Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/gxformat2/lint.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 """Workflow linting entry point - main script.""" |
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2 import argparse |
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3 import os |
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4 import sys |
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5 |
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6 from gxformat2._scripts import ensure_format2 |
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7 from gxformat2.linting import LintContext |
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8 from gxformat2.markdown_parse import validate_galaxy_markdown |
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9 from gxformat2.normalize import Inputs |
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10 from gxformat2.yaml import ordered_load, ordered_load_path |
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11 |
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12 EXIT_CODE_SUCCESS = 0 |
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13 EXIT_CODE_LINT_FAILED = 1 |
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14 EXIT_CODE_FORMAT_ERROR = 2 |
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15 EXIT_CODE_FILE_PARSE_FAILED = 3 |
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16 |
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17 LINT_FAILED_NO_OUTPUTS = "Workflow contained no outputs" |
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18 LINT_FAILED_OUTPUT_NO_LABEL = "Workflow contained output without a label" |
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19 |
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20 |
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21 def ensure_key(lint_context, has_keys, key, has_class=None, has_value=None): |
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22 if key not in has_keys: |
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23 lint_context.error("expected to find key [{key}] but absent", key=key) |
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24 return None |
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25 |
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26 value = has_keys[key] |
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27 return ensure_key_has_value(lint_context, has_keys, key, value, has_class=has_class, has_value=has_value) |
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28 |
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29 |
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30 def ensure_key_if_present(lint_context, has_keys, key, default=None, has_class=None): |
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31 if key not in has_keys: |
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32 return default |
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33 |
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34 value = has_keys[key] |
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35 return ensure_key_has_value(lint_context, has_keys, key, value, has_class=has_class, has_value=None) |
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36 |
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37 |
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38 def ensure_key_has_value(lint_context, has_keys, key, value, has_class=None, has_value=None): |
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39 if has_class is not None and not isinstance(value, has_class): |
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40 lint_context.error("expected value [{value}] with key [{key}] to be of class {clazz}", key=key, value=value, clazz=has_class) |
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41 if has_value is not None and value != has_value: |
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42 lint_context.error("expected value [{value}] with key [{key}] to be {expected_value}", key=key, value=value, expected_value=has_value) |
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43 return value |
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44 |
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45 |
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46 def _lint_step_errors(lint_context, step): |
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47 step_errors = step.get("errors") |
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48 if step_errors is not None: |
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49 lint_context.warn("tool step contains error indicated during Galaxy export - %s" % step_errors) |
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50 |
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51 |
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52 def lint_ga_path(lint_context, path): |
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53 """Apply linting of native workflows to specified path.""" |
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54 workflow_dict = ordered_load_path(path) |
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55 return lint_ga(lint_context, workflow_dict, path=path) |
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56 |
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57 |
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58 def lint_ga(lint_context, workflow_dict, path=None): |
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59 """Lint a native/legacy style Galaxy workflow and populate the corresponding LintContext.""" |
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60 ensure_key(lint_context, workflow_dict, "format-version", has_value="0.1") |
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61 ensure_key(lint_context, workflow_dict, "a_galaxy_workflow", has_value="true") |
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62 |
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63 native_steps = ensure_key(lint_context, workflow_dict, "steps", has_class=dict) or {} |
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64 |
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65 found_outputs = False |
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66 found_output_without_label = False |
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67 for order_index_str, step in native_steps.items(): |
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68 if not order_index_str.isdigit(): |
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69 lint_context.error("expected step_key to be integer not [{value}]", value=order_index_str) |
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70 |
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71 workflow_outputs = ensure_key_if_present(lint_context, step, "workflow_outputs", default=[], has_class=list) |
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72 for workflow_output in workflow_outputs: |
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73 found_outputs = True |
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74 |
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75 if not workflow_output.get("label"): |
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76 found_output_without_label = True |
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77 |
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78 step_type = step.get("type") |
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79 if step_type == "subworkflow": |
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80 subworkflow = ensure_key(lint_context, step, "subworkflow", has_class=dict) |
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81 lint_ga(lint_context, subworkflow) |
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82 |
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83 _lint_step_errors(lint_context, step) |
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84 _lint_tool_if_present(lint_context, step) |
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85 |
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86 _validate_report(lint_context, workflow_dict) |
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87 if not found_outputs: |
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88 lint_context.warn(LINT_FAILED_NO_OUTPUTS) |
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89 |
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90 if found_output_without_label: |
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91 lint_context.warn(LINT_FAILED_OUTPUT_NO_LABEL) |
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92 |
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93 _lint_training(lint_context, workflow_dict) |
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94 |
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95 |
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96 def lint_format2(lint_context, workflow_dict, path=None): |
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97 """Lint a Format 2 Galaxy workflow and populate the corresponding LintContext.""" |
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98 from gxformat2.schema.v19_09 import load_document |
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99 from schema_salad.exceptions import SchemaSaladException # type: ignore |
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100 try: |
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101 load_document("file://" + os.path.normpath(path)) |
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102 except SchemaSaladException as e: |
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103 lint_context.error("Validation failed " + str(e)) |
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104 |
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105 steps = ensure_key_if_present(lint_context, workflow_dict, 'steps', default={}, has_class=dict) |
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106 for key, step in steps.items(): |
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107 _lint_step_errors(lint_context, step) |
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108 _lint_tool_if_present(lint_context, step) |
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109 |
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110 _validate_input_types(lint_context, workflow_dict) |
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111 _validate_report(lint_context, workflow_dict) |
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112 _lint_training(lint_context, workflow_dict) |
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113 |
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114 |
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115 def _validate_input_types(lint_context: LintContext, workflow_dict: dict): |
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116 try: |
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117 inputs = Inputs(workflow_dict) |
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118 except Exception: |
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119 # bad document, can't process inputs... |
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120 return |
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121 for input_def in inputs._inputs: |
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122 input_type = input_def.get("type") |
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123 if "default" in input_def: |
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124 input_default = input_def['default'] |
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125 if input_type == "int": |
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126 if not isinstance(input_default, int): |
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127 lint_context.error('Input default is of invalid type') |
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128 elif input_type == "float": |
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129 if not isinstance(input_default, (int, float)): |
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130 lint_context.error('Input default is of invalid type') |
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131 elif input_type == "string": |
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132 if not isinstance(input_default, str): |
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133 lint_context.error('Input default is of invalid type') |
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134 |
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135 |
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136 def _lint_tool_if_present(lint_context, step_dict): |
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137 tool_id = step_dict.get('tool_id') |
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138 if tool_id and 'testtoolshed' in tool_id: |
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139 lint_context.warn('Step references a tool from the test tool shed, this should be replaced with a production tool') |
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140 |
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141 |
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142 def _validate_report(lint_context, workflow_dict): |
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143 report_dict = ensure_key_if_present(lint_context, workflow_dict, "report", default=None, has_class=dict) |
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144 if report_dict is not None: |
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145 markdown = ensure_key(lint_context, report_dict, "markdown", has_class=str) |
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146 if isinstance(markdown, str): |
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147 try: |
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148 validate_galaxy_markdown(markdown) |
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149 except ValueError as e: |
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150 lint_context.error("Report markdown validation failed [%s]" % e) |
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151 |
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152 |
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153 def _lint_training(lint_context, workflow_dict): |
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154 if lint_context.training_topic is None: |
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155 return |
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156 |
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157 if "tags" not in workflow_dict: |
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158 lint_context.warn("Missing tag(s).") |
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159 else: |
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160 tags = workflow_dict["tags"] |
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161 if lint_context.training_topic not in tags: |
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162 lint_context.warn("Missing expected training topic (%s) as workflow tag." % lint_context.training_topic) |
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163 # Move up into individual lints - all workflows should have docs. |
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164 format2_dict = ensure_format2(workflow_dict) |
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165 if "doc" not in format2_dict: |
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166 lint_context.warn("Missing workflow documentation (annotation or doc element)") |
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167 elif not format2_dict["doc"]: |
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168 lint_context.warn("Empty workflow documentation (annotation or doc element)") |
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169 |
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170 |
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171 def main(argv=None): |
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172 """Script entry point for linting workflows.""" |
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173 if argv is None: |
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174 argv = sys.argv |
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175 args = _parser().parse_args(argv[1:]) |
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176 path = args.path |
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177 with open(path, "r") as f: |
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178 try: |
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179 workflow_dict = ordered_load(f) |
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180 except Exception: |
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181 return EXIT_CODE_FILE_PARSE_FAILED |
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182 workflow_class = workflow_dict.get("class") |
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183 lint_func = lint_format2 if workflow_class == "GalaxyWorkflow" else lint_ga |
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184 lint_context = LintContext(training_topic=args.training_topic) |
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185 lint_func(lint_context, workflow_dict, path=path) |
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186 lint_context.print_messages() |
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187 if lint_context.found_errors: |
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188 return EXIT_CODE_FORMAT_ERROR |
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189 elif lint_context.found_warns: |
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190 return EXIT_CODE_LINT_FAILED |
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191 else: |
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192 return EXIT_CODE_SUCCESS |
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193 |
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194 |
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195 def _parser(): |
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196 parser = argparse.ArgumentParser() |
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197 parser.add_argument("--training-topic", |
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198 required=False, |
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199 help='If this is a training workflow, specify a training topic.') |
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200 parser.add_argument('path', metavar='PATH', type=str, |
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201 help='workflow path') |
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202 return parser |
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203 |
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204 |
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205 if __name__ == "__main__": |
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206 sys.exit(main()) |
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207 |
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208 |
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209 __all__ = ('main', 'lint_format2', 'lint_ga') |