Mercurial > repos > guerler > springsuite

annotate planemo/lib/python3.7/site-packages/galaxy/tool_util/linters/inputs.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 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
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36 if param_type == "select":
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37 dynamic_options = param.get("dynamic_options", None)
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38 if dynamic_options is None:
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39 dynamic_options = param.find("options")
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40
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41 select_options = _find_with_attribute(param, 'option', 'value')
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42 if any(['value' not in option.attrib for option in select_options]):
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43 lint_ctx.error("Option without value")
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44
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45 if dynamic_options is None and len(select_options) == 0:
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46 message = "No options defined for select [%s]" % param_name
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47 lint_ctx.warn(message)
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48
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49 # TODO: Validate type, much more...
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50
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51 conditional_selects = tool_xml.findall("./inputs//conditional")
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52 for conditional in conditional_selects:
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53 conditional_name = conditional.get('name')
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54 if not conditional_name:
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55 lint_ctx.error("Conditional without a name")
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56 if conditional.get("value_from"):
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57 # Probably only the upload tool use this, no children elements
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58 continue
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59 first_param = conditional.find("param")
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60 if first_param is None:
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61 lint_ctx.error("Conditional '%s' has no child <param>" % conditional_name)
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62 continue
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63 first_param_type = first_param.get('type')
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64 if first_param_type not in ['select', 'boolean']:
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65 lint_ctx.warn("Conditional '%s' first param should have type=\"select\" /> or type=\"boolean\"" % conditional_name)
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66 continue
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67
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68 if first_param_type == 'select':
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69 select_options = _find_with_attribute(first_param, 'option', 'value')
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70 option_ids = [option.get('value') for option in select_options]
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71 else: # boolean
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72 option_ids = [
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73 first_param.get('truevalue', 'true'),
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74 first_param.get('falsevalue', 'false')
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75 ]
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76
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77 if string_as_bool(first_param.get('optional', False)):
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78 lint_ctx.warn("Conditional test parameter cannot be optional")
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79
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80 whens = conditional.findall('./when')
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81 if any('value' not in when.attrib for when in whens):
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82 lint_ctx.error("When without value")
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83
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84 when_ids = [w.get('value') for w in whens]
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85
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86 for option_id in option_ids:
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87 if option_id not in when_ids:
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88 lint_ctx.warn("No <when /> block found for %s option '%s' inside conditional '%s'" % (first_param_type, option_id, conditional_name))
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89
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90 for when_id in when_ids:
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91 if when_id not in option_ids:
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92 if first_param_type == 'select':
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93 lint_ctx.warn("No <option /> found for when block '%s' inside conditional '%s'" % (when_id, conditional_name))
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94 else:
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95 lint_ctx.warn("No truevalue/falsevalue found for when block '%s' inside conditional '%s'" % (when_id, conditional_name))
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96
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97 if datasource:
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98 for datasource_tag in ('display', 'uihints'):
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99 if not any([param.tag == datasource_tag for param in inputs]):
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100 lint_ctx.info("%s tag usually present in data sources" % datasource_tag)
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101
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102 if num_inputs:
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103 lint_ctx.info("Found %d input parameters.", num_inputs)
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104 else:
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105 if datasource:
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106 lint_ctx.info("No input parameters, OK for data sources")
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107 else:
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108 lint_ctx.warn("Found no input parameters.")
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109
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110
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111 def lint_repeats(tool_xml, lint_ctx):
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112 """Lint repeat blocks in tool inputs."""
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113 repeats = tool_xml.findall("./inputs//repeat")
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114 for repeat in repeats:
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115 if "name" not in repeat.attrib:
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116 lint_ctx.error("Repeat does not specify name attribute.")
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117 if "title" not in repeat.attrib:
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118 lint_ctx.error("Repeat does not specify title attribute.")
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119
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120
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121 def _find_with_attribute(element, tag, attribute, test_value=None):
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122 rval = []
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123 for el in (element.findall('./%s' % tag) or []):
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124 if attribute not in el.attrib:
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125 continue
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126 value = el.attrib[attribute]
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127 if test_value is not None:
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128 if value == test_value:
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129 rval.append(el)
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130 else:
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131 rval.append(el)
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132 return rval