Mercurial > repos > mvdbeek > docker_scriptrunner

annotate scriptrunner.py @ 2:495946ffc2d6 draft default tip

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planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
author mvdbeek
date Sun, 22 Jul 2018 13:38:01 -0400
parents 21d312776891
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1 # DockerToolFactory.py
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2 # see https://github.com/mvdbeek/scriptrunner
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3
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mvdbeek
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4 from __future__ import print_function
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5 import sys
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6 import shutil
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7 import subprocess
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8 import os
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mvdbeek
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9 import time
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10 import tempfile
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11 import argparse
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12 import math
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13 from os.path import abspath
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15 progname = os.path.split(sys.argv[0])[1]
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16 verbose = False
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17 debug = False
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19 html_escape_table = {
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20 "&": "&",
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21 ">": ">",
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22 "<": "&lt;",
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23 "$": "\$"
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24 }
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27 def timenow():
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28 """Return current time as a string."""
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29 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
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30
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32 def html_escape(text):
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33 """Produce entities within text."""
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34 return "".join(html_escape_table.get(c, c) for c in text)
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37 def cmd_exists(cmd):
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38 return subprocess.call("type " + cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
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41 def construct_bind(host_path, container_path=False, binds=None, ro=True):
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42 # TODO remove container_path if it's alwyas going to be the same as host_path
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43 """Build or extend binds dictionary with container path. binds is used
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
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44 to mount all files using the docker-py client."""
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45 if not binds:
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46 binds = {}
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47 if isinstance(host_path, list):
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48 for k, v in enumerate(host_path):
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49 if not container_path:
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50 container_path = host_path[k]
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51 binds[host_path[k]] = {'bind': container_path, 'ro': ro}
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52 container_path = False # could be more elegant
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53 return binds
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54 else:
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55 if not container_path:
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56 container_path = host_path
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57 binds[host_path] = {'bind': container_path, 'ro': ro}
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58 return binds
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59
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60
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61 def switch_to_docker(opts):
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62 import docker # need local import, as container does not have docker-py
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63 user_id = os.getuid()
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64 group_id = os.getgid()
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65 docker_client = docker.APIClient()
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66 toolfactory_path = abspath(sys.argv[0])
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67 binds = construct_bind(host_path=opts.script_path, ro=False)
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68 binds = construct_bind(binds=binds, host_path=abspath(opts.output_dir), ro=False)
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69 if len(opts.input_file) > 0:
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70 binds = construct_bind(binds=binds, host_path=opts.input_file, ro=True)
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71 if not opts.output_file == 'None':
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72 binds = construct_bind(binds=binds, host_path=opts.output_file, ro=False)
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73 if opts.make_HTML:
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74 binds = construct_bind(binds=binds, host_path=opts.output_html, ro=False)
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75 binds = construct_bind(binds=binds, host_path=toolfactory_path)
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76 volumes = list(binds.keys())
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77 sys.argv = [abspath(opts.output_dir) if sys.argv[i - 1] == '--output_dir' else arg for i, arg in enumerate(sys.argv)] # inject absolute path of working_dir
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78 cmd = ['python', '-u'] + sys.argv + ['--dockerized', '1', "--user_id", str(user_id), "--group_id", str(group_id)]
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79 image_exists = [True for image in docker_client.images() if opts.docker_image in image['RepoTags']]
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80 if not image_exists:
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81 docker_client.pull(opts.docker_image)
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82 container = docker_client.create_container(
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83 image=opts.docker_image,
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84 volumes=volumes,
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85 command=cmd,
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86 host_config=docker_client.create_host_config(binds=binds))
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87 docker_client.start(container=container[u'Id'])
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88 exit_code = docker_client.wait(container=container[u'Id'])['StatusCode']
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89 logs = docker_client.logs(container=container[u'Id'])
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90 print(logs, end="", file=sys.stderr)
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91 docker_client.remove_container(container[u'Id'])
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92 return exit_code
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93
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95 class ScriptRunner:
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96 """class is a wrapper for an arbitrary script
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97 """
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98
2
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99 def __init__(self, opts=None, treatbashSpecial=True, image_tag='base'):
0
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100 """
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101 cleanup inputs, setup some outputs
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102 """
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103 self.opts = opts
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104 self.scriptname = 'script'
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105 self.treatbashSpecial = treatbashSpecial
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106 self.image_tag = image_tag
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107 os.chdir(abspath(opts.output_dir))
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108 self.thumbformat = 'png'
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109 s = open(self.opts.script_path, 'r').readlines()
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110 s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
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111 self.script = '\n'.join(s)
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112 fhandle, self.sfile = tempfile.mkstemp(prefix='script', suffix=".%s" % (opts.interpreter))
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113 tscript = open(self.sfile, 'w') # use self.sfile as script source for Popen
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114 tscript.write(self.script)
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115 tscript.close()
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116 self.indentedScript = '\n'.join([' %s' % html_escape(x) for x in s]) # for restructured text in help
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117 self.escapedScript = '\n'.join([html_escape(x) for x in s])
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118 self.elog = os.path.join(self.opts.output_dir, "%s_error.log" % self.scriptname)
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119 if opts.output_dir: # may not want these complexities
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120 self.tlog = os.path.join(self.opts.output_dir, "%s_runner.log" % self.scriptname)
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121 art = '%s.%s' % (self.scriptname, opts.interpreter)
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122 artpath = os.path.join(self.opts.output_dir, art) # need full path
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123 artifact = open(artpath, 'w') # use self.sfile as script source for Popen
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124 artifact.write(self.script)
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125 artifact.close()
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126 self.cl = []
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127 self.html = []
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128 self.cl.append(opts.interpreter)
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129 if self.treatbashSpecial and opts.interpreter in ['bash', 'sh']:
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130 self.cl.append(self.sfile)
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131 else:
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132 self.cl.append('-') # stdin
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133 for input in opts.input_file:
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134 self.cl.append(input)
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135 if opts.output_file == 'None': # If tool generates only HTML, set output name to toolname
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136 self.cl.append(str(self.scriptname) + '.out')
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137 self.cl.append(opts.output_file)
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138 for param in opts.additional_parameters:
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139 param, value = param.split(',')
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140 self.cl.append('--' + param)
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141 self.cl.append(value)
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142 self.outFormats = opts.output_format
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143 self.inputFormats = [formats for formats in opts.input_formats]
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144 self.test1Input = '%s_test1_input.xls' % self.scriptname
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145 self.test1Output = '%s_test1_output.xls' % self.scriptname
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146 self.test1HTML = '%s_test1_output.html' % self.scriptname
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147
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148 def compressPDF(self, inpdf=None, thumbformat='png'):
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149 """
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150 inpdf is absolute path to PDF
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151 """
2
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152 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf, self.myName)
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153 hlog = os.path.join(self.opts.output_dir, "compress_%s.txt" % os.path.basename(inpdf))
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154 sto = open(hlog, 'a')
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155 our_env = os.environ.copy()
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156 our_tmp = our_env.get('TMP', None)
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157 if not our_tmp:
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158 our_env['TMP'] = tempfile.gettempdir()
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159 outpdf = '%s_compressed' % inpdf
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160 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH", "-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf, inpdf]
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161 x = subprocess.Popen(cl, stdout=sto, stderr=sto, cwd=self.opts.output_dir, env=our_env)
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162 retval1 = x.wait()
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163 sto.close()
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164 if retval1 == 0:
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165 os.unlink(inpdf)
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166 shutil.move(outpdf, inpdf)
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167 os.unlink(hlog)
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168 hlog = os.path.join(self.opts.output_dir, "thumbnail_%s.txt" % os.path.basename(inpdf))
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169 sto = open(hlog, 'w')
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170 outpng = '%s.%s' % (os.path.splitext(inpdf)[0], thumbformat)
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171 cl2 = ['convert', inpdf, outpng]
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172 x = subprocess.Popen(cl2, stdout=sto, stderr=sto, cwd=self.opts.output_dir, env=our_env)
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173 retval2 = x.wait()
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174 sto.close()
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175 if retval2 == 0:
2
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176 os.unlink(hlog)
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177 retval = retval1 or retval2
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178 return retval
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179
2
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180 def getfSize(self, fpath, outpath):
0
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181 """
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182 format a nice file size string
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183 """
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184 size = ''
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185 fp = os.path.join(outpath, fpath)
0
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186 if os.path.isfile(fp):
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187 size = '0 B'
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188 n = float(os.path.getsize(fp))
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mvdbeek
parents:
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189 if n > 2**20:
2
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parents: 0
diff changeset
190 size = '%1.1f MB' % (n / 2**20)
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
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191 elif n > 2**10:
2
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mvdbeek
parents: 0
diff changeset
192 size = '%1.1f KB' % (n / 2**10)
0
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mvdbeek
parents:
diff changeset
193 elif n > 0:
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mvdbeek
parents:
diff changeset
194 size = '%d B' % (int(n))
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mvdbeek
parents:
diff changeset
195 return size
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mvdbeek
parents:
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196
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mvdbeek
parents:
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197 def makeHtml(self):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
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198 """ Create an HTML file content to list all the artifacts found in the output_dir
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mvdbeek
parents:
diff changeset
199 """
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200
2
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201 galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
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202 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
parents: 0
diff changeset
203 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
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204 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
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mvdbeek
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205 <title></title>
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mvdbeek
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206 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
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mvdbeek
parents: 0
diff changeset
207 </head>
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mvdbeek
parents: 0
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208 <body>
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mvdbeek
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diff changeset
209 <div class="toolFormBody">
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mvdbeek
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210 """
0
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parents:
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211 galhtmlpostfix = """</div></body></html>\n"""
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
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212
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mvdbeek
parents:
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213 flist = os.listdir(self.opts.output_dir)
2
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mvdbeek
parents: 0
diff changeset
214 flist = [x for x in flist if x != 'Rplots.pdf']
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
215 flist.sort()
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mvdbeek
parents:
diff changeset
216 html = []
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
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217 html.append(galhtmlprefix % progname)
2
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mvdbeek
parents: 0
diff changeset
218 html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.scriptname, timenow()))
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
219 fhtml = []
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
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220 if len(flist) > 0:
2
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
parents: 0
diff changeset
221 logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
222 logfiles.sort()
2
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mvdbeek
parents: 0
diff changeset
223 logfiles = [x for x in logfiles if abspath(x) != abspath(self.tlog)]
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
parents: 0
diff changeset
224 logfiles.append(abspath(self.tlog)) # make it the last one
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
225 pdflist = []
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
226 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
2
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
parents: 0
diff changeset
227 for rownum, fname in enumerate(flist):
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
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diff changeset
228 dname, e = os.path.splitext(fname)
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
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diff changeset
229 sfsize = self.getfSize(fname, self.opts.output_dir)
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
parents: 0
diff changeset
230 if e.lower() == '.pdf': # compress and make a thumbnail
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
parents: 0
diff changeset
231 thumb = '%s.%s' % (dname, self.thumbformat)
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
parents: 0
diff changeset
232 pdff = os.path.join(self.opts.output_dir, fname)
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
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diff changeset
233 retval = self.compressPDF(inpdf=pdff, thumbformat=self.thumbformat)
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
234 if retval == 0:
2
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
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diff changeset
235 pdflist.append((fname, thumb))
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
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diff changeset
236 else:
2
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
parents: 0
diff changeset
237 pdflist.append((fname, fname))
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
parents: 0
diff changeset
238 if (rownum + 1) % 2 == 0:
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
parents: 0
diff changeset
239 fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname, fname, sfsize))
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
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diff changeset
240 else:
2
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mvdbeek
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diff changeset
241 fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname, fname, sfsize))
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
parents: 0
diff changeset
242 for logfname in logfiles: # expect at least tlog - if more
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
parents: 0
diff changeset
243 if abspath(logfname) == abspath(self.tlog): # handled later
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
244 sectionname = 'All tool run'
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
245 if (len(logfiles) > 1):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
246 sectionname = 'Other'
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
247 ourpdfs = pdflist
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
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248 else:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
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249 realname = os.path.basename(logfname)
2
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parents: 0
diff changeset
250 sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
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parents:
diff changeset
251 ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
2
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252 pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] != sectionname] # remove
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
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parents:
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253 nacross = 1
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254 npdf = len(ourpdfs)
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255
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256 if npdf > 0:
2
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
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diff changeset
257 nacross = math.sqrt(npdf)
0
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258 if int(nacross)**2 != npdf:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
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diff changeset
259 nacross += 1
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parents:
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260 nacross = int(nacross)
2
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diff changeset
261 width = min(400, int(1200 / nacross))
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
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parents:
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262 html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
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263 html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>')
2
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
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diff changeset
264 ntogo = nacross # counter for table row padding with empty cells
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
265 html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
2
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
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diff changeset
266 for i, paths in enumerate(ourpdfs):
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
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diff changeset
267 fname, thumb = paths
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diff changeset
268 s = """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d"
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diff changeset
269 alt="Image called %s"/></a></td>\n""" % (fname, thumb, fname, width, fname)
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
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diff changeset
270 if ((i + 1) % nacross == 0):
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
271 s += '</tr>\n'
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parents:
diff changeset
272 ntogo = 0
2
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
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diff changeset
273 if i < (npdf - 1): # more to come
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mvdbeek
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diff changeset
274 s += '<tr>'
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
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diff changeset
275 ntogo = nacross
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
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parents:
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276 else:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
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diff changeset
277 ntogo -= 1
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
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parents:
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278 html.append(s)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
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parents:
diff changeset
279 if html[-1].strip().endswith('</tr>'):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
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280 html.append('</table></div>\n')
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mvdbeek
parents:
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281 else:
2
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mvdbeek
parents: 0
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282 if ntogo > 0: # pad
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
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diff changeset
283 html.append('<td>&nbsp;</td>' * ntogo)
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
284 html.append('</tr></table></div>\n')
2
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mvdbeek
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diff changeset
285 logt = open(logfname, 'r').readlines()
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
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286 logtext = [x for x in logt if x.strip() > '']
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
287 html.append('<div class="toolFormTitle">%s log output</div>' % sectionname)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
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288 if len(logtext) > 1:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
289 html.append('\n<pre>\n')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
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290 html += logtext
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
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291 html.append('\n</pre>\n')
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
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292 else:
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mvdbeek
parents:
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293 html.append('%s is empty<br/>' % logfname)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
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294 if len(fhtml) > 0:
2
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mvdbeek
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diff changeset
295 fhtml.insert(0, '<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n')
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
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296 fhtml.append('</table></div><br/>')
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mvdbeek
parents: 0
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297 html.append('<div class="toolFormTitle">All output files available for downloading</div>\n')
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mvdbeek
parents: 0
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298 html += fhtml # add all non-pdf files to the end of the display
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
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parents:
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299 else:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
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300 html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
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301 html.append(galhtmlpostfix)
2
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mvdbeek
parents: 0
diff changeset
302 with open(self.opts.output_html, 'w') as htmlf:
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
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303 htmlf.write('\n'.join(html))
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
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diff changeset
304 htmlf.write('\n')
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
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305 self.html = html
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
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parents:
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306
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mvdbeek
parents:
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307 def run(self):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
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parents:
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308 """
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
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309 scripts must be small enough not to fill the pipe!
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
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310 """
2
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mvdbeek
parents: 0
diff changeset
311 if self.treatbashSpecial and self.opts.interpreter in ['bash', 'sh']:
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
parents: 0
diff changeset
312 retval = self.runBash()
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
313 else:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
314 if self.opts.output_dir:
2
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
parents: 0
diff changeset
315 ste = open(self.elog, 'w')
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
parents: 0
diff changeset
316 sto = open(self.tlog, 'w')
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
317 sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl))
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
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318 sto.flush()
2
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
parents: 0
diff changeset
319 p = subprocess.Popen(self.cl, shell=False, stdout=sto, stderr=ste, stdin=subprocess.PIPE, cwd=self.opts.output_dir)
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
320 else:
2
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
parents: 0
diff changeset
321 p = subprocess.Popen(self.cl, shell=False, stdin=subprocess.PIPE)
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
322 p.stdin.write(self.script)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
323 p.stdin.close()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
324 retval = p.wait()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
325 if self.opts.output_dir:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
326 sto.close()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
327 ste.close()
2
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mvdbeek
parents: 0
diff changeset
328 err = open(self.elog, 'r').readlines()
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
parents: 0
diff changeset
329 if retval != 0 and err: # problem
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
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diff changeset
330 print(err, end="", file=sys.stderr) # same problem, need to capture docker stdin/stdout
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
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parents:
diff changeset
331 if self.opts.make_HTML:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
332 self.makeHtml()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
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parents:
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333 return retval
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
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334
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
335 def runBash(self):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
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parents:
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336 """
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
337 cannot use - for bash so use self.sfile
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
338 """
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
339 if self.opts.output_dir:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
340 s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl)
2
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mvdbeek
parents: 0
diff changeset
341 sto = open(self.tlog, 'w')
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
342 sto.write(s)
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
343 sto.flush()
2
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mvdbeek
parents: 0
diff changeset
344 p = subprocess.Popen(self.cl, shell=False, stdout=sto, stderr=sto, cwd=self.opts.output_dir)
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
345 else:
2
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
parents: 0
diff changeset
346 p = subprocess.Popen(self.cl, shell=False)
0
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
347 retval = p.wait()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
348 if self.opts.output_dir:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
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parents:
diff changeset
349 sto.close()
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parents:
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350 if self.opts.make_HTML:
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
351 self.makeHtml()
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parents:
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352 return retval
2
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diff changeset
353
0
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354
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mvdbeek
parents:
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355 def change_user_id(new_uid, new_gid):
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
356 """
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
357 To avoid issues with wrong user ids, we change the user id of the 'galaxy' user in the container
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
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parents:
diff changeset
358 to the user id with which the script has been called initially.
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mvdbeek
parents:
diff changeset
359 """
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
360 cmd1 = ["/usr/sbin/usermod", "-d", "/var/home/galaxy", "galaxy"]
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
361 cmd2 = ["/usr/sbin/usermod", "-u", new_uid, "galaxy"]
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
362 cmd3 = ["/usr/sbin/groupmod", "-g", new_gid, "galaxy"]
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
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363 cmd4 = ["/usr/sbin/usermod", "-d", "/home/galaxy", "galaxy"]
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
364 [subprocess.call(cmd) for cmd in [cmd1, cmd2, cmd3, cmd4]]
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
365
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
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366
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
367 def main():
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
diff changeset
368 op = argparse.ArgumentParser()
21d312776891 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
mvdbeek
parents:
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369 a = op.add_argument
2
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diff changeset
370 a('--docker_image', default=None)
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diff changeset
371 a('--script_path', default=None)
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mvdbeek
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diff changeset
372 a('--tool_name', default=None)
495946ffc2d6 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
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diff changeset
373 a('--interpreter', default=None)
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diff changeset
374 a('--output_dir', default='./')
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375 a('--output_html', default=None)
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376 a('--input_file', default='None', nargs='*')
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377 a('--output_file', default='None')
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378 a('--user_email', default='Unknown')
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379 a('--bad_user', default=None)
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380 a('--make_HTML', default=None)
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381 a('--new_tool', default=None)
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382 a('--dockerized', default=0)
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383 a('--group_id', default=None)
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384 a('--user_id', default=None)
0
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385 a('--output_format', default='tabular')
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386 a('--input_format', dest='input_formats', action='append', default=[])
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387 a('--additional_parameters', dest='additional_parameters', action='append', default=[])
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388 opts = op.parse_args()
2
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389 assert not opts.bad_user, 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to admin_users in universe_wsgi.ini' % (opts.bad_user, opts.bad_user)
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390 assert os.path.isfile(opts.script_path), '## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
0
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391 if opts.output_dir:
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392 try:
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393 os.makedirs(opts.output_dir)
2
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394 except Exception:
0
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395 pass
2
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396 if opts.dockerized == 0:
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397 retcode = switch_to_docker(opts)
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398 sys.exit(retcode)
0
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399 change_user_id(opts.user_id, opts.group_id)
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400 os.setgid(int(opts.group_id))
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401 os.setuid(int(opts.user_id))
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402 r = ScriptRunner(opts)
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403 retcode = r.run()
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404 os.unlink(r.sfile)
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405 if retcode:
2
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406 sys.exit(retcode) # indicate failure to job runner
0
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407
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408
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409 if __name__ == "__main__":
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410 main()