Mercurial > repos > fubar > tool_factory_2
comparison toolfactory/rgToolFactory2.py @ 46:f8700bed1e17 draft
Uploaded
| author | fubar |
|---|---|
| date | Tue, 18 Aug 2020 08:25:43 -0400 |
| parents | e7e9732ebed6 |
| children |
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| 45:668c37cc8962 | 46:f8700bed1e17 |
|---|---|
| 171 self.tinputs = gxtp.Inputs() | 171 self.tinputs = gxtp.Inputs() |
| 172 self.toutputs = gxtp.Outputs() | 172 self.toutputs = gxtp.Outputs() |
| 173 self.testparam = [] | 173 self.testparam = [] |
| 174 if ( | 174 if ( |
| 175 self.args.runmode == "Executable" or self.args.runmode == "system" | 175 self.args.runmode == "Executable" or self.args.runmode == "system" |
| 176 ): # binary - no need | 176 ): |
| 177 aCL(self.args.exe_package) # this little CL will just run | 177 if len(self.args.cl_override) > 0: |
| 178 for x in self.args.cl_override.split(' '): | |
| 179 aCL(x) | |
| 180 else: | |
| 181 aCL(self.args.exe_package) # this little CL will just run | |
| 178 else: | 182 else: |
| 179 self.prepScript() | 183 self.prepScript() |
| 184 aCL(self.args.interpreter_name) | |
| 185 aCL(self.sfile) | |
| 186 | |
| 180 self.elog = "%s_error_log.txt" % self.tool_name | 187 self.elog = "%s_error_log.txt" % self.tool_name |
| 181 self.tlog = "%s_runner_log.txt" % self.tool_name | 188 self.tlog = "%s_runner_log.txt" % self.tool_name |
| 182 | 189 |
| 183 if self.args.parampass == "0": | 190 if self.args.parampass == "0": |
| 184 self.clsimple() | 191 self.clsimple() |
| 229 self.clpositional() | 236 self.clpositional() |
| 230 else: | 237 else: |
| 231 self.clargparse() | 238 self.clargparse() |
| 232 | 239 |
| 233 def prepScript(self): | 240 def prepScript(self): |
| 234 aCL = self.cl.append | |
| 235 rx = open(self.args.script_path, "r").readlines() | 241 rx = open(self.args.script_path, "r").readlines() |
| 236 rx = [x.rstrip() for x in rx] | 242 rx = [x.rstrip() for x in rx] |
| 237 rxcheck = [x.strip() for x in rx if x.strip() > ""] | 243 rxcheck = [x.strip() for x in rx if x.strip() > ""] |
| 238 assert len(rxcheck) > 0, "Supplied script is empty. Cannot run" | 244 assert len(rxcheck) > 0, "Supplied script is empty. Cannot run" |
| 239 self.script = "\n".join(rx) | 245 self.script = "\n".join(rx) |
| 253 artifact = open(art, "wb") | 259 artifact = open(art, "wb") |
| 254 if self.args.interpreter_name == "python": | 260 if self.args.interpreter_name == "python": |
| 255 artifact.write(bytes("#!/usr/bin/env python\n", "utf8")) | 261 artifact.write(bytes("#!/usr/bin/env python\n", "utf8")) |
| 256 artifact.write(bytes(self.script, "utf8")) | 262 artifact.write(bytes(self.script, "utf8")) |
| 257 artifact.close() | 263 artifact.close() |
| 258 aCL(self.args.interpreter_name) | 264 |
| 259 aCL(self.sfile) | 265 |
| 260 | 266 |
| 261 def cleanuppar(self): | 267 def cleanuppar(self): |
| 262 """ positional parameters are complicated by their numeric ordinal""" | 268 """ positional parameters are complicated by their numeric ordinal""" |
| 263 for i, p in enumerate(self.infiles): | 269 for i, p in enumerate(self.infiles): |
| 264 if self.args.parampass == "positional": | 270 if self.args.parampass == "positional": |
| 265 assert p[ICLPOS].isdigit(), ( | 271 assert p[ICLPOS].isdigit(), ( |
| 480 """ | 486 """ |
| 481 Create a Galaxy xml tool wrapper for the new script | 487 Create a Galaxy xml tool wrapper for the new script |
| 482 Uses galaxyhtml | 488 Uses galaxyhtml |
| 483 Hmmm. How to get the command line into correct order... | 489 Hmmm. How to get the command line into correct order... |
| 484 """ | 490 """ |
| 485 self.tool.command_line_override = self.xmlcl | 491 if self.args.cl_override: |
| 492 self.tool.command_line_override = self.args.cl_override.split(' ') + self.xmlcl | |
| 493 else: | |
| 494 self.tool.command_line_override = self.xmlcl | |
| 486 if self.args.interpreter_name: | 495 if self.args.interpreter_name: |
| 487 self.tool.interpreter = self.args.interpreter_name | 496 self.tool.interpreter = self.args.interpreter_name |
| 488 if self.args.help_text: | 497 if self.args.help_text: |
| 489 helptext = open(self.args.help_text, "r").readlines() | 498 helptext = open(self.args.help_text, "r").readlines() |
| 490 helptext = [html_escape(x) for x in helptext] | 499 helptext = [html_escape(x) for x in helptext] |
| 497 ) | 506 ) |
| 498 self.tool.version_command = None # do not want | 507 self.tool.version_command = None # do not want |
| 499 requirements = gxtp.Requirements() | 508 requirements = gxtp.Requirements() |
| 500 | 509 |
| 501 if self.args.interpreter_name: | 510 if self.args.interpreter_name: |
| 511 if self.args.dependencies: | |
| 512 for d in self.args.dependencies.split(','): | |
| 513 requirements.append( | |
| 514 gxtp.Requirement( | |
| 515 "package", d, "" | |
| 516 ) | |
| 517 ) | |
| 502 if self.args.interpreter_name == "python": | 518 if self.args.interpreter_name == "python": |
| 503 requirements.append( | 519 requirements.append( |
| 504 gxtp.Requirement( | 520 gxtp.Requirement( |
| 505 "package", "python", self.args.interpreter_version | 521 "package", "python", self.args.interpreter_version |
| 506 ) | 522 ) |
| 689 </command> | 705 </command> |
| 690 """ | 706 """ |
| 691 parser = argparse.ArgumentParser() | 707 parser = argparse.ArgumentParser() |
| 692 a = parser.add_argument | 708 a = parser.add_argument |
| 693 a("--script_path", default="") | 709 a("--script_path", default="") |
| 710 a("--dependencies", default="") | |
| 711 a("--cl_override", default="") | |
| 694 a("--tool_name", default=None) | 712 a("--tool_name", default=None) |
| 695 a("--interpreter_name", default=None) | 713 a("--interpreter_name", default=None) |
| 696 a("--interpreter_version", default=None) | 714 a("--interpreter_version", default=None) |
| 697 a("--exe_package", default=None) | 715 a("--exe_package", default=None) |
| 698 a("--exe_package_version", default=None) | 716 a("--exe_package_version", default=None) |