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openworm / owmeta

Unified, simple data access python library for data & facts about C. elegans anatomy
MIT License
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Implement muscle.innervatedBy() in alpha0.5 #33

Closed slarson closed 10 years ago

slarson commented 10 years ago

There's interest from @wilzh40 to see this accomplished for another part of the project. @mwatts15 do you have everything you need to do this?

slarson commented 10 years ago

@wilzh40 -- @mwatts15 says this should be in the latest version over on the alpha0.5 branch -- now that you have this up per the mailing list can you try it out?

wilzh40 commented 10 years ago

I'm getting an error in the install script after running python setup.py install: File "setup.py", line 32, in insert_worm.do_insert() File "/Users/wilsonzhao/Programming/OpenWorm/PyOpenWorm/db/insert_worm.py", line 232, in do_insert P.connect(configFile='default.conf',do_logging=logging) File "/Users/wilsonzhao/Programming/OpenWorm/PyOpenWorm/PyOpenWorm/init.py", line 160, in connect Configureable.conf.openDatabase() File "/Users/wilsonzhao/Programming/OpenWorm/PyOpenWorm/PyOpenWorm/data.py", line 225, in openDatabase self.source.open() File "/Users/wilsonzhao/Programming/OpenWorm/PyOpenWorm/PyOpenWorm/data.py", line 477, in open self.graph.open(self.conf['rdf.store_conf'],create=True) File "build/bdist.macosx-10.9-intel/egg/rdflib/graph.py", line 378, in open File "build/bdist.macosx-10.9-intel/egg/rdflib/plugins/sleepycat.py", line 89, in open File "build/bdist.macosx-10.9-intel/egg/rdflib/plugins/sleepycat.py", line 66, in _init_db_environment OSError: [Errno 2] No such file or directory: 'BASE/db/worm.db'

mwatts15 commented 10 years ago

Hi @wilzh40. Could you try it since the change I made just now?

wilzh40 commented 10 years ago

Great, it works now on my mac! When I tried running a new install on my linux distro this is what I got: Traceback (most recent call last): File "setup.py", line 32, in insert_worm.do_insert() File "/home/wilson/programming/openworm/PyOpenWorm/db/insert_worm.py", line 232, in do_insert P.connect(configFile='default.conf',do_logging=logging) File "/home/wilson/programming/openworm/PyOpenWorm/PyOpenWorm/init.py", line 136, in connect loadConfig(configFile) File "/home/wilson/programming/openworm/PyOpenWorm/PyOpenWorm/init.py", line 98, in loadConfig Configureable.conf = Data.open(f) File "/home/wilson/programming/openworm/PyOpenWorm/PyOpenWorm/data.py", line 219, in open Configureable.conf = Configure.open(file_name) File "/home/wilson/programming/openworm/PyOpenWorm/PyOpenWorm/configure.py", line 89, in open raise BadConf(e) PyOpenWorm.configure.BadConf: PyOpenWorm

mwatts15 commented 10 years ago

Hi Wilson, I'm not entirely sure what's wrong here. It looks like Requirement isn't able to find PyOpenWorm, which is strange. Could you print the traceback where that exception is raised.

On Thu, Aug 14, 2014 at 5:19 PM, Wilson Zhao notifications@github.com wrote:

Great, it works now on my mac! When I tried running a new install on my linux distro this is what I got: Traceback (most recent call last):

File "setup.py", line 32, in insert_worm.do_insert() File "/home/wilson/programming/openworm/PyOpenWorm/db/insert_worm.py", line 232, in do_insert P.connect(configFile='default.conf',do_logging=logging) File "/home/wilson/programming/openworm/PyOpenWorm/PyOpenWorm/init.py", line 136, in connect loadConfig(configFile) File "/home/wilson/programming/openworm/PyOpenWorm/PyOpenWorm/init.py", line 98, in loadConfig Configureable.conf = Data.open(f) File "/home/wilson/programming/openworm/PyOpenWorm/PyOpenWorm/data.py", line 219, in open Configureable.conf = Configure.open(file_name) File "/home/wilson/programming/openworm/PyOpenWorm/PyOpenWorm/configure.py", line 89, in open raise BadConf(e) PyOpenWorm.configure.BadConf: PyOpenWorm

— Reply to this email directly or view it on GitHub https://github.com/openworm/PyOpenWorm/issues/33#issuecomment-52252797.

Cheers, Mark Watts Department of Computer Science University of Texas at Austin

mwatts15 commented 10 years ago

I just realized, that my request may be confiusing. I was asking to see the exception which triggered the exception handler where the BadConf is thrown. It's almost definitely a DistributionNotFound exception. I'll have a look at the pkg_resources docs to see why the PyOpenWorm package might not be available.

mwatts15 commented 10 years ago

I believe this issue has been fixed since at least 66d3d96b .

If you continue to experience the problem, please reopen this ticket if necessary or create a new ticket with your related issue, referencing this one (#33).