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1 # DockerToolFactory.py
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2 # see https://bitbucket.org/mvdbeek/DockerToolFactory
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3
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4 import sys
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5 import shutil
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6 import subprocess
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7 import os
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8 import time
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9 import tempfile
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10 import argparse
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11 import tarfile
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12 import re
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13 import shutil
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14 import math
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15 import fileinput
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16 from os.path import abspath
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17
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18 progname = os.path.split(sys.argv[0])[1]
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19 myversion = 'V001.1 March 2014'
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20 verbose = False
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21 debug = False
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22 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
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23
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24 # if we do html we need these dependencies specified in a tool_dependencies.xml file and referred to in the generated
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25 # tool xml
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26 toolhtmldepskel = """<?xml version="1.0"?>
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27 <tool_dependency>
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28 <package name="ghostscript" version="9.10">
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29 <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" />
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30 </package>
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31 <package name="graphicsmagick" version="1.3.18">
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32 <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" />
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33 </package>
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34 <readme>
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35 %s
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36 </readme>
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37 </tool_dependency>
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38 """
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39
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40 protorequirements = """<requirements>
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41 <requirement type="package" version="9.10">ghostscript</requirement>
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42 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
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43 <container type="docker">toolfactory/custombuild:%s</container>
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44 </requirements>"""
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45
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46 def timenow():
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47 """return current time as a string
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48 """
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49 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
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50
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51 html_escape_table = {
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52 "&": "&",
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53 ">": ">",
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54 "<": "<",
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55 "$": "\$"
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56 }
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57
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58 def html_escape(text):
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59 """Produce entities within text."""
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60 return "".join(html_escape_table.get(c,c) for c in text)
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61
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62 def cmd_exists(cmd):
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63 return subprocess.call("type " + cmd, shell=True,
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64 stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
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65
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66 def edit_dockerfile(dockerfile):
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67 '''we have to change the userid of galaxy inside the container to the id with which the tool is run,
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68 otherwise we have a mismatch in the file permissions inside the container'''
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69 uid=os.getuid()
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70 for line in fileinput.FileInput(dockerfile, inplace=1):
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71 sys.stdout.write(line.replace("RUN adduser galaxy\n", "RUN adduser galaxy -u {0}\n".format(uid)))
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72
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73 def build_docker(dockerfile, docker_client, image_tag='base'):
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74 '''Given the path to a dockerfile, and a docker_client, build the image, if it does not
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75 exist yet.'''
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76 image_id='toolfactory/custombuild:'+image_tag
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77 existing_images=", ".join(["".join(d['RepoTags']) for d in docker_client.images()])
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78 if image_id in existing_images:
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79 print 'docker container exists, skipping build'
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80 return image_id
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81 print "Building Docker image, using Dockerfile:{0}".format(dockerfile)
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1
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82 build_process=docker_client.build(fileobj=open(dockerfile, 'r'), tag=image_id)
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83 print "succesfully dispatched docker build process, building now"
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84 build_log=[line for line in build_process] #will block until image is built.
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85 return image_id
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86
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87 def construct_bind(host_path, container_path=False, binds=None, ro=True):
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88 #TODO remove container_path if it's alwyas going to be the same as host_path
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89 '''build or extend binds dictionary with container path. binds is used
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90 to mount all files using the docker-py client.'''
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91 if not binds:
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92 binds={}
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93 if isinstance(host_path, list):
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94 for k,v in enumerate(host_path):
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95 if not container_path:
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96 container_path=host_path[k]
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97 binds[host_path[k]]={'bind':container_path, 'ro':ro}
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98 container_path=False #could be more elegant
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99 return binds
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100 else:
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101 if not container_path:
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102 container_path=host_path
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103 binds[host_path]={'bind':container_path, 'ro':ro}
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104 return binds
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105
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106 def switch_to_docker(opts):
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107 import docker #need local import, as container does not have docker-py
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108 docker_client=docker.Client()
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109 toolfactory_path=abspath(sys.argv[0])
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110 dockerfile=os.path.dirname(toolfactory_path)+'/Dockerfile'
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111 edit_dockerfile(dockerfile)
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112 image_id=build_docker(dockerfile, docker_client)
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113 binds=construct_bind(host_path=opts.script_path, ro=False)
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114 binds=construct_bind(binds=binds, host_path=abspath(opts.output_dir), ro=False)
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115 if len(opts.input_tab)>0:
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116 binds=construct_bind(binds=binds, host_path=opts.input_tab, ro=True)
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117 if not opts.output_tab == 'None':
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118 binds=construct_bind(binds=binds, host_path=opts.output_tab, ro=False)
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119 if opts.make_HTML:
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120 binds=construct_bind(binds=binds, host_path=opts.output_html, ro=False)
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121 if opts.make_Tool:
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122 binds=construct_bind(binds=binds, host_path=opts.new_tool, ro=False)
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123 binds=construct_bind(binds=binds, host_path=opts.help_text, ro=True)
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124 binds=construct_bind(binds=binds, host_path=toolfactory_path)
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125 volumes=binds.keys()
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126 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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127 cmd=['python', '-u']+sys.argv+['--dockerized', '1']
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128 container=docker_client.create_container(
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129 image=image_id,
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130 user='galaxy',
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131 volumes=volumes,
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132 command=cmd
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133 )
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134 docker_client.start(container=container[u'Id'], binds=binds)
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135 docker_client.wait(container=container[u'Id'])
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136 logs=docker_client.logs(container=container[u'Id'])
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137 print "".join([log for log in logs])
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138
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139 class ScriptRunner:
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140 """class is a wrapper for an arbitrary script
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141 """
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142
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143 def __init__(self,opts=None,treatbashSpecial=True, image_tag='base'):
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144 """
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145 cleanup inputs, setup some outputs
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146
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147 """
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148 self.opts = opts
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149 self.useGM = cmd_exists('gm')
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150 self.useIM = cmd_exists('convert')
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151 self.useGS = cmd_exists('gs')
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152 self.temp_warned = False # we want only one warning if $TMP not set
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153 self.treatbashSpecial = treatbashSpecial
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154 self.image_tag = image_tag
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155 os.chdir(abspath(opts.output_dir))
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156 self.thumbformat = 'png'
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157 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
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158 self.toolid = self.toolname
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159 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
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160 self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
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161 self.xmlfile = '%s.xml' % self.toolname
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162 s = open(self.opts.script_path,'r').readlines()
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163 s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
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164 self.script = '\n'.join(s)
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165 fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))
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166 tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
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167 tscript.write(self.script)
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168 tscript.close()
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169 self.indentedScript = '\n'.join([' %s' % html_escape(x) for x in s]) # for restructured text in help
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170 self.escapedScript = '\n'.join([html_escape(x) for x in s])
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171 self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname)
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172 if opts.output_dir: # may not want these complexities
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173 self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname)
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174 art = '%s.%s' % (self.toolname,opts.interpreter)
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175 artpath = os.path.join(self.opts.output_dir,art) # need full path
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176 artifact = open(artpath,'w') # use self.sfile as script source for Popen
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177 artifact.write(self.script)
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178 artifact.close()
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179 self.cl = []
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180 self.html = []
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181 a = self.cl.append
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182 a(opts.interpreter)
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183 if self.treatbashSpecial and opts.interpreter in ['bash','sh']:
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184 a(self.sfile)
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185 else:
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186 a('-') # stdin
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187 for input in opts.input_tab:
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188 a(input)
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189 if opts.output_tab == 'None': #If tool generates only HTML, set output name to toolname
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190 a(str(self.toolname)+'.out')
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191 a(opts.output_tab)
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192 for param in opts.additional_parameters:
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193 param, value=param.split(',')
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194 a('--'+param)
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195 a(value)
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196 #print self.cl
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197 self.outFormats = opts.output_format
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198 self.inputFormats = [formats for formats in opts.input_formats]
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199 self.test1Input = '%s_test1_input.xls' % self.toolname
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200 self.test1Output = '%s_test1_output.xls' % self.toolname
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201 self.test1HTML = '%s_test1_output.html' % self.toolname
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202
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203 def makeXML(self):
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204 """
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205 Create a Galaxy xml tool wrapper for the new script as a string to write out
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206 fixme - use templating or something less fugly than this example of what we produce
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207
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208 <tool id="reverse" name="reverse" version="0.01">
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209 <description>a tabular file</description>
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210 <command interpreter="python">
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211 reverse.py --script_path "$runMe" --interpreter "python"
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212 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
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213 </command>
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214 <inputs>
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215 <param name="input1" type="data" format="tabular" label="Select a suitable input file from your history"/>
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216
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217 </inputs>
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218 <outputs>
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219 <data format=opts.output_format name="tab_file"/>
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220
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221 </outputs>
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222 <help>
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223
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224 **What it Does**
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225
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226 Reverse the columns in a tabular file
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227
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228 </help>
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229 <configfiles>
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230 <configfile name="runMe">
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231
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232 # reverse order of columns in a tabular file
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233 import sys
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234 inp = sys.argv[1]
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235 outp = sys.argv[2]
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236 i = open(inp,'r')
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237 o = open(outp,'w')
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238 for row in i:
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239 rs = row.rstrip().split('\t')
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240 rs.reverse()
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241 o.write('\t'.join(rs))
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242 o.write('\n')
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243 i.close()
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244 o.close()
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245
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246
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247 </configfile>
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248 </configfiles>
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249 </tool>
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250
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251 """
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252 newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
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253 %(tooldesc)s
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254 %(requirements)s
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255 <command interpreter="python">
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256 %(command)s
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257 </command>
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258 <inputs>
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259 %(inputs)s
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260 </inputs>
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261 <outputs>
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262 %(outputs)s
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263 </outputs>
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264 <configfiles>
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265 <configfile name="runMe">
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266 %(script)s
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267 </configfile>
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268 </configfiles>
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269
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270 %(tooltests)s
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271
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272 <help>
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273
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274 %(help)s
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275
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276 </help>
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277 </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
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278
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279 newCommand="""
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280 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
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281 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s """
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282 # may NOT be an input or htmlout - appended later
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283 tooltestsTabOnly = """
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284 <tests>
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285 <test>
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286 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
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287 <param name="runMe" value="$runMe"/>
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288 <output name="tab_file" file="%(test1Output)s" ftype="tabular"/>
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289 </test>
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290 </tests>
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291 """
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292 tooltestsHTMLOnly = """
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293 <tests>
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294 <test>
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295 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
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296 <param name="runMe" value="$runMe"/>
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297 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
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298 </test>
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299 </tests>
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300 """
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301 tooltestsBoth = """<tests>
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302 <test>
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303 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
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304 <param name="runMe" value="$runMe"/>
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305 <output name="tab_file" file="%(test1Output)s" ftype="tabular" />
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306 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
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307 </test>
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308 </tests>
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309 """
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310 xdict = {}
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311 #xdict['requirements'] = ''
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312 #if self.opts.make_HTML:
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313 xdict['requirements'] = protorequirements % self.image_tag
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314 xdict['tool_version'] = self.opts.tool_version
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315 xdict['test1Input'] = self.test1Input
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316 xdict['test1HTML'] = self.test1HTML
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317 xdict['test1Output'] = self.test1Output
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318 if self.opts.make_HTML and self.opts.output_tab <> 'None':
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319 xdict['tooltests'] = tooltestsBoth % xdict
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320 elif self.opts.make_HTML:
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321 xdict['tooltests'] = tooltestsHTMLOnly % xdict
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322 else:
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323 xdict['tooltests'] = tooltestsTabOnly % xdict
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324 xdict['script'] = self.escapedScript
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325 # configfile is least painful way to embed script to avoid external dependencies
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326 # but requires escaping of <, > and $ to avoid Mako parsing
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327 if self.opts.help_text:
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328 helptext = open(self.opts.help_text,'r').readlines()
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329 helptext = [html_escape(x) for x in helptext] # must html escape here too - thanks to Marius van den Beek
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330 xdict['help'] = ''.join([x for x in helptext])
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331 else:
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332 xdict['help'] = 'Please ask the tool author (%s) for help as none was supplied at tool generation\n' % (self.opts.user_email)
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333 coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::']
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334 coda.append('\n')
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335 coda.append(self.indentedScript)
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336 coda.append('\n**Attribution**\nThis Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.\n' % (self.opts.user_email,timenow()))
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337 coda.append('See %s for details of that project' % (toolFactoryURL))
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338 coda.append('Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. ')
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339 coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573\n')
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340 xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
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341 if self.opts.tool_desc:
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342 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
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343 else:
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344 xdict['tooldesc'] = ''
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345 xdict['command_outputs'] = ''
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346 xdict['outputs'] = ''
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347 if self.opts.input_tab <> 'None':
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348 xdict['command_inputs'] = '--input_tab'
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349 xdict['inputs']=''
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350 for i,input in enumerate(self.inputFormats):
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351 xdict['inputs' ]+='<param name="input{0}" type="data" format="{1}" label="Select a suitable input file from your history"/> \n'.format(i+1, input)
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352 xdict['command_inputs'] += ' $input{0}'.format(i+1)
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353 else:
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354 xdict['command_inputs'] = '' # assume no input - eg a random data generator
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355 xdict['inputs'] = ''
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356 # I find setting the job name not very logical. can be changed in workflows anyway. xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname
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357 xdict['toolname'] = self.toolname
|
|
|
358 xdict['toolid'] = self.toolid
|
|
|
359 xdict['interpreter'] = self.opts.interpreter
|
|
|
360 xdict['scriptname'] = self.sfile
|
|
|
361 if self.opts.make_HTML:
|
|
|
362 xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"'
|
|
|
363 xdict['outputs'] += ' <data format="html" name="html_file"/>\n'
|
|
|
364 else:
|
|
|
365 xdict['command_outputs'] += ' --output_dir "./"'
|
|
|
366 #print self.opts.output_tab
|
|
|
367 if not self.opts.output_tab:
|
|
|
368 xdict['command_outputs'] += ' --output_tab "$tab_file"'
|
|
|
369 xdict['outputs'] += ' <data format="%s" name="tab_file"/>\n' % self.outFormats
|
|
|
370 xdict['command'] = newCommand % xdict
|
|
|
371 #print xdict['outputs']
|
|
|
372 xmls = newXML % xdict
|
|
|
373 xf = open(self.xmlfile,'w')
|
|
|
374 xf.write(xmls)
|
|
|
375 xf.write('\n')
|
|
|
376 xf.close()
|
|
|
377 # ready for the tarball
|
|
|
378
|
|
|
379
|
|
|
380 def makeTooltar(self):
|
|
|
381 """
|
|
|
382 a tool is a gz tarball with eg
|
|
|
383 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
|
|
|
384 """
|
|
|
385 retval = self.run()
|
|
|
386 if retval:
|
|
|
387 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
|
|
|
388 sys.exit(1)
|
|
|
389 tdir = self.toolname
|
|
|
390 os.mkdir(tdir)
|
|
|
391 self.makeXML()
|
|
|
392 if self.opts.make_HTML:
|
|
|
393 if self.opts.help_text:
|
|
|
394 hlp = open(self.opts.help_text,'r').read()
|
|
|
395 else:
|
|
|
396 hlp = 'Please ask the tool author for help as none was supplied at tool generation\n'
|
|
|
397 if self.opts.include_dependencies:
|
|
|
398 tooldepcontent = toolhtmldepskel % hlp
|
|
|
399 depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w')
|
|
|
400 depf.write(tooldepcontent)
|
|
|
401 depf.write('\n')
|
|
|
402 depf.close()
|
|
|
403 if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
|
|
|
404 testdir = os.path.join(tdir,'test-data')
|
|
|
405 os.mkdir(testdir) # make tests directory
|
|
|
406 for i in self.opts.input_tab:
|
|
|
407 #print i
|
|
|
408 shutil.copyfile(i,os.path.join(testdir,self.test1Input))
|
|
|
409 if not self.opts.output_tab:
|
|
|
410 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
|
|
|
411 if self.opts.make_HTML:
|
|
|
412 shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
|
|
|
413 if self.opts.output_dir:
|
|
|
414 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
|
|
|
415 outpif = '%s.py' % self.toolname # new name
|
|
|
416 outpiname = os.path.join(tdir,outpif) # path for the tool tarball
|
|
|
417 pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
|
|
|
418 notes = ['# %s - a self annotated version of %s generated by running %s\n' % (outpiname,pyin,pyin),]
|
|
|
419 notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
|
|
|
420 notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
|
|
|
421 pi=[line.replace('if opts.dockerized==0:', 'if False:') for line in open(self.pyfile)] #do not run docker in the generated tool
|
|
|
422 notes += pi
|
|
|
423 outpi = open(outpiname,'w')
|
|
|
424 outpi.write(''.join(notes))
|
|
|
425 outpi.write('\n')
|
|
|
426 outpi.close()
|
|
|
427 stname = os.path.join(tdir,self.sfile)
|
|
|
428 if not os.path.exists(stname):
|
|
|
429 shutil.copyfile(self.sfile, stname)
|
|
|
430 xtname = os.path.join(tdir,self.xmlfile)
|
|
|
431 if not os.path.exists(xtname):
|
|
|
432 shutil.copyfile(self.xmlfile,xtname)
|
|
|
433 tarpath = "%s.gz" % self.toolname
|
|
|
434 tar = tarfile.open(tarpath, "w:gz")
|
|
|
435 tar.add(tdir,arcname=self.toolname)
|
|
|
436 tar.close()
|
|
|
437 shutil.copyfile(tarpath,self.opts.new_tool)
|
|
|
438 shutil.rmtree(tdir)
|
|
|
439 ## TODO: replace with optional direct upload to local toolshed?
|
|
|
440 return retval
|
|
|
441
|
|
|
442
|
|
|
443 def compressPDF(self,inpdf=None,thumbformat='png'):
|
|
|
444 """need absolute path to pdf
|
|
|
445 note that GS gets confoozled if no $TMP or $TEMP
|
|
|
446 so we set it
|
|
|
447 """
|
|
|
448 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
|
|
|
449 hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))
|
|
|
450 sto = open(hlog,'a')
|
|
|
451 our_env = os.environ.copy()
|
|
|
452 our_tmp = our_env.get('TMP',None)
|
|
|
453 if not our_tmp:
|
|
|
454 our_tmp = our_env.get('TEMP',None)
|
|
|
455 if not (our_tmp and os.path.exists(our_tmp)):
|
|
|
456 newtmp = os.path.join(self.opts.output_dir,'tmp')
|
|
|
457 try:
|
|
|
458 os.mkdir(newtmp)
|
|
|
459 except:
|
|
|
460 sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp)
|
|
|
461 our_env['TEMP'] = newtmp
|
|
|
462 if not self.temp_warned:
|
|
|
463 sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp)
|
|
|
464 self.temp_warned = True
|
|
|
465 outpdf = '%s_compressed' % inpdf
|
|
|
466 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf]
|
|
|
467 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
|
|
|
468 retval1 = x.wait()
|
|
|
469 sto.close()
|
|
|
470 if retval1 == 0:
|
|
|
471 os.unlink(inpdf)
|
|
|
472 shutil.move(outpdf,inpdf)
|
|
|
473 os.unlink(hlog)
|
|
|
474 hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf))
|
|
|
475 sto = open(hlog,'w')
|
|
|
476 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
|
|
|
477 if self.useGM:
|
|
|
478 cl2 = ['gm', 'convert', inpdf, outpng]
|
|
|
479 else: # assume imagemagick
|
|
|
480 cl2 = ['convert', inpdf, outpng]
|
|
|
481 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
|
|
|
482 retval2 = x.wait()
|
|
|
483 sto.close()
|
|
|
484 if retval2 == 0:
|
|
|
485 os.unlink(hlog)
|
|
|
486 retval = retval1 or retval2
|
|
|
487 return retval
|
|
|
488
|
|
|
489
|
|
|
490 def getfSize(self,fpath,outpath):
|
|
|
491 """
|
|
|
492 format a nice file size string
|
|
|
493 """
|
|
|
494 size = ''
|
|
|
495 fp = os.path.join(outpath,fpath)
|
|
|
496 if os.path.isfile(fp):
|
|
|
497 size = '0 B'
|
|
|
498 n = float(os.path.getsize(fp))
|
|
|
499 if n > 2**20:
|
|
|
500 size = '%1.1f MB' % (n/2**20)
|
|
|
501 elif n > 2**10:
|
|
|
502 size = '%1.1f KB' % (n/2**10)
|
|
|
503 elif n > 0:
|
|
|
504 size = '%d B' % (int(n))
|
|
|
505 return size
|
|
|
506
|
|
|
507 def makeHtml(self):
|
|
|
508 """ Create an HTML file content to list all the artifacts found in the output_dir
|
|
|
509 """
|
|
|
510
|
|
|
511 galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
|
512 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
|
|
513 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
|
|
|
514 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
|
|
|
515 <title></title>
|
|
|
516 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
|
|
|
517 </head>
|
|
|
518 <body>
|
|
|
519 <div class="toolFormBody">
|
|
|
520 """
|
|
|
521 galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>"""
|
|
|
522 galhtmlpostfix = """</div></body></html>\n"""
|
|
|
523
|
|
|
524 flist = os.listdir(self.opts.output_dir)
|
|
|
525 flist = [x for x in flist if x <> 'Rplots.pdf']
|
|
|
526 flist.sort()
|
|
|
527 html = []
|
|
|
528 html.append(galhtmlprefix % progname)
|
|
|
529 html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow()))
|
|
|
530 fhtml = []
|
|
|
531 if len(flist) > 0:
|
|
|
532 logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections
|
|
|
533 logfiles.sort()
|
|
|
534 logfiles = [x for x in logfiles if abspath(x) <> abspath(self.tlog)]
|
|
|
535 logfiles.append(abspath(self.tlog)) # make it the last one
|
|
|
536 pdflist = []
|
|
|
537 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
|
|
|
538 for rownum,fname in enumerate(flist):
|
|
|
539 dname,e = os.path.splitext(fname)
|
|
|
540 sfsize = self.getfSize(fname,self.opts.output_dir)
|
|
|
541 if e.lower() == '.pdf' : # compress and make a thumbnail
|
|
|
542 thumb = '%s.%s' % (dname,self.thumbformat)
|
|
|
543 pdff = os.path.join(self.opts.output_dir,fname)
|
|
|
544 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
|
|
|
545 if retval == 0:
|
|
|
546 pdflist.append((fname,thumb))
|
|
|
547 else:
|
|
|
548 pdflist.append((fname,fname))
|
|
|
549 if (rownum+1) % 2 == 0:
|
|
|
550 fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
|
|
|
551 else:
|
|
|
552 fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
|
|
|
553 for logfname in logfiles: # expect at least tlog - if more
|
|
|
554 if abspath(logfname) == abspath(self.tlog): # handled later
|
|
|
555 sectionname = 'All tool run'
|
|
|
556 if (len(logfiles) > 1):
|
|
|
557 sectionname = 'Other'
|
|
|
558 ourpdfs = pdflist
|
|
|
559 else:
|
|
|
560 realname = os.path.basename(logfname)
|
|
|
561 sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log
|
|
|
562 ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
|
|
|
563 pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove
|
|
|
564 nacross = 1
|
|
|
565 npdf = len(ourpdfs)
|
|
|
566
|
|
|
567 if npdf > 0:
|
|
|
568 nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))
|
|
|
569 if int(nacross)**2 != npdf:
|
|
|
570 nacross += 1
|
|
|
571 nacross = int(nacross)
|
|
|
572 width = min(400,int(1200/nacross))
|
|
|
573 html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)
|
|
|
574 html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>')
|
|
|
575 ntogo = nacross # counter for table row padding with empty cells
|
|
|
576 html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
|
|
|
577 for i,paths in enumerate(ourpdfs):
|
|
|
578 fname,thumb = paths
|
|
|
579 s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d"
|
|
|
580 alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)
|
|
|
581 if ((i+1) % nacross == 0):
|
|
|
582 s += '</tr>\n'
|
|
|
583 ntogo = 0
|
|
|
584 if i < (npdf - 1): # more to come
|
|
|
585 s += '<tr>'
|
|
|
586 ntogo = nacross
|
|
|
587 else:
|
|
|
588 ntogo -= 1
|
|
|
589 html.append(s)
|
|
|
590 if html[-1].strip().endswith('</tr>'):
|
|
|
591 html.append('</table></div>\n')
|
|
|
592 else:
|
|
|
593 if ntogo > 0: # pad
|
|
|
594 html.append('<td> </td>'*ntogo)
|
|
|
595 html.append('</tr></table></div>\n')
|
|
|
596 logt = open(logfname,'r').readlines()
|
|
|
597 logtext = [x for x in logt if x.strip() > '']
|
|
|
598 html.append('<div class="toolFormTitle">%s log output</div>' % sectionname)
|
|
|
599 if len(logtext) > 1:
|
|
|
600 html.append('\n<pre>\n')
|
|
|
601 html += logtext
|
|
|
602 html.append('\n</pre>\n')
|
|
|
603 else:
|
|
|
604 html.append('%s is empty<br/>' % logfname)
|
|
|
605 if len(fhtml) > 0:
|
|
|
606 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')
|
|
|
607 fhtml.append('</table></div><br/>')
|
|
|
608 html.append('<div class="toolFormTitle">All output files available for downloading</div>\n')
|
|
|
609 html += fhtml # add all non-pdf files to the end of the display
|
|
|
610 else:
|
|
|
611 html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
|
|
|
612 html.append(galhtmlpostfix)
|
|
|
613 htmlf = file(self.opts.output_html,'w')
|
|
|
614 htmlf.write('\n'.join(html))
|
|
|
615 htmlf.write('\n')
|
|
|
616 htmlf.close()
|
|
|
617 self.html = html
|
|
|
618
|
|
|
619
|
|
|
620 def run(self):
|
|
|
621 """
|
|
|
622 scripts must be small enough not to fill the pipe!
|
|
|
623 """
|
|
|
624 if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']:
|
|
|
625 retval = self.runBash()
|
|
|
626 else:
|
|
|
627 if self.opts.output_dir:
|
|
|
628 ste = open(self.elog,'w')
|
|
|
629 sto = open(self.tlog,'w')
|
|
|
630 sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl))
|
|
|
631 sto.flush()
|
|
|
632 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
|
|
|
633 else:
|
|
|
634 p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)
|
|
|
635 p.stdin.write(self.script)
|
|
|
636 p.stdin.close()
|
|
|
637 retval = p.wait()
|
|
|
638 if self.opts.output_dir:
|
|
|
639 sto.close()
|
|
|
640 ste.close()
|
|
|
641 err = open(self.elog,'r').readlines()
|
|
|
642 if retval <> 0 and err: # problem
|
|
|
643 print >> sys.stderr,err #same problem, need to capture docker stdin/stdout
|
|
|
644 if self.opts.make_HTML:
|
|
|
645 self.makeHtml()
|
|
|
646 return retval
|
|
|
647
|
|
|
648 def runBash(self):
|
|
|
649 """
|
|
|
650 cannot use - for bash so use self.sfile
|
|
|
651 """
|
|
|
652 if self.opts.output_dir:
|
|
|
653 s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl)
|
|
|
654 sto = open(self.tlog,'w')
|
|
|
655 sto.write(s)
|
|
|
656 sto.flush()
|
|
|
657 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
|
|
|
658 else:
|
|
|
659 p = subprocess.Popen(self.cl,shell=False)
|
|
|
660 retval = p.wait()
|
|
|
661 if self.opts.output_dir:
|
|
|
662 sto.close()
|
|
|
663 if self.opts.make_HTML:
|
|
|
664 self.makeHtml()
|
|
|
665 return retval
|
|
|
666
|
|
|
667
|
|
|
668 def main():
|
|
|
669 u = """
|
|
|
670 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
|
|
|
671 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
|
|
|
672 </command>
|
|
|
673 """
|
|
|
674 op = argparse.ArgumentParser()
|
|
|
675 a = op.add_argument
|
|
|
676 a('--script_path',default=None)
|
|
|
677 a('--tool_name',default=None)
|
|
|
678 a('--interpreter',default=None)
|
|
|
679 a('--output_dir',default='./')
|
|
|
680 a('--output_html',default=None)
|
|
|
681 a('--input_tab',default='None', nargs='*')
|
|
|
682 a('--output_tab',default='None')
|
|
|
683 a('--user_email',default='Unknown')
|
|
|
684 a('--bad_user',default=None)
|
|
|
685 a('--make_Tool',default=None)
|
|
|
686 a('--make_HTML',default=None)
|
|
|
687 a('--help_text',default=None)
|
|
|
688 a('--tool_desc',default=None)
|
|
|
689 a('--new_tool',default=None)
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690 a('--tool_version',default=None)
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691 a('--include_dependencies',default=None)
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692 a('--dockerized',default=0)
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693 a('--output_format', default='tabular')
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694 a('--input_format', dest='input_formats', action='append', default=[])
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695 a('--additional_parameters', dest='additional_parameters', action='append', default=[])
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696 opts = op.parse_args()
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697 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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698 assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
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699 assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
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700 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
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701 if opts.output_dir:
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702 try:
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703 os.makedirs(opts.output_dir)
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|
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704 except:
|
|
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705 pass
|
|
|
706 if opts.dockerized==0:
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|
707 switch_to_docker(opts)
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|
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708 return
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|
|
709 r = ScriptRunner(opts)
|
|
|
710 if opts.make_Tool:
|
|
|
711 retcode = r.makeTooltar()
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|
|
712 else:
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|
|
713 retcode = r.run()
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|
|
714 os.unlink(r.sfile)
|
|
|
715 if retcode:
|
|
|
716 sys.exit(retcode) # indicate failure to job runner
|
|
|
717
|
|
|
718
|
|
|
719 if __name__ == "__main__":
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|
|
720 main()
|
|
|
721
|
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722
|
