Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/linters/inputs.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 """This module contains a linting functions for tool inputs.""" |
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2 from galaxy.util import string_as_bool |
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3 from ._util import is_datasource, is_valid_cheetah_placeholder |
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4 from ..parser.util import _parse_name |
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5 |
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6 |
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7 def lint_inputs(tool_xml, lint_ctx): |
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8 """Lint parameters in a tool's inputs block.""" |
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9 datasource = is_datasource(tool_xml) |
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10 inputs = tool_xml.findall("./inputs//param") |
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11 num_inputs = 0 |
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12 for param in inputs: |
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13 num_inputs += 1 |
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14 param_attrib = param.attrib |
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15 has_errors = False |
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16 if "type" not in param_attrib: |
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17 lint_ctx.error("Found param input with no type specified.") |
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18 has_errors = True |
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19 if "name" not in param_attrib and "argument" not in param_attrib: |
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20 lint_ctx.error("Found param input with no name specified.") |
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21 has_errors = True |
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22 |
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23 if has_errors: |
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24 continue |
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25 |
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26 param_type = param_attrib["type"] |
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27 param_name = _parse_name(param_attrib.get("name"), param_attrib.get("argument")) |
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28 |
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29 if not is_valid_cheetah_placeholder(param_name): |
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30 lint_ctx.warn("Param input [%s] is not a valid Cheetah placeholder.", param_name) |
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31 |
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32 if param_type == "data": |
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33 if "format" not in param_attrib: |
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34 lint_ctx.warn("Param input [%s] with no format specified - 'data' format will be assumed.", param_name) |
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35 elif param_type == "select": |
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36 dynamic_options = param.get("dynamic_options", None) |
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37 if dynamic_options is None: |
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38 dynamic_options = param.find("options") |
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39 |
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40 select_options = param.findall('./option') |
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41 if any(['value' not in option.attrib for option in select_options]): |
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42 lint_ctx.error("Select [%s] has option without value", param_name) |
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43 |
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44 if dynamic_options is None and len(select_options) == 0: |
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45 message = "No options defined for select [%s]" % param_name |
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46 lint_ctx.warn(message) |
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47 # TODO: Validate type, much more... |
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48 |
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49 conditional_selects = tool_xml.findall("./inputs//conditional") |
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50 for conditional in conditional_selects: |
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51 conditional_name = conditional.get('name') |
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52 if not conditional_name: |
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53 lint_ctx.error("Conditional without a name") |
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54 if conditional.get("value_from"): |
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55 # Probably only the upload tool use this, no children elements |
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56 continue |
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57 first_param = conditional.find("param") |
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58 if first_param is None: |
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59 lint_ctx.error("Conditional '%s' has no child <param>" % conditional_name) |
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60 continue |
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61 first_param_type = first_param.get('type') |
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62 if first_param_type not in ['select', 'boolean']: |
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63 lint_ctx.warn("Conditional '%s' first param should have type=\"select\" /> or type=\"boolean\"" % conditional_name) |
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64 continue |
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65 |
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66 if first_param_type == 'select': |
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67 select_options = _find_with_attribute(first_param, 'option', 'value') |
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68 option_ids = [option.get('value') for option in select_options] |
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69 else: # boolean |
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70 option_ids = [ |
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71 first_param.get('truevalue', 'true'), |
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72 first_param.get('falsevalue', 'false') |
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73 ] |
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74 |
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75 if string_as_bool(first_param.get('optional', False)): |
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76 lint_ctx.warn("Conditional test parameter cannot be optional") |
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77 |
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78 whens = conditional.findall('./when') |
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79 if any('value' not in when.attrib for when in whens): |
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80 lint_ctx.error("When without value") |
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81 |
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82 when_ids = [w.get('value') for w in whens] |
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83 |
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84 for option_id in option_ids: |
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85 if option_id not in when_ids: |
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86 lint_ctx.warn(f"No <when /> block found for {first_param_type} option '{option_id}' inside conditional '{conditional_name}'") |
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87 |
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88 for when_id in when_ids: |
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89 if when_id not in option_ids: |
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90 if first_param_type == 'select': |
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91 lint_ctx.warn(f"No <option /> found for when block '{when_id}' inside conditional '{conditional_name}'") |
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92 else: |
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93 lint_ctx.warn(f"No truevalue/falsevalue found for when block '{when_id}' inside conditional '{conditional_name}'") |
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94 |
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95 if datasource: |
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96 for datasource_tag in ('display', 'uihints'): |
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97 if not any([param.tag == datasource_tag for param in inputs]): |
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98 lint_ctx.info("%s tag usually present in data sources" % datasource_tag) |
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99 |
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100 if num_inputs: |
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101 lint_ctx.info("Found %d input parameters.", num_inputs) |
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102 else: |
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103 if datasource: |
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104 lint_ctx.info("No input parameters, OK for data sources") |
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105 else: |
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106 lint_ctx.warn("Found no input parameters.") |
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107 |
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108 |
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109 def lint_repeats(tool_xml, lint_ctx): |
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110 """Lint repeat blocks in tool inputs.""" |
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111 repeats = tool_xml.findall("./inputs//repeat") |
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112 for repeat in repeats: |
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113 if "name" not in repeat.attrib: |
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114 lint_ctx.error("Repeat does not specify name attribute.") |
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115 if "title" not in repeat.attrib: |
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116 lint_ctx.error("Repeat does not specify title attribute.") |
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117 |
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118 |
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119 def _find_with_attribute(element, tag, attribute, test_value=None): |
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120 rval = [] |
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121 for el in (element.findall('./%s' % tag) or []): |
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122 if attribute not in el.attrib: |
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123 continue |
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124 value = el.attrib[attribute] |
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125 if test_value is not None: |
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126 if value == test_value: |
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127 rval.append(el) |
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128 else: |
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129 rval.append(el) |
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130 return rval |