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1 <tool name="tf_apikey_mutate" id="tf_apikey_mutate" version="0.001">
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2 <!--Source in git at: https://github.com/fubar2/galaxy-->
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3 <!--Created by toolfactory@galaxy.org at 21/05/2023 10:01:12 using the Galaxy Tool Factory.-->
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4 <description>Rotates all API keys in a ToolFactory instance </description>
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5 <requirements>
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6 <requirement version="1.1.1" type="package">bioblend</requirement>
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7 <requirement version="3.10.12" type="package">python</requirement>
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8 <requirement type="package">six</requirement>
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9 </requirements>
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10 <stdio>
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11 <exit_code range="1:" level="fatal"/>
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12 </stdio>
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13 <version_command><![CDATA[echo "0.001"]]></version_command>
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14 <command><![CDATA[python
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15 $runme --galaxy_root "$__root_dir__" --galaxy_venv "$__root_dir__/.venv"
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16 >
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17 $APIK_mutate_log]]></command>
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18 <configfiles>
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19 <configfile name="runme"><![CDATA[#raw
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20
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21 #!/usr/bin/env python
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22 import argparse
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23 import hashlib
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24 import os
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25 import random
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26 import subprocess
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27 import sys
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28 from time import sleep
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29 from urllib import request
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30 from urllib.error import URLError
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31
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32 from bioblend import galaxy
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33
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34 def add_user(sa_session, security_agent, email, password, key=None, username="admin"):
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35 """
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36 Add Galaxy User.
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37 From John https://gist.github.com/jmchilton/4475646
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38 """
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39 query = sa_session.query(User).filter_by(email=email)
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40 user = None
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41 uexists = False
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42 User.use_pbkdf2 = False
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43 if query.count() > 0:
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44 user = query.first()
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45 user.username = username
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46 user.set_password_cleartext(password)
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47 sa_session.add(user)
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48 sa_session.flush()
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49 uexists = True
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50 else:
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51 user = User(email)
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52 user.username = username
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53 user.set_password_cleartext(password)
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54 sa_session.add(user)
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55 sa_session.flush()
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56
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57 security_agent.create_private_user_role(user)
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58 if not user.default_permissions:
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59 security_agent.user_set_default_permissions(user, history=True, dataset=True)
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60
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61 if key is not None:
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62 query = sa_session.query(APIKeys).filter_by(user_id=user.id).delete()
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63 sa_session.flush()
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64
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65 api_key = APIKeys()
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66 api_key.user_id = user.id
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67 api_key.key = key
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68 sa_session.add(api_key)
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69 sa_session.flush()
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70 return user, uexists
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71
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72 def run_sed(options):
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73 """
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74 eg replacement = 'APIK="%s"' % options.key
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75 line_start = 'APIK='
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76 """
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77 fixme = []
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78 tool_config_file: "tool_conf.xml,../local_tools/local_tool_conf.xml"
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79 # database_connection: "sqlite:///<data_dir>/universe.sqlite?isolation_level=IMMEDIATE"
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80 tfc = 'tool_conf.xml,%s/local_tools/local_tool_conf.xml' % options.galaxy_root
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81 fixfile = "%s/config/galaxy.yml" % options.galaxy_root
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82 fixme.append((' virtualenv: ', ' virtualenv: "%s"' % options.galaxy_venv, fixfile))
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83 fixme.append((' galaxy_root: ', ' galaxyroot: "%s"' % options.galaxy_root, fixfile))
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84 fixme.append((' tool_config_file: ', ' tool_config_file: "%s"' % tfc, fixfile))
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85 fixfile = "%s/local_tools/toolfactory/toolfactory.py" % options.galaxy_root
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86 fixme.append((' self.GALAXY_ADMIN_KEY =', ' self.GALAXY_ADMIN_KEY = "%s"' % options.key, fixfile ))
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87 fixme.append((' self.GALAXY_URL = ' , ' self.GALAXY_URL = "%s"' % options.galaxy_url, fixfile ))
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88 fixfile = "%s/local_tools/toolfactory/install_tf_deps.sh" % options.galaxy_root
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89 fixme.append(('APIK=', 'APIK="%s"' % options.key, fixfile ))
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90 fixme.append(('LOCALTOOLDIR=', 'LOCALTOOLDIR="%s"' % os.path.join(os.path.abspath(options.galaxy_root), "local_tools"), fixfile ))
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91 fixfile = "%s/local_tools/toolfactory/localplanemotest.sh" % options.galaxy_root
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92 fixme.append(('GALAXY_URL=', 'GALAXY_URL=%s' % options.galaxy_url, fixfile))
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93 fixme.append(('API_KEY=', 'API_KEY=%s' % options.key, fixfile))
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94 fixfile = "%s/local_tools/toolfactory/toolfactory_fast_test.sh" % options.galaxy_root
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95 fixme.append(('GALAXY_URL=', 'GALAXY_URL=%s' % options.galaxy_url, fixfile))
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96 fixme.append(('API_KEY=', 'API_KEY=%s' % options.key, fixfile))
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97 fixme.append(('GALAXY_VENV=', 'GALAXY_VENV=%s' % options.galaxy_venv, fixfile))
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98 fixme.append(('API_KEY_USER=', 'API_KEY_USER=%s' % options.botkey, fixfile))
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99 for line_start, line_replacement, file_to_edit in fixme:
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100 cmd = ["sed", "-i", "s#.*%s.*#%s#g" % (line_start, line_replacement), file_to_edit]
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101 print("## executing", ' '.join(cmd))
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102 res = subprocess.run(cmd)
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103 if not res.returncode == 0:
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104 print('### Non zero %d return code from %s ' % (res.returncode, ''.join(cmd)))
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105
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106
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107 if __name__ == "__main__":
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108 print('starting!', file=sys.stderr)
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109 apikey = "%s" % hash(random.random())
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110 apikey2 = "%s" % hash(random.random())
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111 parser = argparse.ArgumentParser(description="Create Galaxy Admin User.")
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112 parser.add_argument("--galaxy_url", help="Galaxy server URL", default="http://localhost:8080")
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113 parser.add_argument("--galaxy_root", help="Galaxy root directory path", default="/work/galaxytf")
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114 parser.add_argument("--galaxy_venv", help="Galaxy venv path", default="/work/galaxytf/.venv")
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115 parser.add_argument("--user", help="Username - an email address.", default="toolfactory@galaxy.org")
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116 parser.add_argument("--password", help="Password", default="ChangeMe!")
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117 parser.add_argument("--password2", help="Password", default=apikey2)
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118 parser.add_argument("--key", help="API-Key.", default=apikey)
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119 parser.add_argument("--botkey", help="bot API-Key.", default=apikey2)
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120 parser.add_argument("--username", default="tfadmin")
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121 parser.add_argument("args", nargs=argparse.REMAINDER)
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122 options = parser.parse_args()
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123 sys.path.insert(1, options.galaxy_root)
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124 sys.path.insert(1, os.path.join(options.galaxy_root, "lib"))
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125 sys.path.insert(1, os.path.join(options.galaxy_venv, "lib", "python3.10", "site-packages"))
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126 from galaxy.model import User, APIKeys
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127 from galaxy.model.mapping import init
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128 from galaxy.model.orm.scripts import get_config
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129 cnf = get_config(argv=['-c','galaxy', ],cwd=options.galaxy_root)
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130 print('cnf=%s' % cnf, file=sys.stderr)
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131 cdb_url = cnf["db_url"]
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132 # or perhaps "postgresql:///ubuntu?host=/var/run/postgresql"
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133 # this is harder to please get_config(sys.argv, use_argparse=False)["db_url"]
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134 print('### Using cdb_url', cdb_url, file=sys.stderr)
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135 mapping = init("/tmp/", cdb_url)
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136 sa_session = mapping.context
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137 security_agent = mapping.security_agent
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138 usr, uexists = add_user(
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139 sa_session, security_agent, options.user, options.password, key=options.key, username=options.username
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140 )
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141 print("added user", options.user, "apikey", options.key, file=sys.stderr)
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142
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143 usr, uexists = add_user(
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144 sa_session, security_agent, 'test@bx.psu.edu', options.password2, key=options.botkey, username='bot'
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145 )
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146 run_sed(options)
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147 print('Evil deeds done', file=sys.stderr)
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148
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149
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150 #end raw]]></configfile>
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151 </configfiles>
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152 <inputs/>
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153 <outputs>
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154 <data name="APIK_mutate_log" format="txt" label="APIK_mutate_log" hidden="false"/>
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155 </outputs>
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156 <tests>
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157 <test>
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158 <output name="APIK_mutate_log" value="APIK_mutate_log_sample" compare="sim_size" delta="100"/>
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159 </test>
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160 </tests>
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161 <help><![CDATA[
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162
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163 **What it Does**
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164
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165 Regenerates fresh API keys for the ToolFactory administrative user and rewrites them into all the relevant utility code.
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166
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167 The Docker image is constructed with a new set of keys but they are identical in every image, so running this tool
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168 in that image makes sure that while it is running, it is not using the distributed keys. It will do the same thing for a
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169 local disk installation but has already been run once at first boot. No real harm running it again to recycle all your keys
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170 if you like.
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171
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172 Will break the ToolFactory if it breaks.
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173 Safe in Docker since it's not persistent :)
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174 Use at your own peril.
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175 This is a crazy tool to run.
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176
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177 This script consistently fails tool test, but actually works fine on a ToolFactory docker or local installation.
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178 It reuses code from the initial configuration to create new, random API keys for the admin logins.
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179
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180
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181 ]]></help>
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182 <citations>
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183 <citation type="doi">10.1093/bioinformatics/bts573</citation>
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184 </citations>
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185 </tool>
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186
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