Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/parser/factory.py @ 0:4f3585e2f14b draft default tip
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author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """Constructors for concrete tool and input source objects.""" |
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2 |
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3 import logging |
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4 |
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5 from galaxy.tool_util.loader import load_tool_with_refereces |
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6 from galaxy.util.yaml_util import ordered_load |
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7 from .cwl import CwlToolSource |
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8 from .interface import InputSource |
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9 from .xml import XmlInputSource, XmlToolSource |
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10 from .yaml import YamlInputSource, YamlToolSource |
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11 from ..fetcher import ToolLocationFetcher |
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12 |
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13 log = logging.getLogger(__name__) |
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14 |
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15 |
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16 def get_tool_source(config_file=None, xml_tree=None, enable_beta_formats=True, tool_location_fetcher=None, macro_paths=None): |
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17 """Return a ToolSource object corresponding to supplied source. |
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18 |
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19 The supplied source may be specified as a file path (using the config_file |
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20 parameter) or as an XML object loaded with load_tool_with_refereces. |
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21 """ |
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22 if xml_tree is not None: |
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23 return XmlToolSource(xml_tree, source_path=config_file, macro_paths=macro_paths) |
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24 elif config_file is None: |
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25 raise ValueError("get_tool_source called with invalid config_file None.") |
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26 |
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27 if tool_location_fetcher is None: |
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28 tool_location_fetcher = ToolLocationFetcher() |
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29 |
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30 config_file = tool_location_fetcher.to_tool_path(config_file) |
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31 if not enable_beta_formats: |
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32 tree, macro_paths = load_tool_with_refereces(config_file) |
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33 return XmlToolSource(tree, source_path=config_file, macro_paths=macro_paths) |
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34 |
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35 if config_file.endswith(".yml"): |
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36 log.info("Loading tool from YAML - this is experimental - tool will not function in future.") |
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37 with open(config_file) as f: |
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38 as_dict = ordered_load(f) |
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39 return YamlToolSource(as_dict, source_path=config_file) |
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40 elif config_file.endswith(".json") or config_file.endswith(".cwl"): |
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41 log.info("Loading CWL tool - this is experimental - tool likely will not function in future at least in same way.") |
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42 return CwlToolSource(config_file) |
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43 else: |
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44 tree, macro_paths = load_tool_with_refereces(config_file) |
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45 return XmlToolSource(tree, source_path=config_file, macro_paths=macro_paths) |
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46 |
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47 |
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48 def get_tool_source_from_representation(tool_format, tool_representation): |
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49 # TODO: make sure whatever is consuming this method uses ordered load. |
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50 log.info("Loading dynamic tool - this is experimental - tool may not function in future.") |
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51 if tool_format == "GalaxyTool": |
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52 if "version" not in tool_representation: |
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53 tool_representation["version"] = "1.0.0" # Don't require version for embedded tools. |
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54 return YamlToolSource(tool_representation) |
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55 else: |
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56 raise Exception("Unknown tool representation format [%s]." % tool_format) |
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57 |
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58 |
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59 def get_input_source(content): |
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60 """Wrap dicts or XML elements as InputSource if needed. |
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61 |
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62 If the supplied content is already an InputSource object, |
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63 it is simply returned. This allow Galaxy to uniformly |
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64 consume using the tool input source interface. |
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65 """ |
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66 if not isinstance(content, InputSource): |
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67 if isinstance(content, dict): |
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68 content = YamlInputSource(content) |
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69 else: |
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70 content = XmlInputSource(content) |
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71 return content |
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72 |
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73 |
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74 __all__ = ("get_tool_source", "get_input_source") |