Mercurial > repos > fubar > tool_factory_2
comparison toolfactory/rgToolFactory2.py @ 100:c749364c2283 draft
Uploaded
| author | fubar |
|---|---|
| date | Mon, 23 Nov 2020 03:12:37 +0000 |
| parents | d4d88d393285 |
| children | 557d5f06f213 |
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| 99:d4d88d393285 | 100:c749364c2283 |
|---|---|
| 37 import tarfile | 37 import tarfile |
| 38 import tempfile | 38 import tempfile |
| 39 import time | 39 import time |
| 40 | 40 |
| 41 | 41 |
| 42 from bioblend import ConnectionError | |
| 42 from bioblend import toolshed | 43 from bioblend import toolshed |
| 43 | 44 |
| 44 # import docker | 45 # import docker |
| 45 | 46 |
| 46 import galaxyxml.tool as gxt | 47 import galaxyxml.tool as gxt |
| 779 ) | 780 ) |
| 780 repos = ts.repositories.get_repositories() | 781 repos = ts.repositories.get_repositories() |
| 781 rnames = [x.get("name", "?") for x in repos] | 782 rnames = [x.get("name", "?") for x in repos] |
| 782 rids = [x.get("id", "?") for x in repos] | 783 rids = [x.get("id", "?") for x in repos] |
| 783 sto.write(f"############names={rnames} rids={rids}\n") | 784 sto.write(f"############names={rnames} rids={rids}\n") |
| 785 sto.write(f"############names={repos}\n") | |
| 784 tfcat = "ToolFactory generated tools" | 786 tfcat = "ToolFactory generated tools" |
| 785 if self.args.tool_name not in rnames: | 787 if self.args.tool_name not in rnames: |
| 786 tscat = ts.categories.get_categories() | 788 tscat = ts.categories.get_categories() |
| 787 cnames = [x.get("name", "?").strip() for x in tscat] | 789 cnames = [x.get("name", "?").strip() for x in tscat] |
| 788 cids = [x.get("id", "?") for x in tscat] | 790 cids = [x.get("id", "?") for x in tscat] |
| 802 tid = res.get("id", None) | 804 tid = res.get("id", None) |
| 803 sto.write(f"##########create res={res}\n") | 805 sto.write(f"##########create res={res}\n") |
| 804 else: | 806 else: |
| 805 i = rnames.index(self.args.tool_name) | 807 i = rnames.index(self.args.tool_name) |
| 806 tid = rids[i] | 808 tid = rids[i] |
| 807 res = ts.repositories.update_repository( | 809 try: |
| 808 id=tid, tar_ball_path=self.newtarpath, commit_message=None | 810 res = ts.repositories.update_repository( |
| 809 ) | 811 id=tid, tar_ball_path=self.newtarpath, commit_message=None) |
| 810 sto.write(f"#####update res={res}\n") | 812 sto.write(f"#####update res={res}\n") |
| 813 except ConnectionError: | |
| 814 sto.write("Probably no change to repository - bioblend shed upload failed\n") | |
| 811 sto.close() | 815 sto.close() |
| 812 | 816 |
| 813 def eph_galaxy_load(self): | 817 def eph_galaxy_load(self): |
| 814 """load the new tool from the local toolshed after planemo uploads it""" | 818 """load the new tool from the local toolshed after planemo uploads it""" |
| 815 if os.path.exists(self.tlog): | 819 if os.path.exists(self.tlog): |
| 1239 retcode = r.run() | 1243 retcode = r.run() |
| 1240 r.moveRunOutputs() | 1244 r.moveRunOutputs() |
| 1241 r.makeToolTar() | 1245 r.makeToolTar() |
| 1242 else: | 1246 else: |
| 1243 r.makeToolTar() | 1247 r.makeToolTar() |
| 1244 #r.planemo_shedLoad() | 1248 r.planemo_shedLoad() |
| 1245 r.shedLoad() | 1249 r.shedLoad() |
| 1246 r.eph_galaxy_load() | 1250 r.eph_galaxy_load() |
| 1247 retcode = r.gal_tool_test() # writes outputs | 1251 retcode = r.gal_tool_test() # writes outputs |
| 1248 r.makeToolTar() | 1252 r.makeToolTar() |
| 1249 #r.planemo_shedLoad() | 1253 r.planemo_shedLoad() |
| 1250 r.shedLoad() | 1254 r.shedLoad() |
| 1251 r.eph_galaxy_load() | 1255 r.eph_galaxy_load() |
| 1252 retcode = r.gal_test() | 1256 retcode = r.gal_test() |
| 1253 r.moveRunOutputs() | 1257 r.moveRunOutputs() |
| 1254 r.makeToolTar() | 1258 r.makeToolTar() |