annotate toolfactory/rgToolFactory2.py @ 49:35a912ce0c83 draft

Can now make the bwa example from planemo :)

#!/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
# essential problem is to create two command lines - one for the tool xml and a different
# one to run the executable with the supplied test data and settings
# Be simpler to write the tool, then run it with planemo and soak up the test outputs.



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

import yaml

myversion = "V2.1 July 2020"
verbose = True
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"
IPATHPOS = 0
ICLPOS = 1
IFMTPOS = 2
ILABPOS = 3
IHELPOS = 4
IOCLPOS = 5

# --output_files "$otab.history_name~~~$otab.history_format~~~$otab.CL~~~otab.history_test
ONAMEPOS = 0
OFMTPOS = 1
OCLPOS = 2
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"
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!
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
    """
    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 = {"&": "&amp;", ">": "&gt;", "<": "&lt;", "$": 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("&amp;", "&")
    t = t.replace("&gt;", ">")
    t = t.replace("&lt;", "<")
    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"
        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",
        ], '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.tool = gxt.Tool(
            self.args.tool_name,
            self.tool_id,
            self.args.tool_version,
            self.args.tool_desc,
            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")
        if not os.path.exists(self.tooloutdir):
            os.mkdir(self.tooloutdir)
        if not os.path.exists(self.testdir):
            os.mkdir(self.testdir)  # make tests directory
        if not os.path.exists(self.repdir):
            os.mkdir(self.repdir)
        self.tinputs = gxtp.Inputs()
        self.toutputs = gxtp.Outputs()
        self.testparam = []
        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("$runme")
                else:
                    aCL(self.executeme)  # this little CL will just run
                    aXCL(self.executeme)
            else:
                if self.args.script_path:
                    aCL(self.executeme)
                    aCL(self.sfile)
                    aXCL("$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()
        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)
            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):
        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.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.executeme)
        artifact = open(art, "wb")
        artifact.write(bytes(self.script, "utf8"))
        artifact.close()

    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, test, 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)
            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]
            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):
        """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 but multiple 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...
        """
        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.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.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()
        else:
            self.doXMLparam()
        self.tool.outputs = self.toutputs
        self.tool.inputs = self.tinputs
        if (
            self.args.script_path
        ):
            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"
        )
        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 makeTool(self):
        """write xmls and samples into place
        """
        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)

    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)
        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 not entry.is_file() or entry.name.startswith('.'):
                    continue
                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):
        """

        """
        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 - 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 retval != 0 and err:  # problem
            sys.stderr.write(err)
        logging.debug("run done")
        return retval

    def planemo_shedload(self):
        """
        planemo shed_create --shed_target testtoolshed
        planemo shed_update --check_diff --shed_target testtoolshed
        """
        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)
        else:
            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, genoutputs=True):
        """planemo is a requirement so is available
        """
        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):
        """
        """
        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.returncode)
            )
        else:
            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,
        }
        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>
    """
    parser = argparse.ArgumentParser()
    a = parser.add_argument
    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("--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="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:8080")
    a("--galaxy_api_key", default="fbdd3c2eecd191e88939fffc02eeeaf8")
    a("--toolshed_url", default="http://localhost:9009")
    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.sysexe or args.packages
    ), "## Tool Factory wrapper expects an interpreter or an executable package"
    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)
    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.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


if __name__ == "__main__":
    main()