Mercurial > repos > fubar > tool_factory_2

comparison toolfactory/rgToolFactory2.py @ 76:46db8143adb7 draft

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author fubar
date Mon, 16 Nov 2020 02:42:49 +0000
parents 25dd9364a32a
children 89aca6c67405
comparison
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75:25dd9364a32a 76:46db8143adb7
22 # one to run the executable with the supplied test data and settings 22 # one to run the executable with the supplied test data and settings
23 # Be simpler to write the tool, then run it with planemo and soak up the test outputs. 23 # Be simpler to write the tool, then run it with planemo and soak up the test outputs.
24 24
25 25
26 import argparse 26 import argparse
27 import datetime
28 import json
27 import logging 29 import logging
28 import os 30 import os
29 import re 31 import re
30 import shutil 32 import shutil
31 import subprocess 33 import subprocess
177 self.tool_id, 179 self.tool_id,
178 self.args.tool_version, 180 self.args.tool_version,
179 self.args.tool_desc, 181 self.args.tool_desc,
180 FAKEEXE, 182 FAKEEXE,
181 ) 183 )
184 self.newtarpath = "toolfactory_%s.tgz" % self.tool_name
182 self.tooloutdir = "tfout" 185 self.tooloutdir = "tfout"
183 self.repdir = "TF_run_report_tempdir" 186 self.repdir = "TF_run_report_tempdir"
184 self.testdir = os.path.join(self.tooloutdir, "test-data") 187 self.testdir = os.path.join(self.tooloutdir, "test-data")
185 if not os.path.exists(self.tooloutdir): 188 if not os.path.exists(self.tooloutdir):
186 os.mkdir(self.tooloutdir) 189 os.mkdir(self.tooloutdir)
813 p = subprocess.run(cll, shell=False, stdout=tout, stderr=tout) 816 p = subprocess.run(cll, shell=False, stdout=tout, stderr=tout)
814 tout.write("Ran %s got %d" % (" ".join(cll), p.returncode)) 817 tout.write("Ran %s got %d" % (" ".join(cll), p.returncode))
815 tout.close() 818 tout.close()
816 return p.returncode 819 return p.returncode
817 820
818 def eph_test(self): 821 def eph_test(self, genoutputs=True):
819 """""" 822 """problem getting jobid - ephemeris upload is the job before the one we want - but depends on how many inputs
823 """
820 if os.path.exists(self.tlog): 824 if os.path.exists(self.tlog):
821 tout = open(self.tlog, "a") 825 tout = open(self.tlog, "a")
822 else: 826 else:
823 tout = open(self.tlog, "w") 827 tout = open(self.tlog, "w")
824 cll = [ 828 cll = [
831 "--name", 835 "--name",
832 self.args.tool_name, 836 self.args.tool_name,
833 "--owner", 837 "--owner",
834 "fubar", 838 "fubar",
835 ] 839 ]
836 p = subprocess.run( 840 if genoutputs:
837 cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout 841 dummy, tfile = tempfile.mkstemp()
838 ) 842 p = subprocess.run(
839 tout.write("eph_test Ran %s got %d" % (" ".join(cll), p.returncode)) 843 cll, shell=False, stderr=dummy, stdout=dummy
844 )
845
846 with open('tool_test_output.json','rb') as f:
847 s = json.loads(f.read())
848 print('read %s' % s)
849 cl = s['tests'][0]['data']['job']['command_line'].split()
850 n = cl.index('--script_path')
851 jobdir = cl[n+1]
852 jobdir = jobdir.replace('"','')
853 jobdir = jobdir.split('/configs')[0]
854 print('jobdir=%s' % jobdir)
855
856 #"/home/ross/galthrow/database/jobs_directory/000/649/configs/tmptfxu51gs\"
857 src = os.path.join(jobdir,'working',self.newtarpath)
858 if os.path.exists(src):
859 dest = os.path.join(self.testdir, self.newtarpath)
860 shutil.copyfile(src, dest)
861 else:
862 tout.write('No toolshed archive found after first ephemeris test - not a good sign')
863 ephouts = os.path.join(jobdir,'working','tfout','test-data')
864 with os.scandir(ephouts) as outs:
865 for entry in outs:
866 if not entry.is_file():
867 continue
868 dest = os.path.join(self.tooloutdir, entry.name)
869 src = os.path.join(ephouts, entry.name)
870 shutil.copyfile(src, dest)
871 else:
872 p = subprocess.run(
873 cll, shell=False, stderr=tout, stdout=tout)
874 tout.write("eph_test Ran %s got %d" % (" ".join(cll), p.returncode))
840 tout.close() 875 tout.close()
841 return p.returncode 876 return p.returncode
842 877
843 def planemo_test(self, genoutputs=True): 878 def planemo_test(self, genoutputs=True):
844 """planemo is a requirement so is available for testing 879 """planemo is a requirement so is available for testing
938 else: 973 else:
939 print( 974 print(
940 "### problem - output file %s not found in tooloutdir %s" 975 "### problem - output file %s not found in tooloutdir %s"
941 % (src, self.tooloutdir) 976 % (src, self.tooloutdir)
942 ) 977 )
943 self.newtarpath = "toolfactory_%s.tgz" % self.tool_name
944 tf = tarfile.open(self.newtarpath, "w:gz") 978 tf = tarfile.open(self.newtarpath, "w:gz")
945 tf.add(name=self.tooloutdir, arcname=self.tool_name, filter=exclude_function) 979 tf.add(name=self.tooloutdir, arcname=self.tool_name, filter=exclude_function)
946 tf.close() 980 tf.close()
947 shutil.copyfile(self.newtarpath, self.args.new_tool) 981 shutil.copyfile(self.newtarpath, self.args.new_tool)
948 982
960 dest = os.path.join(self.repdir, ofn) 994 dest = os.path.join(self.repdir, ofn)
961 src = os.path.join(self.tooloutdir, entry.name) 995 src = os.path.join(self.tooloutdir, entry.name)
962 shutil.copyfile(src, dest) 996 shutil.copyfile(src, dest)
963 997
964 998
999
965 def main(): 1000 def main():
966 """ 1001 """
967 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as: 1002 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
968 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" 1003 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath"
969 --tool_name "foo" --interpreter "Rscript" 1004 --tool_name "foo" --interpreter "Rscript"
974 a("--script_path", default=None) 1009 a("--script_path", default=None)
975 a("--history_test", default=None) 1010 a("--history_test", default=None)
976 a("--cl_prefix", default=None) 1011 a("--cl_prefix", default=None)
977 a("--sysexe", default=None) 1012 a("--sysexe", default=None)
978 a("--packages", default=None) 1013 a("--packages", default=None)
979 a("--tool_name", default=None) 1014 a("--tool_name", default="newtool")
980 a("--tool_dir", default=None) 1015 a("--tool_dir", default=None)
981 a("--input_files", default=[], action="append") 1016 a("--input_files", default=[], action="append")
982 a("--output_files", default=[], action="append") 1017 a("--output_files", default=[], action="append")
983 a("--user_email", default="Unknown") 1018 a("--user_email", default="Unknown")
984 a("--bad_user", default=None) 1019 a("--bad_user", default=None)
994 a("--parampass", default="positional") 1029 a("--parampass", default="positional")
995 a("--tfout", default="./tfout") 1030 a("--tfout", default="./tfout")
996 a("--new_tool", default="new_tool") 1031 a("--new_tool", default="new_tool")
997 a("--galaxy_url", default="http://localhost:8080") 1032 a("--galaxy_url", default="http://localhost:8080")
998 a( 1033 a(
999 "--toolshed_url", default="http://localhost:9009" 1034 "--toolshed_url", default="http://localhost:9009")
1000 ) # make sure this is NOT 127.0.0.1 - it won't work if tool_sheds_conf.xml has localhost 1035 # make sure this is identical to tool_sheds_conf.xml localhost != 127.0.0.1 so validation fails
1001 # a("--galaxy_api_key", default="1e62ddad74fe9bf112859f4e9efea48b")
1002 # a("--toolshed_api_key", default="9154c91f2a162bf12fda15764f43846c")
1003
1004 a("--toolshed_api_key", default="fakekey") 1036 a("--toolshed_api_key", default="fakekey")
1005 a("--galaxy_api_key", default="fakekey") 1037 a("--galaxy_api_key", default="fakekey")
1006 a("--galaxy_root", default="/galaxy-central") 1038 a("--galaxy_root", default="/galaxy-central")
1007
1008 args = parser.parse_args() 1039 args = parser.parse_args()
1009 assert not args.bad_user, ( 1040 assert not args.bad_user, (
1010 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to "admin_users" in the Galaxy configuration file' 1041 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to "admin_users" in the Galaxy configuration file'
1011 % (args.bad_user, args.bad_user) 1042 % (args.bad_user, args.bad_user)
1012 ) 1043 )
1029 retcode = r.planemo_test(genoutputs=True) # this fails :( - see PR 1060 retcode = r.planemo_test(genoutputs=True) # this fails :( - see PR
1030 r.moveRunOutputs() 1061 r.moveRunOutputs()
1031 r.makeToolTar() 1062 r.makeToolTar()
1032 retcode = r.planemo_test(genoutputs=False) 1063 retcode = r.planemo_test(genoutputs=False)
1033 r.moveRunOutputs() 1064 r.moveRunOutputs()
1065 print(f"second planemo_test returned {retcode}")
1034 if args.make_Tool == "gentestinstall": 1066 if args.make_Tool == "gentestinstall":
1035 retcode = r.planemo_shedload() # r.shedLoad()
1036 print(f"planemo_shedload returned {retcode}")
1037 r.eph_galaxy_load() 1067 r.eph_galaxy_load()
1038 1068
1039 1069
1040 if __name__ == "__main__": 1070 if __name__ == "__main__":
1041 main() 1071 main()