Mercurial > repos > fubar > tool_factory_2

comparison rgToolFactory2.py @ 7:61381bad936d draft

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Uploaded
author fubar
date Mon, 12 Jan 2015 05:01:29 -0500
parents 81198714ac8e
children 9d58cc32a12d
comparison
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6:81198714ac8e 7:61381bad936d
143 "&": "&", 143 "&": "&",
144 ">": ">", 144 ">": ">",
145 "<": "&lt;", 145 "<": "&lt;",
146 "$": "\$" 146 "$": "\$"
147 } 147 }
148 148 html_unescape_table = dict(zip(html_escape_table.values(),html_escape_table.keys()))
149 def html_escape(text): 149 def html_escape(text):
150 """Produce entities within text.""" 150 """Produce entities within text."""
151 return "".join(html_escape_table.get(c,c) for c in text) 151 return "".join(html_escape_table.get(c,c) for c in text)
152 152
153
154 def html_unescape(text):
155 """Revert entities within text."""
156 return "".join(html_unescape_table.get(c,c) for c in text)
157
153 def cmd_exists(cmd): 158 def cmd_exists(cmd):
154 return subprocess.call("type " + cmd, shell=True, 159 return subprocess.call("type " + cmd, shell=True,
155 stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0 160 stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
156 161
157 def parse_citations(citations_text): 162 def parse_citations(citations_text):
243 a('--INNAMES "%s"' % (self.infile_names)) 248 a('--INNAMES "%s"' % (self.infile_names))
244 if self.opts.output_tab: 249 if self.opts.output_tab:
245 a('--OUTPATH "%s"' % self.opts.output_tab) 250 a('--OUTPATH "%s"' % self.opts.output_tab)
246 for p in opts.additional_parameters: 251 for p in opts.additional_parameters:
247 p = p.replace('"','') 252 p = p.replace('"','')
248 ps = p.split(',') 253 psplit = p.split(',')
249 a('%s="%s"' % (ps[0],ps[1])) 254 param = html_unescape(psplit[0])
255 value = html_unescape(psplit[1])
256 a('%s="%s"' % (param,value))
250 if (self.opts.interpreter == 'Rscript'): 257 if (self.opts.interpreter == 'Rscript'):
251 # pass params on command line 258 # pass params on command line
252 if self.opts.input_tab: 259 if self.opts.input_tab:
253 a('INPATHS="%s"' % self.infile_paths) 260 a('INPATHS="%s"' % self.infile_paths)
254 a('INNAMES="%s"' % self.infile_names) 261 a('INNAMES="%s"' % self.infile_names)
255 if self.opts.output_tab: 262 if self.opts.output_tab:
256 a('OUTPATH="%s"' % self.opts.output_tab) 263 a('OUTPATH="%s"' % self.opts.output_tab)
257 for p in opts.additional_parameters: 264 for p in opts.additional_parameters:
258 p = p.replace('"','') 265 p = p.replace('"','')
259 ps = p.split(',') 266 psplit = p.split(',')
260 a('%s="%s"' % (ps[0],ps[1])) 267 param = html_unescape(psplit[0])
268 value = html_unescape(psplit[1])
269 a('%s="%s"' % (param,value))
261 if (self.opts.interpreter == 'perl'): 270 if (self.opts.interpreter == 'perl'):
262 # pass params on command line 271 # pass params on command line
263 if self.opts.input_tab: 272 if self.opts.input_tab:
264 a('%s' % self.infile_paths) 273 a('%s' % self.infile_paths)
265 a('%s' % self.infile_names) 274 a('%s' % self.infile_names)
266 if self.opts.output_tab: 275 if self.opts.output_tab:
267 a('%s' % self.opts.output_tab) 276 a('%s' % self.opts.output_tab)
268 for p in opts.additional_parameters: 277 for p in opts.additional_parameters:
269 p = p.replace('"','') 278 p = p.replace('"','')
270 ps = p.split(',') 279 psplit = p.split(',')
271 param = ps[0] 280 param = html_unescape(psplit[0])
272 value = ps[1] 281 value = html_unescape(psplit[1])
273 if (value.find(' ') <> -1): 282 if (value.find(' ') <> -1):
274 a('%s="%s"' % (param,value)) 283 a('%s="%s"' % (param,value))
275 else: 284 else:
276 a('%s=%s' % (param,value)) 285 a('%s=%s' % (param,value))
277 if self.opts.interpreter == 'sh' or self.opts.interpreter == 'bash': 286 if self.opts.interpreter == 'sh' or self.opts.interpreter == 'bash':
283 if self.opts.output_tab: 292 if self.opts.output_tab:
284 self.cl.insert(3,'OUTPATH=%s' % (self.opts.output_tab)) 293 self.cl.insert(3,'OUTPATH=%s' % (self.opts.output_tab))
285 a('OUTPATH=%s' % (self.opts.output_tab)) 294 a('OUTPATH=%s' % (self.opts.output_tab))
286 # sets those environment variables for the script 295 # sets those environment variables for the script
287 # additional params appear in CL - yes, it's confusing 296 # additional params appear in CL - yes, it's confusing
288 for i,param in enumerate(opts.additional_parameters): 297 for i,p in enumerate(opts.additional_parameters):
289 psplit = param.split(',') 298 psplit = p.split(',')
290 n = psplit[0] 299 param = html_unescape(psplit[0])
291 v = psplit[1] 300 value = html_unescape(psplit[1])
292 if (v.find(' ') <> -1): 301 if (value.find(' ') <> -1):
293 a('%s="%s"' % (n,v)) 302 a('%s="%s"' % (param,value))
294 self.cl.insert(4+i,'%s="%s"' % (n,v)) 303 self.cl.insert(4+i,'%s="%s"' % (param,value))
295 else: 304 else:
296 a('%s=%s' % (n,v)) 305 a('%s=%s' % (param,value))
297 self.cl.insert(4+i,'%s=%s' % (n,v)) 306 self.cl.insert(4+i,'%s=%s' % (param,value))
298 307
299 308
300 self.outFormats = opts.output_format 309 self.outFormats = opts.output_format
301 self.inputFormats = opts.input_formats 310 self.inputFormats = opts.input_formats
302 self.test1Output = '%s_test1_output.xls' % self.toolname 311 self.test1Output = '%s_test1_output.xls' % self.toolname