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annotate planemo/lib/python3.7/site-packages/galaxy/tool_util/cwl/schema.py @ 0:d30785e31577 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:18:57 -0400
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1 """Abstraction around cwltool and related libraries for loading a CWL artifact."""
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2 import os
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3 from collections import namedtuple
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4
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5 from .cwltool_deps import (
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6 default_loader,
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7 ensure_cwltool_available,
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8 load_tool,
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9 LoadingContext,
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10 resolve_and_validate_document,
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11 )
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12
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13 RawProcessReference = namedtuple("RawProcessReference", ["loading_context", "process_object", "uri"])
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14 ResolvedProcessDefinition = namedtuple("ResolvedProcessDefinition", ["loading_context", "uri", "raw_process_reference"])
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15 REWRITE_EXPRESSIONS = False
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16
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17
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18 class SchemaLoader(object):
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19
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20 def __init__(self, strict=True, validate=True):
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21 self._strict = strict
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22 self._validate = validate
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23
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24 @property
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25 def raw_document_loader(self):
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26 ensure_cwltool_available()
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27 return default_loader(None)
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28
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29 def loading_context(self):
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30 loading_context = LoadingContext()
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31 loading_context.strict = self._strict
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32 loading_context.do_validate = self._validate
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33 loading_context.loader = self.raw_document_loader
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34 loading_context.do_update = True
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35 return loading_context
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36
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37 def raw_process_reference(self, path, loading_context=None):
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38 path = os.path.abspath(path)
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39 uri = "file://" + path
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40 loading_context = loading_context or self.loading_context()
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41 if REWRITE_EXPRESSIONS and not uri.endswith(".galaxy"):
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42 galaxy_path = os.path.abspath(path) + ".galaxy"
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43 from cwl_utils import etools_to_clt
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44 etools_to_clt.main([path, galaxy_path])
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45 galaxy_uri = "file://" + galaxy_path
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46 uri = galaxy_uri
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47 loading_context, process_object, uri = load_tool.fetch_document(uri, loadingContext=loading_context)
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48 return RawProcessReference(loading_context, process_object, uri)
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49
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50 def raw_process_reference_for_object(self, process_object, uri=None, loading_context=None):
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51 if uri is None:
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52 uri = "galaxy://"
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53 loading_context = loading_context or self.loading_context()
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54 process_object["id"] = uri
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55 loading_context, process_object, uri = load_tool.fetch_document(process_object, loadingContext=loading_context)
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56 return RawProcessReference(loading_context, process_object, uri)
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57
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58 def process_definition(self, raw_process_reference):
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59 assert raw_process_reference.loading_context is not None, "No loading context found for raw_process_reference"
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60 loading_context, uri = resolve_and_validate_document(
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61 raw_process_reference.loading_context,
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62 raw_process_reference.process_object,
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63 raw_process_reference.uri,
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64 )
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65 process_def = ResolvedProcessDefinition(
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66 loading_context,
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67 uri,
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68 raw_process_reference,
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69 )
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70 return process_def
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71
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72 def tool(self, **kwds):
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73 process_definition = kwds.get("process_definition", None)
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74 if process_definition is None:
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75 raw_process_reference = kwds.get("raw_process_reference", None)
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76 if raw_process_reference is None:
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77 raw_process_reference = self.raw_process_reference(kwds["path"])
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78 process_definition = self.process_definition(raw_process_reference)
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79
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80 tool = load_tool.make_tool(
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81 process_definition.uri,
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82 process_definition.loading_context,
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83 )
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84 return tool
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85
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86
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87 schema_loader = SchemaLoader()
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88 non_strict_non_validating_schema_loader = SchemaLoader(strict=False, validate=False)