Working on bugfix for #21

gillespy/__init__.py

@@ -1 +1,4 @@
 from .gillespy import *
+import os
+os.environ["PATH"] += os.pathsep + "/usr/local/stochss/StochKit/"
+os.environ["PATH"] += os.pathsep + "/usr/local/stochss/ode/"

gillespy/gillespy.py

@@ -12,9 +12,12 @@
 import matplotlib.pyplot as plt
 import tempfile
 import uuid
-import subprocess
+import subprocess32 as subprocess
 import types
 import random
+import os
+import signal
+import psutil
 
 try:
     import lxml.etree as etree
@@ -239,14 +242,14 @@ def delete_reaction(self, obj):
     def delete_all_reactions(self):
         self.listOfReactions.clear()
 
-    def run(self, number_of_trajectories=1, seed=None, report_level=0, solver=None, stochkit_home=None, debug=False):
+    def run(self, number_of_trajectories=1, seed=None, report_level=0, solver=None, stochkit_home=None, debug=False,timeout=None):
         if solver is not None:
             if isinstance(solver, (type, types.ClassType)) and  issubclass(solver, GillesPySolver):
-                return solver.run(self,t=self.tspan[-1],increment=self.tspan[-1]-self.tspan[-2],seed=seed,number_of_trajectories=number_of_trajectories, stochkit_home=stochkit_home, debug=debug)
+                return solver.run(self,t=self.tspan[-1],increment=self.tspan[-1]-self.tspan[-2],seed=seed,number_of_trajectories=number_of_trajectories, stochkit_home=stochkit_home, debug=debug,timeout=timeout)
             else:
                 raise SimuliationError('argument "solver" to run() must be a subclass of GillesPySolver')
         else:
-            return StochKitSolver.run(self,t=self.tspan[-1],increment=self.tspan[-1]-self.tspan[-2],seed=seed,number_of_trajectories=number_of_trajectories, stochkit_home=stochkit_home, debug=debug)
+            return StochKitSolver.run(self,t=self.tspan[-1],increment=self.tspan[-1]-self.tspan[-2],seed=seed,number_of_trajectories=number_of_trajectories, stochkit_home=stochkit_home, debug=debug,timeout=timeout)
 
 
 class Species():
@@ -318,7 +321,7 @@ class Reaction():
     """
 
     def __init__(self, name = "", reactants = {}, products = {}, 
-                 propensity_function = None, massaction = False, 
+                 propensity_function = None, massaction = True, 
                  rate=None, annotation=None):
         """ 
         Initializes the reaction using short-hand notation. 
@@ -343,8 +346,8 @@ def __init__(self, name = "", reactants = {}, products = {},
         self.name = name
         self.annotation = ""
 
-        if rate is None and propensity_function is None:
-            raise ReactionError("You must specify either a mass-action rate or a propensity function")
+        #if rate is None and propensity_function is None:
+        #    raise ReactionError("You must specify either a mass-action rate or a propensity function")
 
         # We might use this flag in the future to automatically generate
         # the propensity function if set to True.
@@ -378,10 +381,12 @@ def __init__(self, name = "", reactants = {}, products = {},
         if self.massaction:
             self.type = "mass-action"
             if rate is None:
-                raise ReactionError("Reaction : A mass-action propensity has\
-                 to have a rate.")
-            self.marate = rate
-            self.create_mass_action()
+		self.marate=None
+            #    raise ReactionError("Reaction : A mass-action propensity has\
+            #     to have a rate.")
+	    else:
+            	self.marate = rate
+            	self.create_mass_action()
         else:
             self.type = "customized"
 
@@ -642,6 +647,9 @@ def to_model(self,name):
                 type = reac.find('Type').text
             except:
                 raise InvalidStochMLError("No reaction type specified.")
+
+            #reaction  = Reaction(name,{},{},None,False,0.0,None)                                                         
+
 
             reactants  = reac.find('Reactants')
             try:
@@ -820,7 +828,7 @@ class GillesPySolver():
 
     def run(self, model, t=20, number_of_trajectories=1,
             increment=0.05, seed=None, stochkit_home=None, algorithm=None,
-            job_id=None, extra_args='', debug=False):
+            job_id=None, extra_args='', debug=False,timeout=None):
         """ 
         Call out and run the solver. Collect the results.
         """
@@ -873,6 +881,7 @@ def run(self, model, t=20, number_of_trajectories=1,
                                            algorithm)):
                 executable = os.path.join(os.environ.get('STOCHKIT_HOME'), 
                                           algorithm)
+
         if executable is None:
             # try to find the executable in the path
             if os.environ.get('PATH') is not None:
@@ -910,22 +919,37 @@ def run(self, model, t=20, number_of_trajectories=1,
             print "cmd: {0}".format(cmd)
 
         # Execute
-        try:
+        #try:
             #print "CMD: {0}".format(cmd)
-            handle = subprocess.Popen(cmd, stdout = subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
-            return_code = handle.wait()
-        except OSError as e:
-            raise SimuliationError("Solver execution failed: \
-            {0}\n{1}".format(cmd, e))
-
+            #handle = subprocess.Popen(cmd, stdout = subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
+        handle = subprocess.Popen(cmd,shell=True, preexec_fn=os.setsid)
+            #return_code = handle.wait()
         try:
-            stderr = handle.stderr.read()
-        except Exception as e:
-            stderr = 'Error reading stderr: {0}'.format(e)
-        try:
-            stdout = handle.stdout.read()
-        except Exception as e:
-            stdout = 'Error reading stdout: {0}'.format(e)
+            outs, errs = handle.communicate(timeout=timeout)
+            return_code = 0
+        except subprocess.TimeoutExpired:
+	    #os.killpg(os.getpgid(handle.pid),signal.SIGTERM)
+            #print os.getpgid(handle.pid)
+	    parent = psutil.Process(handle.pid)
+	    for child in parent.children(recursive=True):  # or parent.children() for recursive=False
+                child.kill()	    
+            handle.kill()
+            outs, errs = handle.communicate(timeout=timeout)
+            return_code=-1
+            raise SolverTimeoutError("Solver timed out")
+
+        #except OSError as e:
+        #    raise SimuliationError("Solver execution failed: \
+        #    {0}\n{1}".format(cmd, e))
+
+        #try:
+        #    stderr = handle.stderr.read()
+        #except Exception as e:
+        #    stderr = 'Error reading stderr: {0}'.format(e)
+        #try:
+        #    stdout = handle.stdout.read()
+        #except Exception as e:
+        #    stdout = 'Error reading stdout: {0}'.format(e)
 
         if return_code != 0:
             #print stdout
@@ -961,7 +985,7 @@ class StochKitSolver(GillesPySolver):
     @classmethod
     def run(cls, model, t=20, number_of_trajectories=1,
             increment=0.05, seed=None, stochkit_home=None, algorithm='ssa',
-            job_id=None, method=None,debug=False):
+            job_id=None, method=None,debug=False,timeout=None):
 
         # all this is specific to StochKit
         if model.units == "concentration":
@@ -993,7 +1017,7 @@ def run(cls, model, t=20, number_of_trajectories=1,
 
 
         self = StochKitSolver()
-        return GillesPySolver.run(self, model,t, number_of_trajectories, increment, seed, stochkit_home, algorithm, job_id, extra_args=args, debug=debug)
+        return GillesPySolver.run(self, model,t, number_of_trajectories, increment, seed, stochkit_home, algorithm, job_id, extra_args=args, debug=debug,timeout=timeout)
 
     def get_trajectories(self, outdir, debug=False):
         # Collect all the output data
@@ -1048,6 +1072,9 @@ class InvalidStochMLError(Exception):
 class InvalidModelError(Exception):
     pass
 
+class SolverTimeoutError(Exception):
+    pass
+
 class SimulationError(Exception):
     pass