Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/factory.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 import os
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4 from typing import Callable as tCallable # pylint: disable=unused-import
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5 from typing import Any, Dict, Optional, Tuple, Union
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6
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7 from typing_extensions import Text # pylint: disable=unused-import
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8 # move to a regular typing import when Python 3.3-3.6 is no longer supported
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9
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10 from . import load_tool
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11 from .context import LoadingContext, RuntimeContext
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12 from .executors import SingleJobExecutor
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13 from .process import Process
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14
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15
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16 class WorkflowStatus(Exception):
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17 def __init__(self, out, status):
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18 # type: (Dict[Text,Any], Text) -> None
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19 """Signaling exception for the status of a Workflow."""
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20 super(WorkflowStatus, self).__init__("Completed %s" % status)
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21 self.out = out
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22 self.status = status
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23
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24
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25 class Callable(object):
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26 def __init__(self, t, factory): # type: (Process, Factory) -> None
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27 """Initialize."""
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28 self.t = t
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29 self.factory = factory
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30
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31 def __call__(self, **kwargs):
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32 # type: (**Any) -> Union[Text, Dict[Text, Text]]
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33 runtime_context = self.factory.runtime_context.copy()
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34 runtime_context.basedir = os.getcwd()
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35 out, status = self.factory.executor(self.t, kwargs, runtime_context)
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36 if status != "success":
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37 raise WorkflowStatus(out, status)
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38 else:
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39 return out
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40
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41 class Factory(object):
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42 def __init__(self,
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43 executor=None, # type: Optional[tCallable[...,Tuple[Dict[Text,Any], Text]]]
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44 loading_context=None, # type: Optional[LoadingContext]
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45 runtime_context=None # type: Optional[RuntimeContext]
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46 ): # type: (...) -> None
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47 """Easy way to load a CWL document for execution."""
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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): # type: (Union[Text, Dict[Text, 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 Exception("Error loading tool")
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64 return Callable(load, self)