circular import in tool_shed code gives unit test failure
Dear, I've been running unit tests on the latest galaxy-central 7294:663e03e40c86 that have me this error: [localhost] out: ====================================================================== [localhost] out: ERROR: Failure: ImportError (cannot import name install_manager) [localhost] out: ---------------------------------------------------------------------- [localhost] out: Traceback (most recent call last): [localhost] out: File "/Users/pajon01/galaxy-test/galaxy-central/eggs/nose-0.11.1-py2.7.egg/nose/loader.py", line 379, in loadTestsFromName [localhost] out: addr.filename, addr.module) [localhost] out: File "/Users/pajon01/galaxy-test/galaxy-central/eggs/nose-0.11.1-py2.7.egg/nose/importer.py", line 39, in importFromPath [localhost] out: return self.importFromDir(dir_path, fqname) [localhost] out: File "/Users/pajon01/galaxy-test/galaxy-central/eggs/nose-0.11.1-py2.7.egg/nose/importer.py", line 86, in importFromDir [localhost] out: mod = load_module(part_fqname, fh, filename, desc) [localhost] out: File "/Users/pajon01/galaxy-test/galaxy-central/lib/galaxy/tool_shed/install_manager.py", line 10, in <module> [localhost] out: from galaxy.tool_shed.migrate.common import * [localhost] out: File "/Users/pajon01/galaxy-test/galaxy-central/lib/galaxy/tool_shed/migrate/common.py", line 9, in <module> [localhost] out: from galaxy.tool_shed import install_manager [localhost] out: ImportError: cannot import name install_manager [localhost] out: ---------------------------------------------------------------------- I fixed it by commenting out the circular import in tool_shed/install_manager.py hg diff diff -r 663e03e40c86 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py Wed Jun 20 03:39:05 2012 -0400 +++ b/lib/galaxy/tool_shed/install_manager.py Wed Jun 20 16:37:06 2012 +0100 @@ -7,7 +7,7 @@ from galaxy.util.json import from_json_string, to_json_string from galaxy.util.shed_util import * from galaxy.util.odict import odict -from galaxy.tool_shed.migrate.common import * +#from galaxy.tool_shed.migrate.common import * Hope it would be useful to someone else. Kind regards, Anne. -- Anne Pajon, Ph.D. Cancer Research UK - Cambridge Research Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon@cancer.org.uk | +44 (0)1223 404 334 NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered in England and Wales Company Registered Number: 4325234. Registered Charity Number: 1089464 and Scotland SC041666 Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.
Thanks Anne, I'll make sure this fix makes it into my next commit to Galaxy central. Greg On Jun 20, 2012, at 11:42 AM, Anne Pajon wrote:
Dear,
I've been running unit tests on the latest galaxy-central 7294:663e03e40c86 that have me this error:
[localhost] out: ====================================================================== [localhost] out: ERROR: Failure: ImportError (cannot import name install_manager) [localhost] out: ---------------------------------------------------------------------- [localhost] out: Traceback (most recent call last): [localhost] out: File "/Users/pajon01/galaxy-test/galaxy-central/eggs/nose-0.11.1-py2.7.egg/nose/loader.py", line 379, in loadTestsFromName [localhost] out: addr.filename, addr.module) [localhost] out: File "/Users/pajon01/galaxy-test/galaxy-central/eggs/nose-0.11.1-py2.7.egg/nose/importer.py", line 39, in importFromPath [localhost] out: return self.importFromDir(dir_path, fqname) [localhost] out: File "/Users/pajon01/galaxy-test/galaxy-central/eggs/nose-0.11.1-py2.7.egg/nose/importer.py", line 86, in importFromDir [localhost] out: mod = load_module(part_fqname, fh, filename, desc) [localhost] out: File "/Users/pajon01/galaxy-test/galaxy-central/lib/galaxy/tool_shed/install_manager.py", line 10, in <module> [localhost] out: from galaxy.tool_shed.migrate.common import * [localhost] out: File "/Users/pajon01/galaxy-test/galaxy-central/lib/galaxy/tool_shed/migrate/common.py", line 9, in <module> [localhost] out: from galaxy.tool_shed import install_manager [localhost] out: ImportError: cannot import name install_manager
[localhost] out: ----------------------------------------------------------------------
I fixed it by commenting out the circular import in tool_shed/install_manager.py
hg diff diff -r 663e03e40c86 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py Wed Jun 20 03:39:05 2012 -0400 +++ b/lib/galaxy/tool_shed/install_manager.py Wed Jun 20 16:37:06 2012 +0100 @@ -7,7 +7,7 @@ from galaxy.util.json import from_json_string, to_json_string from galaxy.util.shed_util import * from galaxy.util.odict import odict -from galaxy.tool_shed.migrate.common import * +#from galaxy.tool_shed.migrate.common import *
Hope it would be useful to someone else. Kind regards, Anne. -- Anne Pajon, Ph.D. Cancer Research UK - Cambridge Research Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon@cancer.org.uk | +44 (0)1223 404 334
NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose.
We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered in England and Wales Company Registered Number: 4325234. Registered Charity Number: 1089464 and Scotland SC041666 Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.
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participants (2)
-
Anne Pajon -
Greg Von Kuster