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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
children
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1:315a7e9ed6eb 2:495946ffc2d6
1 # DockerToolFactory.py 1 # DockerToolFactory.py
2 # see https://github.com/mvdbeek/scriptrunner 2 # see https://github.com/mvdbeek/scriptrunner
3 3
4 import sys 4 from __future__ import print_function
5 import shutil 5 import sys
6 import subprocess 6 import shutil
7 import os 7 import subprocess
8 import time 8 import os
9 import tempfile 9 import time
10 import tempfile
10 import argparse 11 import argparse
11 import getpass
12 import tarfile
13 import re
14 import shutil
15 import math 12 import math
16 import fileinput 13 from os.path import abspath
17 from os.path import abspath 14
18 15 progname = os.path.split(sys.argv[0])[1]
19 16 verbose = False
20 progname = os.path.split(sys.argv[0])[1]
21 verbose = False
22 debug = False 17 debug = False
23 18
19 html_escape_table = {
20 "&": "&",
21 ">": ">",
22 "<": "&lt;",
23 "$": "\$"
24 }
25
26
24 def timenow(): 27 def timenow():
25 """return current time as a string 28 """Return current time as a string."""
26 """
27 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) 29 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
28 30
29 html_escape_table = {
30 "&": "&amp;",
31 ">": "&gt;",
32 "<": "&lt;",
33 "$": "\$"
34 }
35 31
36 def html_escape(text): 32 def html_escape(text):
37 """Produce entities within text.""" 33 """Produce entities within text."""
38 return "".join(html_escape_table.get(c,c) for c in text) 34 return "".join(html_escape_table.get(c, c) for c in text)
35
39 36
40 def cmd_exists(cmd): 37 def cmd_exists(cmd):
41 return subprocess.call("type " + cmd, shell=True, 38 return subprocess.call("type " + cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
42 stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0 39
43 40
44 def construct_bind(host_path, container_path=False, binds=None, ro=True): 41 def construct_bind(host_path, container_path=False, binds=None, ro=True):
45 #TODO remove container_path if it's alwyas going to be the same as host_path 42 # TODO remove container_path if it's alwyas going to be the same as host_path
46 '''build or extend binds dictionary with container path. binds is used 43 """Build or extend binds dictionary with container path. binds is used
47 to mount all files using the docker-py client.''' 44 to mount all files using the docker-py client."""
48 if not binds: 45 if not binds:
49 binds={} 46 binds = {}
50 if isinstance(host_path, list): 47 if isinstance(host_path, list):
51 for k,v in enumerate(host_path): 48 for k, v in enumerate(host_path):
52 if not container_path: 49 if not container_path:
53 container_path=host_path[k] 50 container_path = host_path[k]
54 binds[host_path[k]]={'bind':container_path, 'ro':ro} 51 binds[host_path[k]] = {'bind': container_path, 'ro': ro}
55 container_path=False #could be more elegant 52 container_path = False # could be more elegant
56 return binds 53 return binds
57 else: 54 else:
58 if not container_path: 55 if not container_path:
59 container_path=host_path 56 container_path = host_path
60 binds[host_path]={'bind':container_path, 'ro':ro} 57 binds[host_path] = {'bind': container_path, 'ro': ro}
61 return binds 58 return binds
62 59
60
63 def switch_to_docker(opts): 61 def switch_to_docker(opts):
64 import docker #need local import, as container does not have docker-py 62 import docker # need local import, as container does not have docker-py
65 user_id = os.getuid() 63 user_id = os.getuid()
66 group_id = os.getgid() 64 group_id = os.getgid()
67 docker_client=docker.Client() 65 docker_client = docker.APIClient()
68 toolfactory_path=abspath(sys.argv[0]) 66 toolfactory_path = abspath(sys.argv[0])
69 binds=construct_bind(host_path=opts.script_path, ro=False) 67 binds = construct_bind(host_path=opts.script_path, ro=False)
70 binds=construct_bind(binds=binds, host_path=abspath(opts.output_dir), ro=False) 68 binds = construct_bind(binds=binds, host_path=abspath(opts.output_dir), ro=False)
71 if len(opts.input_tab)>0: 69 if len(opts.input_file) > 0:
72 binds=construct_bind(binds=binds, host_path=opts.input_tab, ro=True) 70 binds = construct_bind(binds=binds, host_path=opts.input_file, ro=True)
73 if not opts.output_tab == 'None': 71 if not opts.output_file == 'None':
74 binds=construct_bind(binds=binds, host_path=opts.output_tab, ro=False) 72 binds = construct_bind(binds=binds, host_path=opts.output_file, ro=False)
75 if opts.make_HTML: 73 if opts.make_HTML:
76 binds=construct_bind(binds=binds, host_path=opts.output_html, ro=False) 74 binds = construct_bind(binds=binds, host_path=opts.output_html, ro=False)
77 binds=construct_bind(binds=binds, host_path=toolfactory_path) 75 binds = construct_bind(binds=binds, host_path=toolfactory_path)
78 volumes=binds.keys() 76 volumes = list(binds.keys())
79 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 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
80 cmd=['python', '-u']+sys.argv+['--dockerized', '1', "--user_id", str(user_id), "--group_id", str(group_id)] 78 cmd = ['python', '-u'] + sys.argv + ['--dockerized', '1', "--user_id", str(user_id), "--group_id", str(group_id)]
81 image_exists = [ True for image in docker_client.images() if opts.docker_image in image['RepoTags'] ] 79 image_exists = [True for image in docker_client.images() if opts.docker_image in image['RepoTags']]
82 if not image_exists: 80 if not image_exists:
83 docker_client.pull(opts.docker_image) 81 docker_client.pull(opts.docker_image)
84 container=docker_client.create_container( 82 container = docker_client.create_container(
85 image=opts.docker_image, 83 image=opts.docker_image,
86 volumes=volumes, 84 volumes=volumes,
87 command=cmd 85 command=cmd,
88 ) 86 host_config=docker_client.create_host_config(binds=binds))
89 docker_client.start(container=container[u'Id'], binds=binds) 87 docker_client.start(container=container[u'Id'])
90 docker_client.wait(container=container[u'Id']) 88 exit_code = docker_client.wait(container=container[u'Id'])['StatusCode']
91 logs=docker_client.logs(container=container[u'Id']) 89 logs = docker_client.logs(container=container[u'Id'])
92 print "".join([log for log in logs]) 90 print(logs, end="", file=sys.stderr)
93 docker_client.remove_container(container[u'Id']) 91 docker_client.remove_container(container[u'Id'])
92 return exit_code
93
94 94
95 class ScriptRunner: 95 class ScriptRunner:
96 """class is a wrapper for an arbitrary script 96 """class is a wrapper for an arbitrary script
97 """ 97 """
98 98
99 def __init__(self,opts=None,treatbashSpecial=True, image_tag='base'): 99 def __init__(self, opts=None, treatbashSpecial=True, image_tag='base'):
100 """ 100 """
101 cleanup inputs, setup some outputs 101 cleanup inputs, setup some outputs
102
103 """ 102 """
104 self.opts = opts 103 self.opts = opts
105 self.scriptname = 'script' 104 self.scriptname = 'script'
106 self.useIM = cmd_exists('convert')
107 self.useGS = cmd_exists('gs')
108 self.temp_warned = False # we want only one warning if $TMP not set
109 self.treatbashSpecial = treatbashSpecial 105 self.treatbashSpecial = treatbashSpecial
110 self.image_tag = image_tag 106 self.image_tag = image_tag
111 os.chdir(abspath(opts.output_dir)) 107 os.chdir(abspath(opts.output_dir))
112 self.thumbformat = 'png' 108 self.thumbformat = 'png'
113 s = open(self.opts.script_path,'r').readlines() 109 s = open(self.opts.script_path, 'r').readlines()
114 s = [x.rstrip() for x in s] # remove pesky dos line endings if needed 110 s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
115 self.script = '\n'.join(s) 111 self.script = '\n'.join(s)
116 fhandle,self.sfile = tempfile.mkstemp(prefix='script',suffix=".%s" % (opts.interpreter)) 112 fhandle, self.sfile = tempfile.mkstemp(prefix='script', suffix=".%s" % (opts.interpreter))
117 tscript = open(self.sfile,'w') # use self.sfile as script source for Popen 113 tscript = open(self.sfile, 'w') # use self.sfile as script source for Popen
118 tscript.write(self.script) 114 tscript.write(self.script)
119 tscript.close() 115 tscript.close()
120 self.indentedScript = '\n'.join([' %s' % html_escape(x) for x in s]) # for restructured text in help 116 self.indentedScript = '\n'.join([' %s' % html_escape(x) for x in s]) # for restructured text in help
121 self.escapedScript = '\n'.join([html_escape(x) for x in s]) 117 self.escapedScript = '\n'.join([html_escape(x) for x in s])
122 self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.scriptname) 118 self.elog = os.path.join(self.opts.output_dir, "%s_error.log" % self.scriptname)
123 if opts.output_dir: # may not want these complexities 119 if opts.output_dir: # may not want these complexities
124 self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.scriptname) 120 self.tlog = os.path.join(self.opts.output_dir, "%s_runner.log" % self.scriptname)
125 art = '%s.%s' % (self.scriptname,opts.interpreter) 121 art = '%s.%s' % (self.scriptname, opts.interpreter)
126 artpath = os.path.join(self.opts.output_dir,art) # need full path 122 artpath = os.path.join(self.opts.output_dir, art) # need full path
127 artifact = open(artpath,'w') # use self.sfile as script source for Popen 123 artifact = open(artpath, 'w') # use self.sfile as script source for Popen
128 artifact.write(self.script) 124 artifact.write(self.script)
129 artifact.close() 125 artifact.close()
130 self.cl = [] 126 self.cl = []
131 self.html = [] 127 self.html = []
132 a = self.cl.append 128 self.cl.append(opts.interpreter)
133 a(opts.interpreter) 129 if self.treatbashSpecial and opts.interpreter in ['bash', 'sh']:
134 if self.treatbashSpecial and opts.interpreter in ['bash','sh']: 130 self.cl.append(self.sfile)
135 a(self.sfile)
136 else: 131 else:
137 a('-') # stdin 132 self.cl.append('-') # stdin
138 for input in opts.input_tab: 133 for input in opts.input_file:
139 a(input) 134 self.cl.append(input)
140 if opts.output_tab == 'None': #If tool generates only HTML, set output name to toolname 135 if opts.output_file == 'None': # If tool generates only HTML, set output name to toolname
141 a(str(self.scriptname)+'.out') 136 self.cl.append(str(self.scriptname) + '.out')
142 a(opts.output_tab) 137 self.cl.append(opts.output_file)
143 for param in opts.additional_parameters: 138 for param in opts.additional_parameters:
144 param, value=param.split(',') 139 param, value = param.split(',')
145 a('--'+param) 140 self.cl.append('--' + param)
146 a(value) 141 self.cl.append(value)
147 self.outFormats = opts.output_format 142 self.outFormats = opts.output_format
148 self.inputFormats = [formats for formats in opts.input_formats] 143 self.inputFormats = [formats for formats in opts.input_formats]
149 self.test1Input = '%s_test1_input.xls' % self.scriptname 144 self.test1Input = '%s_test1_input.xls' % self.scriptname
150 self.test1Output = '%s_test1_output.xls' % self.scriptname 145 self.test1Output = '%s_test1_output.xls' % self.scriptname
151 self.test1HTML = '%s_test1_output.html' % self.scriptname 146 self.test1HTML = '%s_test1_output.html' % self.scriptname
152 147
153 148 def compressPDF(self, inpdf=None, thumbformat='png'):
154 def compressPDF(self,inpdf=None,thumbformat='png'): 149 """
155 """need absolute path to pdf 150 inpdf is absolute path to PDF
156 note that GS gets confoozled if no $TMP or $TEMP 151 """
157 so we set it 152 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf, self.myName)
158 """ 153 hlog = os.path.join(self.opts.output_dir, "compress_%s.txt" % os.path.basename(inpdf))
159 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName) 154 sto = open(hlog, 'a')
160 hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))
161 sto = open(hlog,'a')
162 our_env = os.environ.copy() 155 our_env = os.environ.copy()
163 our_tmp = our_env.get('TMP',None) 156 our_tmp = our_env.get('TMP', None)
164 if not our_tmp: 157 if not our_tmp:
165 our_tmp = our_env.get('TEMP',None) 158 our_env['TMP'] = tempfile.gettempdir()
166 if not (our_tmp and os.path.exists(our_tmp)):
167 newtmp = os.path.join(self.opts.output_dir,'tmp')
168 try:
169 os.mkdir(newtmp)
170 except:
171 sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp)
172 our_env['TEMP'] = newtmp
173 if not self.temp_warned:
174 sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp)
175 self.temp_warned = True
176 outpdf = '%s_compressed' % inpdf 159 outpdf = '%s_compressed' % inpdf
177 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf] 160 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH", "-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf, inpdf]
178 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env) 161 x = subprocess.Popen(cl, stdout=sto, stderr=sto, cwd=self.opts.output_dir, env=our_env)
179 retval1 = x.wait() 162 retval1 = x.wait()
180 sto.close() 163 sto.close()
181 if retval1 == 0: 164 if retval1 == 0:
182 os.unlink(inpdf) 165 os.unlink(inpdf)
183 shutil.move(outpdf,inpdf) 166 shutil.move(outpdf, inpdf)
184 os.unlink(hlog) 167 os.unlink(hlog)
185 hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf)) 168 hlog = os.path.join(self.opts.output_dir, "thumbnail_%s.txt" % os.path.basename(inpdf))
186 sto = open(hlog,'w') 169 sto = open(hlog, 'w')
187 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat) 170 outpng = '%s.%s' % (os.path.splitext(inpdf)[0], thumbformat)
188 cl2 = ['convert', inpdf, outpng] 171 cl2 = ['convert', inpdf, outpng]
189 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env) 172 x = subprocess.Popen(cl2, stdout=sto, stderr=sto, cwd=self.opts.output_dir, env=our_env)
190 retval2 = x.wait() 173 retval2 = x.wait()
191 sto.close() 174 sto.close()
192 if retval2 == 0: 175 if retval2 == 0:
193 os.unlink(hlog) 176 os.unlink(hlog)
194 retval = retval1 or retval2 177 retval = retval1 or retval2
195 return retval 178 return retval
196 179
197 180 def getfSize(self, fpath, outpath):
198 def getfSize(self,fpath,outpath):
199 """ 181 """
200 format a nice file size string 182 format a nice file size string
201 """ 183 """
202 size = '' 184 size = ''
203 fp = os.path.join(outpath,fpath) 185 fp = os.path.join(outpath, fpath)
204 if os.path.isfile(fp): 186 if os.path.isfile(fp):
205 size = '0 B' 187 size = '0 B'
206 n = float(os.path.getsize(fp)) 188 n = float(os.path.getsize(fp))
207 if n > 2**20: 189 if n > 2**20:
208 size = '%1.1f MB' % (n/2**20) 190 size = '%1.1f MB' % (n / 2**20)
209 elif n > 2**10: 191 elif n > 2**10:
210 size = '%1.1f KB' % (n/2**10) 192 size = '%1.1f KB' % (n / 2**10)
211 elif n > 0: 193 elif n > 0:
212 size = '%d B' % (int(n)) 194 size = '%d B' % (int(n))
213 return size 195 return size
214 196
215 def makeHtml(self): 197 def makeHtml(self):
216 """ Create an HTML file content to list all the artifacts found in the output_dir 198 """ Create an HTML file content to list all the artifacts found in the output_dir
217 """ 199 """
218 200
219 galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> 201 galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
220 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> 202 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
221 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> 203 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
222 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> 204 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
223 <title></title> 205 <title></title>
224 <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> 206 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
225 </head> 207 </head>
226 <body> 208 <body>
227 <div class="toolFormBody"> 209 <div class="toolFormBody">
228 """ 210 """
229 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/>"""
230 galhtmlpostfix = """</div></body></html>\n""" 211 galhtmlpostfix = """</div></body></html>\n"""
231 212
232 flist = os.listdir(self.opts.output_dir) 213 flist = os.listdir(self.opts.output_dir)
233 flist = [x for x in flist if x <> 'Rplots.pdf'] 214 flist = [x for x in flist if x != 'Rplots.pdf']
234 flist.sort() 215 flist.sort()
235 html = [] 216 html = []
236 html.append(galhtmlprefix % progname) 217 html.append(galhtmlprefix % progname)
237 html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.scriptname,timenow())) 218 html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.scriptname, timenow()))
238 fhtml = [] 219 fhtml = []
239 if len(flist) > 0: 220 if len(flist) > 0:
240 logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections 221 logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections
241 logfiles.sort() 222 logfiles.sort()
242 logfiles = [x for x in logfiles if abspath(x) <> abspath(self.tlog)] 223 logfiles = [x for x in logfiles if abspath(x) != abspath(self.tlog)]
243 logfiles.append(abspath(self.tlog)) # make it the last one 224 logfiles.append(abspath(self.tlog)) # make it the last one
244 pdflist = [] 225 pdflist = []
245 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf']) 226 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
246 for rownum,fname in enumerate(flist): 227 for rownum, fname in enumerate(flist):
247 dname,e = os.path.splitext(fname) 228 dname, e = os.path.splitext(fname)
248 sfsize = self.getfSize(fname,self.opts.output_dir) 229 sfsize = self.getfSize(fname, self.opts.output_dir)
249 if e.lower() == '.pdf' : # compress and make a thumbnail 230 if e.lower() == '.pdf': # compress and make a thumbnail
250 thumb = '%s.%s' % (dname,self.thumbformat) 231 thumb = '%s.%s' % (dname, self.thumbformat)
251 pdff = os.path.join(self.opts.output_dir,fname) 232 pdff = os.path.join(self.opts.output_dir, fname)
252 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat) 233 retval = self.compressPDF(inpdf=pdff, thumbformat=self.thumbformat)
253 if retval == 0: 234 if retval == 0:
254 pdflist.append((fname,thumb)) 235 pdflist.append((fname, thumb))
255 else: 236 else:
256 pdflist.append((fname,fname)) 237 pdflist.append((fname, fname))
257 if (rownum+1) % 2 == 0: 238 if (rownum + 1) % 2 == 0:
258 fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize)) 239 fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname, fname, sfsize))
259 else: 240 else:
260 fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize)) 241 fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname, fname, sfsize))
261 for logfname in logfiles: # expect at least tlog - if more 242 for logfname in logfiles: # expect at least tlog - if more
262 if abspath(logfname) == abspath(self.tlog): # handled later 243 if abspath(logfname) == abspath(self.tlog): # handled later
263 sectionname = 'All tool run' 244 sectionname = 'All tool run'
264 if (len(logfiles) > 1): 245 if (len(logfiles) > 1):
265 sectionname = 'Other' 246 sectionname = 'Other'
266 ourpdfs = pdflist 247 ourpdfs = pdflist
267 else: 248 else:
268 realname = os.path.basename(logfname) 249 realname = os.path.basename(logfname)
269 sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log 250 sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log
270 ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname] 251 ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
271 pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove 252 pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] != sectionname] # remove
272 nacross = 1 253 nacross = 1
273 npdf = len(ourpdfs) 254 npdf = len(ourpdfs)
274 255
275 if npdf > 0: 256 if npdf > 0:
276 nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2))) 257 nacross = math.sqrt(npdf)
277 if int(nacross)**2 != npdf: 258 if int(nacross)**2 != npdf:
278 nacross += 1 259 nacross += 1
279 nacross = int(nacross) 260 nacross = int(nacross)
280 width = min(400,int(1200/nacross)) 261 width = min(400, int(1200 / nacross))
281 html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname) 262 html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)
282 html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>') 263 html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>')
283 ntogo = nacross # counter for table row padding with empty cells 264 ntogo = nacross # counter for table row padding with empty cells
284 html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>') 265 html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
285 for i,paths in enumerate(ourpdfs): 266 for i, paths in enumerate(ourpdfs):
286 fname,thumb = paths 267 fname, thumb = paths
287 s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d" 268 s = """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d"
288 alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname) 269 alt="Image called %s"/></a></td>\n""" % (fname, thumb, fname, width, fname)
289 if ((i+1) % nacross == 0): 270 if ((i + 1) % nacross == 0):
290 s += '</tr>\n' 271 s += '</tr>\n'
291 ntogo = 0 272 ntogo = 0
292 if i < (npdf - 1): # more to come 273 if i < (npdf - 1): # more to come
293 s += '<tr>' 274 s += '<tr>'
294 ntogo = nacross 275 ntogo = nacross
295 else: 276 else:
296 ntogo -= 1 277 ntogo -= 1
297 html.append(s) 278 html.append(s)
298 if html[-1].strip().endswith('</tr>'): 279 if html[-1].strip().endswith('</tr>'):
299 html.append('</table></div>\n') 280 html.append('</table></div>\n')
300 else: 281 else:
301 if ntogo > 0: # pad 282 if ntogo > 0: # pad
302 html.append('<td>&nbsp;</td>'*ntogo) 283 html.append('<td>&nbsp;</td>' * ntogo)
303 html.append('</tr></table></div>\n') 284 html.append('</tr></table></div>\n')
304 logt = open(logfname,'r').readlines() 285 logt = open(logfname, 'r').readlines()
305 logtext = [x for x in logt if x.strip() > ''] 286 logtext = [x for x in logt if x.strip() > '']
306 html.append('<div class="toolFormTitle">%s log output</div>' % sectionname) 287 html.append('<div class="toolFormTitle">%s log output</div>' % sectionname)
307 if len(logtext) > 1: 288 if len(logtext) > 1:
308 html.append('\n<pre>\n') 289 html.append('\n<pre>\n')
309 html += logtext 290 html += logtext
310 html.append('\n</pre>\n') 291 html.append('\n</pre>\n')
311 else: 292 else:
312 html.append('%s is empty<br/>' % logfname) 293 html.append('%s is empty<br/>' % logfname)
313 if len(fhtml) > 0: 294 if len(fhtml) > 0:
314 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') 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')
315 fhtml.append('</table></div><br/>') 296 fhtml.append('</table></div><br/>')
316 html.append('<div class="toolFormTitle">All output files available for downloading</div>\n') 297 html.append('<div class="toolFormTitle">All output files available for downloading</div>\n')
317 html += fhtml # add all non-pdf files to the end of the display 298 html += fhtml # add all non-pdf files to the end of the display
318 else: 299 else:
319 html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter) 300 html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
320 html.append(galhtmlpostfix) 301 html.append(galhtmlpostfix)
321 htmlf = file(self.opts.output_html,'w') 302 with open(self.opts.output_html, 'w') as htmlf:
322 htmlf.write('\n'.join(html)) 303 htmlf.write('\n'.join(html))
323 htmlf.write('\n') 304 htmlf.write('\n')
324 htmlf.close()
325 self.html = html 305 self.html = html
326 306
327
328 def run(self): 307 def run(self):
329 """ 308 """
330 scripts must be small enough not to fill the pipe! 309 scripts must be small enough not to fill the pipe!
331 """ 310 """
332 if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']: 311 if self.treatbashSpecial and self.opts.interpreter in ['bash', 'sh']:
333 retval = self.runBash() 312 retval = self.runBash()
334 else: 313 else:
335 if self.opts.output_dir: 314 if self.opts.output_dir:
336 ste = open(self.elog,'w') 315 ste = open(self.elog, 'w')
337 sto = open(self.tlog,'w') 316 sto = open(self.tlog, 'w')
338 sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl)) 317 sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl))
339 sto.flush() 318 sto.flush()
340 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir) 319 p = subprocess.Popen(self.cl, shell=False, stdout=sto, stderr=ste, stdin=subprocess.PIPE, cwd=self.opts.output_dir)
341 else: 320 else:
342 p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE) 321 p = subprocess.Popen(self.cl, shell=False, stdin=subprocess.PIPE)
343 p.stdin.write(self.script) 322 p.stdin.write(self.script)
344 p.stdin.close() 323 p.stdin.close()
345 retval = p.wait() 324 retval = p.wait()
346 if self.opts.output_dir: 325 if self.opts.output_dir:
347 sto.close() 326 sto.close()
348 ste.close() 327 ste.close()
349 err = open(self.elog,'r').readlines() 328 err = open(self.elog, 'r').readlines()
350 if retval <> 0 and err: # problem 329 if retval != 0 and err: # problem
351 print >> sys.stderr,err #same problem, need to capture docker stdin/stdout 330 print(err, end="", file=sys.stderr) # same problem, need to capture docker stdin/stdout
352 if self.opts.make_HTML: 331 if self.opts.make_HTML:
353 self.makeHtml() 332 self.makeHtml()
354 return retval 333 return retval
355 334
356 def runBash(self): 335 def runBash(self):
357 """ 336 """
358 cannot use - for bash so use self.sfile 337 cannot use - for bash so use self.sfile
359 """ 338 """
360 if self.opts.output_dir: 339 if self.opts.output_dir:
361 s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl) 340 s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl)
362 sto = open(self.tlog,'w') 341 sto = open(self.tlog, 'w')
363 sto.write(s) 342 sto.write(s)
364 sto.flush() 343 sto.flush()
365 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir) 344 p = subprocess.Popen(self.cl, shell=False, stdout=sto, stderr=sto, cwd=self.opts.output_dir)
366 else: 345 else:
367 p = subprocess.Popen(self.cl,shell=False) 346 p = subprocess.Popen(self.cl, shell=False)
368 retval = p.wait() 347 retval = p.wait()
369 if self.opts.output_dir: 348 if self.opts.output_dir:
370 sto.close() 349 sto.close()
371 if self.opts.make_HTML: 350 if self.opts.make_HTML:
372 self.makeHtml() 351 self.makeHtml()
373 return retval 352 return retval
374 353
375 354
376 def change_user_id(new_uid, new_gid): 355 def change_user_id(new_uid, new_gid):
377 """ 356 """
378 To avoid issues with wrong user ids, we change the user id of the 'galaxy' user in the container 357 To avoid issues with wrong user ids, we change the user id of the 'galaxy' user in the container
379 to the user id with which the script has been called initially. 358 to the user id with which the script has been called initially.
384 cmd4 = ["/usr/sbin/usermod", "-d", "/home/galaxy", "galaxy"] 363 cmd4 = ["/usr/sbin/usermod", "-d", "/home/galaxy", "galaxy"]
385 [subprocess.call(cmd) for cmd in [cmd1, cmd2, cmd3, cmd4]] 364 [subprocess.call(cmd) for cmd in [cmd1, cmd2, cmd3, cmd4]]
386 365
387 366
388 def main(): 367 def main():
389 u = """
390 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
391 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
392 </command>
393 """
394 op = argparse.ArgumentParser() 368 op = argparse.ArgumentParser()
395 a = op.add_argument 369 a = op.add_argument
396 a('--docker_image',default=None) 370 a('--docker_image', default=None)
397 a('--script_path',default=None) 371 a('--script_path', default=None)
398 a('--tool_name',default=None) 372 a('--tool_name', default=None)
399 a('--interpreter',default=None) 373 a('--interpreter', default=None)
400 a('--output_dir',default='./') 374 a('--output_dir', default='./')
401 a('--output_html',default=None) 375 a('--output_html', default=None)
402 a('--input_tab',default='None', nargs='*') 376 a('--input_file', default='None', nargs='*')
403 a('--output_tab',default='None') 377 a('--output_file', default='None')
404 a('--user_email',default='Unknown') 378 a('--user_email', default='Unknown')
405 a('--bad_user',default=None) 379 a('--bad_user', default=None)
406 a('--make_HTML',default=None) 380 a('--make_HTML', default=None)
407 a('--new_tool',default=None) 381 a('--new_tool', default=None)
408 a('--dockerized',default=0) 382 a('--dockerized', default=0)
409 a('--group_id',default=None) 383 a('--group_id', default=None)
410 a('--user_id',default=None) 384 a('--user_id', default=None)
411 a('--output_format', default='tabular') 385 a('--output_format', default='tabular')
412 a('--input_format', dest='input_formats', action='append', default=[]) 386 a('--input_format', dest='input_formats', action='append', default=[])
413 a('--additional_parameters', dest='additional_parameters', action='append', default=[]) 387 a('--additional_parameters', dest='additional_parameters', action='append', default=[])
414 opts = op.parse_args() 388 opts = op.parse_args()
415 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) 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)
416 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R' 390 assert os.path.isfile(opts.script_path), '## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
417 if opts.output_dir: 391 if opts.output_dir:
418 try: 392 try:
419 os.makedirs(opts.output_dir) 393 os.makedirs(opts.output_dir)
420 except: 394 except Exception:
421 pass 395 pass
422 if opts.dockerized==0: 396 if opts.dockerized == 0:
423 switch_to_docker(opts) 397 retcode = switch_to_docker(opts)
424 return 398 sys.exit(retcode)
425 change_user_id(opts.user_id, opts.group_id) 399 change_user_id(opts.user_id, opts.group_id)
426 os.setgid(int(opts.group_id)) 400 os.setgid(int(opts.group_id))
427 os.setuid(int(opts.user_id)) 401 os.setuid(int(opts.user_id))
428 r = ScriptRunner(opts) 402 r = ScriptRunner(opts)
429 retcode = r.run() 403 retcode = r.run()
430 os.unlink(r.sfile) 404 os.unlink(r.sfile)
431 if retcode: 405 if retcode:
432 sys.exit(retcode) # indicate failure to job runner 406 sys.exit(retcode) # indicate failure to job runner
433 407
434 408
435 if __name__ == "__main__": 409 if __name__ == "__main__":
436 main() 410 main()