Mercurial > repos > shellac > guppy_basecaller

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 """Utilities for Galaxy workflows."""
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2 import json
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3 import os
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4 from collections import namedtuple
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5
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6 import yaml
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7 from bioblend.galaxy.client import Client
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8 from ephemeris import generate_tool_list_from_ga_workflow_files
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9 from ephemeris import shed_tools
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10 from gxformat2.converter import python_to_workflow
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11 from gxformat2.interface import BioBlendImporterGalaxyInterface
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12 from gxformat2.interface import ImporterGalaxyInterface
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13
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14 from planemo.io import warn
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15
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16 FAILED_REPOSITORIES_MESSAGE = "Failed to install one or more repositories."
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17
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18
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19 def load_shed_repos(runnable):
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20 if runnable.type.name != "galaxy_workflow":
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21 return []
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22
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23 path = runnable.path
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24 if path.endswith(".ga"):
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25 generate_tool_list_from_ga_workflow_files.generate_tool_list_from_workflow([path], "Tools from workflows", "tools.yml")
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26 with open("tools.yml", "r") as f:
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27 tools = yaml.safe_load(f)["tools"]
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28
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29 else:
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30 # It'd be better to just infer this from the tool shed ID somehow than
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31 # require explicit annotation like this... I think?
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32 with open(path, "r") as f:
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33 workflow = yaml.safe_load(f)
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34
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35 tools = workflow.get("tools", [])
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36
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37 return tools
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38
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39
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40 def install_shed_repos(runnable, admin_gi, ignore_dependency_problems):
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41 tools_info = load_shed_repos(runnable)
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42 if tools_info:
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43 install_tool_manager = shed_tools.InstallRepositoryManager(admin_gi)
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44 install_results = install_tool_manager.install_repositories(tools_info)
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45 if install_results.errored_repositories:
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46 if ignore_dependency_problems:
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47 warn(FAILED_REPOSITORIES_MESSAGE)
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48 else:
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49 raise Exception(FAILED_REPOSITORIES_MESSAGE)
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50
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51
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52 def import_workflow(path, admin_gi, user_gi, from_path=False):
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53 """Import a workflow path to specified Galaxy instance."""
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54 if not from_path:
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55 importer = BioBlendImporterGalaxyInterface(
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56 admin_gi=admin_gi,
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57 user_gi=user_gi
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58 )
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59 workflow = _raw_dict(path, importer)
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60 return importer.import_workflow(workflow)
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61 else:
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62 # TODO: Update bioblend to allow from_path.
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63 path = os.path.abspath(path)
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64 payload = dict(
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65 from_path=path
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66 )
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67 workflows_url = user_gi._make_url(user_gi.workflows)
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68 workflow = Client._post(user_gi.workflows, payload, url=workflows_url)
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69 return workflow
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70
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71
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72 def _raw_dict(path, importer=None):
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73 if path.endswith(".ga"):
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74 with open(path, "r") as f:
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75 workflow = json.load(f)
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76 else:
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77 if importer is None:
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78 importer = DummyImporterGalaxyInterface()
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79
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80 workflow_directory = os.path.dirname(path)
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81 workflow_directory = os.path.abspath(workflow_directory)
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82 with open(path, "r") as f:
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83 workflow = yaml.safe_load(f)
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84 workflow = python_to_workflow(workflow, importer, workflow_directory)
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85
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86 return workflow
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87
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88
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89 def find_tool_ids(path):
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90 tool_ids = []
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91 workflow = _raw_dict(path)
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92 for (order_index, step) in workflow["steps"].items():
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93 tool_id = step.get("tool_id")
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94 tool_ids.append(tool_id)
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95
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96 return tool_ids
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97
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98
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99 WorkflowOutput = namedtuple("WorkflowOutput", ["order_index", "output_name", "label"])
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100
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101
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102 def describe_outputs(path):
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103 """Return a list of :class:`WorkflowOutput` objects for target workflow."""
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104 workflow = _raw_dict(path)
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105 outputs = []
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106 for (order_index, step) in workflow["steps"].items():
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107 step_outputs = step.get("workflow_outputs", [])
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108 for step_output in step_outputs:
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109 output = WorkflowOutput(
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110 int(order_index),
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111 step_output["output_name"],
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112 step_output["label"],
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113 )
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114 outputs.append(output)
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115 return outputs
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116
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117
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118 class DummyImporterGalaxyInterface(ImporterGalaxyInterface):
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119
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120 def import_workflow(self, workflow, **kwds):
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121 return None
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122
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123
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124 __all__ = (
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125 "import_workflow",
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126 "describe_outputs",
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127 )