Mercurial > repos > mvdbeek > docker_toolfactory_alpha

comparison DockerToolFactory.py @ 0:7e0392d4531c

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Initial Commit.
author m.vandenbeek@gmail.com
date Tue, 02 Dec 2014 15:14:12 +0100
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children 5d70248d1e01
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-1:000000000000 0:7e0392d4531c
1 # DockerToolFactory.py
2 # see https://bitbucket.org/mvdbeek/DockerToolFactory
3
4 import sys
5 import shutil
6 import subprocess
7 import os
8 import time
9 import tempfile
10 import argparse
11 import tarfile
12 import re
13 import shutil
14 import math
15 import fileinput
16 from os.path import abspath
17
18 progname = os.path.split(sys.argv[0])[1]
19 myversion = 'V001.1 March 2014'
20 verbose = False
21 debug = False
22 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
23
24 # if we do html we need these dependencies specified in a tool_dependencies.xml file and referred to in the generated
25 # tool xml
26 toolhtmldepskel = """<?xml version="1.0"?>
27 <tool_dependency>
28 <package name="ghostscript" version="9.10">
29 <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" />
30 </package>
31 <package name="graphicsmagick" version="1.3.18">
32 <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" />
33 </package>
34 <readme>
35 %s
36 </readme>
37 </tool_dependency>
38 """
39
40 protorequirements = """<requirements>
41 <requirement type="package" version="9.10">ghostscript</requirement>
42 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
43 <container type="docker">toolfactory/custombuild:%s</container>
44 </requirements>"""
45
46 def timenow():
47 """return current time as a string
48 """
49 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
50
51 html_escape_table = {
52 "&": "&amp;",
53 ">": "&gt;",
54 "<": "&lt;",
55 "$": "\$"
56 }
57
58 def html_escape(text):
59 """Produce entities within text."""
60 return "".join(html_escape_table.get(c,c) for c in text)
61
62 def cmd_exists(cmd):
63 return subprocess.call("type " + cmd, shell=True,
64 stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
65
66 def edit_dockerfile(dockerfile):
67 '''we have to change the userid of galaxy inside the container to the id with which the tool is run,
68 otherwise we have a mismatch in the file permissions inside the container'''
69 uid=os.getuid()
70 for line in fileinput.FileInput(dockerfile, inplace=1):
71 sys.stdout.write(line.replace("RUN adduser galaxy\n", "RUN adduser galaxy -u {0}\n".format(uid)))
72
73 def build_docker(dockerfile, docker_client, image_tag='base'):
74 '''Given the path to a dockerfile, and a docker_client, build the image, if it does not
75 exist yet.'''
76 image_id='toolfactory/custombuild:'+image_tag
77 existing_images=", ".join(["".join(d['RepoTags']) for d in docker_client.images()])
78 if image_id in existing_images:
79 print 'docker container exists, skipping build'
80 return image_id
81 print "Building Docker image, using Dockerfile:{0}".format(dockerfile)
82 build_process=docker_client.build(fileobj=open(dockerfile, 'r'), image_tag=image_id)
83 print "succesfully dispatched docker build process, building now"
84 build_log=[line for line in build_process] #will block until image is built.
85 return image_id
86
87 def construct_bind(host_path, container_path=False, binds=None, ro=True):
88 #TODO remove container_path if it's alwyas going to be the same as host_path
89 '''build or extend binds dictionary with container path. binds is used
90 to mount all files using the docker-py client.'''
91 if not binds:
92 binds={}
93 if isinstance(host_path, list):
94 for k,v in enumerate(host_path):
95 if not container_path:
96 container_path=host_path[k]
97 binds[host_path[k]]={'bind':container_path, 'ro':ro}
98 container_path=False #could be more elegant
99 return binds
100 else:
101 if not container_path:
102 container_path=host_path
103 binds[host_path]={'bind':container_path, 'ro':ro}
104 return binds
105
106 def switch_to_docker(opts):
107 import docker #need local import, as container does not have docker-py
108 docker_client=docker.Client()
109 toolfactory_path=abspath(sys.argv[0])
110 dockerfile=os.path.dirname(toolfactory_path)+'/Dockerfile'
111 edit_dockerfile(dockerfile)
112 image_id=build_docker(dockerfile, docker_client)
113 binds=construct_bind(host_path=opts.script_path, ro=False)
114 binds=construct_bind(binds=binds, host_path=abspath(opts.output_dir), ro=False)
115 if len(opts.input_tab)>0:
116 binds=construct_bind(binds=binds, host_path=opts.input_tab, ro=True)
117 if not opts.output_tab == 'None':
118 binds=construct_bind(binds=binds, host_path=opts.output_tab, ro=False)
119 if opts.make_HTML:
120 binds=construct_bind(binds=binds, host_path=opts.output_html, ro=False)
121 if opts.make_Tool:
122 binds=construct_bind(binds=binds, host_path=opts.new_tool, ro=False)
123 binds=construct_bind(binds=binds, host_path=opts.help_text, ro=True)
124 binds=construct_bind(binds=binds, host_path=toolfactory_path)
125 volumes=binds.keys()
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
127 cmd=['python', '-u']+sys.argv+['--dockerized', '1']
128 container=docker_client.create_container(
129 image=image_id,
130 user='galaxy',
131 volumes=volumes,
132 command=cmd
133 )
134 docker_client.start(container=container[u'Id'], binds=binds)
135 docker_client.wait(container=container[u'Id'])
136 logs=docker_client.logs(container=container[u'Id'])
137 print "".join([log for log in logs])
138
139 class ScriptRunner:
140 """class is a wrapper for an arbitrary script
141 """
142
143 def __init__(self,opts=None,treatbashSpecial=True, image_tag='base'):
144 """
145 cleanup inputs, setup some outputs
146
147 """
148 self.opts = opts
149 self.useGM = cmd_exists('gm')
150 self.useIM = cmd_exists('convert')
151 self.useGS = cmd_exists('gs')
152 self.temp_warned = False # we want only one warning if $TMP not set
153 self.treatbashSpecial = treatbashSpecial
154 self.image_tag = image_tag
155 os.chdir(abspath(opts.output_dir))
156 self.thumbformat = 'png'
157 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
158 self.toolid = self.toolname
159 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
160 self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
161 self.xmlfile = '%s.xml' % self.toolname
162 s = open(self.opts.script_path,'r').readlines()
163 s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
164 self.script = '\n'.join(s)
165 fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))
166 tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
167 tscript.write(self.script)
168 tscript.close()
169 self.indentedScript = '\n'.join([' %s' % html_escape(x) for x in s]) # for restructured text in help
170 self.escapedScript = '\n'.join([html_escape(x) for x in s])
171 self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname)
172 if opts.output_dir: # may not want these complexities
173 self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname)
174 art = '%s.%s' % (self.toolname,opts.interpreter)
175 artpath = os.path.join(self.opts.output_dir,art) # need full path
176 artifact = open(artpath,'w') # use self.sfile as script source for Popen
177 artifact.write(self.script)
178 artifact.close()
179 self.cl = []
180 self.html = []
181 a = self.cl.append
182 a(opts.interpreter)
183 if self.treatbashSpecial and opts.interpreter in ['bash','sh']:
184 a(self.sfile)
185 else:
186 a('-') # stdin
187 for input in opts.input_tab:
188 a(input)
189 if opts.output_tab == 'None': #If tool generates only HTML, set output name to toolname
190 a(str(self.toolname)+'.out')
191 a(opts.output_tab)
192 for param in opts.additional_parameters:
193 param, value=param.split(',')
194 a('--'+param)
195 a(value)
196 #print self.cl
197 self.outFormats = opts.output_format
198 self.inputFormats = [formats for formats in opts.input_formats]
199 self.test1Input = '%s_test1_input.xls' % self.toolname
200 self.test1Output = '%s_test1_output.xls' % self.toolname
201 self.test1HTML = '%s_test1_output.html' % self.toolname
202
203 def makeXML(self):
204 """
205 Create a Galaxy xml tool wrapper for the new script as a string to write out
206 fixme - use templating or something less fugly than this example of what we produce
207
208 <tool id="reverse" name="reverse" version="0.01">
209 <description>a tabular file</description>
210 <command interpreter="python">
211 reverse.py --script_path "$runMe" --interpreter "python"
212 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
213 </command>
214 <inputs>
215 <param name="input1" type="data" format="tabular" label="Select a suitable input file from your history"/>
216
217 </inputs>
218 <outputs>
219 <data format=opts.output_format name="tab_file"/>
220
221 </outputs>
222 <help>
223
224 **What it Does**
225
226 Reverse the columns in a tabular file
227
228 </help>
229 <configfiles>
230 <configfile name="runMe">
231
232 # reverse order of columns in a tabular file
233 import sys
234 inp = sys.argv[1]
235 outp = sys.argv[2]
236 i = open(inp,'r')
237 o = open(outp,'w')
238 for row in i:
239 rs = row.rstrip().split('\t')
240 rs.reverse()
241 o.write('\t'.join(rs))
242 o.write('\n')
243 i.close()
244 o.close()
245
246
247 </configfile>
248 </configfiles>
249 </tool>
250
251 """
252 newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
253 %(tooldesc)s
254 %(requirements)s
255 <command interpreter="python">
256 %(command)s
257 </command>
258 <inputs>
259 %(inputs)s
260 </inputs>
261 <outputs>
262 %(outputs)s
263 </outputs>
264 <configfiles>
265 <configfile name="runMe">
266 %(script)s
267 </configfile>
268 </configfiles>
269
270 %(tooltests)s
271
272 <help>
273
274 %(help)s
275
276 </help>
277 </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
278
279 newCommand="""
280 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
281 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s """
282 # may NOT be an input or htmlout - appended later
283 tooltestsTabOnly = """
284 <tests>
285 <test>
286 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
287 <param name="runMe" value="$runMe"/>
288 <output name="tab_file" file="%(test1Output)s" ftype="tabular"/>
289 </test>
290 </tests>
291 """
292 tooltestsHTMLOnly = """
293 <tests>
294 <test>
295 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
296 <param name="runMe" value="$runMe"/>
297 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
298 </test>
299 </tests>
300 """
301 tooltestsBoth = """<tests>
302 <test>
303 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
304 <param name="runMe" value="$runMe"/>
305 <output name="tab_file" file="%(test1Output)s" ftype="tabular" />
306 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
307 </test>
308 </tests>
309 """
310 xdict = {}
311 #xdict['requirements'] = ''
312 #if self.opts.make_HTML:
313 xdict['requirements'] = protorequirements % self.image_tag
314 xdict['tool_version'] = self.opts.tool_version
315 xdict['test1Input'] = self.test1Input
316 xdict['test1HTML'] = self.test1HTML
317 xdict['test1Output'] = self.test1Output
318 if self.opts.make_HTML and self.opts.output_tab <> 'None':
319 xdict['tooltests'] = tooltestsBoth % xdict
320 elif self.opts.make_HTML:
321 xdict['tooltests'] = tooltestsHTMLOnly % xdict
322 else:
323 xdict['tooltests'] = tooltestsTabOnly % xdict
324 xdict['script'] = self.escapedScript
325 # configfile is least painful way to embed script to avoid external dependencies
326 # but requires escaping of <, > and $ to avoid Mako parsing
327 if self.opts.help_text:
328 helptext = open(self.opts.help_text,'r').readlines()
329 helptext = [html_escape(x) for x in helptext] # must html escape here too - thanks to Marius van den Beek
330 xdict['help'] = ''.join([x for x in helptext])
331 else:
332 xdict['help'] = 'Please ask the tool author (%s) for help as none was supplied at tool generation\n' % (self.opts.user_email)
333 coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::']
334 coda.append('\n')
335 coda.append(self.indentedScript)
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()))
337 coda.append('See %s for details of that project' % (toolFactoryURL))
338 coda.append('Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. ')
339 coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573\n')
340 xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
341 if self.opts.tool_desc:
342 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
343 else:
344 xdict['tooldesc'] = ''
345 xdict['command_outputs'] = ''
346 xdict['outputs'] = ''
347 if self.opts.input_tab <> 'None':
348 xdict['command_inputs'] = '--input_tab'
349 xdict['inputs']=''
350 for i,input in enumerate(self.inputFormats):
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)
352 xdict['command_inputs'] += ' $input{0}'.format(i+1)
353 else:
354 xdict['command_inputs'] = '' # assume no input - eg a random data generator
355 xdict['inputs'] = ''
356 # I find setting the job name not very logical. can be changed in workflows anyway. xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname
357 xdict['toolname'] = self.toolname
358 xdict['toolid'] = self.toolid
359 xdict['interpreter'] = self.opts.interpreter
360 xdict['scriptname'] = self.sfile
361 if self.opts.make_HTML:
362 xdict['command_outputs'] += ' --output_dir "$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>&nbsp;</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)
690 a('--tool_version',default=None)
691 a('--include_dependencies',default=None)
692 a('--dockerized',default=0)
693 a('--output_format', default='tabular')
694 a('--input_format', dest='input_formats', action='append', default=[])
695 a('--additional_parameters', dest='additional_parameters', action='append', default=[])
696 opts = op.parse_args()
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)
698 assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
699 assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
700 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
701 if opts.output_dir:
702 try:
703 os.makedirs(opts.output_dir)
704 except:
705 pass
706 if opts.dockerized==0:
707 switch_to_docker(opts)
708 return
709 r = ScriptRunner(opts)
710 if opts.make_Tool:
711 retcode = r.makeTooltar()
712 else:
713 retcode = r.run()
714 os.unlink(r.sfile)
715 if retcode:
716 sys.exit(retcode) # indicate failure to job runner
717
718
719 if __name__ == "__main__":
720 main()
721
722