--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/ToolFactory_tester.py	Mon Apr 26 04:18:54 2021 +0000
@@ -0,0 +1,202 @@
+# 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
+
+import argparse
+import copy
+import os
+import subprocess
+import shutil
+import sys
+import tarfile
+import tempfile
+import time
+
+myversion = "V2.2 April 2021"
+verbose = True
+debug = True
+toolFactoryURL = "https://github.com/fubar2/toolfactory"
+
+def timenow():
+    """return current time as a string"""
+    return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))
+
+class ToolTester():
+    # 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
+    # uncompress passed tar, run planemo and rebuild a new tarball with tests
+
+    def __init__(self, args=None, in_tool_archive='/galaxy-central/tools/newtool/newtool_toolshed.gz', new_tool_archive=None):
+        self.args = args
+        self.new_tool_archive = new_tool_archive
+        assert tarfile.is_tarfile(in_tool_archive)
+        # this is not going to go well with arbitrary names. TODO introspect tool xml!
+        self.tooloutdir = "./tfout"
+        self.repdir = "./TF_run_report"
+        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)
+        if not os.path.exists(self.repdir):
+            os.mkdir(self.repdir)
+        tff = tarfile.open(in_tool_archive, "r:*")
+        flist = tff.getnames()
+        ourdir = os.path.commonpath(flist) # eg pyrevpos
+        self.tool_name = ourdir
+        ourxmls = [x for x in flist if x.lower().endswith('.xml') and os.path.split(x)[0] == ourdir]
+        assert len(ourxmls) > 0
+        self.ourxmls = ourxmls # [os.path.join(tool_path,x) for x in ourxmls]
+        res = tff.extractall()
+        tff.close()
+        self.update_tests(ourdir)
+        self.makeTool()
+        self.moveRunOutputs()
+        self.makeToolTar()
+
+    def call_planemo(self,xmlpath,ourdir):
+        penv = os.environ
+        penv['HOME'] = '/home/ross/galaxy-release_21.01'
+        toolfile = os.path.split(xmlpath)[1]
+        tool_name = self.tool_name
+        tool_test_output = f"{tool_name}_planemo_test_report.html"
+        cll = [
+            "planemo",
+            "test",
+            "--test_output",
+            os.path.abspath(tool_test_output),
+            "--galaxy_root",
+            self.args.galaxy_root,
+            "--update_test_data",
+            os.path.abspath(xmlpath),
+        ]
+        print(cll)
+        p = subprocess.run(
+            cll,
+            capture_output=True,
+            encoding='utf8',
+            env = penv,
+            shell=False,
+        )
+        return p
+
+    def makeTool(self):
+        """write xmls and input samples into place"""
+        for xreal in self.ourxmls:
+            x = os.path.split(xreal)[1]
+            xout = os.path.join(self.tooloutdir,x)
+            shutil.copyfile(xreal, xout)
+        # 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" % p["infilename"])
+            # shutil.copyfile(pth, dest)
+
+    def makeToolTar(self):
+        """move outputs into test-data and prepare the tarball"""
+        excludeme = "_planemo_test_report.html"
+
+        def exclude_function(tarinfo):
+            filename = tarinfo.name
+            return None if filename.endswith(excludeme) else tarinfo
+
+        newtar = 'new_%s_toolshed.gz' % self.tool_name
+        ttf = tarfile.open(newtar, "w:gz")
+        ttf.add(name=self.tooloutdir,
+            arcname=self.tool_name,
+            filter=exclude_function)
+        ttf.close()
+        shutil.copyfile(newtar, self.new_tool_archive)
+
+    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:
+                    _, ext = os.path.splitext(entry.name)
+                    if ext in [".tgz", ".json"]:
+                        continue
+                    if ext in [".yml", ".xml", ".yaml"]:
+                        newname = f"{entry.name.replace('.','_')}.txt"
+                    else:
+                        newname = entry.name
+                else:
+                    newname = f"{entry.name}.txt"
+                dest = os.path.join(self.repdir, newname)
+                src = os.path.join(self.tooloutdir, entry.name)
+                shutil.copyfile(src, dest)
+        with os.scandir('.') as outs:
+            for entry in outs:
+                if not entry.is_file():
+                    continue
+                if "." in entry.name:
+                    _, ext = os.path.splitext(entry.name)
+                    if ext in [".yml", ".xml", ".yaml"]:
+                        newname = f"{entry.name.replace('.','_')}.txt"
+                    else:
+                        newname = entry.name
+                else:
+                    newname = f"{entry.name}.txt"
+                dest = os.path.join(self.repdir, newname)
+                src =entry.name
+                shutil.copyfile(src, dest)
+        if True or self.args.include_tests:
+            with os.scandir(self.testdir) as outs:
+                for entry in outs:
+                    if (not entry.is_file()) or entry.name.endswith(
+                        "_planemo_test_report.html"
+                    ):
+                        continue
+                    if "." in entry.name:
+                        _, ext = os.path.splitext(entry.name)
+                        if ext in [".tgz", ".json"]:
+                            continue
+                        if ext in [".yml", ".xml", ".yaml"]:
+                            newname = f"{entry.name.replace('.','_')}.txt"
+                        else:
+                            newname = entry.name
+                    else:
+                        newname = f"{entry.name}.txt"
+                    dest = os.path.join(self.repdir, newname)
+                    src = os.path.join(self.testdir, entry.name)
+                    shutil.copyfile(src, dest)
+
+
+    def update_tests(self,ourdir):
+        for xmlf in self.ourxmls:
+            capture = self.call_planemo(xmlf,ourdir)
+            #sys.stderr.write('%s, stdout=%s, stderr=%s' % (xmlf, capture.stdout, capture.stdout))
+            print('%s, stdout=%s, stderr=%s' % (capture.stdout, capture.stdout,xmlf))
+
+def main():
+    """
+    This is a Galaxy wrapper.
+    It expects to be called by a special purpose tool.xml
+
+    """
+    parser = argparse.ArgumentParser()
+    a = parser.add_argument
+    a("--in_tool_archive", default=None)
+    a("--new_tested_tool_archive", default=None)
+    a("--galaxy_root", default="/home/ross/galaxy-release_21.01/")
+    args = parser.parse_args()
+    print('Hello from',os.getcwd())
+    tt = ToolTester(args=args, in_tool_archive=args.in_tool_archive, new_tool_archive=args.new_tested_tool_archive)
+
+if __name__ == "__main__":
+    main()