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annotate planemo/lib/python3.7/site-packages/galaxy/tool_util/linters/tests.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
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1 """This module contains a linting functions for tool tests."""
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2 from ._util import is_datasource
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3
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4
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5 # Misspelled so as not be picked up by nosetests.
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6 def lint_tsts(tool_xml, lint_ctx):
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7 tests = tool_xml.findall("./tests/test")
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8 datasource = is_datasource(tool_xml)
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9
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10 if not tests and not datasource:
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11 lint_ctx.warn("No tests found, most tools should define test cases.")
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12 elif datasource:
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13 lint_ctx.info("No tests found, that should be OK for data_sources.")
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14
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15 num_valid_tests = 0
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16 for test in tests:
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17 has_test = False
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18 if "expect_failure" in test.attrib or "expect_exit_code" in test.attrib:
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19 has_test = True
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20 if len(test.findall("assert_stdout")) > 0:
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21 has_test = True
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22 if len(test.findall("assert_stderr")) > 0:
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23 has_test = True
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24 if len(test.findall("assert_command")) > 0:
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25 has_test = True
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26
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27 output_data_names, output_collection_names = _collect_output_names(tool_xml)
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28 found_output_test = False
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29 for output in test.findall("output"):
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30 found_output_test = True
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31 name = output.attrib.get("name", None)
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32 if not name:
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33 lint_ctx.warn("Found output tag without a name defined.")
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34 else:
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35 if name not in output_data_names:
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36 lint_ctx.error("Found output tag with unknown name [%s], valid names [%s]" % (name, output_data_names))
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37
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38 for output_collection in test.findall("output_collection"):
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39 found_output_test = True
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40 name = output_collection.attrib.get("name", None)
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41 if not name:
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42 lint_ctx.warn("Found output_collection tag without a name defined.")
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43 else:
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44 if name not in output_collection_names:
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45 lint_ctx.warn("Found output_collection tag with unknown name [%s], valid names [%s]" % (name, output_collection_names))
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46
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47 has_test = has_test or found_output_test
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48 if not has_test:
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49 lint_ctx.warn("No outputs or expectations defined for tests, this test is likely invalid.")
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50 else:
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51 num_valid_tests += 1
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52
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53 if num_valid_tests or datasource:
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54 lint_ctx.valid("%d test(s) found.", num_valid_tests)
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55 else:
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56 lint_ctx.warn("No valid test(s) found.")
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57
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58
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59 def _collect_output_names(tool_xml):
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60 output_data_names = []
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61 output_collection_names = []
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62
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63 outputs = tool_xml.findall("./outputs")
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64 if len(outputs) == 1:
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65 for output in list(outputs[0]):
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66 name = output.attrib.get("name", None)
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67 if not name:
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68 continue
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69 if output.tag == "data":
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70 output_data_names.append(name)
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71 elif output.tag == "collection":
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72 output_collection_names.append(name)
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73
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74 return output_data_names, output_collection_names