Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/verify/interactor.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 import io |
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2 import json |
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3 import os |
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4 import re |
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5 import shutil |
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6 import sys |
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7 import tarfile |
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8 import tempfile |
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9 import time |
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10 import zipfile |
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11 from json import dumps |
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12 from logging import getLogger |
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13 |
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14 import requests |
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15 from packaging.version import parse as parse_version, Version |
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16 try: |
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17 from nose.tools import nottest |
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18 except ImportError: |
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19 def nottest(x): |
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20 return x |
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21 |
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22 from galaxy import util |
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23 from galaxy.tool_util.parser.interface import TestCollectionDef, TestCollectionOutputDef |
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24 from galaxy.util.bunch import Bunch |
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25 from . import verify |
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26 from .asserts import verify_assertions |
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27 from .wait import wait_on |
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28 |
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29 log = getLogger(__name__) |
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30 |
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31 # Off by default because it can pound the database pretty heavily |
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32 # and result in sqlite errors on larger tests or larger numbers of |
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33 # tests. |
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34 VERBOSE_ERRORS = util.asbool(os.environ.get("GALAXY_TEST_VERBOSE_ERRORS", False)) |
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35 UPLOAD_ASYNC = util.asbool(os.environ.get("GALAXY_TEST_UPLOAD_ASYNC", True)) |
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36 ERROR_MESSAGE_DATASET_SEP = "--------------------------------------" |
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37 DEFAULT_TOOL_TEST_WAIT = int(os.environ.get("GALAXY_TEST_DEFAULT_WAIT", 86400)) |
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38 |
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39 DEFAULT_FTYPE = 'auto' |
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40 # This following default dbkey was traditionally hg17 before Galaxy 18.05, |
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41 # restore this behavior by setting GALAXY_TEST_DEFAULT_DBKEY to hg17. |
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42 DEFAULT_DBKEY = os.environ.get("GALAXY_TEST_DEFAULT_DBKEY", "?") |
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43 |
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44 |
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45 class OutputsDict(dict): |
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46 """Ordered dict that can also be accessed by index. |
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47 |
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48 >>> out = OutputsDict() |
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49 >>> out['item1'] = 1 |
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50 >>> out['item2'] = 2 |
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51 >>> out[1] == 2 == out['item2'] |
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52 True |
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53 """ |
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54 |
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55 def __getitem__(self, item): |
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56 if isinstance(item, int): |
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57 return self[list(self.keys())[item]] |
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58 else: |
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59 return super().__getitem__(item) |
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60 |
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61 |
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62 def stage_data_in_history(galaxy_interactor, tool_id, all_test_data, history=None, force_path_paste=False, maxseconds=DEFAULT_TOOL_TEST_WAIT): |
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63 # Upload any needed files |
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64 upload_waits = [] |
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65 |
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66 assert tool_id |
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67 |
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68 if UPLOAD_ASYNC: |
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69 for test_data in all_test_data: |
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70 upload_waits.append(galaxy_interactor.stage_data_async(test_data, |
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71 history, |
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72 tool_id, |
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73 force_path_paste=force_path_paste, |
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74 maxseconds=maxseconds)) |
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75 for upload_wait in upload_waits: |
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76 upload_wait() |
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77 else: |
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78 for test_data in all_test_data: |
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79 upload_wait = galaxy_interactor.stage_data_async(test_data, |
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80 history, |
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81 tool_id, |
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82 force_path_paste=force_path_paste, |
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83 maxseconds=maxseconds) |
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84 upload_wait() |
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85 |
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86 |
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87 class GalaxyInteractorApi: |
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88 |
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89 def __init__(self, **kwds): |
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90 self.api_url = "%s/api" % kwds["galaxy_url"].rstrip("/") |
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91 self.master_api_key = kwds["master_api_key"] |
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92 self.api_key = self.__get_user_key(kwds.get("api_key"), kwds.get("master_api_key"), test_user=kwds.get("test_user")) |
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93 if kwds.get('user_api_key_is_admin_key', False): |
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94 self.master_api_key = self.api_key |
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95 self.keep_outputs_dir = kwds["keep_outputs_dir"] |
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96 self.download_attempts = kwds.get("download_attempts", 1) |
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97 self.download_sleep = kwds.get("download_sleep", 1) |
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98 # Local test data directories. |
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99 self.test_data_directories = kwds.get("test_data") or [] |
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100 |
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101 self._target_galaxy_version = None |
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102 |
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103 self.uploads = {} |
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104 |
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105 @property |
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106 def target_galaxy_version(self): |
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107 if self._target_galaxy_version is None: |
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108 self._target_galaxy_version = parse_version(self._get('version').json()['version_major']) |
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109 return self._target_galaxy_version |
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110 |
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111 @property |
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112 def supports_test_data_download(self): |
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113 return self.target_galaxy_version >= Version("19.01") |
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114 |
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115 def __get_user_key(self, user_key, admin_key, test_user=None): |
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116 if not test_user: |
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117 test_user = "test@bx.psu.edu" |
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118 if user_key: |
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119 return user_key |
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120 test_user = self.ensure_user_with_email(test_user) |
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121 return self._post("users/%s/api_key" % test_user['id'], key=admin_key).json() |
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122 |
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123 # def get_tools(self): |
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124 # response = self._get("tools?in_panel=false") |
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125 # assert response.status_code == 200, "Non 200 response from tool index API. [%s]" % response.content |
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126 # return response.json() |
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127 |
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128 def get_tests_summary(self): |
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129 response = self._get("tools/tests_summary") |
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130 assert response.status_code == 200, "Non 200 response from tool tests available API. [%s]" % response.content |
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131 return response.json() |
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132 |
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133 def get_tool_tests(self, tool_id, tool_version=None): |
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134 url = "tools/%s/test_data" % tool_id |
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135 if tool_version is not None: |
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136 url += "?tool_version=%s" % tool_version |
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137 response = self._get(url) |
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138 assert response.status_code == 200, "Non 200 response from tool test API. [%s]" % response.content |
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139 return response.json() |
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140 |
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141 def verify_output_collection(self, output_collection_def, output_collection_id, history, tool_id): |
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142 data_collection = self._get("dataset_collections/%s" % output_collection_id, data={"instance_type": "history"}).json() |
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143 |
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144 def verify_dataset(element, element_attrib, element_outfile): |
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145 hda = element["object"] |
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146 self.verify_output_dataset( |
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147 history, |
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148 hda_id=hda["id"], |
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149 outfile=element_outfile, |
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150 attributes=element_attrib, |
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151 tool_id=tool_id |
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152 ) |
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153 |
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154 verify_collection(output_collection_def, data_collection, verify_dataset) |
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155 |
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156 def verify_output(self, history_id, jobs, output_data, output_testdef, tool_id, maxseconds): |
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157 outfile = output_testdef.outfile |
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158 attributes = output_testdef.attributes |
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159 name = output_testdef.name |
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160 |
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161 self.wait_for_jobs(history_id, jobs, maxseconds) |
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162 hid = self.__output_id(output_data) |
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163 # TODO: Twill version verifies dataset is 'ok' in here. |
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164 try: |
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165 self.verify_output_dataset(history_id=history_id, hda_id=hid, outfile=outfile, attributes=attributes, tool_id=tool_id) |
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166 except AssertionError as e: |
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167 raise AssertionError("Output {}: {}".format(name, str(e))) |
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168 |
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169 primary_datasets = attributes.get('primary_datasets', {}) |
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170 if primary_datasets: |
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171 job_id = self._dataset_provenance(history_id, hid)["job_id"] |
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172 outputs = self._get("jobs/%s/outputs" % (job_id)).json() |
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173 |
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174 for designation, (primary_outfile, primary_attributes) in primary_datasets.items(): |
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175 primary_output = None |
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176 for output in outputs: |
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177 if output["name"] == f'__new_primary_file_{name}|{designation}__': |
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178 primary_output = output |
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179 break |
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180 |
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181 if not primary_output: |
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182 msg_template = "Failed to find primary dataset with designation [%s] for output with name [%s]" |
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183 msg_args = (designation, name) |
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184 raise Exception(msg_template % msg_args) |
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185 |
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186 primary_hda_id = primary_output["dataset"]["id"] |
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187 try: |
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188 self.verify_output_dataset(history_id, primary_hda_id, primary_outfile, primary_attributes, tool_id=tool_id) |
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189 except AssertionError as e: |
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190 raise AssertionError("Primary output {}: {}".format(name, str(e))) |
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191 |
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192 def wait_for_jobs(self, history_id, jobs, maxseconds): |
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193 for job in jobs: |
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194 self.wait_for_job(job['id'], history_id, maxseconds) |
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195 |
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196 def verify_output_dataset(self, history_id, hda_id, outfile, attributes, tool_id): |
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197 fetcher = self.__dataset_fetcher(history_id) |
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198 test_data_downloader = self.__test_data_downloader(tool_id) |
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199 verify_hid( |
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200 outfile, |
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201 hda_id=hda_id, |
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202 attributes=attributes, |
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203 dataset_fetcher=fetcher, |
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204 test_data_downloader=test_data_downloader, |
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205 keep_outputs_dir=self.keep_outputs_dir |
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206 ) |
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207 self._verify_metadata(history_id, hda_id, attributes) |
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208 |
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209 def _verify_metadata(self, history_id, hid, attributes): |
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210 """Check dataset metadata. |
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211 |
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212 ftype on output maps to `file_ext` on the hda's API description, `name`, `info`, |
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213 `dbkey` and `tags` all map to the API description directly. Other metadata attributes |
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214 are assumed to be datatype-specific and mapped with a prefix of `metadata_`. |
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215 """ |
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216 metadata = attributes.get('metadata', {}).copy() |
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217 for key in metadata.copy().keys(): |
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218 if key not in ['name', 'info', 'tags', 'created_from_basename']: |
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219 new_key = "metadata_%s" % key |
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220 metadata[new_key] = metadata[key] |
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221 del metadata[key] |
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222 elif key == "info": |
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223 metadata["misc_info"] = metadata["info"] |
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224 del metadata["info"] |
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225 expected_file_type = attributes.get('ftype', None) |
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226 if expected_file_type: |
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227 metadata["file_ext"] = expected_file_type |
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228 |
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229 if metadata: |
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230 time.sleep(5) |
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231 dataset = self._get(f"histories/{history_id}/contents/{hid}").json() |
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232 for key, value in metadata.items(): |
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233 try: |
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234 dataset_value = dataset.get(key, None) |
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235 |
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236 def compare(val, expected): |
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237 if str(val) != str(expected): |
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238 msg = "Dataset metadata verification for [%s] failed, expected [%s] but found [%s]. Dataset API value was [%s]." |
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239 msg_params = (key, value, dataset_value, dataset) |
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240 msg = msg % msg_params |
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241 raise Exception(msg) |
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242 |
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243 if isinstance(dataset_value, list): |
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244 value = str(value).split(",") |
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245 if len(value) != len(dataset_value): |
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246 msg = "Dataset metadata verification for [%s] failed, expected [%s] but found [%s], lists differ in length. Dataset API value was [%s]." |
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247 msg_params = (key, value, dataset_value, dataset) |
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248 msg = msg % msg_params |
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249 raise Exception(msg) |
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250 for val, expected in zip(dataset_value, value): |
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251 compare(val, expected) |
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252 else: |
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253 compare(dataset_value, value) |
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254 except KeyError: |
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255 msg = "Failed to verify dataset metadata, metadata key [%s] was not found." % key |
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256 raise Exception(msg) |
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257 |
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258 def wait_for_job(self, job_id, history_id=None, maxseconds=DEFAULT_TOOL_TEST_WAIT): |
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259 self.wait_for(lambda: self.__job_ready(job_id, history_id), maxseconds=maxseconds) |
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260 |
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261 def wait_for(self, func, what='tool test run', **kwd): |
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262 walltime_exceeded = int(kwd.get("maxseconds", DEFAULT_TOOL_TEST_WAIT)) |
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263 wait_on(func, what, walltime_exceeded) |
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264 |
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265 def get_job_stdio(self, job_id): |
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266 job_stdio = self.__get_job_stdio(job_id).json() |
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267 return job_stdio |
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268 |
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269 def __get_job(self, job_id): |
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270 return self._get('jobs/%s' % job_id) |
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271 |
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272 def __get_job_stdio(self, job_id): |
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273 return self._get('jobs/%s?full=true' % job_id) |
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274 |
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275 def new_history(self, history_name='test_history', publish_history=False): |
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276 create_response = self._post("histories", {"name": history_name}) |
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277 try: |
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278 create_response.raise_for_status() |
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279 except Exception as e: |
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280 raise Exception(f"Error occured while creating history with name '{history_name}': {e}") |
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281 history_id = create_response.json()['id'] |
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282 if publish_history: |
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283 self.publish_history(history_id) |
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284 return history_id |
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285 |
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286 def publish_history(self, history_id): |
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287 response = self._put(f'histories/{history_id}', json.dumps({'published': True})) |
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288 response.raise_for_status() |
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289 |
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290 @nottest |
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291 def test_data_path(self, tool_id, filename): |
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292 response = self._get(f"tools/{tool_id}/test_data_path?filename={filename}", admin=True) |
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293 return response.json() |
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294 |
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295 @nottest |
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296 def test_data_download(self, tool_id, filename, mode='file', is_output=True): |
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297 result = None |
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298 local_path = None |
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299 |
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300 if self.supports_test_data_download: |
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301 response = self._get(f"tools/{tool_id}/test_data_download?filename={filename}", admin=True) |
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302 if response.status_code == 200: |
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303 if mode == 'file': |
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304 result = response.content |
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305 elif mode == 'directory': |
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306 prefix = os.path.basename(filename) |
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307 path = tempfile.mkdtemp(prefix=prefix) |
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308 fileobj = io.BytesIO(response.content) |
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309 if zipfile.is_zipfile(fileobj): |
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310 with zipfile.ZipFile(fileobj) as contents: |
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311 contents.extractall(path=path) |
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312 else: |
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313 # Galaxy < 21.01 |
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314 with tarfile.open(fileobj=fileobj) as tar_contents: |
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315 tar_contents.extractall(path=path) |
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316 result = path |
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317 else: |
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318 # We can only use local data |
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319 local_path = self.test_data_path(tool_id, filename) |
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320 |
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321 if result is None and (local_path is None or not os.path.exists(local_path)): |
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322 for test_data_directory in self.test_data_directories: |
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323 local_path = os.path.join(test_data_directory, filename) |
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324 if os.path.exists(local_path): |
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325 break |
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326 |
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327 if result is None and local_path is not None and os.path.exists(local_path): |
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328 if mode == 'file': |
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329 with open(local_path, mode='rb') as f: |
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330 result = f.read() |
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331 elif mode == 'directory': |
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332 # Make a copy, since we are going to clean up the returned path |
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333 path = tempfile.mkdtemp() |
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334 shutil.copytree(local_path, path) |
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335 result = path |
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336 |
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337 if result is None: |
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338 if is_output: |
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339 raise AssertionError(f"Test output file ({filename}) is missing. If you are using planemo, try adding --update_test_data to generate it.") |
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340 else: |
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341 raise AssertionError(f"Test input file ({filename}) cannot be found.") |
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342 |
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343 return result |
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344 |
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345 def __output_id(self, output_data): |
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346 # Allow data structure coming out of tools API - {id: <id>, output_name: <name>, etc...} |
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347 # or simple id as comes out of workflow API. |
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348 try: |
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349 output_id = output_data.get('id') |
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350 except AttributeError: |
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351 output_id = output_data |
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352 return output_id |
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353 |
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354 def stage_data_async(self, test_data, history_id, tool_id, force_path_paste=False, maxseconds=DEFAULT_TOOL_TEST_WAIT): |
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355 fname = test_data['fname'] |
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356 tool_input = { |
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357 "file_type": test_data['ftype'], |
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358 "dbkey": test_data['dbkey'], |
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359 } |
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360 metadata = test_data.get("metadata", {}) |
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361 if not hasattr(metadata, "items"): |
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362 raise Exception(f"Invalid metadata description found for input [{fname}] - [{metadata}]") |
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363 for name, value in test_data.get('metadata', {}).items(): |
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364 tool_input["files_metadata|%s" % name] = value |
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365 |
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366 composite_data = test_data['composite_data'] |
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367 if composite_data: |
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368 files = {} |
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369 for i, file_name in enumerate(composite_data): |
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370 if force_path_paste: |
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371 file_path = self.test_data_path(tool_id, file_name) |
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372 tool_input.update({ |
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373 "files_%d|url_paste" % i: "file://" + file_path |
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374 }) |
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375 else: |
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376 file_content = self.test_data_download(tool_id, file_name, is_output=False) |
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377 files["files_%s|file_data" % i] = file_content |
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378 tool_input.update({ |
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379 "files_%d|type" % i: "upload_dataset", |
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380 }) |
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381 name = test_data['name'] |
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382 else: |
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383 name = os.path.basename(fname) |
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384 tool_input.update({ |
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385 "files_0|NAME": name, |
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386 "files_0|type": "upload_dataset", |
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387 }) |
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388 files = {} |
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389 if force_path_paste: |
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390 file_name = self.test_data_path(tool_id, fname) |
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391 tool_input.update({ |
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392 "files_0|url_paste": "file://" + file_name |
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393 }) |
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394 else: |
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395 file_content = self.test_data_download(tool_id, fname, is_output=False) |
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396 files = { |
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397 "files_0|file_data": file_content |
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398 } |
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399 submit_response_object = self.__submit_tool(history_id, "upload1", tool_input, extra_data={"type": "upload_dataset"}, files=files) |
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400 submit_response = ensure_tool_run_response_okay(submit_response_object, "upload dataset %s" % name) |
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401 assert "outputs" in submit_response, "Invalid response from server [%s], expecting outputs in response." % submit_response |
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402 outputs = submit_response["outputs"] |
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403 assert len(outputs) > 0, "Invalid response from server [%s], expecting an output dataset." % submit_response |
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404 dataset = outputs[0] |
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405 hid = dataset['id'] |
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406 self.uploads[os.path.basename(fname)] = self.uploads[fname] = self.uploads[name] = {"src": "hda", "id": hid} |
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407 assert "jobs" in submit_response, "Invalid response from server [%s], expecting jobs in response." % submit_response |
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408 jobs = submit_response["jobs"] |
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409 assert len(jobs) > 0, "Invalid response from server [%s], expecting a job." % submit_response |
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410 return lambda: self.wait_for_job(jobs[0]["id"], history_id, maxseconds=maxseconds) |
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411 |
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412 def run_tool(self, testdef, history_id, resource_parameters=None): |
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413 # We need to handle the case where we've uploaded a valid compressed file since the upload |
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414 # tool will have uncompressed it on the fly. |
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415 resource_parameters = resource_parameters or {} |
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416 inputs_tree = testdef.inputs.copy() |
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417 for key, value in inputs_tree.items(): |
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418 values = [value] if not isinstance(value, list) else value |
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419 new_values = [] |
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420 for value in values: |
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421 if isinstance(value, TestCollectionDef): |
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422 hdca_id = self._create_collection(history_id, value) |
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423 new_values = [dict(src="hdca", id=hdca_id)] |
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424 elif value in self.uploads: |
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425 new_values.append(self.uploads[value]) |
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426 else: |
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427 new_values.append(value) |
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428 inputs_tree[key] = new_values |
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429 |
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430 if resource_parameters: |
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431 inputs_tree["__job_resource|__job_resource__select"] = "yes" |
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432 for key, value in resource_parameters.items(): |
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433 inputs_tree["__job_resource|%s" % key] = value |
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434 |
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435 # HACK: Flatten single-value lists. Required when using expand_grouping |
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436 for key, value in inputs_tree.items(): |
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437 if isinstance(value, list) and len(value) == 1: |
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438 inputs_tree[key] = value[0] |
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shellac
parents:
diff
changeset
|
439 |
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shellac
parents:
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changeset
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440 submit_response = None |
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shellac
parents:
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changeset
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441 for _ in range(DEFAULT_TOOL_TEST_WAIT): |
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parents:
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changeset
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442 submit_response = self.__submit_tool(history_id, tool_id=testdef.tool_id, tool_input=inputs_tree) |
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shellac
parents:
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changeset
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443 if _are_tool_inputs_not_ready(submit_response): |
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shellac
parents:
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changeset
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444 print("Tool inputs not ready yet") |
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parents:
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changeset
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445 time.sleep(1) |
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shellac
parents:
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changeset
|
446 continue |
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shellac
parents:
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changeset
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447 else: |
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shellac
parents:
diff
changeset
|
448 break |
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shellac
parents:
diff
changeset
|
449 |
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shellac
parents:
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changeset
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450 submit_response_object = ensure_tool_run_response_okay(submit_response, "execute tool", inputs_tree) |
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shellac
parents:
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changeset
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451 try: |
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shellac
parents:
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changeset
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452 return Bunch( |
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parents:
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453 inputs=inputs_tree, |
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parents:
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changeset
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454 outputs=self.__dictify_outputs(submit_response_object), |
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shellac
parents:
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changeset
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455 output_collections=self.__dictify_output_collections(submit_response_object), |
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shellac
parents:
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changeset
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456 jobs=submit_response_object['jobs'], |
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parents:
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changeset
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457 ) |
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shellac
parents:
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changeset
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458 except KeyError: |
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parents:
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changeset
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459 message = "Error creating a job for these tool inputs - %s" % submit_response_object['err_msg'] |
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shellac
parents:
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460 raise RunToolException(message, inputs_tree) |
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shellac
parents:
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changeset
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461 |
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shellac
parents:
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changeset
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462 def _create_collection(self, history_id, collection_def): |
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parents:
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changeset
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463 create_payload = dict( |
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parents:
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464 name=collection_def.name, |
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parents:
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465 element_identifiers=dumps(self._element_identifiers(collection_def)), |
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shellac
parents:
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466 collection_type=collection_def.collection_type, |
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parents:
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467 history_id=history_id, |
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shellac
parents:
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changeset
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468 ) |
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parents:
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469 return self._post("dataset_collections", data=create_payload).json()["id"] |
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shellac
parents:
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changeset
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470 |
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shellac
parents:
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changeset
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471 def _element_identifiers(self, collection_def): |
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parents:
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472 element_identifiers = [] |
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shellac
parents:
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473 for element_dict in collection_def.elements: |
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parents:
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474 element_identifier = element_dict["element_identifier"] |
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parents:
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475 element_def = element_dict["element_definition"] |
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shellac
parents:
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changeset
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476 if isinstance(element_def, TestCollectionDef): |
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shellac
parents:
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changeset
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477 subelement_identifiers = self._element_identifiers(element_def) |
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shellac
parents:
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changeset
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478 element = dict( |
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shellac
parents:
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changeset
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479 name=element_identifier, |
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shellac
parents:
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changeset
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480 src="new_collection", |
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shellac
parents:
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changeset
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481 collection_type=element_def.collection_type, |
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shellac
parents:
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changeset
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482 element_identifiers=subelement_identifiers |
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shellac
parents:
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changeset
|
483 ) |
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shellac
parents:
diff
changeset
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484 else: |
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shellac
parents:
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changeset
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485 element = self.uploads[element_def["value"]].copy() |
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parents:
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changeset
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486 element["name"] = element_identifier |
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shellac
parents:
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changeset
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487 tags = element_def.get("attributes").get("tags") |
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shellac
parents:
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488 if tags: |
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shellac
parents:
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changeset
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489 element["tags"] = tags.split(",") |
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parents:
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490 element_identifiers.append(element) |
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shellac
parents:
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changeset
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491 return element_identifiers |
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shellac
parents:
diff
changeset
|
492 |
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shellac
parents:
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changeset
|
493 def __dictify_output_collections(self, submit_response): |
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shellac
parents:
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changeset
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494 output_collections_dict = {} |
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shellac
parents:
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changeset
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495 for output_collection in submit_response['output_collections']: |
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shellac
parents:
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changeset
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496 output_collections_dict[output_collection.get("output_name")] = output_collection |
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shellac
parents:
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497 return output_collections_dict |
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shellac
parents:
diff
changeset
|
498 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
499 def __dictify_outputs(self, datasets_object): |
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shellac
parents:
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changeset
|
500 # Convert outputs list to a dictionary that can be accessed by |
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shellac
parents:
diff
changeset
|
501 # output_name so can be more flexible about ordering of outputs |
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shellac
parents:
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changeset
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502 # but also allows fallback to legacy access as list mode. |
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shellac
parents:
diff
changeset
|
503 outputs_dict = OutputsDict() |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
504 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
505 for output in datasets_object['outputs']: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
506 outputs_dict[output.get("output_name")] = output |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
507 return outputs_dict |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
508 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
509 def output_hid(self, output_data): |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
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510 return output_data['id'] |
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shellac
parents:
diff
changeset
|
511 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
512 def delete_history(self, history): |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
513 self._delete(f"histories/{history}") |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
514 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
515 def __job_ready(self, job_id, history_id=None): |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
516 if job_id is None: |
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shellac
parents:
diff
changeset
|
517 raise ValueError("__job_ready passed empty job_id") |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
518 job_json = self._get("jobs/%s" % job_id).json() |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
519 state = job_json['state'] |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
520 try: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
521 return self._state_ready(state, error_msg="Job in error state.") |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
522 except Exception: |
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shellac
parents:
diff
changeset
|
523 if VERBOSE_ERRORS and history_id is not None: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
524 self._summarize_history(history_id) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
525 raise |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
526 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
527 def _summarize_history(self, history_id): |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
528 if history_id is None: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
529 raise ValueError("_summarize_history passed empty history_id") |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
530 print("Problem in history with id %s - summary of history's datasets and jobs below." % history_id) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
531 try: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
532 history_contents = self.__contents(history_id) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
533 except Exception: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
534 print("*TEST FRAMEWORK FAILED TO FETCH HISTORY DETAILS*") |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
535 return |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
536 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
537 for history_content in history_contents: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
538 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
539 dataset = history_content |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
540 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
541 print(ERROR_MESSAGE_DATASET_SEP) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
542 dataset_id = dataset.get('id', None) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
543 print("| %d - %s (HID - NAME) " % (int(dataset['hid']), dataset['name'])) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
544 if history_content['history_content_type'] == 'dataset_collection': |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
545 history_contents_json = self._get("histories/{}/contents/dataset_collections/{}".format(history_id, history_content["id"])).json() |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
546 print("| Dataset Collection: %s" % history_contents_json) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
547 print("|") |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
548 continue |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
549 |
4f3585e2f14b
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shellac
parents:
diff
changeset
|
550 try: |
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parents:
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changeset
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551 dataset_info = self._dataset_info(history_id, dataset_id) |
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parents:
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changeset
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552 print("| Dataset State:") |
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parents:
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changeset
|
553 print(self.format_for_summary(dataset_info.get("state"), "Dataset state is unknown.")) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
554 print("| Dataset Blurb:") |
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shellac
parents:
diff
changeset
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555 print(self.format_for_summary(dataset_info.get("misc_blurb", ""), "Dataset blurb was empty.")) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
556 print("| Dataset Info:") |
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shellac
parents:
diff
changeset
|
557 print(self.format_for_summary(dataset_info.get("misc_info", ""), "Dataset info is empty.")) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
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558 print("| Peek:") |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
559 print(self.format_for_summary(dataset_info.get("peek", ""), "Peek unavilable.")) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
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560 except Exception: |
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shellac
parents:
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changeset
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561 print("| *TEST FRAMEWORK ERROR FETCHING DATASET DETAILS*") |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
562 try: |
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shellac
parents:
diff
changeset
|
563 provenance_info = self._dataset_provenance(history_id, dataset_id) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
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564 print("| Dataset Job Standard Output:") |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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|
565 print(self.format_for_summary(provenance_info.get("stdout", ""), "Standard output was empty.")) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
566 print("| Dataset Job Standard Error:") |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
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567 print(self.format_for_summary(provenance_info.get("stderr", ""), "Standard error was empty.")) |
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shellac
parents:
diff
changeset
|
568 except Exception: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
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569 print("| *TEST FRAMEWORK ERROR FETCHING JOB DETAILS*") |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
570 print("|") |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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changeset
|
571 try: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
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572 jobs_json = self._get("jobs?history_id=%s" % history_id).json() |
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shellac
parents:
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changeset
|
573 for job_json in jobs_json: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
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574 print(ERROR_MESSAGE_DATASET_SEP) |
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shellac
parents:
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575 print("| Job %s" % job_json["id"]) |
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shellac
parents:
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576 print("| State: ") |
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shellac
parents:
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577 print(self.format_for_summary(job_json.get("state", ""), "Job state is unknown.")) |
4f3585e2f14b
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shellac
parents:
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changeset
|
578 print("| Update Time:") |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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579 print(self.format_for_summary(job_json.get("update_time", ""), "Job update time is unknown.")) |
4f3585e2f14b
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parents:
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580 print("| Create Time:") |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
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581 print(self.format_for_summary(job_json.get("create_time", ""), "Job create time is unknown.")) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
582 print("|") |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
583 print(ERROR_MESSAGE_DATASET_SEP) |
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shellac
parents:
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|
584 except Exception: |
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shellac
parents:
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changeset
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585 print(ERROR_MESSAGE_DATASET_SEP) |
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shellac
parents:
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changeset
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586 print("*TEST FRAMEWORK FAILED TO FETCH HISTORY JOBS*") |
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shellac
parents:
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changeset
|
587 print(ERROR_MESSAGE_DATASET_SEP) |
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shellac
parents:
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changeset
|
588 |
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shellac
parents:
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589 def format_for_summary(self, blob, empty_message, prefix="| "): |
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590 contents = "\n".join(f"{prefix}{line.strip()}" for line in io.StringIO(blob).readlines() if line.rstrip("\n\r")) |
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parents:
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591 return contents or f"{prefix}*{empty_message}*" |
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parents:
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changeset
|
592 |
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parents:
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changeset
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593 def _dataset_provenance(self, history_id, id): |
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shellac
parents:
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594 provenance = self._get(f"histories/{history_id}/contents/{id}/provenance").json() |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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595 return provenance |
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parents:
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|
596 |
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parents:
diff
changeset
|
597 def _dataset_info(self, history_id, id): |
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parents:
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598 dataset_json = self._get(f"histories/{history_id}/contents/{id}").json() |
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shellac
parents:
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changeset
|
599 return dataset_json |
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shellac
parents:
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changeset
|
600 |
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shellac
parents:
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changeset
|
601 def __contents(self, history_id): |
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shellac
parents:
diff
changeset
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602 history_contents_response = self._get("histories/%s/contents" % history_id) |
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parents:
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603 history_contents_response.raise_for_status() |
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shellac
parents:
diff
changeset
|
604 return history_contents_response.json() |
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shellac
parents:
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changeset
|
605 |
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shellac
parents:
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changeset
|
606 def _state_ready(self, state_str, error_msg): |
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shellac
parents:
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|
607 if state_str == 'ok': |
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parents:
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608 return True |
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shellac
parents:
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609 elif state_str == 'error': |
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shellac
parents:
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610 raise Exception(error_msg) |
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shellac
parents:
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changeset
|
611 return None |
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shellac
parents:
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changeset
|
612 |
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shellac
parents:
diff
changeset
|
613 def __submit_tool(self, history_id, tool_id, tool_input, extra_data=None, files=None): |
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shellac
parents:
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changeset
|
614 extra_data = extra_data or {} |
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parents:
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changeset
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615 data = dict( |
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shellac
parents:
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616 history_id=history_id, |
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parents:
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|
617 tool_id=tool_id, |
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shellac
parents:
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changeset
|
618 inputs=dumps(tool_input), |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
619 **extra_data |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
620 ) |
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shellac
parents:
diff
changeset
|
621 return self._post("tools", files=files, data=data) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
622 |
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shellac
parents:
diff
changeset
|
623 def ensure_user_with_email(self, email, password=None): |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
624 admin_key = self.master_api_key |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
625 all_users_response = self._get('users', key=admin_key) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
626 try: |
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parents:
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changeset
|
627 all_users_response.raise_for_status() |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
628 except requests.exceptions.HTTPError as e: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
629 raise Exception(f"Failed to verify user with email [{email}] exists - perhaps you're targetting the wrong Galaxy server or using an incorrect admin API key. HTTP error: {e}") |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
630 all_users = all_users_response.json() |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
631 try: |
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shellac
parents:
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changeset
|
632 test_user = [user for user in all_users if user["email"] == email][0] |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
633 except IndexError: |
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shellac
parents:
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changeset
|
634 username = re.sub(r"[^a-z-\d]", '--', email.lower()) |
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shellac
parents:
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changeset
|
635 password = password or 'testpass' |
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shellac
parents:
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changeset
|
636 # If remote user middleware is enabled - this endpoint consumes |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
637 # ``remote_user_email`` otherwise it requires ``email``, ``password`` |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
638 # and ``username``. |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
639 data = dict( |
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shellac
parents:
diff
changeset
|
640 remote_user_email=email, |
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shellac
parents:
diff
changeset
|
641 email=email, |
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shellac
parents:
diff
changeset
|
642 password=password, |
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shellac
parents:
diff
changeset
|
643 username=username, |
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shellac
parents:
diff
changeset
|
644 ) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
645 test_user = self._post('users', data, key=admin_key).json() |
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shellac
parents:
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changeset
|
646 return test_user |
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shellac
parents:
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changeset
|
647 |
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shellac
parents:
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changeset
|
648 def __test_data_downloader(self, tool_id): |
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shellac
parents:
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changeset
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649 def test_data_download(filename, mode='file'): |
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shellac
parents:
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650 return self.test_data_download(tool_id, filename, mode=mode) |
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shellac
parents:
diff
changeset
|
651 return test_data_download |
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shellac
parents:
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changeset
|
652 |
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shellac
parents:
diff
changeset
|
653 def __dataset_fetcher(self, history_id): |
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shellac
parents:
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changeset
|
654 def fetcher(hda_id, base_name=None): |
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shellac
parents:
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|
655 url = f"histories/{history_id}/contents/{hda_id}/display?raw=true" |
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shellac
parents:
diff
changeset
|
656 if base_name: |
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shellac
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657 url += "&filename=%s" % base_name |
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658 response = None |
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659 for _ in range(self.download_attempts): |
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660 response = self._get(url) |
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661 if response.status_code == 500: |
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662 print(f"Retrying failed download with status code {response.status_code}") |
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663 time.sleep(self.download_sleep) |
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664 continue |
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665 else: |
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666 break |
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667 |
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668 response.raise_for_status() |
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669 return response.content |
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670 |
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671 return fetcher |
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672 |
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673 def api_key_header(self, key, admin, anon): |
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674 header = {} |
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675 if not anon: |
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676 if not key: |
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677 key = self.api_key if not admin else self.master_api_key |
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678 header['x-api-key'] = key |
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679 return header |
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680 |
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681 def _post(self, path, data=None, files=None, key=None, admin=False, anon=False, json=False): |
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682 # If json=True, use post payload using request's json parameter instead of the data |
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683 # parameter (i.e. assume the contents is a jsonified blob instead of form parameters |
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684 # with individual parameters jsonified if needed). |
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685 headers = self.api_key_header(key=key, admin=admin, anon=anon) |
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686 url = f"{self.api_url}/{path}" |
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687 return galaxy_requests_post(url, data=data, files=files, as_json=json, headers=headers) |
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688 |
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689 def _delete(self, path, data=None, key=None, admin=False, anon=False): |
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690 headers = self.api_key_header(key=key, admin=admin, anon=anon) |
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691 return requests.delete(f"{self.api_url}/{path}", params=data, headers=headers) |
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692 |
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693 def _patch(self, path, data=None, key=None, admin=False, anon=False): |
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694 headers = self.api_key_header(key=key, admin=admin, anon=anon) |
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695 return requests.patch(f"{self.api_url}/{path}", data=data, headers=headers) |
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696 |
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697 def _put(self, path, data=None, key=None, admin=False, anon=False): |
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698 headers = self.api_key_header(key=key, admin=admin, anon=anon) |
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699 return requests.put(f"{self.api_url}/{path}", data=data, headers=headers) |
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700 |
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701 def _get(self, path, data=None, key=None, admin=False, anon=False): |
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702 headers = self.api_key_header(key=key, admin=admin, anon=anon) |
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703 if path.startswith("/api"): |
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704 path = path[len("/api"):] |
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705 url = f"{self.api_url}/{path}" |
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706 # no data for GET |
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707 return requests.get(url, params=data, headers=headers) |
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708 |
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709 |
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710 def ensure_tool_run_response_okay(submit_response_object, request_desc, inputs=None): |
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711 if submit_response_object.status_code != 200: |
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712 message = None |
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713 dynamic_param_error = False |
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714 try: |
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715 err_response = submit_response_object.json() |
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716 if "param_errors" in err_response: |
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717 param_errors = err_response["param_errors"] |
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718 if "dbkey" in param_errors: |
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719 dbkey_err_obj = param_errors["dbkey"] |
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720 dbkey_val = dbkey_err_obj.get("parameter_value") |
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721 message = "Invalid dbkey specified [%s]" % dbkey_val |
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722 for value in param_errors.values(): |
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723 if isinstance(value, dict) and value.get("is_dynamic"): |
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724 dynamic_param_error = True |
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725 if message is None: |
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726 message = err_response.get("err_msg") or None |
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|
727 except Exception: |
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|
728 # invalid JSON content. |
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|
729 pass |
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730 if message is None: |
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731 template = "Request to %s failed - invalid JSON content returned from Galaxy server [%s]" |
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732 message = template % (request_desc, submit_response_object.text) |
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733 raise RunToolException(message, inputs, dynamic_param_error=dynamic_param_error) |
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734 submit_response = submit_response_object.json() |
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|
735 return submit_response |
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|
736 |
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|
737 |
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|
738 def _are_tool_inputs_not_ready(submit_response): |
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739 if submit_response.status_code != 400: |
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740 return False |
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741 try: |
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742 submit_json = submit_response.json() |
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743 return submit_json.get("err_code") == 400015 |
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744 except Exception: |
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|
745 return False |
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|
746 |
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747 |
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748 class RunToolException(Exception): |
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749 |
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750 def __init__(self, message, inputs=None, dynamic_param_error=False): |
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751 super().__init__(message) |
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752 self.inputs = inputs |
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753 self.dynamic_param_error = dynamic_param_error |
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754 |
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755 |
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756 # Galaxy specific methods - rest of this can be used with arbitrary files and such. |
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757 def verify_hid(filename, hda_id, attributes, test_data_downloader, hid="", dataset_fetcher=None, keep_outputs_dir=False): |
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758 assert dataset_fetcher is not None |
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759 |
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760 def verify_extra_files(extra_files): |
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761 _verify_extra_files_content(extra_files, hda_id, dataset_fetcher=dataset_fetcher, test_data_downloader=test_data_downloader, keep_outputs_dir=keep_outputs_dir) |
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762 |
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763 data = dataset_fetcher(hda_id) |
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764 item_label = "" |
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765 verify( |
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766 item_label, |
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767 data, |
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768 attributes=attributes, |
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769 filename=filename, |
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770 get_filecontent=test_data_downloader, |
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771 keep_outputs_dir=keep_outputs_dir, |
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772 verify_extra_files=verify_extra_files, |
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773 ) |
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774 |
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775 |
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776 def verify_collection(output_collection_def, data_collection, verify_dataset): |
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777 name = output_collection_def.name |
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778 |
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779 expected_collection_type = output_collection_def.collection_type |
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780 if expected_collection_type: |
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781 collection_type = data_collection["collection_type"] |
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782 if expected_collection_type != collection_type: |
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783 template = "Expected output collection [%s] to be of type [%s], was of type [%s]." |
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784 message = template % (name, expected_collection_type, collection_type) |
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785 raise AssertionError(message) |
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786 |
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787 expected_element_count = output_collection_def.count |
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788 if expected_element_count: |
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789 actual_element_count = len(data_collection["elements"]) |
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790 if expected_element_count != actual_element_count: |
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791 template = "Expected output collection [%s] to have %s elements, but it had %s." |
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792 message = template % (name, expected_element_count, actual_element_count) |
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793 raise AssertionError(message) |
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794 |
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795 def get_element(elements, id): |
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796 for element in elements: |
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797 if element["element_identifier"] == id: |
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798 return element |
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799 return False |
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800 |
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801 def verify_elements(element_objects, element_tests): |
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802 # sorted_test_ids = [None] * len(element_tests) |
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803 expected_sort_order = [] |
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804 |
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805 eo_ids = [_["element_identifier"] for _ in element_objects] |
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806 for element_identifier, element_test in element_tests.items(): |
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807 if isinstance(element_test, dict): |
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808 element_outfile, element_attrib = None, element_test |
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809 else: |
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810 element_outfile, element_attrib = element_test |
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811 if 'expected_sort_order' in element_attrib: |
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812 expected_sort_order.append(element_identifier) |
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813 |
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814 element = get_element(element_objects, element_identifier) |
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815 if not element: |
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816 template = "Failed to find identifier '%s' in the tool generated collection elements %s" |
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817 message = template % (element_identifier, eo_ids) |
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818 raise AssertionError(message) |
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819 |
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820 element_type = element["element_type"] |
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821 if element_type != "dataset_collection": |
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822 verify_dataset(element, element_attrib, element_outfile) |
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823 if element_type == "dataset_collection": |
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824 elements = element["object"]["elements"] |
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825 verify_elements(elements, element_attrib.get("elements", {})) |
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826 |
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827 if len(expected_sort_order) > 0: |
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828 i = 0 |
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829 for element_identifier in expected_sort_order: |
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830 element = None |
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831 while i < len(element_objects): |
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832 if element_objects[i]["element_identifier"] == element_identifier: |
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833 element = element_objects[i] |
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834 i += 1 |
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835 break |
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836 i += 1 |
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837 if element is None: |
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838 template = "Collection identifier '%s' found out of order, expected order of %s for the tool generated collection elements %s" |
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839 message = template % (element_identifier, expected_sort_order, eo_ids) |
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840 raise AssertionError(message) |
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841 |
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842 verify_elements(data_collection["elements"], output_collection_def.element_tests) |
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843 |
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844 |
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845 def _verify_composite_datatype_file_content(file_name, hda_id, base_name=None, attributes=None, dataset_fetcher=None, test_data_downloader=None, keep_outputs_dir=False, mode='file'): |
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846 assert dataset_fetcher is not None |
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847 |
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848 data = dataset_fetcher(hda_id, base_name) |
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849 item_label = "History item %s" % hda_id |
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850 try: |
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851 verify( |
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852 item_label, |
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853 data, |
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854 attributes=attributes, |
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855 filename=file_name, |
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856 get_filecontent=test_data_downloader, |
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857 keep_outputs_dir=keep_outputs_dir, |
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858 mode=mode, |
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859 ) |
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860 except AssertionError as err: |
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861 errmsg = f'Composite file ({base_name}) of {item_label} different than expected, difference:\n' |
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862 errmsg += util.unicodify(err) |
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863 raise AssertionError(errmsg) |
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864 |
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865 |
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866 def _verify_extra_files_content(extra_files, hda_id, dataset_fetcher, test_data_downloader, keep_outputs_dir): |
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867 files_list = [] |
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868 cleanup_directories = [] |
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869 for extra_file_dict in extra_files: |
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870 extra_file_type = extra_file_dict["type"] |
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871 extra_file_name = extra_file_dict["name"] |
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872 extra_file_attributes = extra_file_dict["attributes"] |
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873 extra_file_value = extra_file_dict["value"] |
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874 |
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875 if extra_file_type == 'file': |
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876 files_list.append((extra_file_name, extra_file_value, extra_file_attributes, extra_file_type)) |
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parents:
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|
877 elif extra_file_type == 'directory': |
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parents:
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changeset
|
878 extracted_path = test_data_downloader(extra_file_value, mode='directory') |
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parents:
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|
879 cleanup_directories.append(extracted_path) |
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shellac
parents:
diff
changeset
|
880 for root, directories, files in util.path.safe_walk(extracted_path): |
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shellac
parents:
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changeset
|
881 for filename in files: |
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parents:
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|
882 filename = os.path.join(root, filename) |
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parents:
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changeset
|
883 filename = os.path.relpath(filename, extracted_path) |
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shellac
parents:
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|
884 files_list.append((filename, os.path.join(extracted_path, filename), extra_file_attributes, extra_file_type)) |
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parents:
diff
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|
885 else: |
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shellac
parents:
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|
886 raise ValueError('unknown extra_files type: %s' % extra_file_type) |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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|
887 try: |
4f3585e2f14b
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shellac
parents:
diff
changeset
|
888 for filename, filepath, attributes, extra_file_type in files_list: |
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shellac
parents:
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|
889 _verify_composite_datatype_file_content(filepath, hda_id, base_name=filename, attributes=attributes, dataset_fetcher=dataset_fetcher, test_data_downloader=test_data_downloader, keep_outputs_dir=keep_outputs_dir, mode=extra_file_type) |
4f3585e2f14b
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shellac
parents:
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|
890 finally: |
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shellac
parents:
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changeset
|
891 for path in cleanup_directories: |
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shellac
parents:
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|
892 shutil.rmtree(path) |
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parents:
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|
893 |
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parents:
diff
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|
894 |
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|
895 class NullClientTestConfig: |
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parents:
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|
896 |
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parents:
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|
897 def get_test_config(self, job_data): |
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|
898 return None |
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|
899 |
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|
900 |
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parents:
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|
901 class DictClientTestConfig: |
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|
902 |
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|
903 def __init__(self, tools): |
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parents:
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|
904 self._tools = tools or {} |
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|
905 |
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|
906 def get_test_config(self, job_data): |
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|
907 # TODO: allow short ids, allow versions below outer id instead of key concatenation. |
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parents:
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|
908 tool_id = job_data.get("tool_id") |
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parents:
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|
909 tool_version = job_data.get("tool_version") |
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|
910 tool_test_config = None |
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shellac
parents:
diff
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|
911 tool_version_test_config = None |
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parents:
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|
912 is_default = False |
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shellac
parents:
diff
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|
913 if tool_id in self._tools: |
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shellac
parents:
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|
914 tool_test_config = self._tools[tool_id] |
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shellac
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|
915 if tool_test_config is None: |
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shellac
parents:
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|
916 tool_id = f"{tool_id}/{tool_version}" |
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shellac
parents:
diff
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|
917 if tool_id in self._tools: |
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shellac
parents:
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|
918 tool_version_test_config = self._tools[tool_id] |
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shellac
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|
919 else: |
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shellac
parents:
diff
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|
920 if tool_version in tool_test_config: |
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shellac
parents:
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|
921 tool_version_test_config = tool_test_config[tool_version] |
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shellac
parents:
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|
922 elif "default" in tool_test_config: |
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shellac
parents:
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|
923 tool_version_test_config = tool_test_config["default"] |
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shellac
parents:
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|
924 is_default = True |
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shellac
parents:
diff
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|
925 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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changeset
|
926 if tool_version_test_config: |
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shellac
parents:
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|
927 test_index = job_data.get("test_index") |
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shellac
parents:
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|
928 if test_index in tool_version_test_config: |
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shellac
parents:
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|
929 return tool_version_test_config[test_index] |
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shellac
parents:
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|
930 elif str(test_index) in tool_version_test_config: |
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shellac
parents:
diff
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|
931 return tool_version_test_config[str(test_index)] |
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shellac
parents:
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|
932 if 'default' in tool_version_test_config: |
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shellac
parents:
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|
933 return tool_version_test_config['default'] |
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shellac
parents:
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|
934 elif is_default: |
4f3585e2f14b
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shellac
parents:
diff
changeset
|
935 return tool_version_test_config |
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shellac
parents:
diff
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|
936 return None |
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shellac
parents:
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|
937 |
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shellac
parents:
diff
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|
938 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
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|
939 def verify_tool(tool_id, |
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shellac
parents:
diff
changeset
|
940 galaxy_interactor, |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
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|
941 resource_parameters=None, |
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shellac
parents:
diff
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|
942 register_job_data=None, |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
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|
943 test_index=0, |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
944 tool_version=None, |
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shellac
parents:
diff
changeset
|
945 quiet=False, |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
946 test_history=None, |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
947 no_history_cleanup=False, |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
948 publish_history=False, |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
949 force_path_paste=False, |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
950 maxseconds=DEFAULT_TOOL_TEST_WAIT, |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
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|
951 tool_test_dicts=None, |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
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|
952 client_test_config=None, |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
953 skip_with_reference_data=False, |
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shellac
parents:
diff
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|
954 skip_on_dynamic_param_errors=False): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
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|
955 if resource_parameters is None: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
956 resource_parameters = {} |
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shellac
parents:
diff
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|
957 if client_test_config is None: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
958 client_test_config = NullClientTestConfig() |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
959 tool_test_dicts = tool_test_dicts or galaxy_interactor.get_tool_tests(tool_id, tool_version=tool_version) |
4f3585e2f14b
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shellac
parents:
diff
changeset
|
960 tool_test_dict = tool_test_dicts[test_index] |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
961 if "test_index" not in tool_test_dict: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
962 tool_test_dict["test_index"] = test_index |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
963 if "tool_id" not in tool_test_dict: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
964 tool_test_dict["tool_id"] = tool_id |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
965 if tool_version is None and "tool_version" in tool_test_dict: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
966 tool_version = tool_test_dict.get("tool_version") |
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shellac
parents:
diff
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|
967 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
968 job_data = { |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
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|
969 "tool_id": tool_id, |
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shellac
parents:
diff
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|
970 "tool_version": tool_version, |
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shellac
parents:
diff
changeset
|
971 "test_index": test_index, |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
972 } |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
973 client_config = client_test_config.get_test_config(job_data) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
974 skip_message = None |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
975 if client_config is not None: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
976 job_data.update(client_config) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
977 skip_message = job_data.get("skip") |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
978 |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
979 if not skip_message and skip_with_reference_data: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
980 required_data_tables = tool_test_dict.get("required_data_tables") |
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shellac
parents:
diff
changeset
|
981 required_loc_files = tool_test_dict.get("required_loc_files") |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
982 # TODO: actually hit the API and see if these tables are available. |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
983 if required_data_tables: |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
|
984 skip_message = f"Skipping test because of required data tables ({required_data_tables})" |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
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|
985 if required_loc_files: |
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986 skip_message = f"Skipping test because of required loc files ({required_loc_files})" |
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987 |
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988 if skip_message: |
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989 job_data["status"] = "skip" |
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990 register_job_data(job_data) |
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991 return |
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992 |
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993 tool_test_dict.setdefault('maxseconds', maxseconds) |
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994 testdef = ToolTestDescription(tool_test_dict) |
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995 _handle_def_errors(testdef) |
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996 |
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997 created_history = False |
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998 if test_history is None: |
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999 created_history = True |
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1000 history_name = f"Tool Test History for {tool_id}/{tool_version}-{test_index}" |
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1001 test_history = galaxy_interactor.new_history(history_name=history_name, publish_history=publish_history) |
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1002 |
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1003 # Upload data to test_history, run the tool and check the outputs - record |
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1004 # API input, job info, tool run exception, as well as exceptions related to |
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1005 # job output checking and register they with the test plugin so it can |
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1006 # record structured information. |
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1007 tool_inputs = None |
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1008 job_stdio = None |
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1009 job_output_exceptions = None |
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1010 tool_execution_exception = None |
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1011 input_staging_exception = None |
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1012 expected_failure_occurred = False |
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1013 begin_time = time.time() |
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1014 try: |
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1015 try: |
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1016 stage_data_in_history( |
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1017 galaxy_interactor, |
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1018 tool_id, |
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1019 testdef.test_data(), |
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1020 history=test_history, |
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1021 force_path_paste=force_path_paste, |
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1022 maxseconds=maxseconds, |
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1023 ) |
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1024 except Exception as e: |
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1025 input_staging_exception = e |
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1026 raise |
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1027 try: |
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1028 tool_response = galaxy_interactor.run_tool(testdef, test_history, resource_parameters=resource_parameters) |
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1029 data_list, jobs, tool_inputs = tool_response.outputs, tool_response.jobs, tool_response.inputs |
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1030 data_collection_list = tool_response.output_collections |
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1031 except RunToolException as e: |
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1032 tool_inputs = e.inputs |
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1033 tool_execution_exception = e |
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1034 if not testdef.expect_failure: |
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1035 raise e |
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1036 else: |
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1037 expected_failure_occurred = True |
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1038 except Exception as e: |
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1039 tool_execution_exception = e |
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1040 raise e |
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1041 |
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1042 if not expected_failure_occurred: |
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1043 assert data_list or data_collection_list |
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1044 |
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1045 try: |
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1046 job_stdio = _verify_outputs(testdef, test_history, jobs, tool_id, data_list, data_collection_list, galaxy_interactor, quiet=quiet) |
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1047 except JobOutputsError as e: |
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1048 job_stdio = e.job_stdio |
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1049 job_output_exceptions = e.output_exceptions |
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1050 raise e |
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1051 except Exception as e: |
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1052 job_output_exceptions = [e] |
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1053 raise e |
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1054 finally: |
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1055 if register_job_data is not None: |
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1056 end_time = time.time() |
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1057 job_data["time_seconds"] = end_time - begin_time |
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1058 if tool_inputs is not None: |
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1059 job_data["inputs"] = tool_inputs |
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1060 if job_stdio is not None: |
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1061 job_data["job"] = job_stdio |
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1062 status = "success" |
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1063 if job_output_exceptions: |
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1064 job_data["output_problems"] = [util.unicodify(_) for _ in job_output_exceptions] |
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1065 status = "failure" |
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1066 if tool_execution_exception: |
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1067 job_data["execution_problem"] = util.unicodify(tool_execution_exception) |
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1068 dynamic_param_error = getattr(tool_execution_exception, "dynamic_param_error", False) |
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1069 job_data["dynamic_param_error"] = dynamic_param_error |
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1070 status = "error" if not skip_on_dynamic_param_errors or not dynamic_param_error else "skip" |
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1071 if input_staging_exception: |
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1072 job_data["execution_problem"] = "Input staging problem: %s" % util.unicodify(input_staging_exception) |
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1073 status = "error" |
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1074 job_data["status"] = status |
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1075 register_job_data(job_data) |
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1076 |
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1077 if created_history and not no_history_cleanup: |
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1078 galaxy_interactor.delete_history(test_history) |
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1079 |
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1080 |
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1081 def _handle_def_errors(testdef): |
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1082 # If the test generation had an error, raise |
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1083 if testdef.error: |
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1084 if testdef.exception: |
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1085 if isinstance(testdef.exception, Exception): |
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1086 raise testdef.exception |
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1087 else: |
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1088 raise Exception(testdef.exception) |
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1089 else: |
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1090 raise Exception("Test parse failure") |
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1091 |
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1092 |
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1093 def _verify_outputs(testdef, history, jobs, tool_id, data_list, data_collection_list, galaxy_interactor, quiet=False): |
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1094 assert len(jobs) == 1, "Test framework logic error, somehow tool test resulted in more than one job." |
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1095 job = jobs[0] |
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1096 |
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1097 maxseconds = testdef.maxseconds |
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1098 if testdef.num_outputs is not None: |
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1099 expected = testdef.num_outputs |
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1100 actual = len(data_list) + len(data_collection_list) |
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1101 if expected != actual: |
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1102 message_template = "Incorrect number of outputs - expected %d, found %s." |
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1103 message = message_template % (expected, actual) |
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1104 raise Exception(message) |
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1105 found_exceptions = [] |
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1106 |
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1107 def register_exception(e): |
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1108 if not found_exceptions and not quiet: |
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1109 # Only print this stuff out once. |
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1110 for stream in ['stdout', 'stderr']: |
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1111 if stream in job_stdio: |
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1112 print(_format_stream(job_stdio[stream], stream=stream, format=True), file=sys.stderr) |
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1113 found_exceptions.append(e) |
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1114 |
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1115 if testdef.expect_failure: |
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1116 if testdef.outputs: |
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1117 raise Exception("Cannot specify outputs in a test expecting failure.") |
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1118 |
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1119 # Wait for the job to complete and register expections if the final |
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1120 # status was not what test was expecting. |
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1121 job_failed = False |
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1122 try: |
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1123 galaxy_interactor.wait_for_job(job['id'], history, maxseconds) |
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1124 except Exception as e: |
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1125 job_failed = True |
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1126 if not testdef.expect_failure: |
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1127 found_exceptions.append(e) |
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1128 |
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1129 job_stdio = galaxy_interactor.get_job_stdio(job['id']) |
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1130 |
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1131 if not job_failed and testdef.expect_failure: |
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1132 error = AssertionError("Expected job to fail but Galaxy indicated the job successfully completed.") |
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1133 register_exception(error) |
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1134 |
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1135 expect_exit_code = testdef.expect_exit_code |
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1136 if expect_exit_code is not None: |
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1137 exit_code = job_stdio["exit_code"] |
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1138 if str(expect_exit_code) != str(exit_code): |
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1139 error = AssertionError(f"Expected job to complete with exit code {expect_exit_code}, found {exit_code}") |
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1140 register_exception(error) |
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1141 |
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1142 for output_index, output_dict in enumerate(testdef.outputs): |
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1143 # Get the correct hid |
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1144 name = output_dict["name"] |
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1145 outfile = output_dict["value"] |
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1146 attributes = output_dict["attributes"] |
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1147 output_testdef = Bunch(name=name, outfile=outfile, attributes=attributes) |
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1148 try: |
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1149 output_data = data_list[name] |
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1150 except (TypeError, KeyError): |
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1151 # Legacy - fall back on ordered data list access if data_list is |
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1152 # just a list (case with twill variant or if output changes its |
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1153 # name). |
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1154 if hasattr(data_list, "values"): |
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1155 output_data = list(data_list.values())[output_index] |
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1156 else: |
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1157 output_data = data_list[len(data_list) - len(testdef.outputs) + output_index] |
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1158 assert output_data is not None |
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1159 try: |
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1160 galaxy_interactor.verify_output(history, jobs, output_data, output_testdef=output_testdef, tool_id=tool_id, maxseconds=maxseconds) |
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1161 except Exception as e: |
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1162 register_exception(e) |
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1163 |
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1164 other_checks = { |
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1165 "command_line": "Command produced by the job", |
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1166 "command_version": "Tool version indicated during job execution", |
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1167 "stdout": "Standard output of the job", |
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1168 "stderr": "Standard error of the job", |
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1169 } |
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1170 # TODO: Only hack the stdio like this for older profile, for newer tool profiles |
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1171 # add some syntax for asserting job messages maybe - or just drop this because exit |
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1172 # code and regex on stdio can be tested directly - so this is really testing Galaxy |
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1173 # core handling more than the tool. |
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1174 job_messages = job_stdio.get("job_messages") or [] |
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1175 stdout_prefix = "" |
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1176 stderr_prefix = "" |
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1177 for job_message in job_messages: |
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1178 message_type = job_message.get("type") |
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1179 if message_type == "regex" and job_message.get("stream") == "stderr": |
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1180 stderr_prefix += (job_message.get("desc") or '') + "\n" |
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1181 elif message_type == "regex" and job_message.get("stream") == "stdout": |
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1182 stdout_prefix += (job_message.get("desc") or '') + "\n" |
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1183 elif message_type == "exit_code": |
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1184 stderr_prefix += (job_message.get("desc") or '') + "\n" |
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1185 else: |
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1186 raise Exception(f"Unknown job message type [{message_type}] in [{job_message}]") |
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1187 |
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1188 for what, description in other_checks.items(): |
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1189 if getattr(testdef, what, None) is not None: |
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1190 try: |
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1191 raw_data = job_stdio[what] |
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1192 assertions = getattr(testdef, what) |
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1193 if what == "stdout": |
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1194 data = stdout_prefix + raw_data |
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1195 elif what == "stderr": |
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1196 data = stderr_prefix + raw_data |
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1197 else: |
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1198 data = raw_data |
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1199 verify_assertions(data, assertions) |
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1200 except AssertionError as err: |
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1201 errmsg = '%s different than expected\n' % description |
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1202 errmsg += util.unicodify(err) |
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1203 register_exception(AssertionError(errmsg)) |
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1204 |
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1205 for output_collection_def in testdef.output_collections: |
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1206 try: |
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1207 name = output_collection_def.name |
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1208 # TODO: data_collection_list is clearly a bad name for dictionary. |
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1209 if name not in data_collection_list: |
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1210 template = "Failed to find output [%s], tool outputs include [%s]" |
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1211 message = template % (name, ",".join(data_collection_list.keys())) |
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1212 raise AssertionError(message) |
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1213 |
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1214 # Data collection returned from submission, elements may have been populated after |
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1215 # the job completed so re-hit the API for more information. |
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1216 data_collection_id = data_collection_list[name]["id"] |
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1217 galaxy_interactor.verify_output_collection(output_collection_def, data_collection_id, history, tool_id) |
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1218 except Exception as e: |
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1219 register_exception(e) |
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1220 |
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1221 if found_exceptions: |
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1222 raise JobOutputsError(found_exceptions, job_stdio) |
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1223 else: |
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1224 return job_stdio |
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1225 |
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1226 |
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1227 def _format_stream(output, stream, format): |
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1228 output = output or '' |
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1229 if format: |
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1230 msg = "---------------------- >> begin tool %s << -----------------------\n" % stream |
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1231 msg += output + "\n" |
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1232 msg += "----------------------- >> end tool %s << ------------------------\n" % stream |
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1233 else: |
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1234 msg = output |
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1235 return msg |
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1236 |
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1237 |
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1238 class JobOutputsError(AssertionError): |
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1239 |
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1240 def __init__(self, output_exceptions, job_stdio): |
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1241 big_message = "\n".join(map(util.unicodify, output_exceptions)) |
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1242 super().__init__(big_message) |
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1243 self.job_stdio = job_stdio |
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1244 self.output_exceptions = output_exceptions |
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1245 |
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1246 |
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1247 class ToolTestDescription: |
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1248 """ |
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1249 Encapsulates information about a tool test, and allows creation of a |
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1250 dynamic TestCase class (the unittest framework is very class oriented, |
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1251 doing dynamic tests in this way allows better integration) |
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1252 """ |
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1253 |
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1254 def __init__(self, processed_test_dict): |
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1255 assert "test_index" in processed_test_dict, "Invalid processed test description, must have a 'test_index' for naming, etc.." |
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1256 test_index = processed_test_dict["test_index"] |
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1257 name = processed_test_dict.get('name', 'Test-%d' % (test_index + 1)) |
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1258 maxseconds = processed_test_dict.get('maxseconds', DEFAULT_TOOL_TEST_WAIT) |
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1259 if maxseconds is not None: |
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1260 maxseconds = int(maxseconds) |
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1261 |
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1262 self.test_index = test_index |
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1263 assert "tool_id" in processed_test_dict, "Invalid processed test description, must have a 'tool_id' for naming, etc.." |
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1264 self.tool_id = processed_test_dict["tool_id"] |
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1265 self.tool_version = processed_test_dict.get("tool_version") |
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1266 self.name = name |
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1267 self.maxseconds = maxseconds |
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1268 self.required_files = processed_test_dict.get("required_files", []) |
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1269 self.required_data_tables = processed_test_dict.get("required_data_tables", []) |
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1270 self.required_loc_files = processed_test_dict.get("required_loc_files", []) |
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1271 |
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1272 inputs = processed_test_dict.get("inputs", {}) |
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1273 loaded_inputs = {} |
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1274 for key, value in inputs.items(): |
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1275 if isinstance(value, dict) and value.get("model_class"): |
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1276 loaded_inputs[key] = TestCollectionDef.from_dict(value) |
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1277 else: |
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1278 loaded_inputs[key] = value |
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1279 |
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1280 self.inputs = loaded_inputs |
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1281 self.outputs = processed_test_dict.get("outputs", []) |
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1282 self.num_outputs = processed_test_dict.get("num_outputs", None) |
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1283 |
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1284 self.error = processed_test_dict.get("error", False) |
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1285 self.exception = processed_test_dict.get("exception", None) |
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1286 |
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1287 self.output_collections = [TestCollectionOutputDef.from_dict(d) for d in processed_test_dict.get("output_collections", [])] |
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1288 self.command_line = processed_test_dict.get("command_line", None) |
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1289 self.command_version = processed_test_dict.get("command_version", None) |
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1290 self.stdout = processed_test_dict.get("stdout", None) |
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1291 self.stderr = processed_test_dict.get("stderr", None) |
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1292 self.expect_exit_code = processed_test_dict.get("expect_exit_code", None) |
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1293 self.expect_failure = processed_test_dict.get("expect_failure", False) |
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1294 |
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1295 def test_data(self): |
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1296 """ |
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1297 Iterator over metadata representing the required files for upload. |
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1298 """ |
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1299 return test_data_iter(self.required_files) |
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1300 |
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1301 def to_dict(self): |
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1302 inputs_dict = {} |
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1303 for key, value in self.inputs.items(): |
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1304 if hasattr(value, "to_dict"): |
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1305 inputs_dict[key] = value.to_dict() |
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1306 else: |
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1307 inputs_dict[key] = value |
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1308 |
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1309 return { |
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1310 "inputs": inputs_dict, |
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1311 "outputs": self.outputs, |
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1312 "output_collections": [_.to_dict() for _ in self.output_collections], |
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1313 "num_outputs": self.num_outputs, |
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1314 "command_line": self.command_line, |
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1315 "command_version": self.command_version, |
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1316 "stdout": self.stdout, |
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1317 "stderr": self.stderr, |
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1318 "expect_exit_code": self.expect_exit_code, |
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1319 "expect_failure": self.expect_failure, |
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1320 "name": self.name, |
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1321 "test_index": self.test_index, |
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1322 "tool_id": self.tool_id, |
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1323 "tool_version": self.tool_version, |
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1324 "required_files": self.required_files, |
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1325 "required_data_tables": self.required_data_tables, |
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1326 "required_loc_files": self.required_loc_files, |
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1327 "error": self.error, |
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1328 "exception": self.exception, |
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1329 } |
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1330 |
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1331 |
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1332 @nottest |
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1333 def test_data_iter(required_files): |
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1334 for fname, extra in required_files: |
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1335 data_dict = dict( |
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1336 fname=fname, |
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1337 metadata=extra.get('metadata', {}), |
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1338 composite_data=extra.get('composite_data', []), |
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1339 ftype=extra.get('ftype', DEFAULT_FTYPE), |
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1340 dbkey=extra.get('dbkey', DEFAULT_DBKEY), |
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1341 ) |
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1342 edit_attributes = extra.get('edit_attributes', []) |
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1343 |
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1344 # currently only renaming is supported |
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1345 for edit_att in edit_attributes: |
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1346 if edit_att.get('type', None) == 'name': |
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1347 new_name = edit_att.get('value', None) |
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1348 assert new_name, 'You must supply the new dataset name as the value tag of the edit_attributes tag' |
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1349 data_dict['name'] = new_name |
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1350 else: |
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1351 raise Exception('edit_attributes type (%s) is unimplemented' % edit_att.get('type', None)) |
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1352 |
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1353 yield data_dict |
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1354 |
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1355 |
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1356 def galaxy_requests_post(url, data=None, files=None, as_json=False, params=None, headers=None): |
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1357 """Handle some Galaxy conventions and work around requests issues. |
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1358 |
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1359 This is admittedly kind of hacky, so the interface may change frequently - be |
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1360 careful on reuse. |
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1361 |
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1362 If ``as_json`` is True, use post payload using request's json parameter instead |
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1363 of the data parameter (i.e. assume the contents is a json-ified blob instead of |
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1364 form parameters with individual parameters json-ified if needed). requests doesn't |
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1365 allow files to be specified with the json parameter - so rewrite the parameters |
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1366 to handle that if as_json is True with specified files. |
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1367 """ |
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1368 params = params or {} |
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1369 data = data or {} |
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1370 |
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1371 # handle encoded files |
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1372 if files is None: |
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1373 # if not explicitly passed, check __files... convention used in tool testing |
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1374 # and API testing code |
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1375 files = data.get("__files", None) |
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1376 if files is not None: |
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1377 del data["__files"] |
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1378 |
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1379 # files doesn't really work with json, so dump the parameters |
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1380 # and do a normal POST with request's data parameter. |
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1381 if bool(files) and as_json: |
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1382 as_json = False |
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1383 new_items = {} |
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1384 for key, val in data.items(): |
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1385 if isinstance(val, dict) or isinstance(val, list): |
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1386 new_items[key] = dumps(val) |
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1387 data.update(new_items) |
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1388 |
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1389 kwd = { |
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1390 'files': files, |
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1391 } |
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1392 if headers: |
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1393 kwd['headers'] = headers |
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1394 if as_json: |
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1395 kwd['json'] = data |
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1396 kwd['params'] = params |
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1397 else: |
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1398 data.update(params) |
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1399 kwd['data'] = data |
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1400 |
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1401 return requests.post(url, **kwd) |