Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/linters/tests.py @ 0:4f3585e2f14b draft default tip
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author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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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 test_expect = ("expect_failure", "expect_exit_code", "expect_num_outputs") |
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19 for te in test_expect: |
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20 if te in test.attrib: |
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21 has_test = True |
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22 break |
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23 test_assert = ("assert_stdout", "assert_stderr", "assert_command") |
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24 for ta in test_assert: |
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25 if len(test.findall(ta)) > 0: |
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26 has_test = True |
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27 break |
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28 |
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29 output_data_names, output_collection_names = _collect_output_names(tool_xml) |
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30 found_output_test = False |
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31 for output in test.findall("output"): |
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32 found_output_test = True |
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33 name = output.attrib.get("name", None) |
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34 if not name: |
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35 lint_ctx.warn("Found output tag without a name defined.") |
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36 else: |
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37 if name not in output_data_names: |
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38 lint_ctx.error(f"Found output tag with unknown name [{name}], valid names [{output_data_names}]") |
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39 |
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40 for output_collection in test.findall("output_collection"): |
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41 found_output_test = True |
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42 name = output_collection.attrib.get("name", None) |
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43 if not name: |
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44 lint_ctx.warn("Found output_collection tag without a name defined.") |
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45 else: |
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46 if name not in output_collection_names: |
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47 lint_ctx.warn(f"Found output_collection tag with unknown name [{name}], valid names [{output_collection_names}]") |
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48 |
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49 has_test = has_test or found_output_test |
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50 if not has_test: |
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51 lint_ctx.warn("No outputs or expectations defined for tests, this test is likely invalid.") |
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52 else: |
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53 num_valid_tests += 1 |
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54 |
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55 if num_valid_tests or datasource: |
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56 lint_ctx.valid("%d test(s) found.", num_valid_tests) |
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57 else: |
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58 lint_ctx.warn("No valid test(s) found.") |
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59 |
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60 |
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61 def _collect_output_names(tool_xml): |
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62 output_data_names = [] |
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63 output_collection_names = [] |
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64 |
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65 outputs = tool_xml.findall("./outputs") |
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66 if len(outputs) == 1: |
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67 for output in list(outputs[0]): |
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68 name = output.attrib.get("name", None) |
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69 if not name: |
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70 continue |
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71 if output.tag == "data": |
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72 output_data_names.append(name) |
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73 elif output.tag == "collection": |
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74 output_collection_names.append(name) |
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75 |
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76 return output_data_names, output_collection_names |