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