Mercurial > repos > fubar > tool_factory_2
comparison toolfactory/rgToolFactory2.py @ 72:a8764cda9dbf draft
Uploaded
| author | fubar |
|---|---|
| date | Sat, 14 Nov 2020 08:04:59 +0000 |
| parents | afa3da660ae3 |
| children | 3d4324df911b |
comparison
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| 71:eea262faed9c | 72:a8764cda9dbf |
|---|---|
| 760 rids = [x.get('id','?') for x in repos] | 760 rids = [x.get('id','?') for x in repos] |
| 761 tout.write(f'############names={rnames} rids={rids}') | 761 tout.write(f'############names={rnames} rids={rids}') |
| 762 cat = 'ToolFactory generated tools' | 762 cat = 'ToolFactory generated tools' |
| 763 if self.args.tool_name not in rnames: | 763 if self.args.tool_name not in rnames: |
| 764 cll = ["planemo", "shed_create", "--shed_target", "local", | 764 cll = ["planemo", "shed_create", "--shed_target", "local", |
| 765 "--directory", self.args.tool_dir, | |
| 765 "--owner","fubar","--name", | 766 "--owner","fubar","--name", |
| 766 self.args.tool_name,"--shed_key", | 767 self.args.tool_name,"--shed_key", |
| 767 self.args.toolshed_api_key,] | 768 self.args.toolshed_api_key,] |
| 768 try: | 769 try: |
| 769 p = subprocess.run( | 770 p = subprocess.run( |
| 786 self.args.tool_name, | 787 self.args.tool_name, |
| 787 "--shed_key", | 788 "--shed_key", |
| 788 self.args.toolshed_api_key, | 789 self.args.toolshed_api_key, |
| 789 "--tar", | 790 "--tar", |
| 790 self.newtarpath, | 791 self.newtarpath, |
| 792 "--directory", self.args.tool_dir, | |
| 791 ] | 793 ] |
| 792 p = subprocess.run(cll, shell=False, stdout=tout, stderr=tout) | 794 p = subprocess.run(cll, shell=False, stdout=tout, stderr=tout) |
| 793 tout.write("Ran %s got %d" % (" ".join(cll), p.returncode)) | 795 tout.write("Ran %s got %d" % (" ".join(cll), p.returncode)) |
| 794 tout.close() | 796 tout.close() |
| 795 return p.returncode | 797 return p.returncode |
| 837 cll = [ | 839 cll = [ |
| 838 "planemo", | 840 "planemo", |
| 839 "test", | 841 "test", |
| 840 "--galaxy_root", | 842 "--galaxy_root", |
| 841 self.args.galaxy_root, | 843 self.args.galaxy_root, |
| 842 "--update_test_data", | 844 "--update_test_data", |
| 843 "--docker", | 845 "--directory", self.args.tool_dir, |
| 844 xreal, | 846 xreal, |
| 845 ] | 847 ] |
| 846 p = subprocess.run( | 848 p = subprocess.run( |
| 847 cll, shell=False, cwd=self.tooloutdir, stderr=dummy, stdout=dummy, | 849 cll, shell=False, cwd=self.tooloutdir, stderr=dummy, stdout=dummy, |
| 848 ) | 850 ) |
| 849 else: | 851 else: |
| 850 cll = ["planemo", "test", "--galaxy_root", | 852 cll = ["planemo", "test", "--galaxy_root", |
| 851 self.args.galaxy_root, "--docker", | 853 self.args.galaxy_root, |
| 854 "--directory", self.args.tool_dir, | |
| 852 xreal,] | 855 xreal,] |
| 853 p = subprocess.run( | 856 p = subprocess.run( |
| 854 cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout | 857 cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout |
| 855 ) | 858 ) |
| 856 tout.close() | 859 tout.close() |
| 949 a("--history_test", default=None) | 952 a("--history_test", default=None) |
| 950 a("--cl_prefix", default=None) | 953 a("--cl_prefix", default=None) |
| 951 a("--sysexe", default=None) | 954 a("--sysexe", default=None) |
| 952 a("--packages", default=None) | 955 a("--packages", default=None) |
| 953 a("--tool_name", default=None) | 956 a("--tool_name", default=None) |
| 957 a("--tool_dir", default=None) | |
| 954 a("--input_files", default=[], action="append") | 958 a("--input_files", default=[], action="append") |
| 955 a("--output_files", default=[], action="append") | 959 a("--output_files", default=[], action="append") |
| 956 a("--user_email", default="Unknown") | 960 a("--user_email", default="Unknown") |
| 957 a("--bad_user", default=None) | 961 a("--bad_user", default=None) |
| 958 a("--make_Tool", default="runonly") | 962 a("--make_Tool", default="runonly") |