Mercurial > repos > shellac > sam_consensus_v3
comparison env/lib/python3.9/site-packages/planemo/tools.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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-1:000000000000 | 0:4f3585e2f14b |
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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 """Fetch URI to a local path.""" | |
21 fetcher = ToolLocationFetcher() | |
22 return fetcher.to_tool_path(uri) | |
23 | |
24 | |
25 def uris_to_paths(ctx, uris): | |
26 """Fetch multiple URIs to a local path.""" | |
27 fetcher = ToolLocationFetcher() | |
28 paths = [] | |
29 for uri in uris: | |
30 path = fetcher.to_tool_path(uri) | |
31 paths.append(path) | |
32 return paths | |
33 | |
34 | |
35 def yield_tool_sources_on_paths(ctx, paths, recursive=False, yield_load_errors=True, exclude_deprecated=False): | |
36 """Walk paths and yield ToolSource objects discovered.""" | |
37 for path in paths: | |
38 for (tool_path, tool_source) in yield_tool_sources(ctx, path, recursive, yield_load_errors): | |
39 if exclude_deprecated and 'deprecated' in tool_path: | |
40 continue | |
41 yield (tool_path, tool_source) | |
42 | |
43 | |
44 def yield_tool_sources(ctx, path, recursive=False, yield_load_errors=True): | |
45 """Walk single path and yield ToolSource objects discovered.""" | |
46 tools = load_tool_sources_from_path( | |
47 path, | |
48 recursive, | |
49 register_load_errors=True, | |
50 ) | |
51 for (tool_path, tool_source) in tools: | |
52 if is_tool_load_error(tool_source): | |
53 if yield_load_errors: | |
54 yield (tool_path, tool_source) | |
55 else: | |
56 error(LOAD_ERROR_MESSAGE % tool_path) | |
57 continue | |
58 | |
59 if not _is_tool_source(ctx, tool_path, tool_source): | |
60 continue | |
61 yield (tool_path, tool_source) | |
62 | |
63 | |
64 def load_tool_sources_from_path(path, recursive, register_load_errors=False): | |
65 """Generate a list for tool sources found down specified path.""" | |
66 return loader_directory.load_tool_sources_from_path( | |
67 path, | |
68 _load_exception_handler, | |
69 recursive=recursive, | |
70 register_load_errors=register_load_errors, | |
71 ) | |
72 | |
73 | |
74 def _load_exception_handler(path, exc_info): | |
75 error(LOAD_ERROR_MESSAGE % path) | |
76 traceback.print_exception(*exc_info, limit=1, file=sys.stderr) | |
77 | |
78 | |
79 def _is_tool_source(ctx, tool_path, tool_source): | |
80 if os.path.basename(tool_path) in SHED_FILES: | |
81 return False | |
82 root = getattr(tool_source, "root", None) | |
83 if root is not None: | |
84 if root.tag != "tool": | |
85 if ctx.verbose: | |
86 info(SKIP_XML_MESSAGE % tool_path) | |
87 return False | |
88 return True | |
89 | |
90 | |
91 __all__ = ( | |
92 "is_tool_load_error", | |
93 "load_tool_sources_from_path", | |
94 "yield_tool_sources", | |
95 "yield_tool_sources_on_paths", | |
96 ) |