Mercurial > repos > fubar > tool_factory_2

comparison toolfactory/rgToolFactory2.py @ 80:f423a77bc669 draft

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Uploaded
author fubar
date Tue, 17 Nov 2020 09:04:25 +0000
parents 89aca6c67405
children 6395be766c2e
comparison
equal deleted inserted replaced
79:2d0272e730d1 80:f423a77bc669
687 url=self.args.toolshed_url, key=self.args.toolshed_api_key, verify=False 687 url=self.args.toolshed_url, key=self.args.toolshed_api_key, verify=False
688 ) 688 )
689 repos = ts.repositories.get_repositories() 689 repos = ts.repositories.get_repositories()
690 rnames = [x.get("name", "?") for x in repos] 690 rnames = [x.get("name", "?") for x in repos]
691 rids = [x.get("id", "?") for x in repos] 691 rids = [x.get("id", "?") for x in repos]
692 sto.write(f"############names={rnames} rids={rids}") 692 sto.write(f"############names={rnames} rids={rids}\n")
693 cat = "ToolFactory generated tools" 693 cat = "ToolFactory generated tools"
694 if self.args.tool_name not in rnames: 694 if self.args.tool_name not in rnames:
695 tscat = ts.categories.get_categories() 695 tscat = ts.categories.get_categories()
696 cnames = [x.get("name", "?") for x in tscat] 696 cnames = [x.get("name", "?") for x in tscat]
697 cids = [x.get("id", "?") for x in tscat] 697 cids = [x.get("id", "?") for x in tscat]
707 remote_repository_url=self.args.toolshed_url, 707 remote_repository_url=self.args.toolshed_url,
708 homepage_url=None, 708 homepage_url=None,
709 category_ids=catID, 709 category_ids=catID,
710 ) 710 )
711 tid = res.get("id", None) 711 tid = res.get("id", None)
712 sto.write(f"##########create res={res}") 712 sto.write(f"##########create res={res}\n")
713 else: 713 else:
714 i = rnames.index(self.args.tool_name) 714 i = rnames.index(self.args.tool_name)
715 tid = rids[i] 715 tid = rids[i]
716 res = ts.repositories.update_repository( 716 res = ts.repositories.update_repository(
717 id=tid, tar_ball_path=self.newtarpath, commit_message=None 717 id=tid, tar_ball_path=self.newtarpath, commit_message=None
718 ) 718 )
719 sto.write(f"#####update res={res}") 719 sto.write(f"#####update res={res}\n")
720 sto.close() 720 sto.close()
721 721
722 def eph_galaxy_load(self): 722 def eph_galaxy_load(self):
723 """load the new tool from the local toolshed after planemo uploads it""" 723 """load the new tool from the local toolshed after planemo uploads it"""
724 if os.path.exists(self.tlog): 724 if os.path.exists(self.tlog):
772 url=self.args.toolshed_url, key=self.args.toolshed_api_key, verify=False 772 url=self.args.toolshed_url, key=self.args.toolshed_api_key, verify=False
773 ) 773 )
774 repos = ts.repositories.get_repositories() 774 repos = ts.repositories.get_repositories()
775 rnames = [x.get("name", "?") for x in repos] 775 rnames = [x.get("name", "?") for x in repos]
776 rids = [x.get("id", "?") for x in repos] 776 rids = [x.get("id", "?") for x in repos]
777 tout.write(f"############names={rnames} rids={rids}")
778 #cat = "ToolFactory generated tools" 777 #cat = "ToolFactory generated tools"
779 if self.args.tool_name not in rnames: 778 if self.args.tool_name not in rnames:
780 cll = [ 779 cll = [
781 "planemo", 780 "planemo",
782 "shed_create", 781 "shed_create",
794 cll, shell=False, cwd=self.tooloutdir, stdout=tout, stderr=tout 793 cll, shell=False, cwd=self.tooloutdir, stdout=tout, stderr=tout
795 ) 794 )
796 except: 795 except:
797 pass 796 pass
798 if p.returncode != 0: 797 if p.returncode != 0:
799 tout.write("Repository %s exists" % self.args.tool_name) 798 tout.write("Repository %s exists\n" % self.args.tool_name)
800 else: 799 else:
801 tout.write("initiated %s" % self.args.tool_name) 800 tout.write("initiated %s\n" % self.args.tool_name)
802 cll = [ 801 cll = [
803 "planemo", 802 "planemo",
804 "shed_upload", 803 "shed_upload",
805 "--shed_target", 804 "--shed_target",
806 "local", 805 "local",
812 self.args.toolshed_api_key, 811 self.args.toolshed_api_key,
813 "--tar", 812 "--tar",
814 self.newtarpath, 813 self.newtarpath,
815 ] 814 ]
816 p = subprocess.run(cll, shell=False, stdout=tout, stderr=tout) 815 p = subprocess.run(cll, shell=False, stdout=tout, stderr=tout)
817 tout.write("Ran %s got %d" % (" ".join(cll), p.returncode)) 816 tout.write("Ran %s got %d\n" % (" ".join(cll), p.returncode))
818 tout.close() 817 tout.close()
819 return p.returncode 818 return p.returncode
820 819
821 def eph_test(self, genoutputs=True): 820 def eph_test(self, genoutputs=True):
822 """problem getting jobid - ephemeris upload is the job before the one we want - but depends on how many inputs 821 """problem getting jobid - ephemeris upload is the job before the one we want - but depends on how many inputs
890 if genoutputs: 889 if genoutputs:
891 dummy, tfile = tempfile.mkstemp() 890 dummy, tfile = tempfile.mkstemp()
892 cll = [ 891 cll = [
893 "planemo", 892 "planemo",
894 "test", 893 "test",
895 "--test_output_xunit",os.path.join(self.repdir,f"{self.tool_name}_xunit.xml")
896 "--test_data", os.path.abspath(self.testdir), 894 "--test_data", os.path.abspath(self.testdir),
897 "--test_output", os.path.abspath(tool_test_path), 895 "--test_output", os.path.abspath(tool_test_path),
898 "--galaxy_root", 896 "--galaxy_root",
899 self.args.galaxy_root, 897 self.args.galaxy_root,
900 "--update_test_data", 898 "--update_test_data",
902 ] 900 ]
903 p = subprocess.run( 901 p = subprocess.run(
904 cll, 902 cll,
905 shell=False, 903 shell=False,
906 cwd=self.tooloutdir, 904 cwd=self.tooloutdir,
907 stderr=tout, 905 stderr=dummy,
908 stdout=tout, 906 stdout=dummy,
909 ) 907 )
908
910 else: 909 else:
911 cll = [ 910 cll = [
912 "planemo", 911 "planemo",
913 "test", 912 "test",
914 "--test_data", self.testdir, 913 "--test_data", os.path.abspath(self.testdir),
915 "--test_output", tool_test_path, 914 "--test_output", os.path.abspath(tool_test_path),
916 "--galaxy_root", 915 "--galaxy_root",
917 self.args.galaxy_root, 916 self.args.galaxy_root,
918 os.path.abspath(xreal), 917 os.path.abspath(xreal),
919 ] 918 ]
920 p = subprocess.run( 919 p = subprocess.run(
951 shutil.copyfile(xreal, xout) 950 shutil.copyfile(xreal, xout)
952 for p in self.infiles: 951 for p in self.infiles:
953 pth = p[IPATHPOS] 952 pth = p[IPATHPOS]
954 dest = os.path.join(self.testdir, "%s_sample" % p[ICLPOS]) 953 dest = os.path.join(self.testdir, "%s_sample" % p[ICLPOS])
955 shutil.copyfile(pth, dest) 954 shutil.copyfile(pth, dest)
956 dest = os.path.join(self.repdir, "%s.%s" % (p[ICLPOS], p[IFMTPOS]))
957 shutil.copyfile(pth, dest)
958 955
959 def makeToolTar(self): 956 def makeToolTar(self):
960 """move outputs into test-data and prepare the tarball""" 957 """move outputs into test-data and prepare the tarball"""
961 excludeme = "tool_test_output" 958 excludeme = "tool_test_output"
962 959
963 def exclude_function(tarinfo): 960 def exclude_function(tarinfo):
964 filename = tarinfo.name 961 filename = tarinfo.name
965 return ( 962 return (
966 None 963 None
967 if filename.startswith(excludeme) or \ 964 if filename.startswith(excludeme)
968 os.path.splitext(filename)[1].startswith(excludeme)
969 else tarinfo 965 else tarinfo
970 ) 966 )
971 967
972 for p in self.outfiles: 968 for p in self.outfiles:
973 src = p[ONAMEPOS] 969 src = p[ONAMEPOS]
988 984
989 def moveRunOutputs(self): 985 def moveRunOutputs(self):
990 """need to move planemo or run outputs into toolfactory collection""" 986 """need to move planemo or run outputs into toolfactory collection"""
991 with os.scandir(self.tooloutdir) as outs: 987 with os.scandir(self.tooloutdir) as outs:
992 for entry in outs: 988 for entry in outs:
993 if not entry.is_file() or entry.name.startswith("."): 989 if not entry.is_file():
990 continue
991 if "." in entry.name:
992 nayme, ext = os.path.splitext(entry.name)
993 if ext in ['.yml','.xml','.json','.yaml']:
994 ext = f'{ext}.txt'
995 else:
996 ext = ".txt"
997 ofn = "%s%s" % (entry.name.replace(".", "_"), ext)
998 dest = os.path.join(self.repdir, ofn)
999 src = os.path.join(self.tooloutdir, entry.name)
1000 shutil.copyfile(src, dest)
1001 with os.scandir(self.testdir) as outs:
1002 for entry in outs:
1003 if not entry.is_file():
994 continue 1004 continue
995 if "." in entry.name: 1005 if "." in entry.name:
996 nayme, ext = os.path.splitext(entry.name) 1006 nayme, ext = os.path.splitext(entry.name)
997 else: 1007 else:
998 ext = ".txt" 1008 ext = ".txt"
999 ofn = "%s%s" % (entry.name.replace(".", "_"), ext) 1009 newname = f"{entry.name}{ext}"
1000 dest = os.path.join(self.repdir, ofn) 1010 dest = os.path.join(self.repdir, newname)
1001 src = os.path.join(self.tooloutdir, entry.name) 1011 src = os.path.join(self.testdir, entry.name)
1002 shutil.copyfile(src, dest) 1012 shutil.copyfile(src, dest)
1003 1013
1004 1014
1005 1015
1006 def main(): 1016 def main():
1066 retcode = r.planemo_test(genoutputs=True) # this fails :( - see PR 1076 retcode = r.planemo_test(genoutputs=True) # this fails :( - see PR
1067 r.moveRunOutputs() 1077 r.moveRunOutputs()
1068 r.makeToolTar() 1078 r.makeToolTar()
1069 retcode = r.planemo_test(genoutputs=False) 1079 retcode = r.planemo_test(genoutputs=False)
1070 r.moveRunOutputs() 1080 r.moveRunOutputs()
1081 r.makeToolTar()
1071 print(f"second planemo_test returned {retcode}") 1082 print(f"second planemo_test returned {retcode}")
1072 if args.make_Tool == "gentestinstall": 1083 if args.make_Tool == "gentestinstall":
1084 r.shedLoad()
1073 r.eph_galaxy_load() 1085 r.eph_galaxy_load()
1074 1086
1075 1087
1076 if __name__ == "__main__": 1088 if __name__ == "__main__":
1077 main() 1089 main()