comparison toolfactory/rgToolFactory2.py @ 66:bc1977b1f7b5 draft

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65:ed1ecd161295

                  --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:

        rnames = [x.get('name','?') for x in repos]
        rids = [x.get('id','?') for x in repos]
        tout.write(f'############names={rnames} rids={rids}')
        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:
                p = subprocess.run(

                "planemo",
                "test",
                "--galaxy_root",
                self.args.galaxy_root,
                "--update_test_data",
                xreal,
            ]
            p = subprocess.run(
                    cll, shell=False, cwd=self.tooloutdir, stderr=dummy, stdout=dummy,
                )
        else:
            cll = ["planemo", "test", "--galaxy_root",
                self.args.galaxy_root,
                xreal,]
            p = subprocess.run(
                    cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout
                )
        tout.close()

            shutil.copyfile(pth, dest)

    def makeToolTar(self):
        """ move outputs into test-data and prepare the tarball
        """
        for p in self.outfiles:
            src = p[ONAMEPOS]
            if os.path.isfile(src):
                dest = os.path.join(self.testdir, "%s_sample" % src)
                shutil.copyfile(src, dest)

                    "### problem - output file %s not found in tooloutdir %s"
                    % (src, self.tooloutdir)
                )
        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)

    def moveRunOutputs(self):
        """need to move planemo or run outputs into toolfactory collection

                    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)
                if entry.name.startswith('tool_test_output'):
                    os.unlink(src)


def main():
    """
    This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:

    for i, x in enumerate(args.additional_parameters):
        args.additional_parameters[i] = args.additional_parameters[i].replace('"', "")
    r = ScriptRunner(args)
    r.writeShedyml()
    r.makeTool()
    retcode = r.planemo_test(genoutputs=True)  # this fails :( - see PR
    r.moveRunOutputs()
    r.makeToolTar()
    retcode = r.planemo_test(genoutputs=False)
    r.moveRunOutputs()
    if args.make_Tool == "gentestinstall":
        retcode = r.planemo_shedload() #r.shedLoad()
        print(f'planemo_shedload returned {retcode}')
        r.eph_galaxy_load()



if __name__ == "__main__":
    main()

66:bc1977b1f7b5

                  --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:

        rnames = [x.get('name','?') for x in repos]
        rids = [x.get('id','?') for x in repos]
        tout.write(f'############names={rnames} rids={rids}')
        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:
                p = subprocess.run(

                "planemo",
                "test",
                "--galaxy_root",
                self.args.galaxy_root,
                "--update_test_data",
                "--docker",
                xreal,
            ]
            p = subprocess.run(
                    cll, shell=False, cwd=self.tooloutdir, stderr=dummy, stdout=dummy,
                )
        else:
            cll = ["planemo", "test", "--galaxy_root",
                self.args.galaxy_root, "--docker",
                xreal,]
            p = subprocess.run(
                    cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout
                )
        tout.close()

            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)  or os.path.splitext(filename)[1].startswith(excludeme) else tarinfo

        for p in self.outfiles:
            src = p[ONAMEPOS]
            if os.path.isfile(src):
                dest = os.path.join(self.testdir, "%s_sample" % src)
                shutil.copyfile(src, dest)

                    "### problem - output file %s not found in tooloutdir %s"
                    % (src, self.tooloutdir)
                )
        self.newtarpath = "toolfactory_%s.tgz" % self.tool_name
        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

                    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 main():
    """
    This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:

    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:
        retcode = r.planemo_test(genoutputs=True)  # this fails :( - see PR
        r.moveRunOutputs()
        r.makeToolTar()
        retcode = r.planemo_test(genoutputs=False)
        r.moveRunOutputs()
        if args.make_Tool == "gentestinstall":
            retcode = r.planemo_shedload() #r.shedLoad()
            print(f'planemo_shedload returned {retcode}')
            r.eph_galaxy_load()



if __name__ == "__main__":
    main()