Mercurial > repos > sanbi-uwc > build_ctb_gene

annotate build_ctb_gene.py @ 38:65df0b64db15 draft

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planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit d7d335bdd8e18529d643b7ce55a311db71f957bc
author sanbi-uwc
date Wed, 01 Jun 2016 07:37:28 -0400
parents 8f16164019bd
children 2a9a2575c8a4
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1 #!/usr/bin/env python
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2 from __future__ import print_function
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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3 import argparse
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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4 import os
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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5 import sys
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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6 import glob
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7 import shlex
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8 import shutil
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9 import datetime
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10 import time
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11 import random
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12 from subprocess import check_call, check_output, CalledProcessError
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13 import socket
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14 try:
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15 from urllib.parse import urlparse
8f16164019bd planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 3cb86dfb85e313a464efbce8529442c8fc4630a5
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16 except ImportError:
8f16164019bd planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 3cb86dfb85e313a464efbce8529442c8fc4630a5
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17 from urlparse import urlparse
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18 import logging
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20 log = logging.getLogger(__name__)
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22
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23 def inspect_docker(cmd_str):
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24 output = None
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25 try:
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26 output = check_output(cmd_str, shell=True)
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27 except CalledProcessError:
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28 print("Error running get_docker_port by build_ctb_gene", file=sys.stderr)
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29 return None
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30 return output
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32
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33 class BuildCtbRunner(object):
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34 def __init__(self, args=None):
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35 """
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36 Initializes an object to run CtbRunner in Galaxy.
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37 """
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38 # Check whether the options are specified and saves them into the object
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39 # assert args != None
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40 self.args = args
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41 self.outputdir = args.outputdir
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42 self.mount_point = None
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43 self.docker_instance_name = "build_ctb_gene_" + str(random.randrange(0, 1000, 2))
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44
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45 def build_ctb_gene(self):
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46 cmdline_str = "build_ctb_gene test {}".format(self.args.input_file)
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47 cmdline_str = self.newSplit(cmdline_str)
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48 try:
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49 check_call(cmdline_str)
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50 except CalledProcessError:
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51 print("Error running the build_ctb_gene goterms", file=sys.stderr)
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52 return None
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53 else:
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54 # self.copy_output_file_to_dataset()
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55 print("Building a new DB, current time: %s" % str(datetime.date.today()))
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56 print("GFF File - Input: %s" % str(self.args.input_file))
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57 return True
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58
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59 def newSplit(self, value):
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60 lex = shlex.shlex(value)
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61 lex.quotes = '"'
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62 lex.whitespace_split = True
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63 lex.commenters = ''
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64 return list(lex)
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65
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66 def copy_output_file_to_dataset(self):
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67 """
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68 Retrieves the output files from the gx working directory and copy them to the Galaxy output directory
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69 """
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70 # retrieve neo4j files to the working gx directory
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71 mp = self.mount_point + "/graph.db"
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72 result_file = glob.glob(mp + '/*')
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73 for file_name in result_file:
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74 if os.path.isfile(file_name):
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75 shutil.copy2(file_name, self.args.outputdir)
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76 elif os.path.isdir(file_name):
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77 # create the parent dir before copytree
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78 os.chdir(self.args.outputdir)
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79 shutil.copytree(file_name, file_name.rsplit('/', 1)[-1])
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80
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81 def docker_stop(self):
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82 stop_cmd = 'docker stop build_ctb_gene'
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83 stop_cmd_str = self.newSplit(stop_cmd)
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84 try:
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85 check_call(stop_cmd_str)
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86 except CalledProcessError:
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87 print("Error running docker stop build_ctb_gene", file=sys.stderr)
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88 return None
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89 else:
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90 return True
27
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91
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92 def docker_run(self):
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93 self.mount_point = "{}".format(self.outputdir)
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94 try:
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95 os.makedirs(self.mount_point)
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96 except os.error as e:
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97 print("Error creating mount point {mount_point}: {error}".format(mount_point=self.mount_point, error=e.strerror))
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98
36
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99 cmd_str = "docker run -d -P -v {}:/data -e NEO4J_AUTH=none --name {} thoba/neo4j_galaxy_ie".format(
29
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100 self.mount_point, self.docker_instance_name)
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101 cmd = self.newSplit(cmd_str)
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102 try:
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103 check_call(cmd)
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104 except CalledProcessError:
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105 print("Error running docker run by build_ctb_gene", file=sys.stderr)
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106
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107
4
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108 def main():
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109 parser = argparse.ArgumentParser(description="Tool used to extract data about genes using locus_tags")
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110 parser.add_argument('--outputdir')
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111 parser.add_argument('--input_file')
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112 args = parser.parse_args()
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113
26
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114 ctb_gene_runner = BuildCtbRunner(args)
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115
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116 # boot up a neo4j docker container
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117 ctb_gene_runner.docker_run()
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118
29
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119 # get the port of the docker container
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120 cmd_str = "docker inspect --format='{{(index (index .NetworkSettings.Ports \"7474/tcp\") 0).HostPort}}' %s" % ctb_gene_runner.docker_instance_name
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121
35
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122 # TODO: randomise the ports/names/mount_point and use the auto kill image
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123 neo4j_container_info = inspect_docker(cmd_str)
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124 if neo4j_container_info is None:
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125 exit(1)
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126 else:
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127 neo4j_port = neo4j_container_info[:-1]
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128 neo4j_url = 'http://localhost:{}/db/data/'.format(neo4j_port)
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129 try:
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130 os.environ["NEO4J_REST_URL"] = neo4j_url
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131 except (OSError, ValueError), e:
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132 print("Error setting the NEO4J db environmental values", e)
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133
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134 # make the output directory
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135 if not os.path.exists(args.outputdir):
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136 os.makedirs(args.outputdir)
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137
37
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138 url = urlparse(neo4j_url)
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139 if '@' in url.netloc:
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140 (host, port) = url.netloc.split('@')[1].split(':')
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141 else:
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142 (host, port) = url.netloc.split(':')
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143 timeout = int(os.environ.get('NEO4J_WAIT_TIMEOUT', 30)) # time to wait till neo4j
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144 connected = False
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145 #print('host, port', host, port)
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146 while timeout > 0:
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147 try:
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148 socket.create_connection((host, port), 1)
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149 except socket.error:
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150 timeout -= 1
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151 time.sleep(1)
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152 else:
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153 connected = True
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154 break
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155 if not connected:
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156 sys.exit('timed out trying to connect to {}'.format(neo4j_url))
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157
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158 status = ctb_gene_runner.build_ctb_gene()
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159 if status is None:
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160 exit(1)
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161
11
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162
14
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163 if __name__ == "__main__": main()