Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/tools.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 """Planemo-specific wrappers around galaxy-tool-util tool functionality."""
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2 from __future__ import absolute_import
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3
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4 import os
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5 import sys
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6 import traceback
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7
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8 from galaxy.tool_util import loader_directory
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9 from galaxy.tool_util.fetcher import ToolLocationFetcher
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10
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11 from planemo.io import error, info
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12
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13 is_tool_load_error = loader_directory.is_tool_load_error
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14 SKIP_XML_MESSAGE = "Skipping XML file - does not appear to be a tool %s."
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15 SHED_FILES = ["tool_dependencies.xml", "repository_dependencies.xml"]
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16 LOAD_ERROR_MESSAGE = "Error loading tool with path %s"
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17
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18
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19 def uri_to_path(ctx, uri):
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20 fetcher = ToolLocationFetcher()
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21 return fetcher.to_tool_path(uri)
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22
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23
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24 def uris_to_paths(ctx, uris):
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25 fetcher = ToolLocationFetcher()
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26 paths = []
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27 for uri in uris:
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28 path = fetcher.to_tool_path(uri)
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29 paths.append(path)
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30 return paths
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31
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32
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33 def yield_tool_sources_on_paths(ctx, paths, recursive=False, yield_load_errors=True, exclude_deprecated=False):
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34 for path in paths:
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35 for (tool_path, tool_source) in yield_tool_sources(ctx, path, recursive, yield_load_errors):
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36 if exclude_deprecated and 'deprecated' in tool_path:
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37 continue
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38 yield (tool_path, tool_source)
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39
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40
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41 def yield_tool_sources(ctx, path, recursive=False, yield_load_errors=True):
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42 tools = load_tool_sources_from_path(
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43 path,
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44 recursive,
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45 register_load_errors=True,
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46 )
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47 for (tool_path, tool_source) in tools:
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48 if is_tool_load_error(tool_source):
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49 if yield_load_errors:
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50 yield (tool_path, tool_source)
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51 else:
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52 error(LOAD_ERROR_MESSAGE % tool_path)
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53 continue
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54
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55 if not _is_tool_source(ctx, tool_path, tool_source):
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56 continue
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57 yield (tool_path, tool_source)
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58
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59
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60 def load_tool_sources_from_path(path, recursive, register_load_errors=False):
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61 """Generator for tool sources on a path."""
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62 return loader_directory.load_tool_sources_from_path(
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63 path,
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64 _load_exception_handler,
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65 recursive=recursive,
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66 register_load_errors=register_load_errors,
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67 )
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68
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69
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70 def _load_exception_handler(path, exc_info):
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71 error(LOAD_ERROR_MESSAGE % path)
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72 traceback.print_exception(*exc_info, limit=1, file=sys.stderr)
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73
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74
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75 def _is_tool_source(ctx, tool_path, tool_source):
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76 if os.path.basename(tool_path) in SHED_FILES:
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77 return False
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78 root = getattr(tool_source, "root", None)
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79 if root is not None:
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80 if root.tag != "tool":
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81 if ctx.verbose:
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82 info(SKIP_XML_MESSAGE % tool_path)
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83 return False
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84 return True
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85
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86
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87 __all__ = (
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88 "is_tool_load_error",
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89 "load_tool_sources_from_path",
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90 "yield_tool_sources",
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91 "yield_tool_sources_on_paths",
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92 )