Mercurial > repos > fubar > rglasso_1_9_8

comparison rgToolFactory.py @ 7:ef0297b352d8 draft

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Uploaded
author fubar
date Fri, 19 Dec 2014 18:22:38 -0500
parents 42637d352d09
children 4b62ea84c318
comparison
equal deleted inserted replaced
6:42637d352d09 7:ef0297b352d8
151 artifact.close() 151 artifact.close()
152 self.cl = [] 152 self.cl = []
153 self.html = [] 153 self.html = []
154 a = self.cl.append 154 a = self.cl.append
155 a(opts.interpreter) 155 a(opts.interpreter)
156 if self.treatbashSpecial and opts.interpreter in ['bash','sh']: 156 # cannot use pipe input on test - change so always eg Rscript myscript.R
157 a(self.sfile) 157 #if self.treatbashSpecial and opts.interpreter in ['bash','sh']:
158 else: 158 # a(self.sfile)
159 a('-') # stdin 159 #else:
160 a(opts.input_tab) 160 # a('-') # stdin
161 a(opts.output_tab) 161 #a(opts.input_tab)
162 #a(opts.output_tab)
163 a(self.sfile)
162 self.outFormats = 'tabular' # TODO make this an option at tool generation time 164 self.outFormats = 'tabular' # TODO make this an option at tool generation time
163 self.inputFormats = 'tabular' # TODO make this an option at tool generation time 165 self.inputFormats = 'tabular' # TODO make this an option at tool generation time
164 self.test1Input = '%s_test1_input.xls' % self.toolname 166 self.test1Input = '%s_test1_input.xls' % self.toolname
165 self.test1Output = '%s_test1_output.xls' % self.toolname 167 self.test1Output = '%s_test1_output.xls' % self.toolname
166 self.test1HTML = '%s_test1_output.html' % self.toolname 168 self.test1HTML = '%s_test1_output.html' % self.toolname
536 htmlf.write('\n'.join(html)) 538 htmlf.write('\n'.join(html))
537 htmlf.write('\n') 539 htmlf.write('\n')
538 htmlf.close() 540 htmlf.close()
539 self.html = html 541 self.html = html
540 542
541
542 def run(self): 543 def run(self):
543 """ 544 """
544 scripts must be small enough not to fill the pipe! 545 scripts must be small enough not to fill the pipe!
545 """ 546 """
546 my_env = os.environ.copy() 547 my_env = os.environ.copy()
547 if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']: 548 if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']:
548 retval = self.runBash(pth) 549 retval = self.runBash()
550 else:
551 if self.opts.output_dir:
552 ste = open(self.elog,'w')
553 sto = open(self.tlog,'w')
554 sto.write('## Toolfactory running %s as %s script\n' % (self.toolname,self.opts.interpreter))
555 sto.flush()
556 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,cwd=self.opts.output_dir,env=my_env)
557 else:
558 p = subprocess.Popen(self.cl,shell=False,cwd=self.opts.output_dir,env=my_env)
559 # p.stdin.write(self.script)
560 #print >> p.stdin, self.script
561 #p.stdin.close()
562 retval = p.wait()
563 if self.opts.output_dir:
564 sto.close()
565 ste.close()
566 # get stderr, allowing for case where it's very large
567 tmp_stderr = open( self.elog, 'rb' )
568 stderr = ''
569 try:
570 while True:
571 stderr += tmp_stderr.read( buffsize )
572 if not stderr or len( stderr ) % buffsize != 0:
573 break
574 except OverflowError:
575 pass
576 tmp_stderr.close()
577 if self.opts.make_HTML:
578 self.makeHtml()
579 return retval
580
581 def old_run(self):
582 """
583 can't use pipe as stdin on test. go figure
584 scripts must be small enough not to fill the pipe!
585 """
586 my_env = os.environ.copy()
587 if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']:
588 retval = self.runBash()
549 else: 589 else:
550 if self.opts.output_dir: 590 if self.opts.output_dir:
551 ste = open(self.elog,'w') 591 ste = open(self.elog,'w')
552 sto = open(self.tlog,'w') 592 sto = open(self.tlog,'w')
553 sto.write('## Toolfactory running %s as %s script\n' % (self.toolname,self.opts.interpreter)) 593 sto.write('## Toolfactory running %s as %s script\n' % (self.toolname,self.opts.interpreter))