Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/verify/asserts/__init__.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 import logging |
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2 import sys |
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3 |
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4 from galaxy.util import unicodify |
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5 from galaxy.util.getargspec import getfullargspec |
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6 |
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7 log = logging.getLogger(__name__) |
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8 |
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9 assertion_module_names = ['text', 'tabular', 'xml', 'hdf5', 'archive', 'size'] |
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10 |
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11 # Code for loading modules containing assertion checking functions, to |
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12 # create a new module of assertion functions, create the needed python |
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13 # source file "test/base/asserts/<MODULE_NAME>.py" and add |
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14 # <MODULE_NAME> to the list of assertion module names defined above. |
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15 assertion_modules = [] |
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16 for assertion_module_name in assertion_module_names: |
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17 full_assertion_module_name = 'galaxy.tool_util.verify.asserts.' + assertion_module_name |
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18 try: |
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19 # Dynamically import module |
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20 __import__(full_assertion_module_name) |
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21 assertion_module = sys.modules[full_assertion_module_name] |
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22 assertion_modules.append(assertion_module) |
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23 except Exception: |
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24 log.exception('Failed to load assertion module: %s', assertion_module_name) |
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25 |
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26 |
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27 def verify_assertions(data, assertion_description_list): |
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28 """ This function takes a list of assertions and a string to check |
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29 these assertions against. """ |
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30 for assertion_description in assertion_description_list: |
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31 verify_assertion(data, assertion_description) |
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32 |
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33 |
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34 def verify_assertion(data, assertion_description): |
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35 tag = assertion_description["tag"] |
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36 assert_function_name = "assert_" + tag |
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37 assert_function = None |
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38 for assertion_module in assertion_modules: |
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39 if hasattr(assertion_module, assert_function_name): |
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40 assert_function = getattr(assertion_module, assert_function_name) |
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41 |
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42 if assert_function is None: |
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43 errmsg = "Unable to find test function associated with XML tag '%s'. Check your tool file syntax." % tag |
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44 raise AssertionError(errmsg) |
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45 |
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46 assert_function_args = getfullargspec(assert_function).args |
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47 args = {} |
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48 for attribute, value in assertion_description["attributes"].items(): |
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49 if attribute in assert_function_args: |
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50 args[attribute] = value |
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51 |
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52 # Three special arguments automatically populated independently of |
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53 # tool XML attributes. output is passed in as the contents of the |
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54 # output file. verify_assertions_function is passed in as the |
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55 # verify_assertions function defined above, this allows |
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56 # recursively checking assertions on subsections of |
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57 # output. children is the parsed version of the child elements of |
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58 # the XML element describing this assertion. See |
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59 # assert_element_text in test/base/asserts/xml.py as an example of |
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60 # how to use verify_assertions_function and children in conjuction |
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61 # to apply assertion checking to a subset of the input. The parsed |
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62 # version of an elements child elements do not need to just define |
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63 # assertions, developers of assertion functions can also use the |
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64 # child elements in novel ways to define inputs the assertion |
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65 # checking function (for instance consider the following fictional |
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66 # assertion function for checking column titles of tabular output |
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67 # - <has_column_titles><with_name name="sequence"><with_name |
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68 # name="probability"></has_column_titles>.) |
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69 if "output" in assert_function_args: |
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70 # If the assert_function will have an attribute called "output" |
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71 # the data passed from the test to the function will be unicodified. |
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72 # This is because most of the assert functions are working on pure |
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73 # text files. |
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74 args["output"] = unicodify(data) |
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75 if "output_bytes" in assert_function_args: |
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76 # This will read in data as bytes and will not change it prior passing |
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77 # it to the assert_function |
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78 args["output_bytes"] = data |
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79 |
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80 if "verify_assertions_function" in assert_function_args: |
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81 args["verify_assertions_function"] = verify_assertions |
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82 |
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83 if "children" in assert_function_args: |
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84 args["children"] = assertion_description["children"] |
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85 |
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86 # TODO: Verify all needed function arguments are specified. |
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87 assert_function(**args) |