Mercurial > repos > bcclaywell > argo_navis

annotate venv/lib/python2.7/site-packages/planemo/tool_lint.py @ 0:d67268158946 draft

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planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author bcclaywell
date Mon, 12 Oct 2015 17:43:33 -0400
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d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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1 import os
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2
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3 from planemo.io import info
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4 from planemo.io import error
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5
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6 import planemo.linters.xsd
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7
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8 from planemo.tools import load_tool_elements_from_path, is_tool_load_error
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9 from galaxy.tools.lint import lint_xml
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10
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11 SKIP_XML_MESSAGE = "Skipping XML file - does not appear to be a tool %s."
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12 LINTING_TOOL_MESSAGE = "Linting tool %s"
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13 SHED_FILES = ["tool_dependencies.xml", "repository_dependencies.xml"]
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15
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16 def lint_tools_on_path(ctx, paths, lint_args, **kwds):
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17 assert_tools = kwds.get("assert_tools", True)
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18 recursive = kwds.get("recursive", False)
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19 exit = 0
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20 valid_tools = 0
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21 for path in paths:
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22 for (tool_path, tool_xml) in yield_tool_xmls(ctx, path, recursive):
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23 if handle_tool_load_error(tool_path, tool_xml):
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24 exit = 1
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25 continue
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26 info("Linting tool %s" % tool_path)
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27 if not lint_xml(tool_xml, **lint_args):
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28 error("Failed linting")
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29 exit = 1
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30 else:
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31 valid_tools += 1
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32 if exit == 0 and valid_tools == 0 and assert_tools:
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33 exit = 2
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34 return exit
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35
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36
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37 def handle_tool_load_error(tool_path, tool_xml):
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38 """ Return True if tool_xml is tool load error (invalid XML), and
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39 print a helpful error message.
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40 """
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41 is_error = False
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42 if is_tool_load_error(tool_xml):
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43 info("Could not lint %s due to malformed xml." % tool_path)
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44 is_error = True
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45 return is_error
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46
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47
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48 def yield_tool_xmls(ctx, path, recursive=False):
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49 tools = load_tool_elements_from_path(
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50 path,
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51 recursive,
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52 register_load_errors=True,
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53 )
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54 for (tool_path, tool_xml) in tools:
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55 if is_tool_load_error(tool_xml):
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56 yield (tool_path, tool_xml)
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57 continue
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58 if not _is_tool_xml(ctx, tool_path, tool_xml):
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59 continue
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60 yield (tool_path, tool_xml)
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61
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62
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63 def build_lint_args(ctx, **kwds):
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64 report_level = kwds.get("report_level", "all")
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65 fail_level = kwds.get("fail_level", "warn")
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66 skip = kwds.get("skip", None)
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67 if skip is None:
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68 skip = ctx.global_config.get("lint_skip", "")
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69 if isinstance(skip, list):
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70 skip = ",".join(skip)
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71
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72 skip_types = [s.strip() for s in skip.split(",")]
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73 lint_args = dict(
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74 level=report_level,
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75 fail_level=fail_level,
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76 extra_modules=_lint_extra_modules(**kwds),
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77 skip_types=skip_types,
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78 )
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79 return lint_args
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80
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81
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82 def _lint_extra_modules(**kwds):
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83 xsd = kwds.get("xsd", False)
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84 if xsd:
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85 return [planemo.linters.xsd]
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86 else:
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87 return []
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88
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89
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90 def _is_tool_xml(ctx, tool_path, tool_xml):
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91 if os.path.basename(tool_path) in SHED_FILES:
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92 return False
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93 if tool_xml.getroot().tag != "tool":
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94 if ctx.verbose:
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95 info(SKIP_XML_MESSAGE % tool_path)
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96 return False
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97 return True