comparison toolfactory/rgToolFactory2.py @ 28:ad564ab3cf7b draft

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# 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 sys
import subprocess
import shutil
import os
import time
import tempfile
import argparse
import tarfile
import re
import galaxyxml.tool as gxt
import galaxyxml.tool.parameters as gxtp
import logging


progname = os.path.split(sys.argv[0])[1]
myversion = 'V2.1 July 2020'
verbose = True
debug = True
toolFactoryURL = 'https://github.com/fubar2/toolfactory'
ourdelim = '~~~'


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 = {
    "&": "&",
    ">": ">",
    "<": "&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
        """
        lastclredirect = None
        self.cl = []
        aCL = self.cl.append
        if args.output_dir:  # simplify for the tool tarball
            os.chdir(args.output_dir)
        self.args = args
        # a sanitizer now does this but..
        self.tool_name = re.sub('[^a-zA-Z0-9_]+', '', args.tool_name)
        self.tool_id = self.tool_name
        self.xmlfile = '%s.xml' % self.tool_name
        if self.args.interpreter_name == "Executable":  # binary - no need
            aCL(self.args.exe_package)  # this little CL will just run
        else:  # a script has been provided
            rx = open(self.args.script_path, 'r').readlines()
            # remove pesky dos line endings if needed
            rx = [x.rstrip() for x in rx]
            self.script = '\n'.join(rx)
            fhandle, self.sfile = tempfile.mkstemp(
                prefix=self.tool_name, suffix=".%s" % (args.interpreter_name))
            # use self.sfile as script source for Popen
            tscript = open(self.sfile, 'w')
            tscript.write(self.script)
            tscript.close()
            self.indentedScript = "  %s" % '\n'.join(
                [' %s' % html_escape(x) for x in rx])  # for restructured text in help
            self.escapedScript = "%s" % '\n'.join(
                [' %s' % html_escape(x) for x in rx])
            aCL(self.args.interpreter_name)
            aCL(self.sfile)
        self.elog = os.path.join(self.args.output_dir,
                                 "%s_error.log" % self.tool_name)
        if args.output_dir:  # may not want these complexities
            self.tlog = os.path.join(
                self.args.output_dir, "%s_runner.log" % self.tool_name)
            art = '%s.%s' % (self.tool_name, args.interpreter_name)
            artpath = os.path.join(
                self.args.output_dir,
                art)  # need full path
            # use self.sfile as script source for Popen
            artifact = open(artpath, 'w')
            artifact.write(self.script)
            artifact.close()
        self.infile_paths = []
        self.infile_format = []
        self.infile_cl = []
        self.infile_label = []
        self.infile_help = []
        if self.args.input_files:
            aif = [x.split(ourdelim) for x in self.args.input_files]
            # transpose the input_files array passed as
            # --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label~~~$input_help"
            laif = list(map(list, zip(*aif)))
            self.infile_paths, self.infile_cl, self.infile_format, self.infile_label, self.infile_help = laif
            self.infile_name = []
            # positionals have integers indicating order - need valid internal
            # names
            for i, scl in enumerate(self.infile_cl):
                if scl.isdigit():
                    scl = 'input%s' % scl
                if scl.upper() in ['STDOUT', 'STDIN']:
                    scl = 'input%d' % (i + 1)
                # make a list of internal names for each input file
                self.infile_name.append(scl)
        # list all (cl param) pairs - positional needs sorting by cl index so decorate
        clsuffix = []
        clsuffix.append([self.args.output_cl, self.args.output_tab])
        if self.args.parampass == '0':  # only need two
            aCL('<')
            aCL('%s' % self.infile_paths[0])
            aCL('>')
            aCL('%s' % self.args.output_tab)
        else:
            for i, p in enumerate(self.infile_paths):
                # decorator is cl - sort for positional
                clsuffix.append([self.infile_cl[i], p])
            for p in self.args.additional_parameters:
                psplit = p.split(ourdelim)
                pform = psplit[5]
                if pform == 'STDOUT':
                    lastclredirect = ['>', psplit[1]]
                else:
                    clsuffix.append([pform, psplit[1]])  # cl,value
            clsuffix.sort()
            if self.args.parampass == "positional":
                # inputs in order then params in order TODO fix ordering using
                # self.infile_cl
                for (k, v) in clsuffix:
                    if ' ' in v:
                        aCL("v")
                    else:
                        aCL(v)
            elif self.args.parampass == "argparse":
                # inputs then params in argparse named form
                for (k, v) in clsuffix:
                    if ' ' in v:
                        aCL('--%s' % k)
                        aCL('"%s"' % v)
                    else:
                        aCL('--%s' % k)
                        aCL('%s' % v)
            if lastclredirect:
                for v in lastclredirect:
                    aCL(v)  # add the stdout parameter last
        self.test1Output = '%s_test1_output.xls' % self.tool_name
        self.test1HTML = '%s_test1_output.html' % self.tool_name

    def makeXML(self):
        """
        Create a Galaxy xml tool wrapper for the new script
        Uses galaxyhtml
        """
        # need interp and executable (?script) or else executable only
        if self.args.interpreter_name:
            exe = "$runMe"  # our dynamic script from the tool builder
            interp = self.args.interpreter_name
        else:
            interp = None
            exe = self.args.exe_package
        assert exe is not None, 'No interpeter or executable passed in to makeXML'
        tool = gxt.Tool(self.args.tool_name, self.tool_id,
                        self.args.tool_version, self.args.tool_desc, exe)
        if interp:
            tool.interpreter = interp
        if self.args.help_text:
            helptext = open(self.args.help_text, 'r').readlines()
            # must html escape here too - thanks to Marius van den Beek
            helptext = [html_escape(x) for x in helptext]
            tool.help = ''.join([x for x in helptext])
        else:
            tool.help = 'Please ask the tool author (%s) for help \
              as none was supplied at tool generation\n' % (self.args.user_email)
        tool.version_command = None  # do not want
        inputs = gxtp.Inputs()
        outputs = gxtp.Outputs()
        requirements = gxtp.Requirements()
        testparam = []
        is_positional = (self.args.parampass == 'positional')
        if self.args.include_dependencies == "yes":
            requirements.append(gxtp.Requirement('package', 'ghostscript'))
            requirements.append(gxtp.Requirement('package', 'graphicsmagick'))
        if self.args.interpreter_name:
            if self.args.interpreter_name == 'python':  # always needed for this runner script
                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:  # uses exe not interpreter
                requirements.append(gxtp.Requirement(
                    'package', self.args.exe_package, self.args.exe_package_version))
        tool.requirements = requirements
        for i, infpath in enumerate(self.infile_paths):
            if self.args.parampass == 0:
                assert len(
                    self.infile_name) == 1, 'Maximum one "<" if parampass is 0 - more than one input files supplied'
            newname = self.infile_name[i]
            if len(newname) > 1:
                ndash = 2
            else:
                ndash = 1
            if not len(self.infile_label[i]) > 0:
                alab = self.infile_name[i]
            else:
                alab = self.infile_label[i]
            aninput = gxtp.DataParam(self.infile_name[i], optional=False, label=alab, help=self.infile_help[i],
                                     format=self.infile_format[i], multiple=False, num_dashes=ndash)
            if self.args.parampass == '0':
                aninput.command_line_override = '< $%s' % self.infile_name[i]
            aninput.positional = is_positional
            inputs.append(aninput)
        for parm in self.args.additional_parameters:
            newname, newval, newlabel, newhelp, newtype, newcl = parm.split(
                ourdelim)
            if not len(newlabel) > 0:
                newlabel = newname
            if len(newname) > 1:
                ndash = 2
            else:
                ndash = 1
            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 = is_positional
            inputs.append(aparm)
            tparm = gxtp.TestParam(newname, value=newval)
            testparam.append(tparm)
        tool.inputs = inputs
        configfiles = gxtp.Configfiles()
        configfiles.append(gxtp.Configfile(name="runMe", text=self.script))
        tool.configfiles = configfiles
        if self.args.output_tab:
            ext = self.args.output_format
            aparm = gxtp.OutputData(
                self.args.output_cl, format=ext, num_dashes=ndash)
            if is_positional:
                aparm.command_line_override = '> $output1'
            aparm.positional = is_positional
            outputs.append(aparm)
        tool.outputs = outputs
        tests = gxtp.Tests()
        test_a = gxtp.Test()
        ext = self.infile_format[0].split(',')[0]
        if is_positional:
            param = gxtp.TestParam(
                'input1', value='input1.%s' % ext, ftype=ext)
        else:
            param = gxtp.TestParam(self.infile_name[0], value='%s.%s' % (
                self.infile_name[0], ext), ftype=ext)
        test_a.append(param)
        param = gxtp.TestParam('job_name', value='test_a')
        test_a.append(param)
        param = gxtp.TestParam('runMe', value="$runMe")
        test_a.append(param)
        for aparam in testparam:
            test_a.append(aparam)
        test_out = gxtp.TestOutput(
            name=self.args.output_cl, value=self.test1Output)
        test_a.append(test_out)
        tests.append(test_a)
        tool.tests = tests
        tool.add_comment('Created by %s at %s using the Galaxy Tool Factory.' % (
            self.args.user_email, timenow()))
        tool.add_comment('Source in git at: %s' % (toolFactoryURL))
        tool.add_comment(
            'Cite: Creating re-usable tools from scripts doi: 10.1093/bioinformatics/bts573')
        exml = tool.export()
        xf = open(self.xmlfile, '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 ...
        """
        retval = self.run()
        if retval:
            sys.stderr.write(
                '## Run failed. Cannot build yet. Please fix and retry')
            sys.exit(1)
        tdir = 'tdir_%s' % self.tool_name
        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 i, infile in enumerate(self.infile_paths):
            dest = os.path.join(testdir, '%s.%s' %
                                (self.infile_name[i], self.infile_format[i]))
            if infile != dest:
                shutil.copyfile(infile, dest)
        if self.args.output_tab and os.path.exists(self.args.output_tab):
            shutil.copyfile(self.args.output_tab,
                            os.path.join(testdir, self.test1Output))
        else:
            print('#### no output_tab %s exists' % self.args.output_tab)
        if self.args.output_dir:
            if os.path.exists(self.tlog):
                shutil.copyfile(self.tlog, os.path.join(
                    testdir, 'test1_out.log'))
        stname = os.path.join(tdir, self.sfile)
        if not os.path.exists(stname):
            shutil.copyfile(self.sfile, stname)
        xtname = os.path.join(tdir, self.xmlfile)
        if not os.path.exists(xtname):
            shutil.copyfile(self.xmlfile, xtname)
        tarpath = "%s.tar.gz" % self.tool_name
        tar = tarfile.open(tarpath, "w:gz")
        tar.add(tdir, recursive=True, arcname='%s' % self.tool_name)
        tar.close()
        shutil.copyfile(tarpath, self.args.new_tool)
        shutil.rmtree(tdir)
        # TODO: replace with optional direct upload to local toolshed?
        return retval

    def run(self):
        """
        Some devteam tools have this defensive stderr read so I'm keeping with the faith
        Feel free to update.
        """
        logging.debug('run cl=%s' % str(self.cl))
        scl = ' '.join(self.cl)
        err = None
        if self.args.parampass != '0':
            ste = open(self.elog, 'wb')
            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, cwd=self.args.output_dir)
            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.infile_paths[0], 'rb')
            sto = open(self.args.output_tab, '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 self.args.output_dir:
            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('--output_dir', default='./')
    a('--input_files', default=[], action="append")
    a("--input_formats", default="tabular")
    a('--output_tab', default=None)
    a('--output_format', default='tabular')
    a('--output_cl', default=None)
    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('--new_tool', default=None)
    a('--tool_version', default=None)
    a('--include_dependencies', default=None)
    a('--citations', default=None)
    a('--additional_parameters', dest='additional_parameters',
      action='append', default=[])
    a('--edit_additional_parameters', action="store_true", default=False)
    a('--parampass', default="positional")
    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 - eg --interpreter_name=Rscript or an executable package findable by the dependency management 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'
    if args.output_dir:
        try:
            os.makedirs(args.output_dir)
        except BaseException:
            pass
    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()