annotate toolfactory/rgToolFactory2.py @ 99:d4d88d393285 draft

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# replace with shebang for biocontainer
# 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.
# well well. sh run_tests.sh --id rgtf2 --report_file tool_tests_tool_conf.html functional.test_toolbox
# does the needful. Use GALAXY_TEST_SAVE /foo to save outputs - only the tar.gz - not the rest sadly
# GALAXY_TEST_NO_CLEANUP GALAXY_TEST_TMP_DIR=wherever
# planemo test --engine docker_galaxy --test_data ./test-data/ --docker_extra_volume ./test-data rgToolFactory2.xml

import argparse
import datetime
import json
import logging
import os
import re
import shutil
import subprocess
import sys
import tarfile
import tempfile
import time


from bioblend import toolshed

# import docker

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.sysexe:
            self.executeme = self.args.sysexe
        else:
            if self.args.packages:
                self.executeme = self.args.packages.split(",")[0].split(":")[0]
            else:
                self.executeme = None
        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.newtool = gxt.Tool(
            self.args.tool_name,
            self.tool_id,
            self.args.tool_version,
            self.args.tool_desc,
            FAKEEXE,
        )
        self.newtarpath = "toolfactory_%s.tgz" % self.tool_name
        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.script_path:
                aCL(self.executeme)
                aCL(self.sfile)
                aXCL(self.executeme)
                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
        aXCL = self.xmlcl.append

        if len(self.infiles) > 0:
            aCL("<")
            aCL(self.infiles[0][IPATHPOS])
            aXCL("<")
            aXCL("$%s" % self.infiles[0][ICLPOS])
        if len(self.outfiles) > 0:
            aCL(">")
            aCL(self.outfiles[0][OCLPOS])
            aXCL(">")
            aXCL("$%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:
                aparm.positional = int(oldcl)
            self.tinputs.append(aparm)
            tparm = gxtp.TestParam(newname, value=newval)
            self.testparam.append(tparm)

    def doNoXMLparam(self):
        """filter style package - stdin to stdout"""
        if len(self.infiles) > 0:
            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)
        if len(self.outfiles) > 0:
            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.newtool.command_override = self.command_override  # config file
        else:
            self.newtool.command_override = self.xmlcl
        if self.args.help_text:
            helptext = open(self.args.help_text, "r").readlines()
            safertext = [html_escape(x) for x in helptext]
            if False and self.args.script_path:
                scrp = self.script.split("\n")
                scrpt = ["   %s" % x for x in scrp]  # try to stop templating
                scrpt.insert(0, "```\n")
                if len(scrpt) > 300:
                    safertext = (
                        safertext + scrpt[:100] + \
                        [">500 lines - stuff deleted", "......"] + scrpt[-100:]
                    )
                else:
                    safertext = safertext + scrpt
                safertext.append("\n```")
            self.newtool.help = "\n".join([x for x in safertext])
        else:
            self.newtool.help = (
                "Please ask the tool author (%s) for help \
              as none was supplied at tool generation\n"
                % (self.args.user_email)
            )
        self.newtool.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.newtool.requirements = requirements
        if self.args.parampass == "0":
            self.doNoXMLparam()
        else:
            self.doXMLparam()
        self.newtool.outputs = self.toutputs
        self.newtool.inputs = self.tinputs
        if self.args.script_path:
            configfiles = gxtp.Configfiles()
            configfiles.append(gxtp.Configfile(name="runme", text=self.script))
            self.newtool.configfiles = configfiles
        tests = gxtp.Tests()
        test_a = gxtp.Test()
        for tp in self.testparam:
            test_a.append(tp)
        tests.append(test_a)
        self.newtool.tests = tests
        self.newtool.add_comment(
            "Created by %s at %s using the Galaxy Tool Factory."
            % (self.args.user_email, timenow())
        )
        self.newtool.add_comment("Source in git at: %s" % (toolFactoryURL))
        self.newtool.add_comment(
            "Cite: Creating re-usable tools from scripts doi: \
            10.1093/bioinformatics/bts573"
        )
        exml0 = self.newtool.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
        exml = exml.replace('range="1:"', 'range="1000:"')
        xf = open("%s.xml" % self.tool_name, "w")
        xf.write(exml)
        xf.write("\n")
        xf.close()
        # ready for the tarball

    def run(self):
        """
        generate test outputs by running a command line
        won't work if command or test override in play - planemo is the
        easiest way to generate test outputs for that case so is
        automagically selected
        """
        scl = " ".join(self.cl)
        err = None
        if self.args.parampass != "0":
            if os.path.exists(self.elog):
                ste = open(self.elog, "a")
            else:
                ste = open(self.elog, "w")
            if self.lastclredirect:
                sto = open(self.lastclredirect[1], "wb")  # is name of an output file
            else:
                if os.path.exists(self.tlog):
                    sto = open(self.tlog, "a")
                else:
                    sto = open(self.tlog, "w")
                sto.write(
                    "## Executing Toolfactory generated command line = %s\n" % scl
                )
            sto.flush()
            subp = subprocess.run(self.cl, shell=False, stdout=sto, stderr=ste)
            sto.close()
            ste.close()
            retval = subp.returncode
        else:  # work around special case - stdin and write to stdout
            if len(self.infiles) > 0:
                sti = open(self.infiles[0][IPATHPOS], "rb")
            else:
                sti = sys.stdin
            if len(self.outfiles) > 0:
                sto = open(self.outfiles[0][ONAMEPOS], "wb")
            else:
                sto = sys.stdout
            subp = subprocess.run(self.cl, shell=False, stdout=sto, stdin=sti)
            sto.write("## Executing Toolfactory generated command line = %s\n" % scl)
            retval = subp.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 gal_tool_test(self):
        """
        This handy script writes test outputs even if they don't exist
        galaxy-tool-test [-h] [-u GALAXY_URL] [-k KEY] [-a ADMIN_KEY] [--force_path_paste] [-t TOOL_ID] [--tool-version TOOL_VERSION]
        [-i TEST_INDEX] [-o OUTPUT] [--append] [-j OUTPUT_JSON] [--verbose] [-c CLIENT_TEST_CONFIG]
        galaxy-tool-test -u http://localhost:8080 -a 3c9afe09f1b7892449d266109639c104 -o /tmp/foo -t hello -j /tmp/foo/hello.json --verbose
        handy - just leaves outputs in -o
        """
        if os.path.exists(self.tlog):
            tout = open(self.tlog, "a")
        else:
            tout = open(self.tlog, "w")
        testouts = tempfile.mkdtemp(suffix=None, prefix="tftemp")
        dummy, tfile = tempfile.mkstemp()
        cll = [
            os.path.join(self.args.tool_dir,"galaxy-tool-test"),
            "-u",
            self.args.galaxy_url,
            "-k",
            self.args.galaxy_api_key,
            "-t",
            self.args.tool_name,
            "-o",
            testouts,
        ]
        subp = subprocess.run(
           cll, shell=False, stderr=dummy, stdout=dummy
        )
        outfiles = []
        for p in self.outfiles:
            oname = p[ONAMEPOS]
            outfiles.append(oname)
        with os.scandir(testouts) as outs:
            for entry in outs:
                if not entry.is_file():
                    continue
                dest = os.path.join(self.tooloutdir, entry.name)
                src = os.path.join(testouts, entry.name)
                shutil.copyfile(src, dest)
                dest = os.path.join(self.testdir, entry.name)
                src = os.path.join(testouts, entry.name)
                shutil.copyfile(src, dest)
                dest = os.path.join(self.repdir,f"{entry.name}_sample")
                tout.write(f"## found and moved output {entry.name} to {dest}\n")
        tout.close()
        shutil.rmtree(testouts)
        return subp.returncode

    def gal_test(self):
        """
        Uses the built in galaxy tool tester run_test.sh

        export GALAXY_TEST_SAVE="./foo" && export GALAXY_TEST_NO_CLEANUP="1" \
        && export GALAXY_TEST_TMP_DIR=./foo && sh run_tests.sh --id rgtf2 --report_file tool_tests_tool_conf.html functional.test_toolbox

        """
        testdir = tempfile.mkdtemp(suffix=None, prefix="tftemp")
        tool_test_rep = f"{self.tool_name}_galaxy_test_report_html.html"
        if os.path.exists(self.tlog):
            tout = open(self.tlog, "a")
        else:
            tout = open(self.tlog, "w")

        ourenv = os.environ
        ourenv["GALAXY_TEST_SAVE"] = testdir
        ourenv["GALAXY_TEST_NO_CLEANUP"] = "1"
        ourenv["GALAXY_TEST_TMP_DIR"] = testdir

        cll = [
       "sh", f"{self.args.galaxy_root}/run_tests.sh", "--id", self.args.tool_name,
       "--report_file", os.path.join(testdir,tool_test_rep), "functional.test_toolbox",
        ]
        subp = subprocess.run(
            cll, env = ourenv,
            shell=False, cwd=self.args.galaxy_root, stderr=tout, stdout=tout
        )
        src = os.path.join(testdir, tool_test_rep)
        if os.path.isfile(src):
            dest = os.path.join(self.repdir, tool_test_rep)
            shutil.copyfile(src, dest)
        else:
            tout.write(f"### {src} not found\n")
        tout.close()
        return subp.returncode


    def shedLoad(self):
        """
        {'deleted': False,
              'description': 'Tools for manipulating data',
              'id': '175812cd7caaf439',
              'model_class': 'Category',
              'name': 'Text Manipulation',
              'url': '/api/categories/175812cd7caaf439'}]


        """
        if os.path.exists(self.tlog):
            sto = open(self.tlog, "a")
        else:
            sto = open(self.tlog, "w")

        ts = toolshed.ToolShedInstance(
            url=self.args.toolshed_url, key=self.args.toolshed_api_key, verify=False
        )
        repos = ts.repositories.get_repositories()
        rnames = [x.get("name", "?") for x in repos]
        rids = [x.get("id", "?") for x in repos]
        sto.write(f"############names={rnames} rids={rids}\n")
        tfcat = "ToolFactory generated tools"
        if self.args.tool_name not in rnames:
            tscat = ts.categories.get_categories()
            cnames = [x.get("name", "?").strip() for x in tscat]
            cids = [x.get("id", "?") for x in tscat]
            catID = None
            if tfcat.strip() in cnames:
                ci = cnames.index(tfcat)
                catID = cids[ci]
            res = ts.repositories.create_repository(
                name=self.args.tool_name,
                synopsis="Synopsis:%s" % self.args.tool_desc,
                description=self.args.tool_desc,
                type="unrestricted",
                remote_repository_url=self.args.toolshed_url,
                homepage_url=None,
                category_ids=catID,
            )
            tid = res.get("id", None)
            sto.write(f"##########create res={res}\n")
        else:
            i = rnames.index(self.args.tool_name)
            tid = rids[i]
        res = ts.repositories.update_repository(
            id=tid, tar_ball_path=self.newtarpath, commit_message=None
        )
        sto.write(f"#####update res={res}\n")
        sto.close()

    def eph_galaxy_load(self):
        """load the new tool from the local toolshed after planemo uploads it"""
        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",
            "ToolFactory",
        ]
        tout.write("running\n%s\n" % " ".join(cll))
        subp = subprocess.run(cll, shell=False, stderr=tout, stdout=tout)
        tout.write(
            "installed %s - got retcode %d\n" % (self.args.tool_name, subp.returncode)
        )
        tout.close()
        return subp.returncode

    def planemo_shedLoad(self):
        """
        planemo shed_create --shed_target testtoolshed
        planemo shed_init --name=<name>
                  --owner=<shed_username>
                  --description=<short description>
                  [--remote_repository_url=<URL to .shed.yml on github>]
                  [--homepage_url=<Homepage for tool.>]
                  [--long_description=<long description>]
                  [--category=<category name>]*


        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")
        ts = toolshed.ToolShedInstance(
            url=self.args.toolshed_url, key=self.args.toolshed_api_key, verify=False
        )
        repos = ts.repositories.get_repositories()
        rnames = [x.get("name", "?") for x in repos]
        rids = [x.get("id", "?") for x in repos]
        #cat = "ToolFactory generated tools"
        if self.args.tool_name not in rnames:
            cll = [
                "planemo",
                "shed_create",
                "--shed_target",
                "local",
                "--owner",
                "fubar",
                "--name",
                self.args.tool_name,
                "--shed_key",
                self.args.toolshed_api_key,
            ]
            try:
                subp = subprocess.run(
                    cll, shell=False, cwd=self.tooloutdir, stdout=tout, stderr=tout
                )
            except:
                pass
            if subp.returncode != 0:
                tout.write("Repository %s exists\n" % self.args.tool_name)
            else:
                tout.write("initiated %s\n" % 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,
        ]
        subp = subprocess.run(cll, shell=False, stdout=tout, stderr=tout)
        tout.write("Ran %s got %d\n" % (" ".join(cll),subp.returncode))
        tout.close()
        return subp.returncode

    def eph_test(self, genoutputs=True):
        """problem getting jobid - ephemeris upload is the job before the one we want - but depends on how many inputs
        """
        if os.path.exists(self.tlog):
            tout = open(self.tlog, "a")
        else:
            tout = open(self.tlog, "w")
        cll = [
            "shed-tools",
            "test",
            "-g",
            self.args.galaxy_url,
            "-a",
            self.args.galaxy_api_key,
            "--name",
            self.args.tool_name,
            "--owner",
            "fubar",
        ]
        if genoutputs:
            dummy, tfile = tempfile.mkstemp()
            subp = subprocess.run(
               cll, shell=False, stderr=dummy, stdout=dummy
            )

            with open('tool_test_output.json','rb') as f:
                s = json.loads(f.read())
                print('read %s' % s)
                cl = s['tests'][0]['data']['job']['command_line'].split()
                n = cl.index('--script_path')
                jobdir = cl[n+1]
                jobdir = jobdir.replace('"','')
                jobdir = jobdir.split('/configs')[0]
                print('jobdir=%s' % jobdir)

                #"/home/ross/galthrow/database/jobs_directory/000/649/configs/tmptfxu51gs\"
            src = os.path.join(jobdir,'working',self.newtarpath)
            if os.path.exists(src):
                dest = os.path.join(self.testdir, self.newtarpath)
                shutil.copyfile(src, dest)
            else:
                tout.write('No toolshed archive found after first ephemeris test - not a good sign')
            ephouts = os.path.join(jobdir,'working','tfout','test-data')
            with os.scandir(ephouts) as outs:
                for entry in outs:
                    if not entry.is_file():
                        continue
                    dest = os.path.join(self.tooloutdir, entry.name)
                    src = os.path.join(ephouts, entry.name)
                    shutil.copyfile(src, dest)
        else:
            subp = subprocess.run(
               cll, shell=False,  stderr=tout, stdout=tout)
            tout.write("eph_test Ran %s got %d" % (" ".join(cll), subp.returncode))
        tout.close()
        return subp.returncode

    def planemo_test_biocontainer(self, genoutputs=True):
        """planemo is a requirement so is available for testing but testing in a biocontainer
        requires some fiddling to use the hacked galaxy-central .venv

        Planemo runs:
python ./scripts/functional_tests.py -v --with-nosehtml --html-report-file
/export/galaxy-central/database/job_working_directory/000/17/working/TF_run_report_tempdir/tacrev_planemo_test_report.html
--with-xunit --xunit-file /tmp/tmpt90p7f9h/xunit.xml --with-structureddata
--structured-data-file
/export/galaxy-central/database/job_working_directory/000/17/working/tfout/tool_test_output.json functional.test_toolbox


        for the planemo-biocontainer,
        planemo test --conda_dependency_resolution --skip_venv --galaxy_root /galthrow/ rgToolFactory2.xml

        """
        xreal = "%s.xml" % self.tool_name
        tool_test_path = os.path.join(self.repdir,f"{self.tool_name}_planemo_test_report.html")
        if os.path.exists(self.tlog):
            tout = open(self.tlog, "a")
        else:
            tout = open(self.tlog, "w")
        if genoutputs:
            dummy, tfile = tempfile.mkstemp()
            cll = [
                ".", os.path.join(self.args.galaxy_root,'.venv','bin','activate'),"&&",
                "planemo",
                "test",
                "--test_data", self.testdir,
                "--test_output", tool_test_path,
                "--skip_venv",
                "--galaxy_root",
                self.args.galaxy_root,
                "--update_test_data",
                xreal,
            ]
            subp = subprocess.run(
                cll,
                shell=False,
                cwd=self.tooloutdir,
                stderr=dummy,
                stdout=dummy,
            )

        else:
            cll = [
                ".", os.path.join(self.args.galaxy_root,'.venv','bin','activate'),"&&",
                "planemo",
                "test",
                "--test_data", os.path.self.testdir,
                "--test_output", os.path.tool_test_path,
                "--skip_venv",
                "--galaxy_root",
                self.args.galaxy_root,
                xreal,
            ]
            subp = subprocess.run(
                cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout
            )
        tout.close()
        return subp.returncode

    def planemo_test(self, genoutputs=True):
        """planemo is a requirement so is available for testing but needs a different call if
        in the biocontainer - see above
        and for generating test outputs if command or test overrides are supplied
        test outputs are sent to repdir for display
        planemo test --engine docker_galaxy  --galaxy_root /galaxy-central pyrevpos/pyrevpos.xml

        Planemo runs:
python ./scripts/functional_tests.py -v --with-nosehtml --html-report-file
/export/galaxy-central/database/job_working_directory/000/17/working/TF_run_report_tempdir/tacrev_planemo_test_report.html
--with-xunit --xunit-file /tmp/tmpt90p7f9h/xunit.xml --with-structureddata
--structured-data-file
/export/galaxy-central/database/job_working_directory/000/17/working/tfout/tool_test_output.json functional.test_toolbox


        for the planemo-biocontainer,
        planemo test --conda_dependency_resolution --skip_venv --galaxy_root /galthrow/ rgToolFactory2.xml

        """
        xreal = "%s.xml" % self.tool_name
        tool_test_path = os.path.join(self.repdir,f"{self.tool_name}_planemo_test_report.html")
        if os.path.exists(self.tlog):
            tout = open(self.tlog, "a")
        else:
            tout = open(self.tlog, "w")
        if genoutputs:
            dummy, tfile = tempfile.mkstemp()
            cll = [
                "planemo",
                "test",
                "--galaxy_root",
                self.args.galaxy_root,
                "--update_test_data",
                xreal,
            ]
            subp = subprocess.run(
                cll,
                shell=False,
                cwd=self.testdir,
                stderr=dummy,
                stdout=dummy,
            )

        else:
            cll = [
                "planemo",
                "test",
                "--test_data", self.testdir,
                "--test_output",tool_test_path,
                "--galaxy_root",
                self.args.galaxy_root,
                xreal,
            ]
            subp = subprocess.run(
                cll, shell=False, cwd=self.testdir, stderr=tout, stdout=tout
            )
        tout.close()
        return subp.returncode


    def writeShedyml(self):
        """for planemo"""
        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,
            "synopsis": self.args.tool_desc,
            "category": "TF Generated Tools",
        }
        yaml.dump(odict, yamlf, allow_unicode=True)
        yamlf.close()

    def makeTool(self):
        """write xmls and input 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):
        """move outputs into test-data and prepare the tarball"""
        excludeme = "tool_test_output"

        def exclude_function(tarinfo):
            filename = tarinfo.name
            return (
                None
                if filename.startswith(excludeme)
                else tarinfo
            )

        for p in self.outfiles:
            oname = p[ONAMEPOS]
            tdest = os.path.join(self.testdir, "%s_sample" % oname)
            if not os.path.isfile(tdest):
                src = os.path.join(self.testdir,oname)
                if os.path.isfile(src):
                    shutil.copyfile(src, tdest)
                    dest = os.path.join(self.repdir, "%s.sample" % (oname))
                    shutil.copyfile(src, dest)
                else:
                    print(
                        "### problem - output file %s not found in testdir %s"
                        % (tdest, self.testdir)
                    )
        tf = tarfile.open(self.newtarpath, "w:gz")
        tf.add(name=self.tooloutdir, arcname=self.tool_name, filter=exclude_function)
        tf.close()
        shutil.copyfile(self.newtarpath, self.args.new_tool)

    def moveRunOutputs(self):
        """need to move planemo or run outputs into toolfactory collection"""
        with os.scandir(self.tooloutdir) as outs:
            for entry in outs:
                if not entry.is_file():
                    continue
                if "." in entry.name:
                    nayme, ext = os.path.splitext(entry.name)
                    if ext in ['.yml','.xml','.json','.yaml']:
                        ext = f'{ext}.txt'
                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)
        with os.scandir(self.testdir) as outs:
            for entry in outs:
                if not entry.is_file():
                    continue
                if "." in entry.name:
                    nayme, ext = os.path.splitext(entry.name)
                else:
                    ext = ".txt"
                newname = f"{entry.name}{ext}"
                dest = os.path.join(self.repdir, newname)
                src = os.path.join(self.testdir, entry.name)
                shutil.copyfile(src, dest)



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="newtool")
    a("--tool_dir", 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("--galaxy_url", default="http://localhost:8080")
    a(
        "--toolshed_url", default="http://localhost:9009")
    # make sure this is identical to tool_sheds_conf.xml  localhost != 127.0.0.1 so validation fails
    a("--toolshed_api_key", default="fakekey")
    a("--galaxy_api_key", default="fakekey")
    a("--galaxy_root", default="/galaxy-central")
    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 == "generate":
        retcode = r.run()
        r.moveRunOutputs()
        r.makeToolTar()
    else:
        r.makeToolTar()
        #r.planemo_shedLoad()
        r.shedLoad()
        r.eph_galaxy_load()
        retcode = r.gal_tool_test()  # writes outputs
        r.makeToolTar()
        #r.planemo_shedLoad()
        r.shedLoad()
        r.eph_galaxy_load()
        retcode = r.gal_test()
        r.moveRunOutputs()
        r.makeToolTar()
        print(f"second galaxy_test returned {retcode}")


if __name__ == "__main__":
    main()