Add execute_command_in_dir_with_realtime_output.

pyneuroml/pynml.py

@@ -10,6 +10,7 @@
 """
 
 from __future__ import absolute_import
+from __future__ import print_function
 import os
 import sys
 import subprocess
@@ -29,6 +30,8 @@
 import random
 import inspect
 import zipfile
+import shlex
+import signal
 
 DEFAULTS = {'v':False, 
             'default_java_max_memory':'400M',
@@ -551,7 +554,8 @@ def run_lems_with_jneuroml_neuron(lems_file_name,
                                   compile_mods = True,
                                   verbose = DEFAULTS['v'],
                                   exit_on_fail = True,
-                                  cleanup=False):
+                                  cleanup=False,
+                                  realtime_output=False):
                                   #jnml_runs_neuron=True):  #jnml_runs_neuron=False is Work in progress!!!
 
     print_comment("Loading LEMS file: %s and running with jNeuroML_NEURON" \
@@ -578,9 +582,21 @@ def run_lems_with_jneuroml_neuron(lems_file_name,
             if not path+":" in os.environ['PYTHONPATH']:
                 os.environ['PYTHONPATH'] = '%s:%s'%(path,os.environ['PYTHONPATH'])
 
+        print_comment('PYTHONPATH for NEURON: %s'%os.environ['PYTHONPATH'], verbose)
+
+        if realtime_output:
+            success = run_jneuroml_with_realtime_output("", 
+                           lems_file_name, 
+                           post_args, 
+                           max_memory = max_memory, 
+                           exec_in_dir = exec_in_dir, 
+                           verbose = verbose, 
+                           exit_on_fail = exit_on_fail)
+
         #print_comment('PYTHONPATH for NEURON: %s'%os.environ['PYTHONPATH'], verbose)
-
-        success = run_jneuroml("", 
+
+        else: 
+            success = run_jneuroml("", 
                            lems_file_name, 
                            post_args, 
                            max_memory = max_memory, 
@@ -959,6 +975,7 @@ def run_jneuroml(pre_args,
     jar_path = get_path_to_jnml_jar()
 
     output = ''
+
 
     try:
         command = 'java -Xmx%s %s -jar  "%s" %s "%s" %s' % \
@@ -971,6 +988,9 @@ def run_jneuroml(pre_args,
                 sys.exit(-1)
             else:
                 return False
+
+    #except KeyboardInterrupt as e:
+    #    raise e
 
     except:
         print_comment('*** Execution of jnml has failed! ***', True)
@@ -984,6 +1004,45 @@ def run_jneuroml(pre_args,
 
     return True
 
+
+# TODO: Refactorinng
+def run_jneuroml_with_realtime_output(pre_args, 
+                                      target_file, 
+                                      post_args, 
+                                      max_memory   = DEFAULTS['default_java_max_memory'], 
+                                      exec_in_dir  = ".",
+                                      verbose      = DEFAULTS['v'],
+                                      exit_on_fail = True):    
+
+    # NOTE: Only tested with Linux
+
+    if 'nogui' in post_args and not os.name == 'nt':
+        pre_jar = " -Djava.awt.headless=true"
+    else:
+        pre_jar = ""
+
+    jar_path = get_path_to_jnml_jar()
+
+    command = ''
+    output = ''
+
+    try:
+        command = 'java -Xmx%s %s -jar  "%s" %s "%s" %s' % \
+              (max_memory, pre_jar, jar_path, pre_args, target_file, post_args)
+        output = execute_command_in_dir_with_realtime_output(command, exec_in_dir, verbose=verbose,
+                                        prefix = ' jNeuroML >>  ')
+    except KeyboardInterrupt as e:
+        raise e
+    except:
+        print_comment('*** Execution of jnml has failed! ***', True)
+        print_comment('*** Command: %s ***'%command, True)
+        if exit_on_fail: 
+            sys.exit(-1)
+        else:
+            return False
+
+    return True
+
 
 def print_comment_v(text):
     print_comment(text, True)
@@ -997,6 +1056,33 @@ def print_comment(text, print_it=DEFAULTS['v']):
         print("%s%s"%(prefix, text.replace("\n", "\n"+prefix)))
 
 
+def execute_command_in_dir_with_realtime_output(command, directory, verbose=DEFAULTS['v'], 
+                                                prefix="Output: ", env=None):
+
+    # NOTE: Only tested with Linux
+    if os.name == 'nt':
+        directory = os.path.normpath(directory)
+
+    print_comment("Executing: (%s) in directory: %s" % (command, directory), verbose)
+    if env is not None:
+        print_comment("Extra env variables %s" % (env), verbose)
+
+    p = None
+    try:
+        p = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, bufsize=1, cwd=directory, env=env)
+        with p.stdout:
+            for line in iter(p.stdout.readline, b''):
+                print(line, end="")
+        p.wait() # wait for the subprocess to exit
+    except KeyboardInterrupt as e:
+        if p:
+            p.kill()
+        #return True
+        raise e
+
+    return True
+
+
 def execute_command_in_dir(command, directory, verbose=DEFAULTS['v'], 
                            prefix="Output: ", env=None):
 
@@ -1244,3 +1330,4 @@ def main(args=None):
 
 if __name__ == "__main__":
     main()
+