Mercurial > repos > shellac > guppy_basecaller

comparison 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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-1:000000000000 0:26e78fe6e8c4
1 """Planemo-specific wrappers around galaxy-tool-util tool functionality."""
2 from __future__ import absolute_import
3
4 import os
5 import sys
6 import traceback
7
8 from galaxy.tool_util import loader_directory
9 from galaxy.tool_util.fetcher import ToolLocationFetcher
10
11 from planemo.io import error, info
12
13 is_tool_load_error = loader_directory.is_tool_load_error
14 SKIP_XML_MESSAGE = "Skipping XML file - does not appear to be a tool %s."
15 SHED_FILES = ["tool_dependencies.xml", "repository_dependencies.xml"]
16 LOAD_ERROR_MESSAGE = "Error loading tool with path %s"
17
18
19 def uri_to_path(ctx, uri):
20 fetcher = ToolLocationFetcher()
21 return fetcher.to_tool_path(uri)
22
23
24 def uris_to_paths(ctx, uris):
25 fetcher = ToolLocationFetcher()
26 paths = []
27 for uri in uris:
28 path = fetcher.to_tool_path(uri)
29 paths.append(path)
30 return paths
31
32
33 def yield_tool_sources_on_paths(ctx, paths, recursive=False, yield_load_errors=True, exclude_deprecated=False):
34 for path in paths:
35 for (tool_path, tool_source) in yield_tool_sources(ctx, path, recursive, yield_load_errors):
36 if exclude_deprecated and 'deprecated' in tool_path:
37 continue
38 yield (tool_path, tool_source)
39
40
41 def yield_tool_sources(ctx, path, recursive=False, yield_load_errors=True):
42 tools = load_tool_sources_from_path(
43 path,
44 recursive,
45 register_load_errors=True,
46 )
47 for (tool_path, tool_source) in tools:
48 if is_tool_load_error(tool_source):
49 if yield_load_errors:
50 yield (tool_path, tool_source)
51 else:
52 error(LOAD_ERROR_MESSAGE % tool_path)
53 continue
54
55 if not _is_tool_source(ctx, tool_path, tool_source):
56 continue
57 yield (tool_path, tool_source)
58
59
60 def load_tool_sources_from_path(path, recursive, register_load_errors=False):
61 """Generator for tool sources on a path."""
62 return loader_directory.load_tool_sources_from_path(
63 path,
64 _load_exception_handler,
65 recursive=recursive,
66 register_load_errors=register_load_errors,
67 )
68
69
70 def _load_exception_handler(path, exc_info):
71 error(LOAD_ERROR_MESSAGE % path)
72 traceback.print_exception(*exc_info, limit=1, file=sys.stderr)
73
74
75 def _is_tool_source(ctx, tool_path, tool_source):
76 if os.path.basename(tool_path) in SHED_FILES:
77 return False
78 root = getattr(tool_source, "root", None)
79 if root is not None:
80 if root.tag != "tool":
81 if ctx.verbose:
82 info(SKIP_XML_MESSAGE % tool_path)
83 return False
84 return True
85
86
87 __all__ = (
88 "is_tool_load_error",
89 "load_tool_sources_from_path",
90 "yield_tool_sources",
91 "yield_tool_sources_on_paths",
92 )