Mercurial > repos > sanbi-uwc > build_ctb_gene

annotate build_ctb_gene.py @ 32:9e33d452ad8c draft

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planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit cca5de2166bbc2fbbab368415853e085d474b6b2
author sanbi-uwc
date Tue, 24 May 2016 04:19:03 -0400
parents bcf4f741b94f
children f9ad7d3cd333
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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
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4 import os
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5 import sys
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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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14 import logging
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16 log = logging.getLogger(__name__)
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19 def inspect_docker(cmd_str):
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20 output = None
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21 try:
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22 output = check_output(cmd_str, shell=True)
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23 except CalledProcessError:
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24 print("Error running get_docker_port by build_ctb_gene", file=sys.stderr)
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25 return output
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28 class BuildCtbRunner(object):
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29 def __init__(self, args=None):
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30 '''
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31 Initializes an object to run CtbRunner in Galaxy.
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32 '''
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33 # Check whether the options are specified and saves them into the object
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34 # assert args != None
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35 self.args = args
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36 self.mount_point = None
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37 self.docker_instance_name = "build_ctb_gene_" + str(random.randrange(0, 1000, 2))
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38
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39 def build_ctb_gene(self):
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40 cmdline_str = "build_ctb_gene goterms {}".format(self.args.input_file)
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41 #cmdline_str = "touch /tmp/foo.bar"
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42 cmdline_str = self.newSplit(cmdline_str)
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43 build_ctb_run = False
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44 try:
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45 check_call(cmdline_str)
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46 build_ctb_run = True
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47 except CalledProcessError:
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48 print("Error running the build_ctb_gene goterms", file=sys.stderr)
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49 if build_ctb_run:
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50 self.copy_output_file_to_dataset()
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51 print("Building a new DB, current time: %s" % str(datetime.date.today()))
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52 # print("Noe4j Database Name: http://%s:%s@%s:%s/db/data/" % (
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53 # self.args.username, self.args.password, self.args.url, self.args.port))
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54 print("GFF File - Input: %s" % str(self.args.input_file))
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55
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56 def newSplit(self, value):
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57 lex = shlex.shlex(value)
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58 lex.quotes = '"'
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59 lex.whitespace_split = True
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60 lex.commenters = ''
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61 return list(lex)
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62
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63 def copy_output_file_to_dataset(self):
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64 '''
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65 Retrieves the output files from the output directory and copies them to the Galaxy output files
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66 '''
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67 # retrieve neo4j files to the working gx directory
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68 mp = self.mount_point + "/graph.db"
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69 result_file = glob.glob(mp + '/*')
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70 for file_name in result_file:
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71 if os.path.isfile(file_name):
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72 shutil.copy2(file_name, self.args.outputdir)
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73 elif os.path.isdir(file_name):
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74 # create the parent dir before copytree
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75 os.chdir(self.args.outputdir)
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76 shutil.copytree(file_name, file_name.rsplit('/', 1)[-1])
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77
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78 def docker_stop(self):
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79 stop_cmd = 'docker stop build_ctb_gene'
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80 stop_cmd_str = self.newSplit(stop_cmd)
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81 try:
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82 check_call(stop_cmd_str)
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83 except CalledProcessError:
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84 print("Error running docker stop build_ctb_gene", file=sys.stderr)
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85
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86 def docker_run(self):
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87 self.mount_point = "{}/neo4j/data".format(os.getcwd())
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89 cmd_str = "docker run -d -P -v {}:/data -e NEO4J_AUTH=none --name {} thoba/neo4j_galaxy_ie".format(
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90 self.mount_point, self.docker_instance_name)
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91 cmd = self.newSplit(cmd_str)
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92 try:
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93 check_call(cmd)
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94 except CalledProcessError:
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95 print("Error running docker run by build_ctb_gene", file=sys.stderr)
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96
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97
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98 def main():
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99 parser = argparse.ArgumentParser(description="Tool used to extract data about genes using locus_tags")
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100 parser.add_argument('--outputdir')
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101 parser.add_argument('--input_file')
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102 args = parser.parse_args()
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103
26
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104 ctb_gene_runner = BuildCtbRunner(args)
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105
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106 # boot up a neo4j docker container
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107 ctb_gene_runner.docker_run()
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108
29
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109 # get the port of the docker container
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110 cmd_str = "docker inspect --format='{{(index (index .NetworkSettings.Ports \"7474/tcp\") 0).HostPort}}' %s" % ctb_gene_runner.docker_instance_name
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111
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112 # TODO: randomise the ports/names/mount_point and use the autokill image
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113 neo4j_url = 'http://localhost:{}/db/data/'.format(
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114 inspect_docker(cmd_str)[:-1])
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115 try:
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116 os.environ["NEO4J_REST_URL"] = neo4j_url
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117 except (OSError, ValueError), e:
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118 print("Error setting the NEO4J db environmental values", e)
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119
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120 # make the output directory
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121 if not os.path.exists(args.outputdir):
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122 os.makedirs(args.outputdir)
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123 time.sleep(60)
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124 ctb_gene_runner.build_ctb_gene()
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125
11
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126
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127 if __name__ == "__main__": main()