Mercurial > repos > fubar > tool_factory_2
diff toolfactory/rgToolFactory2.py @ 38:a30536c100bf draft
Updated history outputs
| author | fubar |
|---|---|
| date | Wed, 12 Aug 2020 01:43:46 -0400 |
| parents | ce2b1f8ea68d |
| children | 2cd6555baf44 |
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--- a/toolfactory/rgToolFactory2.py Mon Aug 10 23:25:51 2020 -0400 +++ b/toolfactory/rgToolFactory2.py Wed Aug 12 01:43:46 2020 -0400 @@ -1,3 +1,4 @@ +#!/usr/bin/env python # rgToolFactory.py # see https://github.com/fubar2/toolfactory # @@ -33,40 +34,45 @@ import galaxyxml.tool as gxt import galaxyxml.tool.parameters as gxtp + import lxml -foo = lxml.__name__ # fug you, flake8. Say my name! Please accept the PR, Helena! - -progname = os.path.split(sys.argv[0])[1] myversion = "V2.1 July 2020" verbose = True debug = True toolFactoryURL = "https://github.com/fubar2/toolfactory" ourdelim = "~~~" -# --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label~~~$input_help" +# --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label +# ~~~$input_help" IPATHPOS = 0 ICLPOS = 1 IFMTPOS = 2 ILABPOS = 3 IHELPOS = 4 IOCLPOS = 5 + # --output_files "$otab.history_name~~~$otab.history_format~~~$otab.CL ONAMEPOS = 0 OFMTPOS = 1 OCLPOS = 2 OOCLPOS = 3 -# --additional_parameters="$i.param_name~~~$i.param_value~~~$i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL" +# --additional_parameters="$i.param_name~~~$i.param_value~~~ +# $i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL~~~i$.param_CLoverride" ANAMEPOS = 0 AVALPOS = 1 ALABPOS = 2 AHELPPOS = 3 ATYPEPOS = 4 ACLPOS = 5 -AOCLPOS = 6 +AOVERPOS = 6 +AOCLPOS = 7 +foo = len(lxml.__version__) +# fug you, flake8. Say my name! + def timenow(): """return current time as a string """ @@ -108,9 +114,11 @@ citation_tuples = [] for citation in citations: if citation.startswith("doi"): - citation_tuples.append(("doi", citation[len("doi"):].strip())) + citation_tuples.append(("doi", citation[len("doi") :].strip())) else: - citation_tuples.append(("bibtex", citation[len("bibtex"):].strip())) + citation_tuples.append( + ("bibtex", citation[len("bibtex") :].strip()) + ) return citation_tuples @@ -144,7 +152,6 @@ ], 'Parameter passing in args.parampass must be "0","positional" or "argparse"' self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name) self.tool_id = self.tool_name - self.xmlfile = "%s.xml" % self.tool_name if self.args.interpreter_name: exe = "$runMe" else: @@ -177,25 +184,41 @@ clsuffix = [] xclsuffix = [] for i, p in enumerate(self.infiles): - appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS]] + if p[IOCLPOS] == "STDIN": + appendme = [ + p[IOCLPOS], + p[ICLPOS], + p[IPATHPOS], + "< %s" % p[IPATHPOS], + ] + xappendme = [ + p[IOCLPOS], + p[ICLPOS], + p[IPATHPOS], + "< $%s" % p[ICLPOS], + ] + else: + appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS], ""] + xappendme = [p[IOCLPOS], p[ICLPOS], "$%s" % p[ICLPOS], ""] clsuffix.append(appendme) - xclsuffix.append([p[IOCLPOS], p[ICLPOS], "$%s" % p[ICLPOS]]) + xclsuffix.append(xappendme) # print('##infile i=%d, appendme=%s' % (i,appendme)) for i, p in enumerate(self.outfiles): if p[OOCLPOS] == "STDOUT": self.lastclredirect = [">", p[ONAMEPOS]] self.lastxclredirect = [">", "$%s" % p[OCLPOS]] - # print('##outfiles i=%d lastclredirect = %s' % (i,self.lastclredirect)) else: - appendme = [p[OOCLPOS], p[OCLPOS], p[ONAMEPOS]] - clsuffix.append(appendme) - xclsuffix.append([p[OOCLPOS], p[OCLPOS], "$%s" % p[ONAMEPOS]]) - # print('##outfiles i=%d' % i,'appendme',appendme) + clsuffix.append([p[OOCLPOS], p[OCLPOS], p[ONAMEPOS], ""]) + xclsuffix.append( + [p[OOCLPOS], p[OCLPOS], "$%s" % p[ONAMEPOS], ""] + ) for p in self.addpar: - appendme = [p[AOCLPOS], p[ACLPOS], p[AVALPOS]] - clsuffix.append(appendme) - xclsuffix.append([p[AOCLPOS], p[ACLPOS], '"$%s"' % p[ANAMEPOS]]) - # print('##adpar %d' % i,'appendme=',appendme) + clsuffix.append( + [p[AOCLPOS], p[ACLPOS], p[AVALPOS], p[AOVERPOS]] + ) + xclsuffix.append( + [p[AOCLPOS], p[ACLPOS], '"$%s"' % p[ANAMEPOS], p[AOVERPOS]] + ) clsuffix.sort() xclsuffix.sort() self.xclsuffix = xclsuffix @@ -213,13 +236,17 @@ 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.args.interpreter_name) ) 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]) + 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) artifact = open(art, "wb") artifact.write(bytes(self.script, "utf8")) @@ -282,13 +309,13 @@ def clpositional(self): # inputs in order then params aCL = self.cl.append - for (o_v, k, v) in self.clsuffix: + for (o_v, k, v, koverride) in self.clsuffix: if " " in v: aCL("%s" % v) else: aCL(v) aXCL = self.xmlcl.append - for (o_v, k, v) in self.xclsuffix: + for (o_v, k, v, koverride) in self.xclsuffix: aXCL(v) if self.lastxclredirect: aXCL(self.lastxclredirect[0]) @@ -300,15 +327,19 @@ aCL = self.cl.append aXCL = self.xmlcl.append # inputs then params in argparse named form - for (o_v, k, v) in self.xclsuffix: - if len(k.strip()) == 1: + for (o_v, k, v, koverride) in self.xclsuffix: + if koverride > "": + k = koverride + elif len(k.strip()) == 1: k = "-%s" % k else: k = "--%s" % k aXCL(k) aXCL(v) - for (o_v, k, v) in self.clsuffix: - if len(k.strip()) == 1: + for (o_v, k, v, koverride) in self.clsuffix: + if koverride > "": + k = koverride + elif len(k.strip()) == 1: k = "-%s" % k else: k = "--%s" % k @@ -339,7 +370,9 @@ 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) + tp = gxtp.TestOutput( + name=newcl, value="%s_sample" % newcl, format=newfmt + ) self.testparam.append(tp) for p in self.infiles: newname = p[ICLPOS] @@ -363,7 +396,7 @@ tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname) self.testparam.append(tparm) for p in self.addpar: - newname, newval, newlabel, newhelp, newtype, newcl, oldcl = p + newname, newval, newlabel, newhelp, newtype, newcl, override, oldcl = p if not len(newlabel) > 0: newlabel = newname ndash = self.getNdash(newname) @@ -434,7 +467,9 @@ 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): @@ -445,7 +480,7 @@ """ self.tool.command_line_override = self.xmlcl if self.args.interpreter_name: - self.tool.interpreter = self.interp + 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] @@ -462,7 +497,9 @@ if self.args.interpreter_name: if self.args.interpreter_name == "python": requirements.append( - gxtp.Requirement("package", "python", self.args.interpreter_version) + gxtp.Requirement( + "package", "python", self.args.interpreter_version + ) ) elif self.args.interpreter_name not in ["bash", "sh"]: requirements.append( @@ -476,14 +513,16 @@ if self.args.exe_package and self.args.parampass != "system": requirements.append( gxtp.Requirement( - "package", self.args.exe_package, self.args.exe_package_version + "package", + self.args.exe_package, + self.args.exe_package_version, ) ) self.tool.requirements = requirements if self.args.parampass == "0": - self.doXMLNoparam() + self.doNoXMLparam() else: - self.doXMLParam() + self.doXMLparam() self.tool.outputs = self.toutputs self.tool.inputs = self.tinputs if self.args.runmode not in ["Executable", "system"]: @@ -505,7 +544,7 @@ "Cite: Creating re-usable tools from scripts doi: 10.1093/bioinformatics/bts573" ) exml = self.tool.export() - xf = open(self.xmlfile, "w") + xf = open('%s.xml' % self.tool_name, "w") xf.write(exml) xf.write("\n") xf.close() @@ -520,7 +559,9 @@ """ retval = self.run() if retval: - sys.stderr.write("## Run failed. Cannot build yet. Please fix and retry") + sys.stderr.write( + "## Run failed. Cannot build yet. Please fix and retry" + ) sys.exit(1) tdir = "tfout" if not os.path.exists(tdir): @@ -549,19 +590,32 @@ 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(testdir, "test1_log.txt")) + shutil.copyfile(self.tlog, os.path.join(testdir, "test1_log_outfiletxt")) if self.args.runmode not in ["Executable", "system"]: stname = os.path.join(tdir, "%s" % (self.sfile)) if not os.path.exists(stname): shutil.copyfile(self.sfile, stname) - xtname = os.path.join(tdir, self.xmlfile) - if not os.path.exists(xtname): - shutil.copyfile(self.xmlfile, xtname) + xreal = '%s.xml' % self.tool_name + xout = os.path.join(tdir,xreal) + shutil.copyfile(xreal, xout) tarpath = "toolfactory_%s.tgz" % self.tool_name tf = tarfile.open(tarpath, "w:gz") tf.add(name=tdir, arcname=self.tool_name) tf.close() shutil.copyfile(tarpath, self.args.new_tool) + shutil.copyfile(xreal,"tool_xml.txt") + repdir = "TF_run_report_tempdir" + if not os.path.exists(repdir): + os.mkdir(repdir) + repoutnames = [x[OCLPOS] for x in self.outfiles] + with os.scandir('.') as outs: + for entry in outs: + if entry.name.endswith('.tgz') or not entry.is_file(): + continue + if entry.name in repoutnames: + shutil.copyfile(entry.name,os.path.join(repdir,entry.name)) + elif entry.name == "%s.xml" % self.tool_name: + shutil.copyfile(entry.name,os.path.join(repdir,"new_tool_xml")) return retval def run(self): @@ -577,12 +631,15 @@ 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", ) ) @@ -654,17 +711,23 @@ '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 ), "## 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: retcode = r.makeTooltar()