Mercurial > repos > fubar > tool_factory_2

comparison toolfactory/rgToolFactory2.py @ 111:223b78754735 draft

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Uploaded
author fubar
date Sun, 29 Nov 2020 07:51:53 +0000
parents ab2474035f81
children 5509dc4c1cf2
comparison
equal deleted inserted replaced
110:ab2474035f81 111:223b78754735
61 ALOT = 10000000 # srsly. command or test overrides use read() so just in case 61 ALOT = 10000000 # srsly. command or test overrides use read() so just in case
62 STDIOXML = """<stdio> 62 STDIOXML = """<stdio>
63 <exit_code range="100:" level="debug" description="shite happens" /> 63 <exit_code range="100:" level="debug" description="shite happens" />
64 </stdio>""" 64 </stdio>"""
65 65
66 # --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label 66 # --input_files="$intab.input_files~~~$intab.input_CL~~~$intab.input_formats\
67 # ~~~$input_help" 67 #~~~$intab.input_label~~~$intab.input_help"
68 IPATHPOS = 0 68 IPATHPOS = 0
69 ICLPOS = 1 69 ICLPOS = 1
70 IFMTPOS = 2 70 IFMTPOS = 2
71 ILABPOS = 3 71 ILABPOS = 3
72 IHELPOS = 4 72 IHELPOS = 4
261 appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS], ""] 261 appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS], ""]
262 xappendme = [p[IOCLPOS], p[ICLPOS], "$%s" % p[ICLPOS], ""] 262 xappendme = [p[IOCLPOS], p[ICLPOS], "$%s" % p[ICLPOS], ""]
263 clsuffix.append(appendme) 263 clsuffix.append(appendme)
264 xclsuffix.append(xappendme) 264 xclsuffix.append(xappendme)
265 for i, p in enumerate(self.outfiles): 265 for i, p in enumerate(self.outfiles):
266 if p[OOCLPOS] == "STDOUT": 266 if p[OCLPOS] == "STDOUT":
267 self.lastclredirect = [">", p[ONAMEPOS]] 267 self.lastclredirect = [">", p[ONAMEPOS]]
268 self.lastxclredirect = [">", "$%s" % p[OCLPOS]] 268 self.lastxclredirect = [">", "$%s" % p[OCLPOS]]
269 else: 269 else:
270 clsuffix.append([p[OOCLPOS], p[OCLPOS], p[ONAMEPOS], ""]) 270 clsuffix.append([p[OOCLPOS], p[OCLPOS], p[ONAMEPOS], ""])
271 xclsuffix.append([p[OOCLPOS], p[OCLPOS], "$%s" % p[ONAMEPOS], ""]) 271 xclsuffix.append([p[OOCLPOS], p[OCLPOS], "$%s" % p[ONAMEPOS], ""])
294 ) 294 )
295 tscript = open(self.sfile, "w") 295 tscript = open(self.sfile, "w")
296 tscript.write(self.script) 296 tscript.write(self.script)
297 tscript.close() 297 tscript.close()
298 self.escapedScript = [cheetah_escape(x) for x in rx] 298 self.escapedScript = [cheetah_escape(x) for x in rx]
299 self.spacedScript = [f" {x}" for x in self.escapedScript] 299 self.spacedScript = [f" {x}" for x in rx]
300 art = "%s.%s" % (self.tool_name, self.executeme) 300 art = "%s.%s" % (self.tool_name, self.executeme)
301 artifact = open(art, "wb") 301 artifact = open(art, "wb")
302 artifact.write(bytes('\n'.join(self.escapedScript),'utf8')) 302 artifact.write(bytes('\n'.join(self.escapedScript),'utf8'))
303 artifact.close() 303 artifact.close()
304 304
305 def cleanuppar(self): 305 def cleanuppar(self):
306 """ positional parameters are complicated by their numeric ordinal""" 306 """ positional parameters are complicated by their numeric ordinal"""
307 for i, p in enumerate(self.infiles): 307 for i, p in enumerate(self.infiles):
308 infp = copy.copy(p)
308 if self.args.parampass == "positional": 309 if self.args.parampass == "positional":
309 assert p[ 310 assert infp[
310 ICLPOS 311 ICLPOS
311 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % ( 312 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
312 p[ICLPOS], 313 infp[ICLPOS],
313 p[ILABPOS], 314 infp[ILABPOS],
314 ) 315 )
315 p.append(p[ICLPOS]) 316 icl = infp[ICLPOS]
316 if p[ICLPOS].isdigit() or self.args.parampass == "0": 317 infp.append(icl)
318 if infp[ICLPOS].isdigit() or self.args.parampass == "0":
317 scl = "input%d" % (i + 1) 319 scl = "input%d" % (i + 1)
318 p[ICLPOS] = scl 320 infp[ICLPOS] = scl
319 self.infiles[i] = p 321 self.infiles[i] = infp
320 for i, p in enumerate( 322 for i, p in enumerate(
321 self.outfiles 323 self.outfiles
322 ): # trying to automagically gather using extensions 324 ):
323 if self.args.parampass == "positional" and p[OCLPOS] != "STDOUT": 325 if self.args.parampass == "positional" and p[OCLPOS] != "STDOUT":
324 assert p[ 326 assert p[
325 OCLPOS 327 OCLPOS
326 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % ( 328 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
327 p[OCLPOS], 329 p[OCLPOS],
328 p[ONAMEPOS], 330 p[ONAMEPOS],
329 ) 331 )
330 p.append(p[OCLPOS]) 332 p.append(p[OCLPOS]) # keep copy
331 if p[OCLPOS].isdigit() or p[OCLPOS] == "STDOUT": 333 if p[OCLPOS].isdigit() or p[OCLPOS] == "STDOUT":
332 scl = p[ONAMEPOS] 334 scl = p[ONAMEPOS]
333 p[OCLPOS] = scl 335 p[OCLPOS] = scl
334 self.outfiles[i] = p 336 self.outfiles[i] = p
335 for i, p in enumerate(self.addpar): 337 for i, p in enumerate(self.addpar):
410 ndash = 1 412 ndash = 1
411 return ndash 413 return ndash
412 414
413 def doXMLparam(self): 415 def doXMLparam(self):
414 """flake8 made me do this...""" 416 """flake8 made me do this..."""
415 for p in self.outfiles: 417 for p in self.outfiles: # --output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL~~~$otab.history_test"
416 newname, newfmt, newcl, test, oldcl = p 418 newname, newfmt, newcl, test, oldcl = p
417 test = test.strip() 419 test = test.strip()
418 ndash = self.getNdash(newcl) 420 ndash = self.getNdash(newcl)
419 aparm = gxtp.OutputData(newcl, format=newfmt, num_dashes=ndash) 421 aparm = gxtp.OutputData(name=newname, format=newfmt, num_dashes=ndash, label=newcl)
420 aparm.positional = self.is_positional 422 aparm.positional = self.is_positional
421 if self.is_positional: 423 if self.is_positional:
422 if oldcl == "STDOUT": 424 if oldcl == "STDOUT":
423 aparm.positional = 9999999 425 aparm.positional = 9999999
424 aparm.command_line_override = "> $%s" % newcl 426 aparm.command_line_override = "> $%s" % newname
425 else: 427 else:
426 aparm.positional = int(oldcl) 428 aparm.positional = int(oldcl)
427 aparm.command_line_override = "$%s" % newcl 429 aparm.command_line_override = "$%s" % newname
428 self.toutputs.append(aparm) 430 self.toutputs.append(aparm)
429 ld = None 431 ld = None
430 if test.strip() > "": 432 if test.strip() > "":
431 if test.startswith("diff"): 433 if test.startswith("diff"):
432 c = "diff" 434 c = "diff"
580 scr = ( 582 scr = (
581 scr[:100] 583 scr[:100]
582 + [">300 lines - stuff deleted", "......"] 584 + [">300 lines - stuff deleted", "......"]
583 + scr[-100:] 585 + scr[-100:]
584 ) 586 )
585 scr.append('\n------\n') 587 scr.append('\n')
586 safertext = safertext + "\n".join(scr) 588 safertext = safertext + "\n".join(scr)
587 self.newtool.help = safertext 589 self.newtool.help = safertext
588 else: 590 else:
589 self.newtool.help = ( 591 self.newtool.help = (
590 "Please ask the tool author (%s) for help \ 592 "Please ask the tool author (%s) for help \
841 remote_repository_url=self.args.toolshed_url, 843 remote_repository_url=self.args.toolshed_url,
842 homepage_url=None, 844 homepage_url=None,
843 category_ids=catID, 845 category_ids=catID,
844 ) 846 )
845 tid = res.get("id", None) 847 tid = res.get("id", None)
848 sto.write(f"#####create_repository {self.args.tool_name} tid={tid} res={res}\n")
846 else: 849 else:
847 i = rnames.index(self.tool_name) 850 i = rnames.index(self.tool_name)
848 tid = rids[i] 851 tid = rids[i]
849 try: 852 try:
850 res = ts.repositories.update_repository( 853 res = ts.repositories.update_repository(
851 id=tid, tar_ball_path=self.newtarpath, commit_message=None 854 id=tid, tar_ball_path=self.newtarpath, commit_message=None
852 ) 855 )
853 sto.write(f"#####update res={res}\n") 856 sto.write(f"#####update res id {id} ={res}\n")
854 except ConnectionError: 857 except ConnectionError:
855 sto.write( 858 sto.write(
856 "Probably no change to repository - bioblend shed upload failed\n" 859 "Is the toolshed running and the API key correct? Bioblend shed upload failed\n"
857 ) 860 )
858 sto.close() 861 sto.close()
859 862
860 def eph_galaxy_load(self): 863 def eph_galaxy_load(self):
861 """load the new tool from the local toolshed after planemo uploads it""" 864 """load the new tool from the local toolshed after planemo uploads it"""