Mercurial > repos > fubar > tool_factory_2

comparison toolfactory/rgToolFactory2.py @ 131:72d190989c68 draft

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author fubar
date Fri, 09 Apr 2021 23:23:12 +0000
parents e8e8071c9d0c
children 65b5e9acf98a
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130:e8e8071c9d0c 131:72d190989c68
42 myversion = "V2.2 February 2021" 42 myversion = "V2.2 February 2021"
43 verbose = True 43 verbose = True
44 debug = True 44 debug = True
45 toolFactoryURL = "https://github.com/fubar2/toolfactory" 45 toolFactoryURL = "https://github.com/fubar2/toolfactory"
46 foo = len(lxml.__version__) 46 foo = len(lxml.__version__)
47 # fug you, flake8. Say my name!
48 FAKEEXE = "~~~REMOVE~~~ME~~~" 47 FAKEEXE = "~~~REMOVE~~~ME~~~"
49 # need this until a PR/version bump to fix galaxyxml prepending the exe even 48 # need this until a PR/version bump to fix galaxyxml prepending the exe even
50 # with override. 49 # with override.
51 50
52 51
214 for c in clp: 213 for c in clp:
215 aCL(c) 214 aCL(c)
216 aXCL(c) 215 aXCL(c)
217 216
218 def clsimple(self): 217 def clsimple(self):
219 """no parameters - uses < and > for i/o""" 218 """no parameters or repeats - uses < and > for i/o"""
220 aCL = self.cl.append 219 aCL = self.cl.append
221 aXCL = self.xmlcl.append 220 aXCL = self.xmlcl.append
222 if len(self.infiles) > 0: 221 if len(self.infiles) > 0:
223 aCL("<") 222 aCL("<")
224 aCL(self.infiles[0]["infilename"]) 223 aCL(self.infiles[0]["infilename"])
256 self.lastxclredirect = [">", "$%s" % p["name"]] 255 self.lastxclredirect = [">", "$%s" % p["name"]]
257 else: 256 else:
258 clsuffix.append([p["name"], p["name"], ""]) 257 clsuffix.append([p["name"], p["name"], ""])
259 xclsuffix.append([p["name"], "$%s" % p["name"], ""]) 258 xclsuffix.append([p["name"], "$%s" % p["name"], ""])
260 for p in self.addpar: 259 for p in self.addpar:
261 clsuffix.append([p["CL"], p["name"], p["override"]]) 260 nam = p["name"]
262 xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]]) 261 rep = p["repeat"] == "1"
262 if rep:
263 over = f" #for $rep in $R_{nam}:\n--{nam} $rep.{nam}\n#end for"
264 else:
265 over = p["override"]
266 clsuffix.append([p["CL"], nam, over])
267 xclsuffix.append([p["CL"], nam, over])
263 for p in self.selpar: 268 for p in self.selpar:
264 clsuffix.append([p["CL"], p["name"], p["override"]]) 269 clsuffix.append([p["CL"], p["name"], p["override"]])
265 xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]]) 270 xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])
266 clsuffix.sort()
267 xclsuffix.sort()
268 self.xclsuffix = xclsuffix 271 self.xclsuffix = xclsuffix
269 self.clsuffix = clsuffix 272 self.clsuffix = clsuffix
270 273
271 def prepclpos(self): 274 def prepclpos(self):
272 clsuffix = [] 275 clsuffix = []
294 self.lastxclredirect = [">", "$%s" % p["name"]] 297 self.lastxclredirect = [">", "$%s" % p["name"]]
295 else: 298 else:
296 clsuffix.append([p["CL"], p["name"], ""]) 299 clsuffix.append([p["CL"], p["name"], ""])
297 xclsuffix.append([p["CL"], "$%s" % p["name"], ""]) 300 xclsuffix.append([p["CL"], "$%s" % p["name"], ""])
298 for p in self.addpar: 301 for p in self.addpar:
299 clsuffix.append([p["CL"], p["name"], p["override"]]) 302 nam = p["name"]
300 xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]]) 303 rep = p["repeat"] == "1" # repeats make NO sense
304 if rep:
305 print(f'### warning. Repeats for {nam} ignored - not permitted in positional parameter command lines!')
306 over = p["override"]
307 clsuffix.append([p["CL"], nam, over])
308 xclsuffix.append([p["CL"], nam, over])
301 for p in self.selpar: 309 for p in self.selpar:
302 clsuffix.append([p["CL"], p["name"], p["override"]]) 310 clsuffix.append([p["CL"], p["name"], p["override"]])
303 xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]]) 311 xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])
304 clsuffix.sort() 312 clsuffix.sort()
305 xclsuffix.sort() 313 xclsuffix.sort()
386 # inputs then params in argparse named form 394 # inputs then params in argparse named form
387 395
388 for (k, v, koverride) in self.xclsuffix: 396 for (k, v, koverride) in self.xclsuffix:
389 if koverride > "": 397 if koverride > "":
390 k = koverride 398 k = koverride
391 elif len(k.strip()) == 1: 399 aXCL(k)
392 k = "-%s" % k 400 else:
393 else: 401 if len(k.strip()) == 1:
394 k = "--%s" % k 402 k = "-%s" % k
395 aXCL(k) 403 else:
396 aXCL(v) 404 k = "--%s" % k
405 aXCL(k)
406 aXCL(v)
397 for (k, v, koverride) in self.clsuffix: 407 for (k, v, koverride) in self.clsuffix:
398 if koverride > "": 408 if koverride > "":
399 k = koverride 409 k = koverride
400 elif len(k.strip()) == 1: 410 elif len(k.strip()) == 1:
401 k = "-%s" % k 411 k = "-%s" % k
478 self.testparam.append(tp) 488 self.testparam.append(tp)
479 for p in self.infiles: 489 for p in self.infiles:
480 newname = p["infilename"] 490 newname = p["infilename"]
481 newfmt = p["format"] 491 newfmt = p["format"]
482 ndash = self.getNdash(newname) 492 ndash = self.getNdash(newname)
493 reps = p.get("repeat",0) == 1
483 if not len(p["label"]) > 0: 494 if not len(p["label"]) > 0:
484 alab = p["CL"] 495 alab = p["CL"]
485 else: 496 else:
486 alab = p["label"] 497 alab = p["label"]
487 aninput = gxtp.DataParam( 498 aninput = gxtp.DataParam(
499 aninput.positional = 9999998 510 aninput.positional = 9999998
500 aninput.command_line_override = "> $%s" % newname 511 aninput.command_line_override = "> $%s" % newname
501 else: 512 else:
502 aninput.positional = int(p["origCL"]) 513 aninput.positional = int(p["origCL"])
503 aninput.command_line_override = "$%s" % newname 514 aninput.command_line_override = "$%s" % newname
504 self.tinputs.append(aninput) 515 if reps:
505 tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname) 516 repe = gxtp.Repeat(name=f"R_{newname}", title=f"Add as many {newlabel} as needed")
506 self.testparam.append(tparm) 517 repe.append(aninput)
518 self.tinputs.append(repe)
519 tparm = gxtp.TestRepeat(name=f"R_{newname}")
520 tparm2 = gxtp.TestParam(newname, value="%s_sample" % newname)
521 tparm.append(tparm2)
522 self.testparam.append(tparm)
523 else:
524 self.tinputs.append(aninput)
525 tparm = gxtp.TestParam(newname, value="%s_sample" % newname)
526 self.testparam.append(tparm)
507 for p in self.addpar: 527 for p in self.addpar:
508 newname = p["name"] 528 newname = p["name"]
509 newval = p["value"] 529 newval = p["value"]
510 newlabel = p["label"] 530 newlabel = p["label"]
511 newhelp = p["help"] 531 newhelp = p["help"]
512 newtype = p["type"] 532 newtype = p["type"]
513 newcl = p["CL"] 533 newcl = p["CL"]
514 oldcl = p["origCL"] 534 oldcl = p["origCL"]
535 reps = p["repeat"] == "1"
515 if not len(newlabel) > 0: 536 if not len(newlabel) > 0:
516 newlabel = newname 537 newlabel = newname
517 ndash = self.getNdash(newname) 538 ndash = self.getNdash(newname)
518 if newtype == "text": 539 if newtype == "text":
519 aparm = gxtp.TextParam( 540 aparm = gxtp.TextParam(
554 % (newtype, newname) 575 % (newtype, newname)
555 ) 576 )
556 aparm.positional = self.is_positional 577 aparm.positional = self.is_positional
557 if self.is_positional: 578 if self.is_positional:
558 aparm.positional = int(oldcl) 579 aparm.positional = int(oldcl)
559 self.tinputs.append(aparm) 580 if reps:
560 tparm = gxtp.TestParam(newname, value=newval) 581 repe = gxtp.Repeat(name=f"R_{newname}", title=f"Add as many {newlabel} as needed")
561 self.testparam.append(tparm) 582 repe.append(aparm)
583 self.tinputs.append(repe)
584 tparm = gxtp.TestRepeat(name=f"R_{newname}")
585 tparm2 = gxtp.TestParam(newname, value=newval)
586 tparm.append(tparm2)
587 self.testparam.append(tparm)
588 else:
589 self.tinputs.append(aparm)
590 tparm = gxtp.TestParam(newname, value=newval)
591 self.testparam.append(tparm)
562 for p in self.selpar: 592 for p in self.selpar:
563 newname = p["name"] 593 newname = p["name"]
564 newval = p["value"] 594 newval = p["value"]
565 newlabel = p["label"] 595 newlabel = p["label"]
566 newhelp = p["help"] 596 newhelp = p["help"]
604 disc = gxtp.DiscoverDatasets( 634 disc = gxtp.DiscoverDatasets(
605 pattern=newdisc, directory=f"{newname}", visible="false" 635 pattern=newdisc, directory=f"{newname}", visible="false"
606 ) 636 )
607 collect.append(disc) 637 collect.append(disc)
608 self.toutputs.append(collect) 638 self.toutputs.append(collect)
609 tparm = gxtp.TestOutputCollection(newname) 639 try:
610 self.testparam.append(tparm) 640 tparm = gxtp.TestOutputCollection(newname) # broken until PR merged.
641 self.testparam.append(tparm)
642 except Exception:
643 print("#### WARNING: Galaxyxml version does not have the PR merged yet - tests for collections must be over-ridden until then!")
611 644
612 def doNoXMLparam(self): 645 def doNoXMLparam(self):
613 """filter style package - stdin to stdout""" 646 """filter style package - stdin to stdout"""
614 if len(self.infiles) > 0: 647 if len(self.infiles) > 0:
615 alab = self.infiles[0]["label"] 648 alab = self.infiles[0]["label"]