Public Access
fix log dump race and unclosed HDF5 data pool file in DamarisGUI
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markusro committed
1 parent
efb01250c8
commit
da1dc4a088
1 file changed
+116
-114
+116
-114
@@ -613,8 +613,9 @@ class DamarisGUI:
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logger.debug("Data cleanup took %.3fs", time.time() - data_cleanup_start)
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# set the text mark for hdf logging
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if self.log.textbuffer.get_mark( "lastdumped" ) is None:
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self.log.textbuffer.create_mark( "lastdumped", self.log.textbuffer.get_end_iter( ), left_gravity=True )
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with self.log.lock:
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if self.log.textbuffer.get_mark( "lastdumped" ) is None:
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self.log.textbuffer.create_mark( "lastdumped", self.log.textbuffer.get_end_iter( ), left_gravity=True )
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loop_run=0
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#user shorter interval because this blocks user events from the GUI
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@@ -991,125 +992,124 @@ class DamarisGUI:
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# now it's time to create the hdf file
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dump_file = None
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if not os.path.isfile( self.dump_filename ):
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if not init:
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logger.warning("Dump file \"%s\" vanished unexpectedly, creating new one", self.dump_filename)
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# have a look to the path and create necessary directories
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dir_stack = [ ]
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dir_trunk = os.path.dirname( os.path.abspath( self.dump_filename ) )
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while dir_trunk != "" and not os.path.isdir( dir_trunk ):
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dir_stack.append( os.path.basename( dir_trunk ) )
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dir_trunk = os.path.dirname( dir_trunk )
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try:
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while len( dir_stack ):
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dir_trunk = os.path.join( dir_trunk, dir_stack.pop( ) )
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if os.path.isdir( dir_trunk ):
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continue
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os.mkdir( dir_trunk )
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except OSError as e:
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logger.error("Could not create dump directory '%s', so hdf5 dumps disabled: %s", dir_trunk, e)
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self.dump_filename = ""
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self.dump_timeinterval = 0
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return True
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try:
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if not os.path.isfile( self.dump_filename ):
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if not init:
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logger.warning("Dump file \"%s\" vanished unexpectedly, creating new one", self.dump_filename)
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# have a look to the path and create necessary directories
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dir_stack = [ ]
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dir_trunk = os.path.dirname( os.path.abspath( self.dump_filename ) )
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while dir_trunk != "" and not os.path.isdir( dir_trunk ):
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dir_stack.append( os.path.basename( dir_trunk ) )
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dir_trunk = os.path.dirname( dir_trunk )
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try:
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while len( dir_stack ):
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dir_trunk = os.path.join( dir_trunk, dir_stack.pop( ) )
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if os.path.isdir( dir_trunk ):
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continue
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os.mkdir( dir_trunk )
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except OSError as e:
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logger.error("Could not create dump directory '%s', so hdf5 dumps disabled: %s", dir_trunk, e)
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self.dump_filename = ""
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self.dump_timeinterval = 0
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return True
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# create new dump file
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dump_file = tables.open_file( self.dump_filename, mode="w", title="DAMARIS experiment data" )
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# write scripts and other useful information
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scriptgroup = dump_file.create_group( "/", "scripts", "Used Scripts" )
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exp_text, res_text = self.sw.get_scripts( )
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if self.si.exp_script:
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dump_file.create_array( scriptgroup, "experiment_script", exp_text.encode('utf-8') )
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if self.si.res_script:
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dump_file.create_array( scriptgroup, "result_script", res_text.encode('utf-8') )
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if self.si.backend_executable:
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dump_file.create_array( scriptgroup, "backend_executable", self.si.backend_executable.encode('utf-8') )
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if self.spool_dir:
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dump_file.create_array( scriptgroup, "spool_directory", self.spool_dir.encode('utf-8') )
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timeline_tablecols = numpy.recarray( 0, dtype=([ ("time", "S17"),
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("experiments", "int64"),
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("results", "int64") ]) )
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timeline_table = dump_file.create_table( "/", "timeline", timeline_tablecols,
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title="Timeline of Experiment" )
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if tables.__version__[ 0 ] == "1":
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logarray = dump_file.create_vlarray( where=dump_file.root,
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name="log",
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atom=tables.StringAtom( length=120 ),
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title="log messages",
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filters=tables.Filters( complevel=9, complib='zlib' ) )
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else:
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logarray = dump_file.create_earray( where=dump_file.root,
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name="log",
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atom=tables.StringAtom( itemsize=120 ),
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shape=(0,),
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title="log messages",
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filters=tables.Filters( complevel=9, complib='zlib' ) )
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# create new dump file
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dump_file = tables.open_file( self.dump_filename, mode="w", title="DAMARIS experiment data" )
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# write scripts and other useful information
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scriptgroup = dump_file.create_group( "/", "scripts", "Used Scripts" )
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exp_text, res_text = self.sw.get_scripts( )
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if self.si.exp_script:
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dump_file.create_array( scriptgroup, "experiment_script", exp_text.encode('utf-8') )
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if self.si.res_script:
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dump_file.create_array( scriptgroup, "result_script", res_text.encode('utf-8') )
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if self.si.backend_executable:
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dump_file.create_array( scriptgroup, "backend_executable", self.si.backend_executable.encode('utf-8') )
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if self.spool_dir:
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dump_file.create_array( scriptgroup, "spool_directory", self.spool_dir.encode('utf-8') )
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timeline_tablecols = numpy.recarray( 0, dtype=([ ("time", "S17"),
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("experiments", "int64"),
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("results", "int64") ]) )
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timeline_table = dump_file.create_table( "/", "timeline", timeline_tablecols,
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title="Timeline of Experiment" )
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if tables.__version__[ 0 ] == "1":
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logarray = dump_file.create_vlarray( where=dump_file.root,
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name="log",
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atom=tables.StringAtom( length=120 ),
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title="log messages",
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filters=tables.Filters( complevel=9, complib='zlib' ) )
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else:
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logarray = dump_file.create_earray( where=dump_file.root,
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name="log",
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atom=tables.StringAtom( itemsize=120 ),
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shape=(0,),
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title="log messages",
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filters=tables.Filters( complevel=9, complib='zlib' ) )
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if dump_file is None and os.path.isfile( self.dump_filename ) and tables.is_pytables_file( self.dump_filename ):
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# prepare for update
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dump_file = tables.open_file( self.dump_filename, mode="r+" )
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if dump_file is None and os.path.isfile( self.dump_filename ) and tables.is_pytables_file( self.dump_filename ):
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# prepare for update
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dump_file = tables.open_file( self.dump_filename, mode="r+" )
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if dump_file is None:
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# exit!
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logger.error("Could not create dump directory '%s', so hdf5 dumps disabled", dir_trunk)
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self.dump_filename = ""
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self.dump_timeinterval = 0
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return True
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if dump_file is None:
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# exit!
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logger.error("Could not create dump directory '%s', so hdf5 dumps disabled", dir_trunk)
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self.dump_filename = ""
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self.dump_timeinterval = 0
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return True
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# no undo please!
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if dump_file.is_undo_enabled( ):
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dump_file.disable_undo( )
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# no undo please!
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if dump_file.is_undo_enabled( ):
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dump_file.disable_undo( )
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# save the data!
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if self.data is not None:
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self.data.write_hdf5( dump_file, where="/", name="data_pool",
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complib=self.dump_complib, complevel=self.dump_complevel,
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incremental=not init, write_interval=self.dump_timeinterval )
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# save the data!
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if self.data is not None:
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self.data.write_hdf5( dump_file, where="/", name="data_pool",
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complib=self.dump_complib, complevel=self.dump_complevel,
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incremental=not init, write_interval=self.dump_timeinterval )
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# Re-enable run button if this was called from save thread
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# NO: this is dangerous as it allows starting a new experiment before cleanup is finished.
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# it will be re-enabled in observe_running_experiment after joining this thread.
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# if not init and threading.current_thread().name == "dump states":
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# gdk.threads_enter()
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# self.toolbar_run_button.set_sensitive(True)
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# gdk.threads_leave()
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# Re-enable run button if this was called from save thread
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# NO: this is dangerous as it allows starting a new experiment before cleanup is finished.
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# it will be re-enabled in observe_running_experiment after joining this thread.
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# if not init and threading.current_thread().name == "dump states":
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# gdk.threads_enter()
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# self.toolbar_run_button.set_sensitive(True)
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# gdk.threads_leave()
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# now save additional information
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e = 0
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r = 0
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if self.si is not None:
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e = self.si.data.get( "__recentexperiment", -1 ) + 1
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r = self.si.data.get( "__recentresult", -1 ) + 1
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timeline_table = dump_file.root.timeline
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timeline_row = timeline_table.row
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timeline_row[ "time" ] = time.strftime( "%Y%m%d %H:%M:%S" )
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timeline_row[ "experiments" ] = e
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timeline_row[ "results" ] = r
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timeline_row.append( )
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timeline_table.flush( )
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# now save additional information
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e = 0
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r = 0
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if self.si is not None:
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e = self.si.data.get( "__recentexperiment", -1 ) + 1
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r = self.si.data.get( "__recentresult", -1 ) + 1
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timeline_table = dump_file.root.timeline
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timeline_row = timeline_table.row
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timeline_row[ "time" ] = time.strftime( "%Y%m%d %H:%M:%S" )
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timeline_row[ "experiments" ] = e
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timeline_row[ "results" ] = r
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timeline_row.append( )
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timeline_table.flush( )
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# save log window information:
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# also save backend's logfile information?
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logtextbuffer = self.log.textbuffer
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last_end = logtextbuffer.get_mark( "lastdumped" )
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if last_end is None:
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last_end = logtextbuffer.create_mark( "lastdumped", logtextbuffer.get_start_iter( ), left_gravity=True )
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#logtext_start = logtextbuffer.get_iter_at_mark( last_end )
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logtext_end = logtextbuffer.get_end_iter( )
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logtextbuffer.move_mark( last_end, logtext_end )
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# Create new iterators after the mark move
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logtext_start = logtextbuffer.get_iter_at_mark( last_end )
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logtext_end = logtextbuffer.get_end_iter( )
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# recode from unicode
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logtext = logtextbuffer.get_text( logtext_start, logtext_end, True )
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# avoid circular references (seems to be necessary with gtk-2.12)
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# del logtextbuffer, logtext_start, logtext_end, last_end
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for l in logtext.splitlines( ):
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dump_file.root.log.append( numpy.array( [ l ], dtype="S120" ) )
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# save log window information:
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# also save backend's logfile information?
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# the dump thread must not race with the GUI thread appending messages
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with self.log.lock:
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logtextbuffer = self.log.textbuffer
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last_end = logtextbuffer.get_mark( "lastdumped" )
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if last_end is None:
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last_end = logtextbuffer.create_mark( "lastdumped", logtextbuffer.get_start_iter( ), left_gravity=True )
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logtext_start = logtextbuffer.get_iter_at_mark( last_end )
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logtext_end = logtextbuffer.get_end_iter( )
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logtext = logtextbuffer.get_text( logtext_start, logtext_end, True )
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logtextbuffer.move_mark( "lastdumped", logtext_end )
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if logtext is not None:
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for l in logtext.splitlines( ):
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dump_file.root.log.append( numpy.array( [ l ], dtype="S120" ) )
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dump_file.flush( )
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dump_file.close( )
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dump_file.flush( )
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finally:
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if dump_file is not None:
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dump_file.close( )
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self.last_dumped = time.time( )
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del dump_file
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return True
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@@ -1351,6 +1351,7 @@ class LogWindow:
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self.textview.connect( "key-press-event", self.textview_keypress)
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apply_font_css(self.textview, "Monospace 10")
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self.textbuffer = self.textview.get_buffer( )
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self.lock = threading.Lock( )
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self.last_timetag = None
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self( "Started in directory %s\n" % os.getcwd( ) )
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@@ -1365,9 +1366,10 @@ class LogWindow:
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timetag_int = math.floor( timetag )
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timetag_ms = int( (timetag - timetag_int) * 1000 )
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date_tag = time.strftime( "%Y%m%d %H:%M:%S.%%03d:\n", time.localtime( timetag_int ) ) % timetag_ms
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self.textbuffer.place_cursor( self.textbuffer.get_end_iter( ) )
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self.textbuffer.insert_at_cursor( date_tag + str( message ) )
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self.textview.scroll_to_mark( self.textbuffer.get_insert( ), 0.1 , False, 0.5, 0.5)
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with self.lock:
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self.textbuffer.place_cursor( self.textbuffer.get_end_iter( ) )
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self.textbuffer.insert_at_cursor( date_tag + str( message ) )
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self.textview.scroll_to_mark( self.textbuffer.get_insert( ), 0.1 , False, 0.5, 0.5)
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def textview_keypress( self, widget, event, data=None ):
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if event.state & gdk.ModifierType.CONTROL_MASK != 0:
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