mattions/neuronvisio — Issue #35: Include also mods into the possible path for mod files
Author: mattions
Created: 2011-12-20 10:49:13+00:00
State: open
Labels: bug

One of the model available on ModelDB, 140471, is storing the mods into the mod files.

The compilation fails and all the software crash.

This is the log:

INFO neuronvisio.modeldb.ModelDB 117 Downloading model for 'Jaffe et al., 2011'
INFO neuronvisio.modeldb.ModelDB 149 Creating Models/140471.zip
INFO neuronvisio.modeldb.ModelDB 158 Done.
INFO neuronvisio.modeldb.ModelDB 119 Download complete.
INFO neuronvisio.modeldb.ModelDB 164 Extracting 'Models/140471.zip' into Models/140471
INFO neuronvisio.modeldb.ModelDB 170 Trancating file at location 1402360.
INFO neuronvisio.modeldb.ModelDB 192 Done.
INFO neuronvisio.controls 457 Path changed to /home/mattions/Work/model/MSN/Neuronvisio/src/Models/140471
Creating x86_64 directory for .o files.

/home/mattions/Work/model/MSN/Neuronvisio/src/Models/140471
*.mod
*.mod
make: *** No rule to make target `mod_func.c.lo', needed by `libnrnmech.la'. Stop.
NEURON mechanisms not found in ./.
NEURON: unable to open font "*helvetica-medium-r-normal*--14*", using "fixed"
1
INFO neuronvisio.controls 471 Loading model in Models/140471
1
1
1
NEURON: syntax error
in figure5.hoc near line 170
insert Ca	// Ca Channesl
^
xopen("figure5.hoc")
execute1("{xopen("figure5.hoc")}")
load_file("figure5.hoc")
xopen("mosinit.hoc")
and others
0
NEURON: syntax error
in figure5.hoc near line 175
insert aabBK	// BK Channels
^
xopen("mosinit.hoc")
execute1("{xopen("mosinit.hoc")}")
load_file("k")
Assertion failed: file cabcode.c, line 1736
NEURON: sec->nnode > 0
in figure5.hoc near line 175
^
doNotify()
INFO neuronvisio.controls 475 Path changed back to /home/mattions/Work/model/MSN/Neuronvisio/src
Exception in thread Thread-1:
Traceback (most recent call last):
File "/usr/lib/python2.7/threading.py", line 552, in __bootstrap_inner
self.run()
File "/usr/local/lib/python2.7/dist-packages/neuron/gui.py", line 36, in run
self.fun()
File "/usr/local/lib/python2.7/dist-packages/neuron/gui.py", line 17, in process_events
h.doNotify()
RuntimeError: hoc error

Segmentation fault

We should include also mods, in the possible path to compilation, and we should manage the compilation a bit more gracefully, maybe using an Exception.