Mercurial > repos > sanbi-uwc > build_ctb_gene

annotate build_ctb_gene.py @ 49:74ad74a4be56 draft default tip

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planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 11bbdc95f9fe5a9f85c3e71c35acfd874c0ab9be
author sanbi-uwc
date Thu, 07 Jul 2016 09:34:47 -0400
parents 515fdc4654a5
children
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1 #!/usr/bin/env python
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2 from __future__ import print_function
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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
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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, Popen, STDOUT, PIPE
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13 import socket
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14 try:
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15 from urllib.parse import urlparse
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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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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 self.neo4j_proc = None
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45
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46 def build_ctb_gene(self):
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47 cmdline_str = "goget goterms {} {}".format(self.args.input_file, self.args.human_interactions)
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48 cmdline_str = self.newSplit(cmdline_str)
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49 try:
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50 check_call(cmdline_str)
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51 except CalledProcessError:
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52 print("Error running the build_ctb_gene goterms", file=sys.stderr)
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53 return None
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54 else:
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55 # self.copy_output_file_to_dataset()
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56 print("Building a new DB, current time: %s" % str(datetime.date.today()))
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57 print("GFF File - Input: %s" % str(self.args.input_file))
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58 return True
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59
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60 def newSplit(self, value):
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61 lex = shlex.shlex(value)
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62 lex.quotes = '"'
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63 lex.whitespace_split = True
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64 lex.commenters = ''
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65 return list(lex)
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66
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67 def copy_output_file_to_dataset(self):
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68 """
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69 Retrieves the output files from the gx working directory and copy them to the Galaxy output directory
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70 """
10
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71 # retrieve neo4j files to the working gx directory
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72 mp = self.mount_point + "/graph.db"
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73 result_file = glob.glob(mp + '/*')
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74 for file_name in result_file:
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75 if os.path.isfile(file_name):
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76 shutil.copy2(file_name, self.args.outputdir)
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77 elif os.path.isdir(file_name):
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78 # create the parent dir before copytree
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79 os.chdir(self.args.outputdir)
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80 shutil.copytree(file_name, file_name.rsplit('/', 1)[-1])
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81
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82 def docker_stop(self):
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83 stop_cmd = 'docker stop build_ctb_gene'
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84 stop_cmd_str = self.newSplit(stop_cmd)
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85 try:
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86 check_call(stop_cmd_str)
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87 except CalledProcessError:
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88 print("Error running docker stop build_ctb_gene", file=sys.stderr)
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89 return None
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90 else:
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91 return True
27
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92
46
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93 def get_docker_output(self):
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94 if self.neo4j_proc is not None:
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95 return_code = self.neo4j_proc.wait()
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96 (output, _) = self.neo4j_proc.communicate()
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97 return 'Return code: {rc}\n{output}'.format(rc=return_code, output=output)
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98
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99 def shutdown_docker(self):
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100 if self.neo4j_proc is not None:
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101 self.neo4j_proc.terminate()
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102
27
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103 def docker_run(self):
38
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104 self.mount_point = "{}".format(self.outputdir)
37
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105 try:
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106 os.makedirs(self.mount_point)
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107 except os.error as e:
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108 print("Error creating mount point {mount_point}: {error}".format(mount_point=self.mount_point, error=e.strerror))
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109
46
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110 cmd_str = "docker run --rm -P -v {mount_point}:/data -e NEO4J_UID={uid} -e NEO4J_GID={gid} -e NEO4J_AUTH=none -e NEO4J_MONITOR_TRAFFIC=false --name {name} thoba/neo4j_galaxy_ie:latest".format(
41
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111 mount_point=self.mount_point,
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112 name=self.docker_instance_name,
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113 uid=os.getuid(),
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114 gid=os.getgid(),
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115 )
27
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116 cmd = self.newSplit(cmd_str)
46
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117 self.neo4j_proc = Popen(cmd, stdout=PIPE, stderr=STDOUT)
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118 time.sleep(30) # give the container time to wake up
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119 if self.neo4j_proc.poll() is not None:
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120 raise CalledProcessError("Error running docker run by build_ctb_gene:\n", self.get_docker_output)
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121
4
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122 def main():
10
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123 parser = argparse.ArgumentParser(description="Tool used to extract data about genes using locus_tags")
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124 parser.add_argument('--outputdir')
4
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125 parser.add_argument('--input_file')
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126 parser.add_argument('--human_interactions')
4
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127 args = parser.parse_args()
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128
26
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129 ctb_gene_runner = BuildCtbRunner(args)
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130
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131 # boot up a neo4j docker container
27
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132 ctb_gene_runner.docker_run()
46
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133
29
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134 # get the port of the docker container
31
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135 cmd_str = "docker inspect --format='{{(index (index .NetworkSettings.Ports \"7474/tcp\") 0).HostPort}}' %s" % ctb_gene_runner.docker_instance_name
29
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136
35
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137 # TODO: randomise the ports/names/mount_point and use the auto kill image
37
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138 neo4j_container_info = inspect_docker(cmd_str)
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139 if neo4j_container_info is None:
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140 exit(1)
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141 else:
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142 neo4j_port = neo4j_container_info[:-1]
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143 neo4j_url = 'http://localhost:{}/db/data/'.format(neo4j_port)
4
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144 try:
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145 os.environ["NEO4J_REST_URL"] = neo4j_url
46
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146 except (OSError, ValueError) as e:
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147 print("Error setting the NEO4J db environmental values", e)
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148
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149 # make the output directory
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150 if not os.path.exists(args.outputdir):
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151 os.makedirs(args.outputdir)
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152
37
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153 url = urlparse(neo4j_url)
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154 if '@' in url.netloc:
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155 (host, port) = url.netloc.split('@')[1].split(':')
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156 else:
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157 (host, port) = url.netloc.split(':')
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158 timeout = int(os.environ.get('NEO4J_WAIT_TIMEOUT', 30)) # time to wait till neo4j
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159 connected = False
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160 #print('host, port', host, port)
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161 while timeout > 0:
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162 try:
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163 socket.create_connection((host, port), 1)
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164 except socket.error:
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165 timeout -= 1
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166 time.sleep(1)
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167 else:
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168 connected = True
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diff changeset
169 break
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170 if not connected:
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171 sys.exit('timed out trying to connect to {}'.format(neo4j_url))
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172
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173 status = ctb_gene_runner.build_ctb_gene()
46
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174 ctb_gene_runner.shutdown_docker()
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175
37
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176 if status is None:
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177 exit(1)
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178
11
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diff changeset
179
14
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180 if __name__ == "__main__": main()