Mercurial > repos > fubar > toolfactory
comparison fubar-galaxytoolfactory-ca7db160878a/rgToolFactory.py @ 3:8c578211a681 draft
Fixed nasty silly bug - fixed locally but not previously propogated
author | fubar |
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date | Fri, 31 Aug 2012 23:04:13 -0400 |
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2:b55b59435fb1 | 3:8c578211a681 |
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1 # rgToolFactory.py | |
2 # see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home | |
3 # | |
4 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012 | |
5 # | |
6 # all rights reserved | |
7 # Licensed under the LGPL | |
8 # suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home | |
9 | |
10 # August 11 2012 | |
11 # changed to use shell=False and cl as a sequence | |
12 | |
13 # This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye. | |
14 # It also serves as the wrapper for the new tool. | |
15 # | |
16 # you paste and run your script | |
17 # Only works for simple scripts that read one input from the history. | |
18 # Optionally can write one new history dataset, | |
19 # and optionally collect any number of outputs into links on an autogenerated HTML page. | |
20 | |
21 # DO NOT install on a public or important site - please. | |
22 | |
23 # installed generated tools are fine if the script is safe. | |
24 # They just run normally and their user cannot do anything unusually insecure | |
25 # but please, practice safe toolshed. | |
26 # Read the fucking code before you install any tool | |
27 # especially this one | |
28 | |
29 # After you get the script working on some test data, you can | |
30 # optionally generate a toolshed compatible gzip file | |
31 # containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for | |
32 # safe and largely automated installation in a production Galaxy. | |
33 | |
34 # If you opt for an HTML output, you get all the script outputs arranged | |
35 # as a single Html history item - all output files are linked, thumbnails for all the pdfs. | |
36 # Ugly but really inexpensive. | |
37 # | |
38 # Patches appreciated please. | |
39 # | |
40 # | |
41 # long route to June 2012 product | |
42 # Behold the awesome power of Galaxy and the toolshed with the tool factory binds to bind them | |
43 # derived from an integrated script model | |
44 # called rgBaseScriptWrapper.py | |
45 # Note to the unwary: | |
46 # This tool allows arbitrary scripting on your Galaxy as the Galaxy user | |
47 # There is nothing stopping a malicious user doing whatever they choose | |
48 # Extremely dangerous!! | |
49 # Totally insecure. So, trusted users only | |
50 # | |
51 # preferred model is a developer using their throw away workstation instance - ie a private site. | |
52 # no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool. | |
53 # | |
54 | |
55 import sys | |
56 import shutil | |
57 import subprocess | |
58 import os | |
59 import time | |
60 import tempfile | |
61 import optparse | |
62 import tarfile | |
63 import re | |
64 import shutil | |
65 import math | |
66 | |
67 progname = os.path.split(sys.argv[0])[1] | |
68 myversion = 'V000.2 June 2012' | |
69 verbose = False | |
70 debug = False | |
71 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory' | |
72 | |
73 def timenow(): | |
74 """return current time as a string | |
75 """ | |
76 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) | |
77 | |
78 | |
79 class ScriptRunner: | |
80 """class is a wrapper for an arbitrary script | |
81 """ | |
82 | |
83 def __init__(self,opts=None,treatbashSpecial=True): | |
84 """ | |
85 cleanup inputs, setup some outputs | |
86 | |
87 """ | |
88 self.treatbashSpecial = treatbashSpecial | |
89 if opts.output_dir: # simplify for the tool tarball | |
90 os.chdir(opts.output_dir) | |
91 self.thumbformat = 'jpg' | |
92 self.opts = opts | |
93 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but.. | |
94 self.toolid = self.toolname | |
95 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later | |
96 self.pyfile = self.myname # crude but efficient - the cruft won't hurt much | |
97 self.xmlfile = '%s.xml' % self.toolname | |
98 s = open(self.opts.script_path,'r').readlines() | |
99 s = [x.rstrip() for x in s] # remove pesky dos line endings if needed | |
100 self.script = '\n'.join(s) | |
101 fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter)) | |
102 tscript = open(self.sfile,'w') # use self.sfile as script source for Popen | |
103 tscript.write(self.script) | |
104 tscript.close() | |
105 self.indentedScript = ''.join([' %s' % x for x in s]) # for restructured text in help | |
106 if opts.output_dir: # may not want these complexities | |
107 self.tlog = os.path.join(opts.output_dir,"%s_runner.log" % self.toolname) | |
108 art = '%s.%s' % (self.toolname,opts.interpreter) | |
109 artpath = os.path.join(self.opts.output_dir,art) # need full path | |
110 artifact = open(artpath,'w') # use self.sfile as script source for Popen | |
111 artifact.write(self.script) | |
112 artifact.close() | |
113 self.cl = [] | |
114 self.html = [] | |
115 a = self.cl.append | |
116 a(opts.interpreter) | |
117 if self.treatbashSpecial and opts.interpreter in ['bash','sh']: | |
118 a(self.sfile) | |
119 else: | |
120 a('-') # stdin | |
121 a(opts.input_tab) | |
122 a(opts.output_tab) | |
123 self.outFormats = 'tabular' # TODO make this an option at tool generation time | |
124 self.inputFormats = 'tabular' # TODO make this an option at tool generation time | |
125 self.test1Input = '%s_test1_input.xls' % self.toolname | |
126 self.test1Output = '%s_test1_output.xls' % self.toolname | |
127 self.test1HTML = '%s_test1_output.html' % self.toolname | |
128 | |
129 def makeXML(self): | |
130 """ | |
131 Create a Galaxy xml tool wrapper for the new script as a string to write out | |
132 fixme - use templating or something less fugly than this example of what we produce | |
133 | |
134 <tool id="reverse" name="reverse" version="0.01"> | |
135 <description>a tabular file</description> | |
136 <command interpreter="python"> | |
137 reverse.py --script_path "$runMe" --interpreter "python" | |
138 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file" | |
139 </command> | |
140 <inputs> | |
141 <param name="input1" type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/> | |
142 | |
143 </inputs> | |
144 <outputs> | |
145 <data format="tabular" name="tab_file" label="${job_name}"/> | |
146 | |
147 </outputs> | |
148 <help> | |
149 | |
150 **What it Does** | |
151 | |
152 Reverse the columns in a tabular file | |
153 | |
154 </help> | |
155 <configfiles> | |
156 <configfile name="runMe"> | |
157 | |
158 # reverse order of columns in a tabular file | |
159 import sys | |
160 inp = sys.argv[1] | |
161 outp = sys.argv[2] | |
162 i = open(inp,'r') | |
163 o = open(outp,'w') | |
164 for row in i: | |
165 rs = row.rstrip().split('\t') | |
166 rs.reverse() | |
167 o.write('\t'.join(rs)) | |
168 o.write('\n') | |
169 i.close() | |
170 o.close() | |
171 | |
172 | |
173 </configfile> | |
174 </configfiles> | |
175 </tool> | |
176 | |
177 """ | |
178 newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s"> | |
179 %(tooldesc)s | |
180 %(command)s | |
181 <inputs> | |
182 %(inputs)s | |
183 </inputs> | |
184 <outputs> | |
185 %(outputs)s | |
186 </outputs> | |
187 <configfiles> | |
188 <configfile name="runMe"> | |
189 %(script)s | |
190 </configfile> | |
191 </configfiles> | |
192 %(tooltests)s | |
193 <help> | |
194 %(help)s | |
195 </help> | |
196 </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto | |
197 | |
198 newCommand="""<command interpreter="python"> | |
199 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s" | |
200 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s | |
201 </command>""" # may NOT be an input or htmlout | |
202 tooltestsTabOnly = """<tests><test> | |
203 <param name="input1" value="%(test1Input)s" ftype="tabular"/> | |
204 <param name="job_name" value="test1"/> | |
205 <param name="runMe" value="$runMe"/> | |
206 <output name="tab_file" file="%(test1Output)s" ftype="tabular"/> | |
207 </test></tests>""" | |
208 tooltestsHTMLOnly = """<tests><test> | |
209 <param name="input1" value="%(test1Input)s" ftype="tabular"/> | |
210 <param name="job_name" value="test1"/> | |
211 <param name="runMe" value="$runMe"/> | |
212 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/> | |
213 </test></tests>""" | |
214 tooltestsBoth = """<tests><test> | |
215 <param name="input1" value="%(test1Input)s" ftype="tabular"/> | |
216 <param name="job_name" value="test1"/> | |
217 <param name="runMe" value="$runMe"/> | |
218 <output name="tab_file" file="%(test1Output)s" ftype="tabular" /> | |
219 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/> | |
220 </test></tests>""" | |
221 xdict = {} | |
222 xdict['tool_version'] = self.opts.tool_version | |
223 xdict['test1Input'] = self.test1Input | |
224 xdict['test1HTML'] = self.test1HTML | |
225 xdict['test1Output'] = self.test1Output | |
226 if self.opts.make_HTML and self.opts.output_tab <> 'None': | |
227 xdict['tooltests'] = tooltestsBoth % xdict | |
228 elif self.opts.make_HTML: | |
229 xdict['tooltests'] = tooltestsHTMLOnly % xdict | |
230 else: | |
231 xdict['tooltests'] = tooltestsTabOnly % xdict | |
232 xdict['script'] = self.script # configfile is least painful way to embed script to avoid external dependencies | |
233 if self.opts.help_text: | |
234 xdict['help'] = open(self.opts.help_text,'r').read() | |
235 else: | |
236 xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation' | |
237 coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::'] | |
238 coda.append(self.indentedScript) | |
239 coda.append('**Attribution** This Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.' % (self.opts.user_email,timenow())) | |
240 coda.append('See %s for details of that project' % (toolFactoryURL)) | |
241 xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda)) | |
242 if self.opts.tool_desc: | |
243 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc | |
244 else: | |
245 xdict['tooldesc'] = '' | |
246 xdict['command_outputs'] = '' | |
247 xdict['outputs'] = '' | |
248 if self.opts.input_tab <> 'None': | |
249 xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something | |
250 xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats | |
251 else: | |
252 xdict['command_inputs'] = '' # assume no input - eg a random data generator | |
253 xdict['inputs'] = '' | |
254 xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname | |
255 xdict['toolname'] = self.toolname | |
256 xdict['toolid'] = self.toolid | |
257 xdict['interpreter'] = self.opts.interpreter | |
258 xdict['scriptname'] = self.sfile | |
259 if self.opts.make_HTML: | |
260 xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" ' | |
261 xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n' | |
262 if self.opts.output_tab <> 'None': | |
263 xdict['command_outputs'] += ' --output_tab "$tab_file"' | |
264 xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats | |
265 xdict['command'] = newCommand % xdict | |
266 xmls = newXML % xdict | |
267 xf = open(self.xmlfile,'w') | |
268 xf.write(xmls) | |
269 xf.write('\n') | |
270 xf.close() | |
271 # ready for the tarball | |
272 | |
273 | |
274 def makeTooltar(self): | |
275 """ | |
276 a tool is a gz tarball with eg | |
277 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ... | |
278 """ | |
279 retval = self.run() | |
280 if retval: | |
281 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry' | |
282 sys.exit(1) | |
283 self.makeXML() | |
284 tdir = self.toolname | |
285 os.mkdir(tdir) | |
286 if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe.. | |
287 testdir = os.path.join(tdir,'test-data') | |
288 os.mkdir(testdir) # make tests directory | |
289 shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input)) | |
290 if self.opts.output_tab <> 'None': | |
291 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output)) | |
292 if self.opts.make_HTML: | |
293 shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML)) | |
294 if self.opts.output_dir: | |
295 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log')) | |
296 op = '%s.py' % self.toolname # new name | |
297 outpiname = os.path.join(tdir,op) # path for the tool tarball | |
298 pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM) | |
299 notes = ['# %s - a self annotated version of %s generated by running %s\n' % (op,pyin,pyin),] | |
300 notes.append('# to make a new Galaxy tool called %s\n' % self.toolname) | |
301 notes.append('# User %s at %s\n' % (self.opts.user_email,timenow())) | |
302 pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm | |
303 notes += pi | |
304 outpi = open(outpiname,'w') | |
305 outpi.write(''.join(notes)) | |
306 outpi.write('\n') | |
307 outpi.close() | |
308 stname = os.path.join(tdir,self.sfile) | |
309 if not os.path.exists(stname): | |
310 shutil.copyfile(self.sfile, stname) | |
311 xtname = os.path.join(tdir,self.xmlfile) | |
312 if not os.path.exists(xtname): | |
313 shutil.copyfile(self.xmlfile,xtname) | |
314 tarpath = "%s.gz" % self.toolname | |
315 tar = tarfile.open(tarpath, "w:gz") | |
316 tar.add(tdir,arcname=self.toolname) | |
317 tar.close() | |
318 shutil.copyfile(tarpath,self.opts.new_tool) | |
319 shutil.rmtree(tdir) | |
320 ## TODO: replace with optional direct upload to local toolshed? | |
321 return retval | |
322 | |
323 def compressPDF(self,inpdf=None,thumbformat='png'): | |
324 """need absolute path to pdf | |
325 """ | |
326 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName) | |
327 hf,hlog = tempfile.mkstemp(suffix="%s.log" % self.toolname) | |
328 sto = open(hlog,'w') | |
329 outpdf = '%s_compressed' % inpdf | |
330 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dBATCH", "-sOutputFile=%s" % outpdf,inpdf] | |
331 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir) | |
332 retval1 = x.wait() | |
333 if retval1 == 0: | |
334 os.unlink(inpdf) | |
335 shutil.move(outpdf,inpdf) | |
336 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat) | |
337 cl2 = ['convert', inpdf, outpng] | |
338 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir) | |
339 retval2 = x.wait() | |
340 sto.close() | |
341 retval = retval1 or retval2 | |
342 return retval | |
343 | |
344 | |
345 def getfSize(self,fpath,outpath): | |
346 """ | |
347 format a nice file size string | |
348 """ | |
349 size = '' | |
350 fp = os.path.join(outpath,fpath) | |
351 if os.path.isfile(fp): | |
352 size = '0 B' | |
353 n = float(os.path.getsize(fp)) | |
354 if n > 2**20: | |
355 size = '%1.1f MB' % (n/2**20) | |
356 elif n > 2**10: | |
357 size = '%1.1f KB)' % (n/2**10) | |
358 elif n > 0: | |
359 size = '%d B' % (int(n)) | |
360 return size | |
361 | |
362 def makeHtml(self): | |
363 """ Create an HTML file content to list all the artifacts found in the output_dir | |
364 """ | |
365 | |
366 galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> | |
367 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> | |
368 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> | |
369 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> | |
370 <title></title> | |
371 <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> | |
372 </head> | |
373 <body> | |
374 <div class="toolFormBody"> | |
375 """ | |
376 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/>""" | |
377 galhtmlpostfix = """</div></body></html>\n""" | |
378 | |
379 flist = os.listdir(self.opts.output_dir) | |
380 flist = [x for x in flist if x <> 'Rplots.pdf'] | |
381 flist.sort() | |
382 html = [] | |
383 html.append(galhtmlprefix % progname) | |
384 html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow())) | |
385 fhtml = [] | |
386 if len(flist) > 0: | |
387 pdflist = [] | |
388 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf']) | |
389 nacross = 1 | |
390 if npdf > 0: | |
391 nacross = int(round(math.log(npdf,2))) | |
392 nacross = max(1,nacross) | |
393 width = min(400,int(1200/nacross)) | |
394 for rownum,fname in enumerate(flist): | |
395 dname,e = os.path.splitext(fname) | |
396 sfsize = self.getfSize(fname,self.opts.output_dir) | |
397 if e.lower() == '.pdf' : # compress and make a thumbnail | |
398 thumb = '%s.%s' % (dname,self.thumbformat) | |
399 pdff = os.path.join(self.opts.output_dir,fname) | |
400 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat) | |
401 if retval == 0: | |
402 pdflist.append((fname,thumb)) | |
403 if (rownum+1) % 2 == 0: | |
404 fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize)) | |
405 else: | |
406 fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize)) | |
407 ntogo = nacross # counter for table row padding with empty cells | |
408 if len(pdflist) > 0: | |
409 html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>') | |
410 for i,paths in enumerate(pdflist): | |
411 fname,thumb = paths | |
412 s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d" | |
413 alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname) | |
414 if ((i+1) % nacross == 0): | |
415 s += '</tr>\n' | |
416 ntogo = 0 | |
417 if i < (npdf - 1): # more to come | |
418 s += '<tr>' | |
419 ntogo = nacross | |
420 else: | |
421 ntogo -= 1 | |
422 html.append(s) | |
423 if html[-1].strip().endswith('</tr>'): | |
424 html.append('</table></div>\n') | |
425 else: | |
426 if ntogo > 0: # pad | |
427 html.append('<td> </td>'*ntogo) | |
428 html.append('</tr></table></div>\n') | |
429 if len(fhtml) > 0: | |
430 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') | |
431 fhtml.append('</table></div><br/>') | |
432 html += fhtml # add all non-pdf files to the end of the display | |
433 else: | |
434 html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter) | |
435 rlog = open(self.tlog,'r').readlines() | |
436 rlog = [x for x in rlog if x.strip() > ''] | |
437 if len(rlog) > 1: | |
438 html.append('<div class="toolFormTitle">%s log</div><pre>\n' % self.opts.interpreter) | |
439 html += rlog | |
440 html.append('</pre>\n') | |
441 html.append(galhtmlattr % (self.toolname)) | |
442 html.append(galhtmlpostfix) | |
443 htmlf = file(self.opts.output_html,'w') | |
444 htmlf.write('\n'.join(html)) | |
445 htmlf.write('\n') | |
446 htmlf.close() | |
447 self.html = html | |
448 | |
449 | |
450 def run(self): | |
451 """ | |
452 scripts must be small enough not to fill the pipe! | |
453 """ | |
454 if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']: | |
455 retval = self.runBash() | |
456 else: | |
457 if self.opts.output_dir: | |
458 sto = open(self.tlog,'w') | |
459 sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl)) | |
460 sto.flush() | |
461 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,stdin=subprocess.PIPE,cwd=self.opts.output_dir) | |
462 else: | |
463 p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE) | |
464 p.stdin.write(self.script) | |
465 p.stdin.close() | |
466 retval = p.wait() | |
467 if self.opts.output_dir: | |
468 sto.close() | |
469 if self.opts.make_HTML: | |
470 self.makeHtml() | |
471 return retval | |
472 | |
473 def runBash(self): | |
474 """ | |
475 cannot use - for bash so use self.sfile | |
476 """ | |
477 if self.opts.output_dir: | |
478 s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl) | |
479 sto = open(self.tlog,'w') | |
480 sto.write(s) | |
481 sto.flush() | |
482 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir) | |
483 else: | |
484 p = subprocess.Popen(self.cl,shell=False) | |
485 retval = p.wait() | |
486 if self.opts.output_dir: | |
487 sto.close() | |
488 if self.opts.make_HTML: | |
489 self.makeHtml() | |
490 return retval | |
491 | |
492 | |
493 def main(): | |
494 u = """ | |
495 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as: | |
496 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript" | |
497 </command> | |
498 """ | |
499 op = optparse.OptionParser() | |
500 a = op.add_option | |
501 a('--script_path',default=None) | |
502 a('--tool_name',default=None) | |
503 a('--interpreter',default=None) | |
504 a('--output_dir',default=None) | |
505 a('--output_html',default=None) | |
506 a('--input_tab',default="None") | |
507 a('--output_tab',default="None") | |
508 a('--user_email',default='Unknown') | |
509 a('--bad_user',default=None) | |
510 a('--make_Tool',default=None) | |
511 a('--make_HTML',default=None) | |
512 a('--help_text',default=None) | |
513 a('--tool_desc',default=None) | |
514 a('--new_tool',default=None) | |
515 a('--tool_version',default=None) | |
516 opts, args = op.parse_args() | |
517 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) | |
518 assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq' | |
519 assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript' | |
520 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R' | |
521 if opts.output_dir: | |
522 try: | |
523 os.makedirs(opts.output_dir) | |
524 except: | |
525 pass | |
526 r = ScriptRunner(opts) | |
527 if opts.make_Tool: | |
528 retcode = r.makeTooltar() | |
529 else: | |
530 retcode = r.run() | |
531 os.unlink(r.sfile) | |
532 if retcode: | |
533 sys.exit(retcode) # indicate failure to job runner | |
534 | |
535 | |
536 if __name__ == "__main__": | |
537 main() | |
538 | |
539 |