.executor(self.t, kwargs, runtime_context)
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33 if status != "success":
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34 raise WorkflowStatus(out, status)
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35 else:
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36 return out
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37
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38
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39 class Factory:
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40 """Easy way to load a CWL document for execution."""
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41
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42 def __init__(
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43 self,
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44 executor: Optional[JobExecutor] = None,
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45 loading_context: Optional[LoadingContext] = None,
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46 runtime_context: Optional[RuntimeContext] = None,
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47 ) -> None:
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48 if executor is None:
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49 executor = SingleJobExecutor()
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50 self.executor = executor
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51 self.loading_context = loading_context
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52 if loading_context is None:
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53 self.loading_context = LoadingContext()
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54 if runtime_context is None:
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55 self.runtime_context = RuntimeContext()
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56 else:
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57 self.runtime_context = runtime_context
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58
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59 def make(self, cwl: Union[str, Dict[str, Any]]) -> Callable:
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60 """Instantiate a CWL object from a CWl document."""
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61 load = load_tool.load_tool(cwl, self.loading_context)
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62 if isinstance(load, int):
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63 raise WorkflowException("Error loading tool")
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64 return Callable(load, self)