Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/galaxy/activity.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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0
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1 """Module provides generic interface to running Galaxy tools and workflows."""
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2
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3 import json
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4 import os
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5 import tempfile
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6 import time
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7
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8 import bioblend
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9 import requests
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10 import yaml
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11 from bioblend.galaxy.client import Client
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12 from bioblend.util import attach_file
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13 from galaxy.tool_util.cwl.util import (
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14 DirectoryUploadTarget,
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15 FileUploadTarget,
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16 galactic_job_json,
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17 invocation_to_output,
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18 output_properties,
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19 output_to_cwl_json,
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20 path_or_uri_to_uri,
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21 tool_response_to_output,
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22 )
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23 from galaxy.tool_util.parser import get_tool_source
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24 from galaxy.util import (
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25 safe_makedirs,
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26 unicodify,
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27 )
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28
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29 from planemo.galaxy.api import summarize_history
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30 from planemo.io import wait_on
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31 from planemo.runnable import (
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32 ErrorRunResponse,
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33 get_outputs,
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34 RunnableType,
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35 SuccessfulRunResponse,
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36 )
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37
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38 DEFAULT_HISTORY_NAME = "CWL Target History"
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39 ERR_NO_SUCH_TOOL = ("Failed to find tool with ID [%s] in Galaxy - cannot execute job. "
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40 "You may need to enable verbose logging and determine why the tool did not load. [%s]")
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41
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42
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43 def execute(ctx, config, runnable, job_path, **kwds):
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44 """Execute a Galaxy activity."""
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45 try:
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46 return _execute(ctx, config, runnable, job_path, **kwds)
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47 except Exception as e:
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48 return ErrorRunResponse(unicodify(e))
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49
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50
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51 def _verified_tool_id(runnable, user_gi):
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52 tool_id = _tool_id(runnable.path)
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53 try:
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54 user_gi.tools.show_tool(tool_id)
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55 except Exception as e:
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56 raise Exception(ERR_NO_SUCH_TOOL % (tool_id, e))
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57 return tool_id
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58
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59
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60 def _inputs_representation(runnable):
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61 if runnable.type == RunnableType.cwl_tool:
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62 inputs_representation = "cwl"
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63 else:
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64 inputs_representation = "galaxy"
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65 return inputs_representation
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66
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67
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68 def log_contents_str(config):
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69 if hasattr(config, "log_contents"):
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70 return config.log_contents
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71 else:
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72 return "No log for this engine type."
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73
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74
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75 def _execute(ctx, config, runnable, job_path, **kwds):
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76 user_gi = config.user_gi
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77 admin_gi = config.gi
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78
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79 history_id = _history_id(user_gi, **kwds)
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80
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81 job_dict, _ = stage_in(ctx, runnable, config, user_gi, history_id, job_path, **kwds)
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82
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83 if runnable.type in [RunnableType.galaxy_tool, RunnableType.cwl_tool]:
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84 response_class = GalaxyToolRunResponse
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85 tool_id = _verified_tool_id(runnable, user_gi)
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86 inputs_representation = _inputs_representation(runnable)
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87 run_tool_payload = dict(
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88 history_id=history_id,
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89 tool_id=tool_id,
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90 inputs=job_dict,
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91 inputs_representation=inputs_representation,
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92 )
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93 ctx.vlog("Post to Galaxy tool API with payload [%s]" % run_tool_payload)
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94 tool_run_response = user_gi.tools._post(run_tool_payload)
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95
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96 job = tool_run_response["jobs"][0]
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97 job_id = job["id"]
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98 try:
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99 final_state = _wait_for_job(user_gi, job_id)
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100 except Exception:
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101 summarize_history(ctx, user_gi, history_id)
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102 raise
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103 if final_state != "ok":
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104 msg = "Failed to run CWL tool job final job state is [%s]." % final_state
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105 summarize_history(ctx, user_gi, history_id)
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106 with open("errored_galaxy.log", "w") as f:
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107 f.write(log_contents_str(config))
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108 raise Exception(msg)
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109
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110 ctx.vlog("Final job state was ok, fetching details for job [%s]" % job_id)
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111 job_info = admin_gi.jobs.show_job(job_id)
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112 response_kwds = {
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113 'job_info': job_info,
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114 'api_run_response': tool_run_response,
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115 }
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116 if ctx.verbose:
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117 summarize_history(ctx, user_gi, history_id)
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118 elif runnable.type in [RunnableType.galaxy_workflow, RunnableType.cwl_workflow]:
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119 response_class = GalaxyWorkflowRunResponse
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120 workflow_id = config.workflow_id(runnable.path)
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121 ctx.vlog("Found Galaxy workflow ID [%s] for path [%s]" % (workflow_id, runnable.path))
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122 # TODO: update bioblend to allow inputs_by.
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123 # invocation = user_gi.worklfows.invoke_workflow(
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124 # workflow_id,
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125 # history_id=history_id,
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126 # inputs=job_dict,
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127 # )
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128 payload = dict(
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129 workflow_id=workflow_id,
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130 history_id=history_id,
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131 inputs=job_dict,
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132 inputs_by="name",
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133 allow_tool_state_corrections=True,
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134 )
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135 invocations_url = "%s/%s/invocations" % (
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136 user_gi._make_url(user_gi.workflows),
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137 workflow_id,
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138 )
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139 invocation = Client._post(user_gi.workflows, payload, url=invocations_url)
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140 invocation_id = invocation["id"]
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141 ctx.vlog("Waiting for invocation [%s]" % invocation_id)
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142 polling_backoff = kwds.get("polling_backoff", 0)
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143 try:
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144 final_invocation_state = _wait_for_invocation(ctx, user_gi, history_id, workflow_id, invocation_id, polling_backoff)
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145 except Exception:
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146 ctx.vlog("Problem waiting on invocation...")
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147 summarize_history(ctx, user_gi, history_id)
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148 raise
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149 ctx.vlog("Final invocation state is [%s]" % final_invocation_state)
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150 final_state = _wait_for_history(ctx, user_gi, history_id, polling_backoff)
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151 if final_state != "ok":
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152 msg = "Failed to run workflow final history state is [%s]." % final_state
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153 summarize_history(ctx, user_gi, history_id)
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154 with open("errored_galaxy.log", "w") as f:
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155 f.write(log_contents_str(config))
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156 raise Exception(msg)
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157 ctx.vlog("Final history state is 'ok'")
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158 response_kwds = {
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159 'workflow_id': workflow_id,
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160 'invocation_id': invocation_id,
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161 }
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162 else:
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163 raise NotImplementedError()
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164
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165 run_response = response_class(
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166 ctx=ctx,
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167 runnable=runnable,
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168 user_gi=user_gi,
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169 history_id=history_id,
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170 log=log_contents_str(config),
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171 **response_kwds
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172 )
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173 output_directory = kwds.get("output_directory", None)
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174 ctx.vlog("collecting outputs from run...")
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175 run_response.collect_outputs(ctx, output_directory)
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176 ctx.vlog("collecting outputs complete")
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177 return run_response
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178
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179
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180 def stage_in(ctx, runnable, config, user_gi, history_id, job_path, **kwds):
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181 files_attached = [False]
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182
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183 def upload_func(upload_target):
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184
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185 def _attach_file(upload_payload, uri, index=0):
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186 uri = path_or_uri_to_uri(uri)
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187 is_path = uri.startswith("file://")
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188 if not is_path or config.use_path_paste:
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189 upload_payload["inputs"]["files_%d|url_paste" % index] = uri
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190 else:
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191 files_attached[0] = True
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192 path = uri[len("file://"):]
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193 upload_payload["files_%d|file_data" % index] = attach_file(path)
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194
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195 if isinstance(upload_target, FileUploadTarget):
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196 file_path = upload_target.path
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197 upload_payload = user_gi.tools._upload_payload(
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198 history_id,
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199 file_type=upload_target.properties.get('filetype', None) or "auto",
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200 )
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201 name = os.path.basename(file_path)
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202 upload_payload["inputs"]["files_0|auto_decompress"] = False
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203 upload_payload["inputs"]["auto_decompress"] = False
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204 _attach_file(upload_payload, file_path)
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205 upload_payload["inputs"]["files_0|NAME"] = name
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206 if upload_target.secondary_files:
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207 _attach_file(upload_payload, upload_target.secondary_files, index=1)
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208 upload_payload["inputs"]["files_1|type"] = "upload_dataset"
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209 upload_payload["inputs"]["files_1|auto_decompress"] = True
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210 upload_payload["inputs"]["file_count"] = "2"
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211 upload_payload["inputs"]["force_composite"] = "True"
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212
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213 ctx.vlog("upload_payload is %s" % upload_payload)
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214 return user_gi.tools._post(upload_payload, files_attached=files_attached[0])
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215 elif isinstance(upload_target, DirectoryUploadTarget):
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216 tar_path = upload_target.tar_path
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217
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218 upload_payload = user_gi.tools._upload_payload(
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219 history_id,
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220 file_type="tar",
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221 )
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222 upload_payload["inputs"]["files_0|auto_decompress"] = False
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223 _attach_file(upload_payload, tar_path)
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224 tar_upload_response = user_gi.tools._post(upload_payload, files_attached=files_attached[0])
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225 convert_response = user_gi.tools.run_tool(
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226 tool_id="CONVERTER_tar_to_directory",
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227 tool_inputs={"input1": {"src": "hda", "id": tar_upload_response["outputs"][0]["id"]}},
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228 history_id=history_id,
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229 )
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230 assert "outputs" in convert_response, convert_response
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231 return convert_response
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diff changeset
232 else:
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233 content = json.dumps(upload_target.object)
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diff changeset
234 return user_gi.tools.paste_content(
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diff changeset
235 content,
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diff changeset
236 history_id,
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diff changeset
237 file_type="expression.json",
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diff changeset
238 )
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diff changeset
239
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240 def create_collection_func(element_identifiers, collection_type):
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241 payload = {
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242 "name": "dataset collection",
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diff changeset
243 "instance_type": "history",
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diff changeset
244 "history_id": history_id,
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245 "element_identifiers": element_identifiers,
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246 "collection_type": collection_type,
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247 "fields": None if collection_type != "record" else "auto",
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248 }
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249 dataset_collections_url = user_gi.url + "/dataset_collections"
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diff changeset
250 dataset_collection = Client._post(user_gi.histories, payload, url=dataset_collections_url)
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251 return dataset_collection
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252
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253 with open(job_path, "r") as f:
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254 job = yaml.safe_load(f)
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255
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256 # Figure out what "." should be here instead.
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257 job_dir = os.path.dirname(job_path)
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258 job_dict, datasets = galactic_job_json(
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259 job,
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260 job_dir,
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261 upload_func,
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262 create_collection_func,
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263 tool_or_workflow="tool" if runnable.type in [RunnableType.cwl_tool, RunnableType.galaxy_tool] else "workflow",
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264 )
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265
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266 if datasets:
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267 final_state = _wait_for_history(ctx, user_gi, history_id)
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268
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269 for (dataset, path) in datasets:
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270 dataset_details = user_gi.histories.show_dataset(
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271 history_id,
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272 dataset["id"],
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273 )
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274 ctx.vlog("Uploaded dataset for path [%s] with metadata [%s]" % (path, dataset_details))
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275 else:
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276 # Mark uploads as ok because nothing to do.
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277 final_state = "ok"
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278
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279 ctx.vlog("final state is %s" % final_state)
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280 if final_state != "ok":
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281 msg = "Failed to run job final job state is [%s]." % final_state
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282 summarize_history(ctx, user_gi, history_id)
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283 with open("errored_galaxy.log", "w") as f:
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284 f.write(log_contents_str(config))
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285 raise Exception(msg)
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286
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287 return job_dict, datasets
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288
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289
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290 class GalaxyBaseRunResponse(SuccessfulRunResponse):
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291
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292 def __init__(
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293 self,
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294 ctx,
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295 runnable,
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296 user_gi,
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297 history_id,
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298 log,
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299 ):
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300 self._ctx = ctx
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301 self._runnable = runnable
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302 self._user_gi = user_gi
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303 self._history_id = history_id
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304 self._log = log
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305
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306 self._job_info = None
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307
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308 self._outputs_dict = None
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309
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310 def to_galaxy_output(self, output):
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311 """Convert runnable output to a GalaxyOutput object.
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312
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313 Subclasses for workflow and tool execution override this.
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314 """
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315 raise NotImplementedError()
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316
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317 def _get_extra_files(self, dataset_details):
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318 extra_files_url = "%s/%s/contents/%s/extra_files" % (
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319 self._user_gi._make_url(self._user_gi.histories), self._history_id, dataset_details["id"]
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320 )
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321 extra_files = Client._get(self._user_gi.jobs, url=extra_files_url)
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322 return extra_files
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323
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324 def _get_metadata(self, history_content_type, content_id):
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325 if history_content_type == "dataset":
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326 return self._user_gi.histories.show_dataset(
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327 self._history_id,
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328 content_id,
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329 )
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330 elif history_content_type == "dataset_collection":
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331 return self._user_gi.histories.show_dataset_collection(
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332 self._history_id,
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333 content_id,
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334 )
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335 else:
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336 raise Exception("Unknown history content type encountered [%s]" % history_content_type)
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337
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338 def collect_outputs(self, ctx, output_directory):
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339 assert self._outputs_dict is None, "collect_outputs pre-condition violated"
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340
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341 outputs_dict = {}
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342 if not output_directory:
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343 # TODO: rather than creating a directory just use
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344 # Galaxy paths if they are available in this
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345 # configuration.
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346 output_directory = tempfile.mkdtemp()
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347
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348 def get_dataset(dataset_details, filename=None):
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349 parent_basename = dataset_details.get("cwl_file_name")
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350 if not parent_basename:
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351 parent_basename = dataset_details.get("name")
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352 file_ext = dataset_details["file_ext"]
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353 if file_ext == "directory":
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354 # TODO: rename output_directory to outputs_directory because we can have output directories
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355 # and this is confusing...
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356 the_output_directory = os.path.join(output_directory, parent_basename)
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357 safe_makedirs(the_output_directory)
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358 destination = self.download_output_to(dataset_details, the_output_directory, filename=filename)
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359 else:
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360 destination = self.download_output_to(dataset_details, output_directory, filename=filename)
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361 if filename is None:
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362 basename = parent_basename
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363 else:
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364 basename = os.path.basename(filename)
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365
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366 return {"path": destination, "basename": basename}
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367
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368 ctx.vlog("collecting outputs to directory %s" % output_directory)
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369 for runnable_output in get_outputs(self._runnable):
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370 output_id = runnable_output.get_id()
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371 if not output_id:
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372 ctx.vlog("Workflow output identified without an ID (label), skipping")
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373 continue
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374 output_dict_value = None
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375 if self._runnable.type in [RunnableType.cwl_workflow, RunnableType.cwl_tool]:
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376 galaxy_output = self.to_galaxy_output(runnable_output)
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377 cwl_output = output_to_cwl_json(
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378 galaxy_output,
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379 self._get_metadata,
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380 get_dataset,
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381 self._get_extra_files,
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382 pseduo_location=True,
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383 )
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384 output_dict_value = cwl_output
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385 else:
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386 # TODO: deprecate this route for finding workflow outputs,
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387 # it is a brittle and bad approach...
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388 output_dataset_id = self.output_dataset_id(runnable_output)
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389 dataset = self._get_metadata("dataset", output_dataset_id)
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390 dataset_dict = get_dataset(dataset)
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391 ctx.vlog("populated destination [%s]" % dataset_dict["path"])
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392
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393 if dataset["file_ext"] == "expression.json":
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394 with open(dataset_dict["path"], "r") as f:
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395 output_dict_value = json.load(f)
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396 else:
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397 output_dict_value = output_properties(**dataset_dict)
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398
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399 outputs_dict[output_id] = output_dict_value
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400
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401 self._outputs_dict = outputs_dict
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402 ctx.vlog("collected outputs [%s]" % self._outputs_dict)
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403
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404 @property
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405 def log(self):
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406 return self._log
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407
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408 @property
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409 def job_info(self):
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410 if self._job_info is not None:
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411 return dict(
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412 stdout=self._job_info["stdout"],
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413 stderr=self._job_info["stderr"],
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414 command_line=self._job_info["command_line"],
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415 )
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416 return None
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417
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418 @property
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419 def outputs_dict(self):
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420 return self._outputs_dict
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421
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422 def download_output_to(self, dataset_details, output_directory, filename=None):
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423 if filename is None:
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424 local_filename = dataset_details.get("cwl_file_name") or dataset_details.get("name")
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425 else:
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426 local_filename = filename
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427 destination = os.path.join(output_directory, local_filename)
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428 self._history_content_download(
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429 self._history_id,
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430 dataset_details["id"],
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431 to_path=destination,
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432 filename=filename,
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433 )
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434 return destination
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435
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436 def _history_content_download(self, history_id, dataset_id, to_path, filename=None):
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437 user_gi = self._user_gi
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438 url = user_gi.url + "/histories/%s/contents/%s/display" % (history_id, dataset_id)
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439
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440 data = {}
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441 if filename:
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442 data["filename"] = filename
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443
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444 r = requests.get(url, params=data, verify=user_gi.verify, stream=True, timeout=user_gi.timeout)
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445 r.raise_for_status()
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446
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447 with open(to_path, 'wb') as fp:
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448 for chunk in r.iter_content(chunk_size=bioblend.CHUNK_SIZE):
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parents:
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449 if chunk:
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450 fp.write(chunk)
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451
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452
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453 class GalaxyToolRunResponse(GalaxyBaseRunResponse):
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454
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455 def __init__(
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diff changeset
456 self,
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parents:
diff changeset
457 ctx,
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parents:
diff changeset
458 runnable,
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parents:
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459 user_gi,
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parents:
diff changeset
460 history_id,
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parents:
diff changeset
461 log,
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parents:
diff changeset
462 job_info,
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parents:
diff changeset
463 api_run_response,
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parents:
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464 ):
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parents:
diff changeset
465 super(GalaxyToolRunResponse, self).__init__(
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parents:
diff changeset
466 ctx=ctx,
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467 runnable=runnable,
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parents:
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468 user_gi=user_gi,
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parents:
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469 history_id=history_id,
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parents:
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470 log=log,
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parents:
diff changeset
471 )
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parents:
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472 self._job_info = job_info
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parents:
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473 self.api_run_response = api_run_response
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parents:
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474
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parents:
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475 def is_collection(self, output):
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parents:
diff changeset
476 # TODO: Make this more rigorous - search both output and output
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parents:
diff changeset
477 # collections - throw an exception if not found in either place instead
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parents:
diff changeset
478 # of just assuming all non-datasets are collections.
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parents:
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479 return self.output_dataset_id(output) is None
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parents:
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480
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parents:
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481 def to_galaxy_output(self, runnable_output):
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parents:
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482 output_id = runnable_output.get_id()
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parents:
diff changeset
483 return tool_response_to_output(self.api_run_response, self._history_id, output_id)
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parents:
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484
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parents:
diff changeset
485 def output_dataset_id(self, output):
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parents:
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486 outputs = self.api_run_response["outputs"]
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parents:
diff changeset
487 output_id = output.get_id()
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parents:
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488 output_dataset_id = None
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parents:
diff changeset
489 self._ctx.vlog("Looking for id [%s] in outputs [%s]" % (output_id, outputs))
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parents:
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490 for output in outputs:
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parents:
diff changeset
491 if output["output_name"] == output_id:
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parents:
diff changeset
492 output_dataset_id = output["id"]
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493
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494 return output_dataset_id
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495
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496
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parents:
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497 class GalaxyWorkflowRunResponse(GalaxyBaseRunResponse):
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498
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parents:
diff changeset
499 def __init__(
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parents:
diff changeset
500 self,
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parents:
diff changeset
501 ctx,
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parents:
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502 runnable,
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parents:
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503 user_gi,
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parents:
diff changeset
504 history_id,
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parents:
diff changeset
505 log,
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parents:
diff changeset
506 workflow_id,
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parents:
diff changeset
507 invocation_id,
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parents:
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508 ):
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parents:
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509 super(GalaxyWorkflowRunResponse, self).__init__(
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parents:
diff changeset
510 ctx=ctx,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
511 runnable=runnable,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
512 user_gi=user_gi,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
513 history_id=history_id,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
514 log=log,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
515 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
516 self._workflow_id = workflow_id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
517 self._invocation_id = invocation_id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
518
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
519 def to_galaxy_output(self, runnable_output):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
520 output_id = runnable_output.get_id()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
521 self._ctx.vlog("checking for output in invocation [%s]" % self._invocation)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
522 return invocation_to_output(self._invocation, self._history_id, output_id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
523
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
524 def output_dataset_id(self, output):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
525 invocation = self._invocation
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
526 if "outputs" in invocation:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
527 # Use newer workflow outputs API.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
528
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
529 output_name = output.get_id()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
530 if output_name in invocation["outputs"]:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
531 return invocation["outputs"][output.get_id()]["id"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
532 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
533 raise Exception("Failed to find output [%s] in invocation outputs [%s]" % (output_name, invocation["outputs"]))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
534 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
535 # Assume the output knows its order_index and such - older line of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
536 # development not worth persuing.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
537 workflow_output = output.workflow_output
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
538 order_index = workflow_output.order_index
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
539
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
540 invocation_steps = invocation["steps"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
541 output_steps = [s for s in invocation_steps if s["order_index"] == order_index]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
542 assert len(output_steps) == 1, "More than one step matching outputs, behavior undefined."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
543 output_step = output_steps[0]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
544 job_id = output_step["job_id"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
545 assert job_id, "Output doesn't define a job_id, behavior undefined."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
546 job_info = self._user_gi.jobs.show_job(job_id, full_details=True)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
547 job_outputs = job_info["outputs"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
548 output_name = workflow_output.output_name
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
549 assert output_name in job_outputs, "No output [%s] found for output job."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
550 job_output = job_outputs[output_name]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
551 assert "id" in job_output, "Job output [%s] does not contain 'id'." % job_output
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
552 return job_output["id"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
553
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
554 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
555 def _invocation(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
556 invocation = self._user_gi.workflows.show_invocation(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
557 self._workflow_id,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
558 self._invocation_id,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
559 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
560 return invocation
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
561
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
562
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
563 def _tool_id(tool_path):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
564 tool_source = get_tool_source(tool_path)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
565 return tool_source.parse_id()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
566
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
567
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
568 def _history_id(gi, **kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
569 history_id = kwds.get("history_id", None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
570 if history_id is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
571 history_name = kwds.get("history_name", DEFAULT_HISTORY_NAME)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
572 history_id = gi.histories.create_history(history_name)["id"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
573 return history_id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
574
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
575
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
576 def _wait_for_invocation(ctx, gi, history_id, workflow_id, invocation_id, polling_backoff=0):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
577
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
578 def state_func():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
579 if _retry_on_timeouts(ctx, gi, lambda gi: has_jobs_in_states(gi, history_id, ["error", "deleted", "deleted_new"])):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
580 raise Exception("Problem running workflow, one or more jobs failed.")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
581
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
582 return _retry_on_timeouts(ctx, gi, lambda gi: gi.workflows.show_invocation(workflow_id, invocation_id))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
583
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
584 return _wait_on_state(state_func, polling_backoff)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
585
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
586
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
587 def _retry_on_timeouts(ctx, gi, f):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
588 gi.timeout = 60
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
589 try_count = 5
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
590 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
591 for try_num in range(try_count):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
592 start_time = time.time()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
593 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
594 return f(gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
595 except Exception:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
596 end_time = time.time()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
597 if end_time - start_time > 45 and (try_num + 1) < try_count:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
598 ctx.vlog("Galaxy seems to have timedout, retrying to fetch status.")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
599 continue
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
600 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
601 raise
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
602 finally:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
603 gi.timeout = None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
604
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
605
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
606 def has_jobs_in_states(gi, history_id, states):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
607 params = {"history_id": history_id}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
608 jobs_url = gi._make_url(gi.jobs)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
609 jobs = Client._get(gi.jobs, params=params, url=jobs_url)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
610
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
611 target_jobs = [j for j in jobs if j["state"] in states]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
612
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
613 return len(target_jobs) > 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
614
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
615
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
616 def _wait_for_history(ctx, gi, history_id, polling_backoff=0):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
617
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
618 def has_active_jobs(gi):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
619 if has_jobs_in_states(gi, history_id, ["new", "upload", "waiting", "queued", "running"]):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
620 return True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
621 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
622 return None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
623
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
624 timeout = 60 * 60 * 24
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
625 wait_on(lambda: _retry_on_timeouts(ctx, gi, has_active_jobs), "active jobs", timeout, polling_backoff)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
626
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
627 def state_func():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
628 return _retry_on_timeouts(ctx, gi, lambda gi: gi.histories.show_history(history_id))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
629
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
630 return _wait_on_state(state_func, polling_backoff)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
631
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
632
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
633 def _wait_for_job(gi, job_id):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
634 def state_func():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
635 return gi.jobs.show_job(job_id, full_details=True)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
636
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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637 return _wait_on_state(state_func)
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shellac
parents:
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638
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shellac
parents:
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639
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shellac
parents:
diff changeset
640 def _wait_on_state(state_func, polling_backoff=0):
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shellac
parents:
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641
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shellac
parents:
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642 def get_state():
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shellac
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643 response = state_func()
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shellac
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644 state = response["state"]
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shellac
parents:
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645 if str(state) not in ["running", "queued", "new", "ready"]:
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shellac
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646 return state
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shellac
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647 else:
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shellac
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648 return None
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shellac
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649 timeout = 60 * 60 * 24
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shellac
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diff changeset
650 final_state = wait_on(get_state, "state", timeout, polling_backoff)
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shellac
parents:
diff changeset
651 return final_state
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shellac
parents:
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652
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shellac
parents:
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653
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shellac
parents:
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654 __all__ = (
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shellac
parents:
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655 "execute",
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shellac
parents:
diff changeset
656 )