Mercurial > repos > fubar > tool_factory_2
diff toolfactory/rgToolFactory2.py @ 49:35a912ce0c83 draft
Can now make the bwa example from planemo :)
| author | fubar |
|---|---|
| date | Thu, 27 Aug 2020 23:11:01 -0400 |
| parents | 5a7a5b06bce0 |
| children | bf432f4486c7 |
line wrap: on
line diff
--- a/toolfactory/rgToolFactory2.py Sun Aug 23 21:03:48 2020 -0400 +++ b/toolfactory/rgToolFactory2.py Thu Aug 27 23:11:01 2020 -0400 @@ -6,7 +6,8 @@ # # all rights reserved # Licensed under the LGPL -# suggestions for improvement and bug fixes welcome at https://github.com/fubar2/toolfactory +# suggestions for improvement and bug fixes welcome at +# https://github.com/fubar2/toolfactory # # July 2020: BCC was fun and I feel like rip van winkle after 5 years. # Decided to @@ -46,6 +47,10 @@ debug = True toolFactoryURL = "https://github.com/fubar2/toolfactory" ourdelim = "~~~" +ALOT = 10000000 # srsly. command or test overrides use read() so just in case +STDIOXML = """<stdio> +<exit_code range="100:" level="debug" description="shite happens" /> +</stdio>""" # --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label # ~~~$input_help" @@ -56,11 +61,13 @@ IHELPOS = 4 IOCLPOS = 5 -# --output_files "$otab.history_name~~~$otab.history_format~~~$otab.CL +# --output_files "$otab.history_name~~~$otab.history_format~~~$otab.CL~~~otab.history_test ONAMEPOS = 0 OFMTPOS = 1 OCLPOS = 2 -OOCLPOS = 3 +OTESTPOS = 3 +OOCLPOS = 4 + # --additional_parameters="$i.param_name~~~$i.param_value~~~ # $i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL~~~i$.param_CLoverride" @@ -76,6 +83,10 @@ foo = len(lxml.__version__) # fug you, flake8. Say my name! +FAKEEXE = "~~~REMOVE~~~ME~~~" +# need this until a PR/version bump to fix galaxyxml prepending the exe even +# with override. + def timenow(): """return current time as a string @@ -120,9 +131,7 @@ if citation.startswith("doi"): citation_tuples.append(("doi", citation[len("doi") :].strip())) else: - citation_tuples.append( - ("bibtex", citation[len("bibtex") :].strip()) - ) + citation_tuples.append(("bibtex", citation[len("bibtex") :].strip())) return citation_tuples @@ -137,7 +146,6 @@ prepare command line cl for running the tool here and prepare elements needed for galaxyxml tool generation """ - self.infiles = [x.split(ourdelim) for x in args.input_files] self.outfiles = [x.split(ourdelim) for x in args.output_files] self.addpar = [x.split(ourdelim) for x in args.additional_parameters] @@ -148,28 +156,31 @@ self.cl = [] self.xmlcl = [] self.is_positional = self.args.parampass == "positional" + if self.args.packages: + self.executeme = self.args.packages.split(",")[0].split(":")[0] + else: + self.executeme = self.args.sysexe + assert ( + self.executeme is not None + ), "No system or managed executable passed in. Cannot build" aCL = self.cl.append + aXCL = self.xmlcl.append assert args.parampass in [ "0", "argparse", "positional", - ], 'Parameter passing in args.parampass must be "0","positional" or "argparse"' + ], 'args.parampass must be "0","positional" or "argparse"' self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name) self.tool_id = self.tool_name - if self.args.interpreter_name: - exe = "$runMe" - else: - exe = self.args.exe_package - assert ( - exe is not None - ), "No interpeter or executable passed in - nothing to run so cannot build" self.tool = gxt.Tool( self.args.tool_name, self.tool_id, self.args.tool_version, self.args.tool_desc, - exe, + FAKEEXE, ) + if self.args.script_path: + self.tool.interpreter = self.executeme self.tooloutdir = "tfout" self.repdir = "TF_run_report_tempdir" self.testdir = os.path.join(self.tooloutdir, "test-data") @@ -182,21 +193,42 @@ self.tinputs = gxtp.Inputs() self.toutputs = gxtp.Outputs() self.testparam = [] - if ( - self.args.runmode == "Executable" or self.args.runmode == "system" - ): - if len(self.args.cl_override) > 0: - for x in self.args.cl_override.split(' '): - aCL(x) + if self.args.script_path: + self.prepScript() + if self.args.command_override: + scos = open(self.args.command_override, "r").readlines() + self.command_override = [x.rstrip() for x in scos] + else: + self.command_override = None + if self.args.test_override: + stos = open(self.args.test_override, "r").readlines() + self.test_override = [x.rstrip() for x in stos] + else: + self.test_override = None + if self.args.cl_prefix: # DIY CL start + clp = self.args.cl_prefix.split(" ") + for c in clp: + aCL(c) + aXCL(c) + else: + if self.args.runmode == "Executable": + if self.args.script_path: + aCL(self.executeme) + aCL(self.sfile) + aXCL("$runme") + else: + aCL(self.executeme) # this little CL will just run + aXCL(self.executeme) else: - aCL(self.args.exe_package) # this little CL will just run - else: - self.prepScript() - aCL(self.args.interpreter_name) - aCL(self.sfile) - - self.elog = "%s_error_log.txt" % self.tool_name - self.tlog = "%s_runner_log.txt" % self.tool_name + if self.args.script_path: + aCL(self.executeme) + aCL(self.sfile) + aXCL("$runme") + else: + aCL(self.executeme) # this little CL will just run + aXCL(self.executeme) + self.elog = os.path.join(self.repdir,"%s_error_log.txt" % self.tool_name) + self.tlog = os.path.join(self.repdir,"%s_runner_log.txt" % self.tool_name) if self.args.parampass == "0": self.clsimple() @@ -222,20 +254,15 @@ xappendme = [p[IOCLPOS], p[ICLPOS], "$%s" % p[ICLPOS], ""] clsuffix.append(appendme) xclsuffix.append(xappendme) - # print('##infile i=%d, appendme=%s' % (i,appendme)) for i, p in enumerate(self.outfiles): if p[OOCLPOS] == "STDOUT": self.lastclredirect = [">", p[ONAMEPOS]] self.lastxclredirect = [">", "$%s" % p[OCLPOS]] else: clsuffix.append([p[OOCLPOS], p[OCLPOS], p[ONAMEPOS], ""]) - xclsuffix.append( - [p[OOCLPOS], p[OCLPOS], "$%s" % p[ONAMEPOS], ""] - ) + xclsuffix.append([p[OOCLPOS], p[OCLPOS], "$%s" % p[ONAMEPOS], ""]) for p in self.addpar: - clsuffix.append( - [p[AOCLPOS], p[ACLPOS], p[AVALPOS], p[AOVERPOS]] - ) + clsuffix.append([p[AOCLPOS], p[ACLPOS], p[AVALPOS], p[AOVERPOS]]) xclsuffix.append( [p[AOCLPOS], p[ACLPOS], '"$%s"' % p[ANAMEPOS], p[AOVERPOS]] ) @@ -255,21 +282,15 @@ assert len(rxcheck) > 0, "Supplied script is empty. Cannot run" self.script = "\n".join(rx) fhandle, self.sfile = tempfile.mkstemp( - prefix=self.tool_name, suffix="_%s" % (self.args.interpreter_name) + prefix=self.tool_name, suffix="_%s" % (self.executeme) ) tscript = open(self.sfile, "w") tscript.write(self.script) tscript.close() - self.indentedScript = " %s" % "\n".join( - [" %s" % html_escape(x) for x in rx] - ) - self.escapedScript = "%s" % "\n".join( - [" %s" % html_escape(x) for x in rx] - ) - art = "%s.%s" % (self.tool_name, self.args.interpreter_name) + self.indentedScript = " %s" % "\n".join([" %s" % html_escape(x) for x in rx]) + self.escapedScript = "%s" % "\n".join([" %s" % html_escape(x) for x in rx]) + art = "%s.%s" % (self.tool_name, self.executeme) artifact = open(art, "wb") - if self.args.interpreter_name == "python": - artifact.write(bytes("#!/usr/bin/env python\n", "utf8")) artifact.write(bytes(self.script, "utf8")) artifact.close() @@ -377,7 +398,7 @@ def doXMLparam(self): """flake8 made me do this...""" for p in self.outfiles: - newname, newfmt, newcl, oldcl = p + newname, newfmt, newcl, test, oldcl = p ndash = self.getNdash(newcl) aparm = gxtp.OutputData(newcl, format=newfmt, num_dashes=ndash) aparm.positional = self.is_positional @@ -389,9 +410,17 @@ aparm.positional = int(oldcl) aparm.command_line_override = "$%s" % newcl self.toutputs.append(aparm) - tp = gxtp.TestOutput( - name=newcl, value="%s_sample" % newcl, format=newfmt - ) + usetest = None + ld = None + if test > '': + if test.startswith('diff'): + usetest = 'diff' + if test.split(':')[1].isdigit: + ld = int(test.split(':')[1]) + else: + usetest = test + tp = gxtp.TestOutput(name=newcl, value="%s_sample" % newcl, format=newfmt, + compare=usetest, lines_diff=ld, delta=None,) self.testparam.append(tp) for p in self.infiles: newname = p[ICLPOS] @@ -457,11 +486,12 @@ self.testparam.append(tparm) def doNoXMLparam(self): + """filter style package - stdin to stdout""" alab = self.infiles[0][ILABPOS] if len(alab) == 0: alab = self.infiles[0][ICLPOS] max1s = ( - "Maximum one input if parampass is 0 - more than one input files supplied - %s" + "Maximum one input if parampass is 0 but multiple input files supplied - %s" % str(self.infiles) ) assert len(self.infiles) == 1, max1s @@ -486,9 +516,7 @@ anout.command_line_override = "> $%s" % newname anout.positional = self.is_positional self.toutputs.append(anout) - tp = gxtp.TestOutput( - name=newname, value="%s_sample" % newname, format=newfmt - ) + tp = gxtp.TestOutput(name=newname, value="%s_sample" % newname, format=newfmt) self.testparam.append(tp) def makeXML(self): @@ -497,12 +525,12 @@ Uses galaxyhtml Hmmm. How to get the command line into correct order... """ - if self.args.cl_override: - self.tool.command_line_override = self.args.cl_override.split(' ') + self.xmlcl + if self.command_override: + self.tool.command_line_override = self.command_override # config file else: self.tool.command_line_override = self.xmlcl - if self.args.interpreter_name: - self.tool.interpreter = self.args.interpreter_name + # if self.args.interpreter_name: + # self.tool.interpreter = self.args.interpreter_name if self.args.help_text: helptext = open(self.args.help_text, "r").readlines() helptext = [html_escape(x) for x in helptext] @@ -515,38 +543,14 @@ ) self.tool.version_command = None # do not want requirements = gxtp.Requirements() - - if self.args.interpreter_name: - if self.args.dependencies: - for d in self.args.dependencies.split(','): - requirements.append( - gxtp.Requirement( - "package", d, "" - ) - ) - if self.args.interpreter_name == "python": - requirements.append( - gxtp.Requirement( - "package", "python", self.args.interpreter_version - ) - ) - elif self.args.interpreter_name not in ["bash", "sh"]: - requirements.append( - gxtp.Requirement( - "package", - self.args.interpreter_name, - self.args.interpreter_version, - ) - ) - else: - if self.args.exe_package and self.args.parampass != "system": - requirements.append( - gxtp.Requirement( - "package", - self.args.exe_package, - self.args.exe_package_version, - ) - ) + if self.args.packages: + for d in self.args.packages.split(","): + if ":" in d: + packg, ver = d.split(":") + else: + packg = d + ver = "" + requirements.append(gxtp.Requirement("package", packg.strip(), ver.strip())) self.tool.requirements = requirements if self.args.parampass == "0": self.doNoXMLparam() @@ -554,9 +558,11 @@ self.doXMLparam() self.tool.outputs = self.toutputs self.tool.inputs = self.tinputs - if self.args.runmode not in ["Executable", "system"]: + if ( + self.args.script_path + ): configfiles = gxtp.Configfiles() - configfiles.append(gxtp.Configfile(name="runMe", text=self.script)) + configfiles.append(gxtp.Configfile(name="runme", text=self.script)) self.tool.configfiles = configfiles tests = gxtp.Tests() test_a = gxtp.Test() @@ -573,75 +579,69 @@ "Cite: Creating re-usable tools from scripts doi: \ 10.1093/bioinformatics/bts573" ) - exml = self.tool.export() - xf = open('%s.xml' % self.tool_name, "w") + exml0 = self.tool.export() + exml = exml0.replace(FAKEEXE, "") # temporary work around until PR accepted + if self.test_override: # cannot do this inside galaxyxml as it expects lxml objects for tests + part1 = exml.split('<tests>')[0] + part2 = exml.split('</tests>')[1] + fixed = '%s\n%s\n%s' % (part1,self.test_override,part2) + exml = fixed + xf = open("%s.xml" % self.tool_name, "w") xf.write(exml) xf.write("\n") xf.close() # ready for the tarball - def makeTooltar(self): - """ - a tool is a gz tarball with eg - /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ... - NOTE names for test inputs and outputs are munged here so must - correspond to actual input and output names used on the generated cl + def makeTool(self): + """write xmls and samples into place """ - retval = self.run() - if retval: - sys.stderr.write( - "## Run failed. Cannot build yet. Please fix and retry" - ) - sys.exit(1) self.makeXML() + if self.args.script_path: + stname = os.path.join(self.tooloutdir, "%s" % (self.sfile)) + if not os.path.exists(stname): + shutil.copyfile(self.sfile, stname) + xreal = "%s.xml" % self.tool_name + xout = os.path.join(self.tooloutdir, xreal) + shutil.copyfile(xreal, xout) for p in self.infiles: pth = p[IPATHPOS] dest = os.path.join(self.testdir, "%s_sample" % p[ICLPOS]) shutil.copyfile(pth, dest) - for p in self.outfiles: - pth = p[OCLPOS] - if p[OOCLPOS] == "STDOUT" or self.args.parampass == "0": - pth = p[ONAMEPOS] - dest = os.path.join(self.testdir, "%s_sample" % p[ONAMEPOS]) - shutil.copyfile(pth, dest) - dest = os.path.join(self.tooloutdir, p[ONAMEPOS]) - shutil.copyfile(pth, dest) - else: - pth = p[OCLPOS] - dest = os.path.join(self.testdir, "%s_sample" % p[OCLPOS]) - shutil.copyfile(pth, dest) - dest = os.path.join(self.tooloutdir, p[OCLPOS]) - shutil.copyfile(pth, dest) - if os.path.exists(self.tlog) and os.stat(self.tlog).st_size > 0: - shutil.copyfile(self.tlog, os.path.join(self.tooloutdir, "test1_log_outfiletxt")) - if self.args.runmode not in ["Executable", "system"]: - stname = os.path.join(self.tooloutdir, "%s" % (self.sfile)) - if not os.path.exists(stname): - shutil.copyfile(self.sfile, stname) - xreal = '%s.xml' % self.tool_name - xout = os.path.join(self.tooloutdir,xreal) - shutil.copyfile(xreal, xout) + + def makeToolTar(self): self.newtarpath = "toolfactory_%s.tgz" % self.tool_name tf = tarfile.open(self.newtarpath, "w:gz") tf.add(name=self.tooloutdir, arcname=self.tool_name) tf.close() shutil.copyfile(self.newtarpath, self.args.new_tool) - shutil.copyfile(xreal,"tool_xml.txt") - repoutnames = [x[OCLPOS] for x in self.outfiles] - with os.scandir('.') as outs: + if os.path.exists(self.tlog) and os.stat(self.tlog).st_size > 0: + shutil.copyfile( + self.tlog, os.path.join(self.tooloutdir, "test1_log_outfiletxt") + ) + + def moveRunOutputs(self): + """need to move files into toolfactory collection after any run - planemo or not + """ + for p in self.outfiles: + naym = p[ONAMEPOS] + src = os.path.join(self.tooloutdir,naym) + if os.path.isfile(src): + dest = os.path.join(self.testdir, "%s_sample" % naym) + shutil.copyfile(naym, dest) + else: + print('### problem - output file %s not found in tooloutdir %s' % (src,self.tooloutdir)) + with os.scandir(self.tooloutdir) as outs: for entry in outs: - if entry.name.endswith('.tgz') or not entry.is_file(): + if not entry.is_file() or entry.name.startswith('.'): continue - if entry.name in repoutnames: - if '.' in entry.name: - ofne = os.path.splitext(entry.name)[1] - else: - ofne = '.txt' - ofn = '%s%s' % (entry.name.replace('.','_'),ofne) - shutil.copyfile(entry.name,os.path.join(self.repdir,ofn)) - elif entry.name == "%s.xml" % self.tool_name: - shutil.copyfile(entry.name,os.path.join(self.repdir,"new_tool_xml.xml")) - return retval + if "." in entry.name: + nayme,ext = os.path.splitext(entry.name) + else: + ext = ".txt" + ofn = "%s%s" % (entry.name.replace(".", "_"), ext) + dest = os.path.join(self.repdir, ofn) + src = os.path.join(self.tooloutdir,entry.name) + shutil.copyfile(src, dest) def run(self): """ @@ -655,15 +655,12 @@ if self.args.parampass != "0": ste = open(self.elog, "wb") if self.lastclredirect: - sto = open( - self.lastclredirect[1], "wb" - ) # is name of an output file + sto = open(self.lastclredirect[1], "wb") # is name of an output file else: sto = open(self.tlog, "wb") sto.write( bytes( - "## Executing Toolfactory generated command line = %s\n" - % scl, + "## Executing Toolfactory generated command line = %s\n" % scl, "utf8", ) ) @@ -683,7 +680,7 @@ pass tmp_stderr.close() retval = p.returncode - else: # work around special case of simple scripts that take stdin and write to stdout + else: # work around special case - stdin and write to stdout sti = open(self.infiles[0][IPATHPOS], "rb") sto = open(self.outfiles[0][ONAMEPOS], "wb") # must use shell to redirect @@ -700,142 +697,222 @@ logging.debug("run done") return retval - def install_load(self): - testres = self.planemo_test() - if testres == 0: - self.planemo_shedload() - self,eph_galaxy_load() - else: - stderr.write('Planemo test failed - tool %s was not installed' % self.args.tool_name) - - def planemo_shedload(self): """ planemo shed_create --shed_target testtoolshed planemo shed_update --check_diff --shed_target testtoolshed """ - cll = ['planemo', 'shed_create', '--shed_target','local'] - p = subprocess.run(cll, shell=False,cwd=self.tooloutdir ) + if os.path.exists(self.tlog): + tout = open(self.tlog,'a') + else: + tout = open(self.tlog,'w') + cll = ["planemo", "shed_create", "--shed_target", "local"] + try: + p = subprocess.run(cll, shell=False, cwd=self.tooloutdir, stdout=tout, stderr = tout) + except: + pass if p.returncode != 0: - print('Repository %s exists' % self.args.tool_name) + print("Repository %s exists" % self.args.tool_name) else: - print('initiated %s' % self.args.tool_name) - cll = ['planemo', 'shed_upload', '--shed_target','local','-r','--owner','fubar', - '--name',self.args.tool_name,'--shed_key',self.args.toolshed_api_key,'--tar',self.newtarpath] - p = subprocess.run(cll, shell=False,cwd=self.tooloutdir) - print('Ran',' '.join(cll),'got',p.returncode) + print("initiated %s" % self.args.tool_name) + cll = [ + "planemo", + "shed_upload", + "--shed_target", + "local", + "--owner", + "fubar", + "--name", + self.args.tool_name, + "--shed_key", + self.args.toolshed_api_key, + "--tar", + self.newtarpath, + ] + print("Run", " ".join(cll)) + p = subprocess.run(cll, shell=False) + print("Ran", " ".join(cll), "got", p.returncode) + tout.close() return p.returncode - - def planemo_test(self): + def planemo_test(self, genoutputs=True): """planemo is a requirement so is available """ - cll = ['planemo', 'test', '--galaxy_root', self.args.galaxy_root, - self.args.tool_name] - p = subprocess.run(cll, shell=False) - ols = os.listdir('.') - for fn in ols: - if '.' in fn: - ofne = os.path.splitext(fn)[1] - else: - ofne = '.txt' - ofn = '%s%s' % (fn.replace('.','_'),ofne) - shutil.copyfile(fn,os.path.join(self.repdir,ofn)) + xreal = "%s.xml" % self.tool_name + if os.path.exists(self.tlog): + tout = open(self.tlog,'a') + else: + tout = open(self.tlog,'w') + if genoutputs: + cll = [ + "planemo", + "test", + "--galaxy_root", + self.args.galaxy_root, + "--update_test_data", + xreal, + ] + else: + cll = ["planemo", "test", "--galaxy_root", self.args.galaxy_root, xreal] + try: + p = subprocess.run(cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout) + except: + pass + tout.close() return p.returncode - def eph_galaxy_load(self): """ """ - cll = ['shed-tools', 'install', '-g', self.args.galaxy_url, '--latest', - '-a', self.args.galaxy_api_key , '--name', self.args.tool_name, '--owner','fubar', - '--toolshed', self.args.toolshed_url, - '--section_label','Generated Tools','--install_tool_dependencies',] - print('running\n',' '.join(cll)) - p = subprocess.run(cll, shell=False) + if os.path.exists(self.tlog): + tout = open(self.tlog,'a') + else: + tout = open(self.tlog,'w') + cll = [ + "shed-tools", + "install", + "-g", + self.args.galaxy_url, + "--latest", + "-a", + self.args.galaxy_api_key, + "--name", + self.args.tool_name, + "--owner", + "fubar", + "--toolshed", + self.args.toolshed_url, + "--section_label", + "Generated Tools", + "--install_tool_dependencies", + ] + print("running\n", " ".join(cll)) + p = subprocess.run(cll, shell=False, stderr=tout, stdout=tout) if p.returncode != 0: - print('Repository %s installation returned %d' % (self.args.tool_name,p.retcode)) + print( + "Repository %s installation returned %d" + % (self.args.tool_name, p.returncode) + ) else: - print('installed %s' % self.args.tool_name) + print("installed %s" % self.args.tool_name) + tout.close() return p.returncode def writeShedyml(self): - yuser = self.args.user_email.split('@')[0] - yfname = os.path.join(self.tooloutdir,'.shed.yml') - yamlf = open(yfname, 'w') - odict = {'name':self.tool_name,'owner':yuser,'type':'unrestricted','description':self.args.tool_desc} + yuser = self.args.user_email.split("@")[0] + yfname = os.path.join(self.tooloutdir, ".shed.yml") + yamlf = open(yfname, "w") + odict = { + "name": self.tool_name, + "owner": yuser, + "type": "unrestricted", + "description": self.args.tool_desc, + } yaml.dump(odict, yamlf, allow_unicode=True) yamlf.close() + + def install_load(self): + _ = self.planemo_test(genoutputs=True) + testres = self.planemo_test(genoutputs=False) + if testres == 0: + if self.args.make_Tool == "install": + self.planemo_shedload() + self.eph_galaxy_load() + else: + os.stderr.write( + "Planemo test failed - tool %s was not installed" % self.args.tool_name + ) + def main(): """ This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as: - <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript" + <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" + --tool_name "foo" --interpreter "Rscript" </command> """ parser = argparse.ArgumentParser() a = parser.add_argument - a("--script_path", default="") - a("--dependencies", default="") - a("--cl_override", default="") + a("--script_path", default=None) + a("--history_test", default=None) + a("--cl_prefix", default=None) + a("--sysexe", default=None) + a("--packages", default=None) a("--tool_name", default=None) - a("--interpreter_name", default=None) - a("--interpreter_version", default=None) - a("--exe_package", default=None) - a("--exe_package_version", default=None) a("--input_files", default=[], action="append") a("--output_files", default=[], action="append") a("--user_email", default="Unknown") a("--bad_user", default=None) - a("--make_Tool", default=None) + a("--make_Tool", default="runonly") a("--help_text", default=None) a("--tool_desc", default=None) a("--tool_version", default=None) a("--citations", default=None) + a("--command_override", default=None) + a("--test_override", default=None) a("--additional_parameters", action="append", default=[]) a("--edit_additional_parameters", action="store_true", default=False) a("--parampass", default="positional") a("--tfout", default="./tfout") a("--new_tool", default="new_tool") a("--runmode", default=None) - a("--galaxy_url", default="http://localhost") - a("--galaxy_api_key", default='fakekey') + a("--galaxy_url", default="http://localhost:8080") + a("--galaxy_api_key", default="fbdd3c2eecd191e88939fffc02eeeaf8") a("--toolshed_url", default="http://localhost:9009") - a("--toolshed_api_key", default=None) - a("--planemo_test", default="yes") + a("--toolshed_api_key", default="d46e5ed0e242ed52c6e1f506b5d7f9f7") + a("--galaxy_root", default="/home/ross/galaxy") args = parser.parse_args() assert not args.bad_user, ( 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to "admin_users" in the Galaxy configuration file' % (args.bad_user, args.bad_user) ) + assert args.tool_name, "## Tool Factory expects a tool name - eg --tool_name=DESeq" assert ( - args.tool_name - ), "## Tool Factory expects a tool name - eg --tool_name=DESeq" - assert ( - args.interpreter_name or args.exe_package + args.sysexe or args.packages ), "## Tool Factory wrapper expects an interpreter or an executable package" - assert args.exe_package or ( - len(args.script_path) > 0 and os.path.isfile(args.script_path) - ), "## Tool Factory wrapper expects a script path - eg --script_path=foo.R if no executable" - args.input_files = [ - x.replace('"', "").replace("'", "") for x in args.input_files - ] + args.input_files = [x.replace('"', "").replace("'", "") for x in args.input_files] # remove quotes we need to deal with spaces in CL params for i, x in enumerate(args.additional_parameters): - args.additional_parameters[i] = args.additional_parameters[i].replace( - '"', "" - ) + args.additional_parameters[i] = args.additional_parameters[i].replace('"', "") r = ScriptRunner(args) - if args.make_Tool: - r.writeShedyml() - retcode = r.makeTooltar() - if retcode == 0: - if args.planemo_test == "yes": - r.install_load() + r.writeShedyml() + r.makeTool() + if args.make_Tool == "runonly": + retcode = r.run() + if retcode: + sys.stderr.write( + "## Run failed with return code %d. Cannot build yet. Please fix and retry" + % retcode + ) + sys.exit(1) + else: + r.moveRunOutputs() + elif args.make_Tool in ["gentestinstall", "generate", "gentest"]: + retcode = r.run() + if retcode: + sys.stderr.write( + "## Run failed with return code %d. Cannot build yet. Please fix and retry" + % retcode + ) + sys.exit(1) + r.moveRunOutputs() + r.makeToolTar() + if args.make_Tool in ["gentestinstall","gentest"]: + r.planemo_test(genoutputs=False) + r.moveRunOutputs() + r.planemo_shedload() + r.eph_galaxy_load() else: - retcode = r.run() - # if retcode: + retcode = r.planemo_test(genoutputs=True) # this fails :( + r.moveRunOutputs() + r.makeToolTar() + retcode = r.planemo_test(genoutputs=False) + r.moveRunOutputs() + if args.make_Tool == "planemotestinstall": + r.planemo_shedload() + r.eph_galaxy_load() + # if retcode: # sys.exit(retcode) # indicate failure to job runner