Mercurial > repos > fubar > mashmap
diff toolfactory/test-data/input1_sample @ 1:0183cad9d13b draft
planemo upload
| author | fubar |
|---|---|
| date | Thu, 22 Feb 2024 10:48:01 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/test-data/input1_sample Thu Feb 22 10:48:01 2024 +0000 @@ -0,0 +1,741 @@ +#!/usr/bin/env python +# rgToolFactory.py +# see https://github.com/fubar2/toolfactory +# +# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012 +# +# all rights reserved +# Licensed under the LGPL +# 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 +# 1. Fix the toolfactory so it works - done for simplest case +# 2. Fix planemo so the toolfactory function works +# 3. Rewrite bits using galaxyxml functions where that makes sense - done +# +# removed all the old complications including making the new tool use this same script +# galaxyxml now generates the tool xml https://github.com/hexylena/galaxyxml +# No support for automatic HTML file creation from arbitrary outputs +# TODO: add option to run that code as a post execution hook +# TODO: add additional history input parameters - currently only one + + +import argparse +import logging +import os +import re +import shutil +import subprocess +import sys +import tarfile +import tempfile +import time + +import galaxyxml.tool as gxt +import galaxyxml.tool.parameters as gxtp + +import lxml + +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 +# ~~~$input_help" +IPATHPOS = 0 +ICLPOS = 1 +IFMTPOS = 2 +ILABPOS = 3 +IHELPOS = 4 +IOCLPOS = 5 + +# --output_files "$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~~~i$.param_CLoverride" +ANAMEPOS = 0 +AVALPOS = 1 +ALABPOS = 2 +AHELPPOS = 3 +ATYPEPOS = 4 +ACLPOS = 5 +AOVERPOS = 6 +AOCLPOS = 7 + + +foo = len(lxml.__version__) +# fug you, flake8. Say my name! + +def timenow(): + """return current time as a string + """ + return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time())) + + +def quote_non_numeric(s): + """return a prequoted string for non-numerics + useful for perl and Rscript parameter passing? + """ + try: + _ = float(s) + return s + except ValueError: + return '"%s"' % s + + +html_escape_table = {"&": "&", ">": ">", "<": "<", "$": r"\$"} + + +def html_escape(text): + """Produce entities within text.""" + return "".join(html_escape_table.get(c, c) for c in text) + + +def html_unescape(text): + """Revert entities within text. Multiple character targets so use replace""" + t = text.replace("&", "&") + t = t.replace(">", ">") + t = t.replace("<", "<") + t = t.replace("\\$", "$") + return t + + +def parse_citations(citations_text): + """ + """ + citations = [c for c in citations_text.split("**ENTRY**") if c.strip()] + citation_tuples = [] + for citation in citations: + if citation.startswith("doi"): + citation_tuples.append(("doi", citation[len("doi") :].strip())) + else: + citation_tuples.append( + ("bibtex", citation[len("bibtex") :].strip()) + ) + return citation_tuples + + +class ScriptRunner: + """Wrapper for an arbitrary script + uses galaxyxml + + """ + + def __init__(self, args=None): + """ + prepare command line cl for running the tool here + and prepare elements needed for galaxyxml tool generation + """ + + self.infiles = [x.split(ourdelim) for x in args.input_files] + self.outfiles = [x.split(ourdelim) for x in args.output_files] + self.addpar = [x.split(ourdelim) for x in args.additional_parameters] + self.args = args + self.cleanuppar() + self.lastclredirect = None + self.lastxclredirect = None + self.cl = [] + self.xmlcl = [] + self.is_positional = self.args.parampass == "positional" + aCL = self.cl.append + assert args.parampass in [ + "0", + "argparse", + "positional", + ], 'Parameter passing in args.parampass must be "0","positional" or "argparse"' + self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name) + self.tool_id = self.tool_name + if self.args.interpreter_name: + exe = "$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, + ) + self.tinputs = gxtp.Inputs() + self.toutputs = gxtp.Outputs() + self.testparam = [] + if ( + self.args.runmode == "Executable" or self.args.runmode == "system" + ): # binary - no need + aCL(self.args.exe_package) # this little CL will just run + else: + self.prepScript() + self.elog = "%s_error_log.txt" % self.tool_name + self.tlog = "%s_runner_log.txt" % self.tool_name + + if self.args.parampass == "0": + self.clsimple() + else: + clsuffix = [] + xclsuffix = [] + for i, p in enumerate(self.infiles): + 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(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], ""] + ) + for p in self.addpar: + 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 + self.clsuffix = clsuffix + if self.args.parampass == "positional": + self.clpositional() + else: + self.clargparse() + + def prepScript(self): + aCL = self.cl.append + rx = open(self.args.script_path, "r").readlines() + rx = [x.rstrip() for x in rx] + rxcheck = [x.strip() for x in rx if x.strip() > ""] + 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) + ) + 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) + artifact = open(art, "wb") + artifact.write(bytes(self.script, "utf8")) + artifact.close() + aCL(self.args.interpreter_name) + aCL(self.sfile) + + def cleanuppar(self): + """ positional parameters are complicated by their numeric ordinal""" + for i, p in enumerate(self.infiles): + if self.args.parampass == "positional": + assert p[ICLPOS].isdigit(), ( + "Positional parameters must be ordinal integers - got %s for %s" + % (p[ICLPOS], p[ILABPOS]) + ) + p.append(p[ICLPOS]) + if p[ICLPOS].isdigit() or self.args.parampass == "0": + scl = "input%d" % (i + 1) + p[ICLPOS] = scl + self.infiles[i] = p + for i, p in enumerate( + self.outfiles + ): # trying to automagically gather using extensions + if self.args.parampass == "positional" and p[OCLPOS] != "STDOUT": + assert p[OCLPOS].isdigit(), ( + "Positional parameters must be ordinal integers - got %s for %s" + % (p[OCLPOS], p[ONAMEPOS]) + ) + p.append(p[OCLPOS]) + if p[OCLPOS].isdigit() or p[OCLPOS] == "STDOUT": + scl = p[ONAMEPOS] + p[OCLPOS] = scl + self.outfiles[i] = p + for i, p in enumerate(self.addpar): + if self.args.parampass == "positional": + assert p[ACLPOS].isdigit(), ( + "Positional parameters must be ordinal integers - got %s for %s" + % (p[ACLPOS], p[ANAMEPOS]) + ) + p.append(p[ACLPOS]) + if p[ACLPOS].isdigit(): + scl = "input%s" % p[ACLPOS] + p[ACLPOS] = scl + self.addpar[i] = p + + def clsimple(self): + """ no parameters - uses < and > for i/o + """ + aCL = self.cl.append + aCL("<") + aCL(self.infiles[0][IPATHPOS]) + aCL(">") + aCL(self.outfiles[0][OCLPOS]) + aXCL = self.xmlcl.append + aXCL("<") + aXCL("$%s" % self.infiles[0][ICLPOS]) + aXCL(">") + aXCL("$%s" % self.outfiles[0][ONAMEPOS]) + + def clpositional(self): + # inputs in order then params + aCL = self.cl.append + 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, koverride) in self.xclsuffix: + aXCL(v) + if self.lastxclredirect: + aXCL(self.lastxclredirect[0]) + aXCL(self.lastxclredirect[1]) + + def clargparse(self): + """ argparse style + """ + aCL = self.cl.append + aXCL = self.xmlcl.append + # inputs then params in argparse named form + 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, koverride) in self.clsuffix: + if koverride > "": + k = koverride + elif len(k.strip()) == 1: + k = "-%s" % k + else: + k = "--%s" % k + aCL(k) + aCL(v) + + def getNdash(self, newname): + if self.is_positional: + ndash = 0 + else: + ndash = 2 + if len(newname) < 2: + ndash = 1 + return ndash + + def doXMLparam(self): + """flake8 made me do this...""" + for p in self.outfiles: + newname, newfmt, newcl, oldcl = p + ndash = self.getNdash(newcl) + aparm = gxtp.OutputData(newcl, format=newfmt, num_dashes=ndash) + aparm.positional = self.is_positional + if self.is_positional: + if oldcl == "STDOUT": + aparm.positional = 9999999 + aparm.command_line_override = "> $%s" % newcl + else: + aparm.positional = int(oldcl) + aparm.command_line_override = "$%s" % newcl + self.toutputs.append(aparm) + tp = gxtp.TestOutput( + name=newcl, value="%s_sample" % newcl, format=newfmt + ) + self.testparam.append(tp) + for p in self.infiles: + newname = p[ICLPOS] + newfmt = p[IFMTPOS] + ndash = self.getNdash(newname) + if not len(p[ILABPOS]) > 0: + alab = p[ICLPOS] + else: + alab = p[ILABPOS] + aninput = gxtp.DataParam( + newname, + optional=False, + label=alab, + help=p[IHELPOS], + format=newfmt, + multiple=False, + num_dashes=ndash, + ) + aninput.positional = self.is_positional + self.tinputs.append(aninput) + tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname) + self.testparam.append(tparm) + for p in self.addpar: + newname, newval, newlabel, newhelp, newtype, newcl, override, oldcl = p + if not len(newlabel) > 0: + newlabel = newname + ndash = self.getNdash(newname) + if newtype == "text": + aparm = gxtp.TextParam( + newname, + label=newlabel, + help=newhelp, + value=newval, + num_dashes=ndash, + ) + elif newtype == "integer": + aparm = gxtp.IntegerParam( + newname, + label=newname, + help=newhelp, + value=newval, + num_dashes=ndash, + ) + elif newtype == "float": + aparm = gxtp.FloatParam( + newname, + label=newname, + help=newhelp, + value=newval, + num_dashes=ndash, + ) + else: + raise ValueError( + 'Unrecognised parameter type "%s" for\ + additional parameter %s in makeXML' + % (newtype, newname) + ) + aparm.positional = self.is_positional + if self.is_positional: + aninput.positional = int(oldcl) + self.tinputs.append(aparm) + self.tparm = gxtp.TestParam(newname, value=newval) + self.testparam.append(tparm) + + def doNoXMLparam(self): + 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" + % str(self.infiles) + ) + assert len(self.infiles) == 1, max1s + newname = self.infiles[0][ICLPOS] + aninput = gxtp.DataParam( + newname, + optional=False, + label=alab, + help=self.infiles[0][IHELPOS], + format=self.infiles[0][IFMTPOS], + multiple=False, + num_dashes=0, + ) + aninput.command_line_override = "< $%s" % newname + aninput.positional = self.is_positional + self.tinputs.append(aninput) + tp = gxtp.TestParam(name=newname, value="%s_sample" % newname) + self.testparam.append(tp) + newname = self.outfiles[0][OCLPOS] + newfmt = self.outfiles[0][OFMTPOS] + anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0) + 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 + ) + self.testparam.append(tp) + + def makeXML(self): + """ + Create a Galaxy xml tool wrapper for the new script + Uses galaxyhtml + Hmmm. How to get the command line into correct order... + """ + self.tool.command_line_override = self.xmlcl + 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] + self.tool.help = "".join([x for x in helptext]) + else: + self.tool.help = ( + "Please ask the tool author (%s) for help \ + as none was supplied at tool generation\n" + % (self.args.user_email) + ) + self.tool.version_command = None # do not want + requirements = gxtp.Requirements() + + if self.args.interpreter_name: + 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, + ) + ) + self.tool.requirements = requirements + if self.args.parampass == "0": + self.doNoXMLparam() + else: + self.doXMLparam() + self.tool.outputs = self.toutputs + self.tool.inputs = self.tinputs + if self.args.runmode not in ["Executable", "system"]: + configfiles = gxtp.Configfiles() + configfiles.append(gxtp.Configfile(name="runMe", text=self.script)) + self.tool.configfiles = configfiles + tests = gxtp.Tests() + test_a = gxtp.Test() + for tp in self.testparam: + test_a.append(tp) + tests.append(test_a) + self.tool.tests = tests + self.tool.add_comment( + "Created by %s at %s using the Galaxy Tool Factory." + % (self.args.user_email, timenow()) + ) + self.tool.add_comment("Source in git at: %s" % (toolFactoryURL)) + self.tool.add_comment( + "Cite: Creating re-usable tools from scripts doi: 10.1093/bioinformatics/bts573" + ) + exml = self.tool.export() + 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 + """ + retval = self.run() + if retval: + sys.stderr.write( + "## Run failed. Cannot build yet. Please fix and retry" + ) + sys.exit(1) + tdir = "tfout" + if not os.path.exists(tdir): + os.mkdir(tdir) + self.makeXML() + testdir = os.path.join(tdir, "test-data") + if not os.path.exists(testdir): + os.mkdir(testdir) # make tests directory + for p in self.infiles: + pth = p[IPATHPOS] + dest = os.path.join(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(testdir, "%s_sample" % p[ONAMEPOS]) + shutil.copyfile(pth, dest) + dest = os.path.join(tdir, p[ONAMEPOS]) + shutil.copyfile(pth, dest) + else: + pth = p[OCLPOS] + dest = os.path.join(testdir, "%s_sample" % p[OCLPOS]) + shutil.copyfile(pth, dest) + dest = os.path.join(tdir, 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(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) + 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): + """ + Some devteam tools have this defensive stderr read so I'm keeping with the faith + Feel free to update. + """ + s = "run cl=%s" % str(self.cl) + + logging.debug(s) + scl = " ".join(self.cl) + err = None + 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 + else: + sto = open(self.tlog, "wb") + sto.write( + bytes( + "## Executing Toolfactory generated command line = %s\n" + % scl, + "utf8", + ) + ) + sto.flush() + p = subprocess.run(self.cl, shell=False, stdout=sto, stderr=ste) + sto.close() + ste.close() + tmp_stderr = open(self.elog, "rb") + err = "" + buffsize = 1048576 + try: + while True: + err += str(tmp_stderr.read(buffsize)) + if not err or len(err) % buffsize != 0: + break + except OverflowError: + pass + tmp_stderr.close() + retval = p.returncode + else: # work around special case of simple scripts that take stdin and write to stdout + sti = open(self.infiles[0][IPATHPOS], "rb") + sto = open(self.outfiles[0][ONAMEPOS], "wb") + # must use shell to redirect + p = subprocess.run(self.cl, shell=False, stdout=sto, stdin=sti) + retval = p.returncode + sto.close() + sti.close() + if os.path.isfile(self.tlog) and os.stat(self.tlog).st_size == 0: + os.unlink(self.tlog) + if os.path.isfile(self.elog) and os.stat(self.elog).st_size == 0: + os.unlink(self.elog) + if p.returncode != 0 and err: # problem + sys.stderr.write(err) + logging.debug("run done") + return retval + + +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> + """ + parser = argparse.ArgumentParser() + a = parser.add_argument + a("--script_path", default="") + 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("--help_text", default=None) + a("--tool_desc", default=None) + a("--tool_version", default=None) + a("--citations", 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) + 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.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 + ] + # 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( + '"', "" + ) + r = ScriptRunner(args) + if args.make_Tool: + retcode = r.makeTooltar() + else: + retcode = r.run() + if retcode: + sys.exit(retcode) # indicate failure to job runner + + +if __name__ == "__main__": + main()