Mercurial > repos > sanbi-uwc > build_ctb_gene

annotate build_ctb_gene.py @ 27:3995dfb6b497 draft

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planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 03cbaf9b605624fc4f6fbad4ccfbbe984d54e990
author sanbi-uwc
date Sun, 22 May 2016 15:34:49 -0400
parents 51a48982f643
children 4864d5866418
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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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18
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19 class BuildCtbRunner(object):
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20 def __init__(self, args=None):
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21 '''
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22 Initializes an object to run CtbRunner in Galaxy.
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23 '''
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24 # Check whether the options are specified and saves them into the object
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25 # assert args != None
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26 self.args = args
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27 self.mount_point = None
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29 def build_ctb_gene(self):
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30 # cmdline_str = "build_ctb_gene goterms {}".format(self.args.input_file)
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31 cmdline_str = "touch /tmp/foo.bar"
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32 cmdline_str = self.newSplit(cmdline_str)
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33 build_ctb_run = False
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34 try:
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35 check_call(cmdline_str)
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36 build_ctb_run = True
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37 except CalledProcessError:
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38 print("Error running the build_ctb_gene goterms", file=sys.stderr)
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39 if build_ctb_run:
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40 self.copy_output_file_to_dataset()
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41 print("Building a new DB, current time: %s" % str(datetime.date.today()))
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42 # print("Noe4j Database Name: http://%s:%s@%s:%s/db/data/" % (
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43 # self.args.username, self.args.password, self.args.url, self.args.port))
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44 print("GFF File - Input: %s" % str(self.args.input_file))
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45
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46 def newSplit(self, value):
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47 lex = shlex.shlex(value)
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48 lex.quotes = '"'
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49 lex.whitespace_split = True
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50 lex.commenters = ''
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51 return list(lex)
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52
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53 def copy_output_file_to_dataset(self):
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54 '''
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55 Retrieves the output files from the output directory and copies them to the Galaxy output files
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56 '''
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57 # retrieve neo4j files to the working gx directory
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58 mp = self.mount_point + "/graph.db"
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59 result_file = glob.glob(mp + '/*')
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60 for file_name in result_file:
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61 if os.path.isfile(file_name):
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62 shutil.copy2(file_name, self.args.outputdir)
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63 elif os.path.isdir(file_name):
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64 # create the parent dir before copytree
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65 os.chdir(self.args.outputdir)
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66 shutil.copytree(file_name, file_name.rsplit('/', 1)[-1])
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67
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68 def docker_stop(self):
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69 stop_cmd = 'docker stop build_ctb_gene'
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70 stop_cmd_str = self.newSplit(stop_cmd)
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71 try:
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72 check_call(stop_cmd_str)
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73 except CalledProcessError:
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74 print("Error running docker stop build_ctb_gene", file=sys.stderr)
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76 def docker_rm(self):
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77 cmd_str = 'docker rm build_ctb_gene'
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78 cmd = self.newSplit(cmd_str)
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79 check_call(cmd)
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80
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81 def docker_run(self):
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82 self.mount_point = "{}/neo4j/data".format(os.getcwd())
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83 cmd_str = "docker run -d -p 7474:7474 -v {}:/data -e NEO4J_AUTH=none --name build_ctb_gene neo4j:2.3".format(
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84 self.mount_point)
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85 cmd = self.newSplit(cmd_str)
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86 check_call(cmd)
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88 def docker_container_check(self):
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89 cmd_str = 'docker ps -a -f name=build_ctb_gene | grep build_ctb_gene'
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90 output = False
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91 try:
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92 output = check_output(cmd_str, shell=True)
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93 except CalledProcessError:
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94 print("Error running docker container check", file=sys.stderr)
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95 if output:
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96 return True
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97 return False
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98
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99
4
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100 def main():
10
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101 parser = argparse.ArgumentParser(description="Tool used to extract data about genes using locus_tags")
27
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102 # parser.add_argument('--outputfile')
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103 parser.add_argument('--outputdir')
4
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104 parser.add_argument('--input_file')
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105 # parser.add_argument('--mount_point')
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106 # parser.add_argument('--username')
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107 # parser.add_argument('--password')
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108 # parser.add_argument('--url')
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109 # parser.add_argument('--port')
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110 args = parser.parse_args()
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111
26
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112 ctb_gene_runner = BuildCtbRunner(args)
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113
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114 # boot up a neo4j docker container
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115 if ctb_gene_runner.docker_container_check():
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116 ctb_gene_runner.docker_stop()
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117 ctb_gene_runner.docker_rm()
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118 ctb_gene_runner.docker_run()
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119
27
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120 # TODO: randomise the ports/names/mount_point and use the autokill image
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121 export_cmd = "export NEO4J_REST_URL=http://localhost:7474/db/data/"
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122 try:
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123 os.system(export_cmd)
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124 except (OSError, ValueError), e:
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125 print("Error exporting the NEO4J db environmental values", e)
4
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126
10
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127 # make the output directory
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128 if not os.path.exists(args.outputdir):
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129 os.makedirs(args.outputdir)
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130 time.sleep(60)
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131 ctb_gene_runner.build_ctb_gene()
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132
11
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133
14
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134 if __name__ == "__main__": main()