Got this in the latest pull of galaxy central... Ideas? Traceback (most recent call last): File "./scripts/set_metadata.py", line 24, in ? import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers File "/mnt/ngs/analysis/svcgalaxy/galaxy-central/lib/galaxy/model/__init__.py", line 13, in ? import galaxy.datatypes.registry File "/mnt/ngs/analysis/svcgalaxy/galaxy-central/lib/galaxy/datatypes/registry.py", line 145 finally: ^ SyntaxError: invalid syntax
Well, lib/galaxy/datatypes/registry.py hasn't changed in over two months. Out of curiousity, I tried downloading a fresh copy of galaxy-central (without any initial configuration or database, either) and didn't encounter the same problem. I even tried messing with that line of code and didn't have any luck reproducing the same traceback. What version of python are you using? -Scott ----- Original Message -----
Got this in the latest pull of galaxy central...
Ideas?
Traceback (most recent call last): File "./scripts/set_metadata.py", line 24, in ? import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers File "/mnt/ngs/analysis/svcgalaxy/galaxy-central/lib/galaxy/model/__init__.py", line 13, in ? import galaxy.datatypes.registry File "/mnt/ngs/analysis/svcgalaxy/galaxy-central/lib/galaxy/datatypes/registry.py", line 145 finally: ^ SyntaxError: invalid syntax ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
We recently ran into that issue as well. It seems that the used finally: syntax is valid from python 2.5, and we were using python 2.4. Loading a more recent version of python helped. Best, Geert Vandeweyer On 11/07/2012 04:54 AM, Scott McManus wrote:
Well, lib/galaxy/datatypes/registry.py hasn't changed in over two months. Out of curiousity, I tried downloading a fresh copy of galaxy-central (without any initial configuration or database, either) and didn't encounter the same problem. I even tried messing with that line of code and didn't have any luck reproducing the same traceback.
What version of python are you using?
-Scott
------------------------------------------------------------------------
Got this in the latest pull of galaxy central...
Ideas?
Traceback (most recent call last): File "./scripts/set_metadata.py", line 24, in ? import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers File "/mnt/ngs/analysis/svcgalaxy/galaxy-central/lib/galaxy/model/__init__.py", line 13, in ? import galaxy.datatypes.registry File "/mnt/ngs/analysis/svcgalaxy/galaxy-central/lib/galaxy/datatypes/registry.py", line 145 finally: ^ SyntaxError: invalid syntax
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi all, It seem that performing the Python version check in the set_metadata.py script (and most of the other scripts) would give a much clearer failure in this situation (accidentally running under Python 2.4). This is what scripts/paster.py does: # ensure supported version from check_python import check_python try: check_python() except: sys.exit(1) Regards, Peter On Wed, Nov 7, 2012 at 9:08 AM, Geert Vandeweyer <geert.vandeweyer2@ua.ac.be> wrote:
We recently ran into that issue as well. It seems that the used finally: syntax is valid from python 2.5, and we were using python 2.4.
Loading a more recent version of python helped.
Best,
Geert Vandeweyer
On 11/07/2012 04:54 AM, Scott McManus wrote:
Well, lib/galaxy/datatypes/registry.py hasn't changed in over two months. Out of curiousity, I tried downloading a fresh copy of galaxy-central (without any initial configuration or database, either) and didn't encounter the same problem. I even tried messing with that line of code and didn't have any luck reproducing the same traceback.
What version of python are you using?
-Scott
________________________________
Got this in the latest pull of galaxy central...
Ideas?
Traceback (most recent call last): File "./scripts/set_metadata.py", line 24, in ? import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers File "/mnt/ngs/analysis/svcgalaxy/galaxy-central/lib/galaxy/model/__init__.py", line 13, in ? import galaxy.datatypes.registry File "/mnt/ngs/analysis/svcgalaxy/galaxy-central/lib/galaxy/datatypes/registry.py", line 145 finally: ^ SyntaxError: invalid syntax
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi Peter, Excellent suggestion. I've replaced the outdated hard-coded minimum version check in set_metadata.py with a call to check_python() in changeset 8171:4b62ed46e5b6. As you note, there are likely other scripts that could benefit from a similar change; patches and pull requests are always welcome. Thanks for using Galaxy, Dan On Nov 7, 2012, at 4:57 AM, Peter Cock wrote:
Hi all,
It seem that performing the Python version check in the set_metadata.py script (and most of the other scripts) would give a much clearer failure in this situation (accidentally running under Python 2.4). This is what scripts/paster.py does:
# ensure supported version from check_python import check_python try: check_python() except: sys.exit(1)
Regards,
Peter
On Wed, Nov 7, 2012 at 9:08 AM, Geert Vandeweyer <geert.vandeweyer2@ua.ac.be> wrote:
We recently ran into that issue as well. It seems that the used finally: syntax is valid from python 2.5, and we were using python 2.4.
Loading a more recent version of python helped.
Best,
Geert Vandeweyer
On 11/07/2012 04:54 AM, Scott McManus wrote:
Well, lib/galaxy/datatypes/registry.py hasn't changed in over two months. Out of curiousity, I tried downloading a fresh copy of galaxy-central (without any initial configuration or database, either) and didn't encounter the same problem. I even tried messing with that line of code and didn't have any luck reproducing the same traceback.
What version of python are you using?
-Scott
________________________________
Got this in the latest pull of galaxy central...
Ideas?
Traceback (most recent call last): File "./scripts/set_metadata.py", line 24, in ? import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers File "/mnt/ngs/analysis/svcgalaxy/galaxy-central/lib/galaxy/model/__init__.py", line 13, in ? import galaxy.datatypes.registry File "/mnt/ngs/analysis/svcgalaxy/galaxy-central/lib/galaxy/datatypes/registry.py", line 145 finally: ^ SyntaxError: invalid syntax
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
I am running under virtualenv and running python 2.6 but I am suspecting that it is not passed on to my cluster that I am running under 2.6....But thanks for pointing me in this direction... On Nov 07, 2012, at 01:08 AM, Geert Vandeweyer <geert.vandeweyer2@ua.ac.be> wrote: We recently ran into that issue as well. It seems that the used finally: syntax is valid from python 2.5, and we were using python 2.4. Loading a more recent version of python helped. Best, Geert Vandeweyer On 11/07/2012 04:54 AM, Scott McManus wrote: Well, lib/galaxy/datatypes/registry.py hasn't changed in over two months. Out of curiousity, I tried downloading a fresh copy of galaxy-central (without any initial configuration or database, either) and didn't encounter the same problem. I even tried messing with that line of code and didn't have any luck reproducing the same traceback. What version of python are you using? -Scott Got this in the latest pull of galaxy central... Ideas? Traceback (most recent call last): File "./scripts/set_metadata.py", line 24, in ? import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers File "/mnt/ngs/analysis/svcgalaxy/galaxy-central/lib/galaxy/model/__init__.py", line 13, in ? import galaxy.datatypes.registry File "/mnt/ngs/analysis/svcgalaxy/galaxy-central/lib/galaxy/datatypes/registry.py", line 145 finally: ^ SyntaxError: invalid syntax ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
participants (5)
-
Anthonius deBoer -
Daniel Blankenberg -
Geert Vandeweyer -
Peter Cock -
Scott McManus