--- a/toolfactory/ToolFactory.py	Tue Apr 27 23:33:49 2021 +0000
+++ b/toolfactory/ToolFactory.py	Fri Apr 30 02:10:32 2021 +0000
@@ -28,6 +28,7 @@
 import tarfile
 import tempfile
 import time
+import urllib
 
 from bioblend import ConnectionError
 from bioblend import galaxy
@@ -70,13 +71,14 @@
             citation_tuples.append(("bibtex", citation[len("bibtex") :].strip()))
     return citation_tuples
 
-class ToolConfUpdater():
+
+class Tool_Conf_Updater():
     # update config/tool_conf.xml with a new tool unpacked in /tools
     # requires highly insecure docker settings - like write to tool_conf.xml and to tools !
     # if in a container possibly not so courageous.
     # Fine on your own laptop but security red flag for most production instances
 
-  def __init__(self, args, tool_conf_path, new_tool_archive_path, new_tool_name, tool_dir):
+    def __init__(self, args, tool_conf_path, new_tool_archive_path, new_tool_name, tool_dir):
         self.args = args
         self.tool_conf_path = os.path.join(args.galaxy_root,tool_conf_path)
         self.tool_dir = os.path.join(args.galaxy_root, tool_dir)
@@ -138,7 +140,7 @@
         if False and self.args.packages and self.args.packages > '':
             self.install_deps()
 
-class ScriptRunner:
+class Tool_Factory:
     """Wrapper for an arbitrary script
     uses galaxyxml
 
@@ -194,9 +196,7 @@
             )
         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:
@@ -209,7 +209,6 @@
                 self.executeme = [self.args.packages.split(",")[0].split(":")[0].strip(), ]
             else:
                 self.executeme = None
-        aCL = self.cl.append
         aXCL = self.xmlcl.append
         assert args.parampass in [
             "0",
@@ -252,13 +251,10 @@
             self.test_override = None
         if self.args.script_path:
             for ex in self.executeme:
-                aCL(ex)
                 aXCL(ex)
-            aCL(self.sfile)
             aXCL("$runme")
         else:
             for ex in self.executeme:
-                aCL(ex)
                 aXCL(ex)
 
         if self.args.parampass == "0":
@@ -273,35 +269,23 @@
 
     def clsimple(self):
         """no parameters or repeats - uses < and > for i/o"""
-        aCL = self.cl.append
         aXCL = self.xmlcl.append
         if len(self.infiles) > 0:
-            aCL("<")
-            aCL(self.infiles[0]["infilename"])
             aXCL("<")
             aXCL("$%s" % self.infiles[0]["infilename"])
         if len(self.outfiles) > 0:
-            aCL(">")
-            aCL(self.outfiles[0]["name"])
             aXCL(">")
             aXCL("$%s" % self.outfiles[0]["name"])
         if self.args.cl_user_suffix:  # DIY CL end
             clp = shlex.split(self.args.cl_user_suffix)
             for c in clp:
-                aCL(c)
                 aXCL(c)
 
     def prepargp(self):
-        clsuffix = []
         xclsuffix = []
         for i, p in enumerate(self.infiles):
             nam = p["infilename"]
             if p["origCL"].strip().upper() == "STDIN":
-                appendme = [
-                    nam,
-                    nam,
-                    "< %s" % nam,
-                ]
                 xappendme = [
                     nam,
                     nam,
@@ -312,16 +296,12 @@
                 over = ""
                 if rep:
                     over = f'#for $rep in $R_{nam}:\n--{nam} "$rep.{nam}"\n#end for'
-                appendme = [p["CL"], p["CL"], ""]
                 xappendme = [p["CL"], "$%s" % p["CL"], over]
-            clsuffix.append(appendme)
             xclsuffix.append(xappendme)
         for i, p in enumerate(self.outfiles):
             if p["origCL"].strip().upper() == "STDOUT":
-                self.lastclredirect = [">", p["name"]]
                 self.lastxclredirect = [">", "$%s" % p["name"]]
             else:
-                clsuffix.append([p["name"], p["name"], ""])
                 xclsuffix.append([p["name"], "$%s" % p["name"], ""])
         for p in self.addpar:
             nam = p["name"]
@@ -330,40 +310,27 @@
                 over = f'#for $rep in $R_{nam}:\n--{nam} "$rep.{nam}"\n#end for'
             else:
                 over = p["override"]
-            clsuffix.append([p["CL"], nam, over])
             xclsuffix.append([p["CL"], '"$%s"' % nam, over])
         for p in self.selpar:
-            clsuffix.append([p["CL"], p["name"], p["override"]])
             xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])
         self.xclsuffix = xclsuffix
-        self.clsuffix = clsuffix
 
     def prepclpos(self):
-        clsuffix = []
         xclsuffix = []
         for i, p in enumerate(self.infiles):
             if p["origCL"].strip().upper() == "STDIN":
-                appendme = [
-                    "999",
-                    p["infilename"],
-                    "< $%s" % p["infilename"],
-                ]
                 xappendme = [
                     "999",
                     p["infilename"],
                     "< $%s" % p["infilename"],
                 ]
             else:
-                appendme = [p["CL"], p["infilename"], ""]
                 xappendme = [p["CL"], "$%s" % p["infilename"], ""]
-            clsuffix.append(appendme)
             xclsuffix.append(xappendme)
         for i, p in enumerate(self.outfiles):
             if p["origCL"].strip().upper() == "STDOUT":
-                self.lastclredirect = [">", p["name"]]
                 self.lastxclredirect = [">", "$%s" % p["name"]]
             else:
-                clsuffix.append([p["CL"], p["name"], ""])
                 xclsuffix.append([p["CL"], "$%s" % p["name"], ""])
         for p in self.addpar:
             nam = p["name"]
@@ -371,15 +338,11 @@
             if rep:
                 print(f'### warning. Repeats for {nam} ignored - not permitted in positional parameter command lines!')
             over = p["override"]
-            clsuffix.append([p["CL"], nam, over])
             xclsuffix.append([p["CL"], '"$%s"' % nam, over])
         for p in self.selpar:
-            clsuffix.append([p["CL"], p["name"], p["override"]])
             xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])
-        clsuffix.sort()
         xclsuffix.sort()
         self.xclsuffix = xclsuffix
-        self.clsuffix = clsuffix
 
     def prepScript(self):
         rx = open(self.args.script_path, "r").readlines()
@@ -443,12 +406,6 @@
 
     def clpositional(self):
         # inputs in order then params
-        aCL = self.cl.append
-        for (k, v, koverride) in self.clsuffix:
-            if " " in v:
-                aCL("%s" % v)
-            else:
-                aCL(v)
         aXCL = self.xmlcl.append
         for (k, v, koverride) in self.xclsuffix:
             aXCL(v)
@@ -458,13 +415,11 @@
         if self.args.cl_user_suffix:  # DIY CL end
             clp = shlex.split(self.args.cl_user_suffix)
             for c in clp:
-                aCL(c)
                 aXCL(c)
 
 
     def clargparse(self):
         """argparse style"""
-        aCL = self.cl.append
         aXCL = self.xmlcl.append
         # inputs then params in argparse named form
 
@@ -479,22 +434,12 @@
                     k = "--%s" % k
                 aXCL(k)
                 aXCL(v)
-        for (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)
         if self.lastxclredirect:
             aXCL(self.lastxclredirect[0])
             aXCL(self.lastxclredirect[1])
         if self.args.cl_user_suffix:  # DIY CL end
             clp = shlex.split(self.args.cl_user_suffix)
             for c in clp:
-                aCL(c)
                 aXCL(c)
 
     def getNdash(self, newname):
@@ -857,80 +802,6 @@
         xf.close()
         # ready for the tarball
 
-    def run(self):  #noqa
-        """
-        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
-        logname = f"{self.tool_name}_runner_log"
-        if self.args.parampass != "0":
-            if self.lastclredirect:
-                logf = open(self.lastclredirect[1], "wb")  # is name of an output file
-            else:
-                logf = open(logname,'w')
-                logf.write("No dependencies so sending CL = '%s' to the fast direct runner instead of planemo to generate tests" % scl)
-            subp = subprocess.run(
-                self.cl, shell=False, stdout=logf, stderr=logf
-            )
-            logf.close()
-            retval = subp.returncode
-        else:  # work around special case - stdin and write to stdout
-            if len(self.infiles) > 0:
-                sti = open(self.infiles[0]["name"], "rb")
-            else:
-                sti = sys.stdin
-            if len(self.outfiles) > 0:
-                sto = open(self.outfiles[0]["name"], "wb")
-            else:
-                sto = sys.stdout
-            subp = subprocess.run(
-                self.cl, shell=False, stdout=sto, stdin=sti
-            )
-            retval = subp.returncode
-            sto.close()
-            sti.close()
-        if retval != 0 and err:  # problem
-            sys.stderr.write(err)
-        for p in self.outfiles:
-            oname = p["name"]
-            tdest = os.path.join(self.testdir, "%s_sample" % oname)
-            if not os.path.isfile(tdest):
-                if os.path.isfile(oname):
-                    shutil.copyfile(oname, tdest)
-                    dest = os.path.join(self.repdir, "%s.sample.%s" % (oname,p['format']))
-                    shutil.copyfile(oname, dest)
-                else:
-                    if report_fail:
-                        tout.write(
-                            "###Tool may have failed - output file %s not found in testdir after planemo run %s."
-                            % (oname, self.testdir)
-                        )
-        for p in self.infiles:
-            pth = p["name"]
-            dest = os.path.join(self.testdir, "%s_sample" % p["infilename"])
-            shutil.copyfile(pth, dest)
-            dest = os.path.join(self.repdir, "%s_sample.%s" % (p["infilename"],p["format"]))
-            shutil.copyfile(pth, dest)
-        with os.scandir('.') as outs:
-            for entry in outs:
-                newname = entry.name
-                if not entry.is_file() or entry.name.endswith('_sample'):
-                    continue
-                if not (entry.name.endswith('.html') or entry.name.endswith('.gz') or entry.name.endswith(".tgz")):
-                    fname, ext = os.path.splitext(entry.name)
-                    if len(ext) > 1:
-                        newname = f"{fname}_{ext[1:]}.txt"
-                    else:
-                        newname = f"{fname}.txt"
-                dest = os.path.join(self.repdir, newname)
-                src = entry.name
-                shutil.copyfile(src, dest)
-        return retval
-
     def writeShedyml(self):
         """for planemo"""
         yuser = self.args.user_email.split("@")[0]
@@ -1068,6 +939,7 @@
     a("--galaxy_venv", default="/galaxy_venv")
     a("--collection", action="append", default=[])
     a("--include_tests", default=False, action="store_true")
+    a("--admin_only", default=False, action="store_true")
     a("--install", default=False, action="store_true")
     a("--run_test", default=False, action="store_true")
     a("--local_tools", default='tools') # relative to $__root_dir__
@@ -1079,30 +951,20 @@
     a("--toolshed_api_key", default="fakekey")
     a("--galaxy_api_key", default="8993d65865e6d6d1773c2c34a1cc207d")
     args = parser.parse_args()
-    assert not args.bad_user, (
-        'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy \
+    if args.admin_only:
+        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.yml Galaxy configuration file'
-        % (args.bad_user, args.bad_user)
+           % (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 in --sysexe or --packages"
-    print('Hello from',os.getcwd())
-    r = ScriptRunner(args)
+    r = Tool_Factory(args)
     r.writeShedyml()
     r.makeTool()
     r.makeToolTar()
-    if args.run_test:
-        if not args.packages or args.packages.strip() == "bash":
-            r.run()
-            r.makeToolTar()
-        else:
-            tt = ToolTester(report_dir=r.repdir, in_tool_archive=r.newtarpath, new_tool_archive=r.args.new_tool, galaxy_root=args.galaxy_root, include_tests=False)
     if args.install:
         #try:
-        tcu = ToolConfUpdater(args=args, tool_dir=args.local_tools,
+        tcu = Tool_Conf_Updater(args=args, tool_dir=args.local_tools,
         new_tool_archive_path=r.newtarpath, tool_conf_path=args.tool_conf_path,
         new_tool_name=r.tool_name)
         #except Exception: