Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/cwl/schema.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 """Abstraction around cwltool and related libraries for loading a CWL artifact.""" |
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2 import os |
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3 import tempfile |
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4 from collections import namedtuple |
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5 |
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6 from .cwltool_deps import ( |
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7 _has_relax_path_checks_flag, |
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8 default_loader, |
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9 ensure_cwltool_available, |
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10 load_tool, |
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11 LoadingContext, |
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12 resolve_and_validate_document, |
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13 ) |
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14 |
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15 RawProcessReference = namedtuple("RawProcessReference", ["loading_context", "process_object", "uri"]) |
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16 ResolvedProcessDefinition = namedtuple("ResolvedProcessDefinition", ["loading_context", "uri", "raw_process_reference"]) |
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17 REWRITE_EXPRESSIONS = False |
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18 |
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19 |
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20 class SchemaLoader: |
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21 |
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22 def __init__(self, strict=True, validate=True): |
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23 self._strict = strict |
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24 self._validate = validate |
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25 |
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26 @property |
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27 def raw_document_loader(self): |
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28 ensure_cwltool_available() |
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29 return default_loader(None) |
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30 |
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31 def loading_context(self): |
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32 loading_context = LoadingContext() |
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33 loading_context.strict = self._strict |
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34 loading_context.do_validate = self._validate |
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35 loading_context.loader = self.raw_document_loader |
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36 loading_context.do_update = True |
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37 if _has_relax_path_checks_flag(): |
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38 loading_context.relax_path_checks = True |
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39 return loading_context |
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40 |
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41 def raw_process_reference(self, path, loading_context=None): |
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42 with tempfile.TemporaryDirectory() as output_dir: |
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43 suffix = '' |
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44 if '#' in path: |
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45 path, suffix = path.split('#') |
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46 print(f""" ------- |
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47 |
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48 {open(path).read()} |
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49 |
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50 ------- |
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51 """) |
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52 processed_path = os.path.join(output_dir, os.path.basename(path)) |
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53 path = os.path.abspath(path) |
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54 uri = "file://" + path |
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55 loading_context = loading_context or self.loading_context() |
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56 if REWRITE_EXPRESSIONS: |
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57 from cwl_utils import cwl_v1_0_expression_refactor |
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58 exit_code = cwl_v1_0_expression_refactor.main([output_dir, path, '--skip-some1', '--skip-some2']) |
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59 if exit_code == 0: |
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60 uri = f"file://{processed_path}" |
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61 print(f""" ------- |
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62 |
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63 {open(processed_path).read()} |
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64 |
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65 ------- |
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66 """) |
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67 if suffix: |
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68 uri = f"{uri}#{suffix}" |
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69 loading_context, process_object, uri = load_tool.fetch_document(uri, loadingContext=loading_context) |
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70 return RawProcessReference(loading_context, process_object, uri) |
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71 |
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72 def raw_process_reference_for_object(self, process_object, uri=None, loading_context=None): |
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73 if uri is None: |
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74 uri = "galaxy://" |
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75 loading_context = loading_context or self.loading_context() |
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76 process_object["id"] = uri |
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77 loading_context, process_object, uri = load_tool.fetch_document(process_object, loadingContext=loading_context) |
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78 return RawProcessReference(loading_context, process_object, uri) |
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79 |
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80 def process_definition(self, raw_process_reference): |
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81 assert raw_process_reference.loading_context is not None, "No loading context found for raw_process_reference" |
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82 loading_context, uri = resolve_and_validate_document( |
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83 raw_process_reference.loading_context, |
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84 raw_process_reference.process_object, |
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85 raw_process_reference.uri, |
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86 ) |
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87 process_def = ResolvedProcessDefinition( |
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88 loading_context, |
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89 uri, |
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90 raw_process_reference, |
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91 ) |
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92 return process_def |
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93 |
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94 def tool(self, **kwds): |
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95 process_definition = kwds.get("process_definition", None) |
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96 if process_definition is None: |
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97 raw_process_reference = kwds.get("raw_process_reference", None) |
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98 if raw_process_reference is None: |
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99 raw_process_reference = self.raw_process_reference(kwds["path"]) |
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100 process_definition = self.process_definition(raw_process_reference) |
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101 |
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102 tool = load_tool.make_tool( |
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103 process_definition.uri, |
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104 process_definition.loading_context, |
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105 ) |
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106 return tool |
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107 |
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108 |
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109 schema_loader = SchemaLoader() |
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110 non_strict_non_validating_schema_loader = SchemaLoader(strict=False, validate=False) |