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From scnakand...@apache.org
Subject [4/5] airavata git commit: cleaning modules
Date Fri, 04 Nov 2016 15:35:57 GMT
http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/example/openmm_example/openmm_streamer.py
----------------------------------------------------------------------
diff --git a/modules/simstream/example/openmm_example/openmm_streamer.py b/modules/simstream/example/openmm_example/openmm_streamer.py
deleted file mode 100644
index da95614..0000000
--- a/modules/simstream/example/openmm_example/openmm_streamer.py
+++ /dev/null
@@ -1,130 +0,0 @@
-from simstream import SimStream, DataReporter
-
-import sys, json
-
-class LogMonitor(object):
-    """
-    A callable class that returns unprocessed lines in an open logfile.
-
-    Instance Variables:
-    logfile -- the path to the logfile to monitor
-    """
-
-    def __init__(self, logfile):
-        """
-        Set up a monitor for a logfile.
-
-        Arguments:
-        logfile -- the path to the logfile to monitor
-        """
-        self.logfile = logfile
-        self._generator = None
-        self._version = sys.version_info[0]
-
-    def __call__(self):
-        """
-        Get the next line from the logfile.
-        """
-        if not self._generator:
-            self._generator = self._monitor_logfile()
-
-        lines = []
-
-        line = self._next()
-        while line is not None:
-            lines.append(line)
-            line = self._next()
-        print(lines)
-        return lines
-
-    def _monitor_logfile(self):
-        """
-        Yield the next set of lines from the logfile.
-        """
-        try:
-            # Make the file persistent for the lifetime of the generator
-            with open(self.logfile) as f:
-                f.seek(0,2) # Move to the end of the file
-                while True:
-                    # Get the next line or indicate the end of the file
-                    line = f.readline()
-                    if line:
-                        yield line.strip()
-                    else:
-                        yield None
-
-        except EnvironmentError as e:
-            # Handle I/O exceptions in an OS-agnostic way
-            print("Error: Could not open file %s: %s" % (self.logfile, e))
-
-    def _next(self):
-        """
-        Python 2/3 agnostic retrieval of generator values.
-        """
-        return self._generator.__next__() if self._version == 3 else self._generator.next()
-
-
-def get_relevant_log_lines(log_lines):
-    import re
-    relevant_lines = []
-    pattern = r'^\[.+\]'
-    for line in log_lines:
-        if re.match(pattern, line) is not None:
-            relevant_lines.append(line)
-    return relevant_lines
-
-
-def calculate_rmsd(trajectory, topology, reference):
-    import mdtraj
-    traj = mdtraj.load(trajectory, top=topology)
-    ref = mdtraj.load(reference)
-    rmsd = mdtraj.rmsd(traj, ref)
-    data = {"step": str(traj.n_frames), "rmsd": str(rmsd[-1])}
-    return data
-
-settings = {}
-
-with open("../settings.json", 'r') as f:
-    settings = json.load(f)
-
-
-if __name__ == "__main__":
-    logfile = sys.argv[1]
-    trajectory = sys.argv[2]
-    topology = sys.argv[3]
-    reference = sys.argv[4]
-
-    open(logfile, 'a').close()
-    open(trajectory, 'a').close()
-
-    log_reporter = DataReporter()
-    log_reporter.add_collector("logger",
-                               LogMonitor(logfile),
-                               settings["url"],
-                               settings["exchange"],
-                               limit=10,
-                               interval=2,
-                               exchange_type="direct", # settings["exchange_type"],
-                               postprocessor=get_relevant_log_lines)
-
-    log_reporter.start_streaming("logger", "openmm.log")
-
-    rmsd_reporter = DataReporter()
-    rmsd_reporter.add_collector("rmsd",
-                                calculate_rmsd,
-                                settings["url"],
-                                settings["exchange"],
-                                limit=1,
-                                interval=2,
-                                exchange_type="direct",  # settings["exchange_type"],
-                                callback_args=[trajectory, topology, reference])
-
-    rmsd_reporter.start_streaming("rmsd", "openmm.rmsd")
-
-    streamer = SimStream(config=settings, reporters={"log_reporter": log_reporter, "rmsd_reporter": rmsd_reporter})
-    streamer.setup()
-
-    try:
-        streamer.start()
-    except KeyboardInterrupt:
-        streamer.stop()

http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/example/openmm_example/test.txt
----------------------------------------------------------------------
diff --git a/modules/simstream/example/openmm_example/test.txt b/modules/simstream/example/openmm_example/test.txt
deleted file mode 100644
index e69de29..0000000

http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/example/settings.json
----------------------------------------------------------------------
diff --git a/modules/simstream/example/settings.json b/modules/simstream/example/settings.json
deleted file mode 100644
index d354d46..0000000
--- a/modules/simstream/example/settings.json
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-    "url": "amqp://guest:guest@localhost:5672",
-    "exchange": "simstream",
-    "queue": "test",
-    "exchange_type": "topic"
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/setup.py
----------------------------------------------------------------------
diff --git a/modules/simstream/setup.py b/modules/simstream/setup.py
deleted file mode 100755
index 2f3b3fd..0000000
--- a/modules/simstream/setup.py
+++ /dev/null
@@ -1,19 +0,0 @@
-"""
-    Setup for simstream module.
-
-    Author: Jeff Kinnison (jkinniso@nd.edu)
-"""
-
-from setuptools import setup, find_packages
-
-setup(
-    name="simstream",
-    version="0.1dev",
-    author="Jeff Kinnison",
-    author_email="jkinniso@nd.edu",
-    packages=find_packages(),
-    description="",
-    install_requires=[
-        "pika >= 0.10.0"
-    ],
-)

http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/simstream/__init__.py
----------------------------------------------------------------------
diff --git a/modules/simstream/simstream/__init__.py b/modules/simstream/simstream/__init__.py
deleted file mode 100755
index 9d403cb..0000000
--- a/modules/simstream/simstream/__init__.py
+++ /dev/null
@@ -1,11 +0,0 @@
-"""
-Utilties for collecting and distributing system data.
-
-Author: Jeff Kinnison (jkinniso@nd.edu)
-"""
-
-from .simstream import SimStream
-from .datareporter import DataReporter, CollectorExistsException, CollectorDoesNotExistException
-from .datacollector import DataCollector
-from .pikaasyncconsumer import PikaAsyncConsumer
-from .pikaproducer import PikaProducer

http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/simstream/datacollector.py
----------------------------------------------------------------------
diff --git a/modules/simstream/simstream/datacollector.py b/modules/simstream/simstream/datacollector.py
deleted file mode 100755
index f7f99c1..0000000
--- a/modules/simstream/simstream/datacollector.py
+++ /dev/null
@@ -1,110 +0,0 @@
-"""
-Utilties for collecting system data.
-
-Author: Jeff Kinnison (jkinniso@nd.edu)
-"""
-
-from .pikaproducer import PikaProducer
-
-from threading import Thread, Lock, Event
-
-import copy
-
-# TODO: Refactor into subclass of Thread
-
-class DataCollector(Thread):
-    """Collects data by running user-specified routines.
-
-    Inherits from: threading.Thread
-
-    Instance variables:
-    name -- the name of the collector
-    limit -- the maximum number of maintained data points
-    interval -- the interval (in seconds) at which data collection is performed
-
-    Public methods:
-    activate -- start collecting data
-    add_routing_key -- add a new streaming endpoint
-    deactivate -- stop further data collection
-    remove_routing_key -- remove a streaming endpoint
-    run -- collect data if active
-    """
-    def __init__(self, name, callback, rabbitmq_url, exchange, exchange_type="direct", limit=250, interval=10,
-                 postprocessor=None, callback_args=[], postprocessor_args=[]):
-        """
-        Arguments:
-        name -- the name of the collector
-        callback -- the data collection function to run
-
-        Keyword arguments:
-        limit -- the maximum number of maintained data points (default 250)
-        interval -- the time interval in seconds at which to collect data
-                    (default: 10)
-        postprocessor -- a function to run on the return value of callback
-                         (default None)
-        callback_args -- the list of arguments to pass to the callback
-                         (default [])
-        postprocessor_args -- the list of arguments to pass to the
-                              postprocessor (default [])
-        """
-        super(DataCollector, self).__init__()
-        self.name = name if name else "Unknown Resource"
-        self.limit = limit
-        self.interval = interval
-        self._callback = callback
-        self._callback_args = callback_args
-        self._postprocessor = postprocessor
-        self._postprocessor_args = postprocessor_args
-        self._data = []
-        self._data_lock = Lock()
-        self._active = False
-        self._producer = PikaProducer(rabbitmq_url, exchange, exchange_type=exchange_type, routing_keys=[])
-
-    def activate(self):
-        """
-        Start collecting data.
-        """
-        self._active = True
-
-    def add_routing_key(self, key):
-        """
-        Add a new producer endpoint.
-        """
-        self._producer.add_routing_key(key)
-
-
-    def deactivate(self):
-        """
-        Stop collecting data.
-        """
-        self._active = False
-
-    def remove_routing_key(self, key):
-        self._producer.remove_routing_key(key)
-        if len(self._producer.endpoints) == 0:
-            self._producer.shutdown()
-
-    def run(self):
-        """
-        Run the callback and postprocessing subroutines and record result.
-
-        Catches generic exceptions because the function being run is not
-        known beforehand.
-        """
-        self._collection_event = Event()
-        while self._active and not self._collection_event.wait(timeout=self.interval):
-            try:
-                result = self._callback(*self._callback_args)
-                result = self._postprocessor(result, *self._postprocessor_args) if self._postprocessor else result
-                #print("Found the value ", result, " in ", self.name)
-                self._data.append(result)
-                if len(self._data) > self.limit:
-                    self._data.pop(0)
-                self._producer(copy.copy(self._data))
-
-            except Exception as e:
-                print("[ERROR] %s" % (e))
-
-    def stop(self):
-        for key in self.producer.routing_keys:
-            self.remove_routing_key(key)

http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/simstream/datareporter.py
----------------------------------------------------------------------
diff --git a/modules/simstream/simstream/datareporter.py b/modules/simstream/simstream/datareporter.py
deleted file mode 100755
index 156cc08..0000000
--- a/modules/simstream/simstream/datareporter.py
+++ /dev/null
@@ -1,169 +0,0 @@
-"""
-Utilties for collecting system data.
-
-Author: Jeff Kinnison (jkinniso@nd.edu)
-"""
-
-# TODO: Refactor to iterate over producers, not collectors. Collectors should
-#       execute concurrently.
-# TODO: Add method to deactivate reporter
-
-from threading import Thread, Event
-
-from .datacollector import DataCollector
-
-
-class CollectorExistsException(Exception):
-    """Thrown when attempting to add a collector with a conflicting name."""
-    pass
-
-
-class CollectorDoesNotExistException(Exception):
-    """Thrown when attempting to access a collector that does not exist."""
-    pass
-
-
-class DataReporter(object):
-    """Manages collecting specified data.
-
-    Subclass of threading.Thread that modifies Thread.join() and Thread.run()
-
-    Instance variables:
-    collectors -- a dict of DataCollectors that are run at interval
-
-    Public methods:
-    add_collector -- add a new DataCollector to the list
-    run -- start the data collection loop
-    join -- end data collection and return control to main thread
-    start_collecting -- begin data collection for all collectors
-    start_collector -- begin data collection for a specific collector
-    stop_collecting -- stop all data collection
-    stop_collector -- stop a running DataCollector
-    """
-
-    def __init__(self, collectors={}):
-        super(DataReporter, self).__init__()
-        self.collectors = {}
-        for key, value in collectors:
-            self.add_collector(
-                key,
-                value.limit,
-                value.callback,
-                value.url,
-                value.exchange,
-                value.postprocessor,
-                value.callback_args,
-                value.postprocessor_args
-            )
-
-    def add_collector(self, name, callback, rabbitmq_url, exchange, limit=250, interval=10, postprocessor=None,
-                      exchange_type="direct", callback_args=[], postprocessor_args=[]):
-        """Add a new collector.
-
-        Arguments:
-        name -- name of the new DataCollector
-        callback -- the data collection callback to run
-
-        Keyword arguments:
-        limit -- the number of data points to store (default 100)
-        postprocessor -- a postprocessing function to run on each data point
-                         (default None)
-        callback_args -- a list of arguments to pass to the callback
-                         (default [])
-        postprocessor_args -- a list of arguments to pass to the postprocessor
-                              (default [])
-
-        Raises:
-        CollectorExistsException if a collector named name already exists
-        """
-        if name in self.collectors:
-            raise CollectorExistsException
-
-        self.collectors[name] = DataCollector(
-            name,
-            callback,
-            rabbitmq_url,
-            exchange,
-            limit=limit,
-            interval=interval,
-            postprocessor=postprocessor,
-            exchange_type=exchange_type,
-            callback_args=callback_args,
-            postprocessor_args=postprocessor_args
-        )
-
-    def start_collecting(self):
-        """
-        Start data collection for all associated collectors.
-        """
-        for collector in self.collectors:
-            self.start_collector(collector)
-
-    def start_collector(self, name):
-        """
-        Activate the specified collector.
-
-        Arguments:
-        name -- the name of the collector to start
-
-        Raises:
-        RuntimeError if the collector has already been started.
-        """
-        try:
-            self.collectors[name].activate()
-            self.collectors[name].start()
-        except RuntimeError as e:
-            print("Error starting collector ", name)
-            print(e)
-
-    def stop_collecting(self):
-        """
-        Stop all collectors.
-        """
-        for collector in self.collectors:
-            self.stop_collector(collector)
-
-    def stop_collector(self, name):
-        """Deactivate the specified collector.
-
-        Arguments:
-        name -- the name of the collector to stop
-
-        Raises:
-        CollectorDoesNotExistException if no collector named name exists
-        """
-        if name not in self.collectors:
-            raise CollectorDoesNotExistException
-
-        try:
-            self.collectors[name].deactivate()
-            self.collectors[name].join()
-        except RuntimeError as e: # Catch deadlock
-            print(e)
-
-
-    def start_streaming(self, collector_name, routing_key):
-        """
-        Begin streaming data from a collector to a particular recipient.
-
-        Arguments:
-        routing_key -- the routing key to reach the intended recipient
-        """
-        if collector_name not in self.collectors: # Make sure collector exists
-            raise CollectorDoesNotExistException
-        self.collectors[collector_name].add_routing_key(routing_key)
-
-    def stop_streaming(self, collector_name, routing_key):
-        """
-        Stop a particular stream.
-
-        Arguments:
-        collector_name -- the collector associated with the producer to stop
-        routing_key -- the routing key to reach the intended recipient
-
-        Raises:
-        ProducerDoesNotExistException if no producer named name exists
-        ValueError if the producer is removed by another call to this method
-                   after the for loop begins
-        """
-        pass

http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/simstream/eventhandler.py
----------------------------------------------------------------------
diff --git a/modules/simstream/simstream/eventhandler.py b/modules/simstream/simstream/eventhandler.py
deleted file mode 100755
index 9f4f3f2..0000000
--- a/modules/simstream/simstream/eventhandler.py
+++ /dev/null
@@ -1,17 +0,0 @@
-"""
-A utility for responding to user-defined events.
-
-Author: Jeff Kinnison (jkinniso)
-"""
-
-
-class EventHandler(object):
-    """
-    """
-    def __init__(self, name, handler, handler_args=[]):
-        self.name = name
-        self._handler = handler
-        self._handler_args
-
-    def __call__(self):
-        pass

http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/simstream/eventmonitor.py
----------------------------------------------------------------------
diff --git a/modules/simstream/simstream/eventmonitor.py b/modules/simstream/simstream/eventmonitor.py
deleted file mode 100755
index d8c79f4..0000000
--- a/modules/simstream/simstream/eventmonitor.py
+++ /dev/null
@@ -1,46 +0,0 @@
-"""
-Utility for monitoring collected data.
-
-Author: Jeff Kinnison (jkinniso@nd.edu)
-"""
-
-# TODO: Add method to add handlers
-# TODO: Add method to create PikaProducer
-# TODO: Add method to use PikaProducer to respond to events
-# TODO: Add method to deactivate monitor
-
-
-class EventCheckerNotCallableException(Exception):
-    pass
-
-
-class EventHandlerNotCallableException(Exception):
-    pass
-
-
-class EventHandlerDoesNotExistException(Exception):
-    pass
-
-
-class EventMonitor(object):
-    """Checks data for user-defined bounds violations.
-
-    Instance variables:
-    handlers -- a dict of EventHandler objects indexed by name
-    """
-    def __init__(self, event_check, handlers={}):
-        self._event_check = event_check
-        self.handlers = handlers
-
-    def __call__(self, val):
-        if not callable(self._event_check):
-            raise EventCheckerNotCallableException
-        self._run_handler(self.event_check(val))
-
-    def _run_handler(self, handler_names):
-        for name in handler_names:
-            if name not in self.handlers:
-                raise EventHandlerDoesNotExistException
-            if not callable(self.handlers[name]):
-                raise EventHandlerNotCallableException
-            self.handlers[name]()

http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/simstream/pikaasyncconsumer.py
----------------------------------------------------------------------
diff --git a/modules/simstream/simstream/pikaasyncconsumer.py b/modules/simstream/simstream/pikaasyncconsumer.py
deleted file mode 100755
index 1c58687..0000000
--- a/modules/simstream/simstream/pikaasyncconsumer.py
+++ /dev/null
@@ -1,203 +0,0 @@
-"""
-Streaming utility for system and simulation data.
-
-author: Jeff Kinnison (jkinniso@nd.edu)
-"""
-
-import json
-import pika
-
-class PikaAsyncConsumer(object):
-    """
-    The primary entry point for routing incoming messages to the proper handler.
-    """
-
-    def __init__(self, rabbitmq_url, exchange_name, queue_name, message_handler,
-                 exchange_type="direct", routing_key="#"):
-        """
-        Create a new instance of Streamer.
-
-        Arguments:
-        rabbitmq_url -- URL to RabbitMQ server
-        exchange_name -- name of RabbitMQ exchange to join
-        queue_name -- name of RabbitMQ queue to join
-
-        Keyword Arguments:
-        exchange_type -- one of 'direct', 'topic', 'fanout', 'headers'
-                         (default 'direct')
-        routing_keys -- the routing key that this consumer listens for
-                        (default '#', receives all messages)
-        """
-        self._connection = None
-        self._channel = None
-        self._shut_down = False
-        self._consumer_tag = None
-        self._url = rabbitmq_url
-        self._message_handler = message_handler
-
-        # The following are necessary to guarantee that both the RabbitMQ
-        # server and Streamer know where to look for messages. These names will
-        # be decided before dispatch and should be recorded in a config file or
-        # else on a per-job basis.
-        self._exchange = exchange_name
-        self._exchange_type = exchange_type
-        self._queue = queue_name
-        self._routing_key = routing_key
-
-    def connect(self):
-        """
-        Create an asynchronous connection to the RabbitMQ server at URL.
-        """
-        return pika.SelectConnection(pika.URLParameters(self._url),
-                                     on_open_callback=self.on_connection_open,
-                                     on_close_callback=self.on_connection_close,
-                                     stop_ioloop_on_close=False)
-
-    def on_connection_open(self, unused_connection):
-        """
-        Actions to perform when the connection opens. This may not happen
-        immediately, so defer action to this callback.
-
-        Arguments:
-        unused_connection -- the created connection (by this point already
-                             available as self._connection)
-        """
-        self._connection.channel(on_open_callback=self.on_channel_open)
-
-    def on_connection_close(self, connection, code, text):
-        """
-        Actions to perform when the connection is unexpectedly closed by the
-        RabbitMQ server.
-
-        Arguments:
-        connection -- the connection that was closed (same as self._connection)
-        code -- response code from the RabbitMQ server
-        text -- response body from the RabbitMQ server
-        """
-        self._channel = None
-        if self._shut_down:
-            self._connection.ioloop.stop()
-        else:
-            self._connection.add_timeout(5, self.reconnect)
-
-    def reconnect(self):
-        """
-        Attempt to reestablish a connection with the RabbitMQ server.
-        """
-        self._connection.ioloop.stop() # Stop the ioloop to completely close
-
-        if not self._shut_down: # Connect and restart the ioloop
-            self._connection = self.connect()
-            self._connection.ioloop.start()
-
-    def on_channel_open(self, channel):
-        """
-        Store the opened channel for future use and set up the exchange and
-        queue to be used.
-
-        Arguments:
-        channel -- the Channel instance opened by the Channel.Open RPC
-        """
-        self._channel = channel
-        self._channel.add_on_close_callback(self.on_channel_close)
-        self.declare_exchange()
-
-
-    def on_channel_close(self, channel, code, text):
-        """
-        Actions to perform when the channel is unexpectedly closed by the
-        RabbitMQ server.
-
-        Arguments:
-        connection -- the connection that was closed (same as self._connection)
-        code -- response code from the RabbitMQ server
-        text -- response body from the RabbitMQ server
-        """
-        self._connection.close()
-
-    def declare_exchange(self):
-        """
-        Set up the exchange that will route messages to this consumer. Each
-        RabbitMQ exchange is uniquely identified by its name, so it does not
-        matter if the exchange has already been declared.
-        """
-        self._channel.exchange_declare(self.declare_exchange_success,
-                                        self._exchange,
-                                        self._exchange_type)
-
-    def declare_exchange_success(self, unused_connection):
-        """
-        Actions to perform on successful exchange declaration.
-        """
-        self.declare_queue()
-
-    def declare_queue(self):
-        """
-        Set up the queue that will route messages to this consumer. Each
-        RabbitMQ queue can be defined with routing keys to use only one
-        queue for multiple jobs.
-        """
-        self._channel.queue_declare(self.declare_queue_success,
-                                    self._queue)
-
-    def declare_queue_success(self, method_frame):
-        """
-        Actions to perform on successful queue declaration.
-        """
-        self._channel.queue_bind(self.munch,
-                                 self._queue,
-                                 self._exchange,
-                                 self._routing_key
-                                )
-
-    def munch(self, unused):
-        """
-        Begin consuming messages from the Airavata API server.
-        """
-        self._channel.add_on_cancel_callback(self.cancel_channel)
-        self._consumer_tag = self._channel.basic_consume(self._process_message)
-
-    def cancel_channel(self, method_frame):
-        if self._channel is not None:
-            self._channel._close()
-
-    def _process_message(self, ch, method, properties, body):
-        """
-        Receive and verify a message, then pass it to the router.
-
-        Arguments:
-        ch -- the channel that routed the message
-        method -- delivery information
-        properties -- message properties
-        body -- the message
-        """
-        print("Received Message: %s" % body)
-        self._message_handler(body)
-        #self._channel.basic_ack(delivery_tag=method.delivery_tag)
-
-    def stop_consuming(self):
-        """
-        Stop the consumer if active.
-        """
-        if self._channel:
-            self._channel.basic_cancel(self.close_channel, self._consumer_tag)
-
-    def close_channel(self):
-        """
-        Close the channel to shut down the consumer and connection.
-        """
-        self._channel.close()
-
-    def start(self):
-        """
-        Start a connection with the RabbitMQ server.
-        """
-        self._connection = self.connect()
-        self._connection.ioloop.start()
-
-    def stop(self):
-        """
-        Stop an active connection with the RabbitMQ server.
-        """
-        self._closing = True
-        self.stop_consuming()

http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/simstream/pikaproducer.py
----------------------------------------------------------------------
diff --git a/modules/simstream/simstream/pikaproducer.py b/modules/simstream/simstream/pikaproducer.py
deleted file mode 100755
index 6ffaf3d..0000000
--- a/modules/simstream/simstream/pikaproducer.py
+++ /dev/null
@@ -1,202 +0,0 @@
-"""
-Utilties for sending data.
-
-Author: Jeff Kinnison (jkinniso@nd.edu)
-"""
-
-import json
-import pika
-
-
-class PikaProducer(object):
-    """
-    Utility for sending job data to a set of endpoints.
-    """
-
-    def __init__(self, rabbitmq_url, exchange, exchange_type="direct", routing_keys=[]):
-        """
-        Instantiate a new PikaProducer.
-
-        Arguments:
-        rabbitmq_url -- the url of the RabbitMQ server to send to
-        exchange -- the name of the exchange to send to
-
-        Keyword Arguments:
-        exchange_type -- one of one of 'direct', 'topic', 'fanout', 'headers'
-                         (default 'direct')
-        routing_key -- the routing keys to the endpoints for this producer
-                       (default [])
-        """
-        self._url = rabbitmq_url
-        self._exchange = exchange
-        self._exchange_type = exchange_type
-        self._routing_keys = routing_keys
-
-        self._connection = None # RabbitMQ connection object
-        self._channel = None    # RabbitMQ channel object
-
-        import random
-        self._name = random.randint(0,100)
-
-    def __call__(self, data):
-        """
-        Publish data to the RabbitMQ server.
-
-        Arguments:
-        data -- JSON serializable data to send
-        """
-        if self._connection is None: # Start the connection if it is inactive
-            self.start()
-        else: # Serialize and send the data
-            message = self.pack_data(data)
-            self.send_data(message)
-
-    def add_routing_key(self, key):
-        """
-        Add a new endpoint that will receive this data.
-
-        Arguments:
-        key -- the routing key for the new endpoint
-        """
-        if key not in self._routing_keys:
-            #print("Adding key %s to %s" % (key, self._name))
-            self._routing_keys.append(key)
-            #print(self._routing_keys)
-
-    def remove_routing_key(self, key):
-        """
-        Stop sending data to an existing endpoint.
-
-        Arguments:
-        key -- the routing key for the existing endpoint
-        """
-        try:
-            self._routing_keys.remove(key)
-        except ValueError:
-            pass
-
-    def pack_data(self, data):
-        """
-        JSON-serialize the data for transport.
-
-        Arguments:
-        data -- JSON-serializable data
-        """
-        try: # Generate a JSON string from the data
-            msg = json.dumps(data)
-        except TypeError as e: # Generate and return an error if serialization fails
-            msg = json.dumps({"err": str(e)})
-        finally:
-            return msg
-
-    def send_data(self, data):
-        """
-        Send the data to all active endpoints.
-
-        Arguments:
-        data -- the message to send
-        """
-        if self._channel is not None: # Make sure the connection is active
-            for key in self._routing_keys: # Send to all endpoints
-                #print(self._exchange, key, self._name)
-                self._channel.basic_publish(exchange = self._exchange,
-                                            routing_key=key,
-                                            body=data)
-
-    def start(self):
-        """
-        Open a connection if one does not exist.
-        """
-        print("Starting new connection")
-        if self._connection is None:
-            print("Creating connection object")
-            self._connection = pika.BlockingConnection(pika.URLParameters(self._url))
-            self._channel = self._connection.channel()
-            self._channel.exchange_declare(exchange=self._exchange,
-                                           type=self._exchange_type)
-
-    def shutdown(self):
-        """
-        Close an existing connection.
-        """
-        if self._channel is not None:
-            self._channel.close()
-
-    def _on_connection_open(self, unused_connection):
-        """
-        Create a new channel if the connection opens successful.
-
-        Arguments:
-        unused_connection -- a reference to self._connection
-        """
-        print("Connection is open")
-        self._connection.channel(on_open_callback=self._on_channel_open)
-
-    def _on_connection_close(self, connection, code, text):
-        """
-        Actions to take when the connection is closed for any reason.
-
-        Arguments:
-        connection -- the connection that was closed (same as self._connection)
-        code -- response code from the RabbitMQ server
-        text -- response body from the RabbitMQ server
-        """
-        print("Connection is closed")
-        self._channel = None
-        self._connection = None
-
-    def _on_channel_open(self, channel):
-        """
-        Actions to take when the channel opens.
-
-        Arguments:
-        channel -- the newly opened channel
-        """
-        print("Channel is open")
-        self._channel = channel
-        self._channel.add_on_close_callback(self._on_channel_close)
-        self._declare_exchange()
-
-    def _on_channel_close(self, channel, code, text):
-        """
-        Actions to take when the channel closes for any reason.
-
-        Arguments:
-        channel -- the channel that was closed (same as self._channel)
-        code -- response code from the RabbitMQ server
-        text -- response body from the RabbitMQ server
-        """
-        print("Channel is closed")
-        self._connection.close()
-
-    def _declare_exchange(self):
-        """
-        Set up the exchange to publish to even if it already exists.
-        """
-        print("Exchange is declared")
-        self._channel.exchange_declare(exchange=self._exchange,
-                                       type=self.exchange_type)
-
-if __name__ == "__main__":
-    import time
-
-    config = {
-        "url": "amqp://guest:guest@localhost:5672",
-        "exchange": "simstream",
-        "routing_key": "test_consumer",
-        "exchange_type": "topic"
-    }
-
-    producer = PikaProducer(config["url"],
-                            config["exchange"],
-                            exchange_type=config["exchange_type"],
-                            routing_keys=[config["routing_key"]])
-    producer.start()
-
-    while True:
-        try:
-            time.sleep(5)
-            data = str(time.time()) + ": Hello SimStream"
-            producer.send_data(data)
-        except KeyboardInterrupt:
-            producer.shutdown()

http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/simstream/simstream/simstream.py
----------------------------------------------------------------------
diff --git a/modules/simstream/simstream/simstream.py b/modules/simstream/simstream/simstream.py
deleted file mode 100755
index 499a8c3..0000000
--- a/modules/simstream/simstream/simstream.py
+++ /dev/null
@@ -1,167 +0,0 @@
-import pika
-
-from .pikaasyncconsumer import PikaAsyncConsumer
-from .datacollector import DataCollector
-from .datareporter import DataReporter
-from .eventhandler import EventHandler
-from .eventmonitor import EventMonitor
-
-
-class ReporterExistsException(Exception):
-    """Thrown when attempting to add a DataReporter with a conflicting name"""
-    pass
-
-
-class SimStream(object):
-    """
-    Manager for routing messages to their correct reporter.
-    """
-
-    DEFAULT_CONFIG_PATH="simstream.cnf"
-
-
-    class MessageParser(object):
-        """
-        Internal message parsing facilities.
-        """
-
-        def __init__(self):
-            self.parsed = None
-
-        def __call__(self, message):
-            pass
-
-
-    def __init__(self, reporters={}, config={}):
-        self.reporters = reporters
-        self.consumer = None
-        self.config = config
-
-    def add_data_reporter(self, reporter):
-        """
-        Add a new DataReporter object.
-
-        Arguments:
-        reporter -- the DataReporter to add
-        """
-        if reporter.name in self.reporters:
-            raise ReporterExistsException
-        self.reporters[reporter.name] = reporter
-
-    def parse_config(self):
-        """
-        Read the config file and set up the specified, data collection and
-        event handling resources.
-        """
-        # TODO: Read in config
-        # TODO: Set up configuration dict
-        pass
-
-    def route_message(self, message):
-        """
-        Send a message to the correct reporter.
-        """
-        # TODO: Create new MessageParser
-        # TODO: Run message through MessageParser
-        # TODO: Route message to the correct DataReporter/EventMonitor
-        parser = MessageParser()
-        parser(message)
-        if parser.reporter_name in self.reporters:
-            self.reporters[parser.reporter_name].start_streaming(
-                    parser.collector_name,
-                    parser.routing_key
-                )
-
-    def start_collecting(self):
-        """
-        Begin collecting data and monitoring for events.
-        """
-        for reporter in self.reporters:
-            self.reporters[reporter].start_collecting()
-
-    def setup(self):
-        """
-        Set up the SimStream instance: create DataCollectors, create
-        EventMonitors, configure AMQP consumer.
-        """
-        self.parse_config()
-        #self.setup_consumer()
-        self.setup_data_collection()
-        self.setup_event_monitoring()
-
-    def setup_data_collection(self):
-        """
-        Set up all DataReporters and DataCollectors.
-        """
-        # TODO: Create and configure all DataReporters
-        # TODO: Create and configure all DataCollectors
-        # TODO: Assign each DataCollector to the correct DataReporter
-        if "reporters" in self.config:
-            for reporter in self.config.reporters:
-                pass
-            for collector in self.config.collectors:
-                pass
-
-    def setup_event_monitoring(self):
-        #TODO: Create and configure all EventMonitors
-        #TODO: Create and configure all EventHandlers
-        #TODO: Assign each EventHandler to the correct EventMonitor
-        #TODO: Assign each EventMonitor to the correct DataCollector
-        pass
-
-    def setup_consumer(self):
-        """
-        Set up and configure the consumer.
-        """
-        if len(self.config) > 0 and self.consumer is None:
-            if "message_handler" in self.config:
-                message_handler = self.config["message_handler"]
-            else:
-                message_handler = self.route_message
-            self.consumer = PikaAsyncConsumer(self.config["url"],
-                                              self.config["exchange"],
-                                              self.config["queue"],
-                                              message_handler,
-                                              exchange_type=self.config["exchange_type"],
-                                              routing_key=self.config["routing_key"]
-                                             )
-
-    def start(self):
-        """
-        Configure and start SimStream.
-        """
-        if self.consumer is None:
-            self.setup()
-        self.start_collecting()
-        #self.consumer.start()
-
-    def stop(self):
-        """
-        Stop all data collection, event monitoring, and message consumption.
-        """
-        self.consumer.stop()
-        self.stop_collecting()
-
-
-if __name__ == "__main__":
-    def print_message(message):
-        with open("test.out", "w") as f:
-            print(message)
-
-    print(SimStream.DEFAULT_CONFIG_PATH)
-
-    config = {
-        "url": "amqp://guest:guest@localhost:5672",
-        "exchange": "simstream",
-        "queue": "simstream_test",
-        "message_handler": print_message,
-        "routing_key": "test_consumer",
-        "exchange_type": "topic"
-    }
-
-    streamer = SimStream(config=config)
-
-    try:
-        streamer.start()
-    except KeyboardInterrupt:
-        streamer.stop()

http://git-wip-us.apache.org/repos/asf/airavata/blob/a82e34ec/modules/xbaya/pom.xml
----------------------------------------------------------------------
diff --git a/modules/xbaya/pom.xml b/modules/xbaya/pom.xml
deleted file mode 100644
index 9878360..0000000
--- a/modules/xbaya/pom.xml
+++ /dev/null
@@ -1,329 +0,0 @@
-<!--Licensed to the Apache Software Foundation (ASF) under one or more contributor
-	license agreements. See the NOTICE file distributed with this work for additional
-	information regarding copyright ownership. The ASF licenses this file to
-	you under the Apache License, Version 2.0 (theƏ "License"); you may not use
-	this file except in compliance with the License. You may obtain a copy of
-	the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required
-	by applicable law or agreed to in writing, software distributed under the
-	License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS
-	OF ANY ~ KIND, either express or implied. See the License for the specific
-	language governing permissions and limitations under the License. -->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-  <modelVersion>4.0.0</modelVersion>
-
-  <groupId>org.airavata </groupId>
-  <artifactId>xbaya</artifactId>
-  <version>0.0.1-SNAPSHOT</version>
-  <packaging>jar</packaging>
-
-  <name>xbaya</name>
-  <url>http://maven.apache.org</url>
- <properties>
-        <!-- Airavata version-->
-        <airavata.version>0.17-SNAPSHOT</airavata.version>
-
-      
-        <!-- Optional parameters to the application, will be embedded in the launcher and can be overriden on the command line -->
-        <app.parameters></app.parameters>
-
-
-        <!-- The Application version used by javapackager -->
-        <app.version>1.0</app.version>
-
-
-        <!-- The app and launcher will be assembled in this folder -->
-        <app.dir>${project.build.directory}/app</app.dir>
-
-        <!-- Native installers will be built in this folder -->
-        <app.installerdir>${project.build.directory}/installer</app.installerdir>
-
-        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-    </properties>
-
-    <profiles>
-        <profile>
-            <id>default</id>
-            <activation>
-                <activeByDefault>true</activeByDefault>
-            </activation>
-            <build>
-                <plugins>
-                    <plugin>
-                        <groupId>org.apache.maven.plugins</groupId>
-                        <artifactId>maven-compiler-plugin</artifactId>
-                        <version>3.3</version>
-                        <configuration>
-                            <source>1.8</source>
-                            <target>1.8</target>
-                        </configuration>
-                    </plugin>
-                </plugins>
-            </build>
-        </profile>
-        <profile>
-            <id>update-deployment</id>
-            <build>
-                <plugins>
-                    <!-- Compile project jar to appdir -->
-                    <plugin>
-                        <groupId>org.apache.maven.plugins</groupId>
-                        <artifactId>maven-jar-plugin</artifactId>
-                        <version>2.6</version>
-                        <configuration>
-                            <outputDirectory>${app.dir}</outputDirectory>
-                        </configuration>
-                    </plugin>
-                    <!-- Copy dependencies to appdir -->
-                    <plugin>
-                        <groupId>org.apache.maven.plugins</groupId>
-                        <artifactId>maven-dependency-plugin</artifactId>
-                        <version>2.10</version>
-                        <configuration>
-                            <excludeScope>provided</excludeScope>
-                            <outputDirectory>${app.dir}</outputDirectory>
-                            <stripVersion>true</stripVersion>
-                        </configuration>
-                        <executions>
-                            <execution>
-                                <phase>package</phase>
-                                <goals>
-                                    <goal>copy-dependencies</goal>
-                                </goals>
-                            </execution>
-                        </executions>
-                    </plugin>
-                    <plugin>
-                        <groupId>org.codehaus.mojo</groupId>
-                        <artifactId>exec-maven-plugin</artifactId>
-                        <version>1.4.0</version>
-                        <!-- Generate app.xml manifest -->
-                        <executions>
-                            <execution>
-                                <id>create-manifest</id>
-                                <phase>package</phase>
-                                <goals>
-                                    <goal>java</goal>
-                                </goals>
-                                <configuration>
-                                    <mainClass>fxlauncher.CreateManifest</mainClass>
-                                    <arguments>
-                                        <argument>${app.url}</argument>
-                                        <argument>${app.mainClass}</argument>
-                                        <argument>${app.dir}</argument>
-                                        <argument>${app.parameters}</argument>
-                                    </arguments>
-                                </configuration>
-                            </execution>
-                            <!-- Embed app.xml inside fxlauncher.xml so we don't need to reference app.xml to start the app -->
-                            <execution>
-                                <id>embed-manifest-in-launcher</id>
-                                <phase>package</phase>
-                                <goals>
-                                    <goal>exec</goal>
-                                </goals>
-                                <configuration>
-                                    <executable>jar</executable>
-                                    <workingDirectory>${app.dir}</workingDirectory>
-                                    <arguments>
-                                        <argument>uf</argument>
-                                        <argument>fxlauncher.jar</argument>
-                                        <argument>app.xml</argument>
-                                    </arguments>
-                                </configuration>
-                            </execution>
-                            <!-- Create native installer. Feel free to add more arguments as needed.
-                             https://docs.oracle.com/javase/8/docs/technotes/tools/windows/javapackager.html
-                             -->
-                            <execution>
-                                <id>installer</id>
-                                <phase>install</phase>
-                                <goals>
-                                    <goal>exec</goal>
-                                </goals>
-                                <configuration>
-                                    <executable>${env.JAVA_HOME}/bin/javapackager</executable>
-                                    <arguments>
-                                        <argument>-deploy</argument>
-                                        <argument>-native</argument>
-                                        <argument>-outdir</argument>
-                                        <argument>${app.installerdir}</argument>
-                                        <argument>-outfile</argument>
-                                        <argument>${app.filename}</argument>
-                                        <argument>-srcdir</argument>
-                                        <argument>${app.dir}</argument>
-                                        <argument>-srcfiles</argument>
-                                        <argument>fxlauncher.jar</argument>
-                                        <argument>-appclass</argument>
-                                        <argument>fxlauncher.Launcher</argument>
-                                        <argument>-name</argument>
-                                        <argument>${project.name}</argument>
-                                        <argument>-title</argument>
-                                        <argument>${project.name}</argument>
-                                        <argument>-vendor</argument>
-                                        <argument>${app.vendor}</argument>
-                                        <argument>-BappVersion=${app.version}</argument>
-                                    </arguments>
-                                </configuration>
-                            </execution>
-                            <!-- Copy application artifacts to remote site using scp (optional) -->
-                            <execution>
-                                <id>deploy-app</id>
-                                <goals>
-                                    <goal>exec</goal>
-                                </goals>
-                                <configuration>
-                                    <executable>scp</executable>
-                                    <arguments>
-                                        <argument>-r</argument>
-                                        <argument>${app.dir}/.</argument>
-                                        <argument>${app.deploy.target}</argument>
-                                    </arguments>
-                                </configuration>
-                            </execution>
-                        </executions>
-                    </plugin>
-                    <plugin>
-                        <groupId>org.apache.maven.plugins</groupId>
-                        <artifactId>maven-compiler-plugin</artifactId>
-                        <version>3.3</version>
-                        <configuration>
-                            <source>1.8</source>
-                            <target>1.8</target>
-                        </configuration>
-                    </plugin>
-                </plugins>
-            </build>
-        </profile>
-    </profiles>
-
-
-  <dependencies>
-  <!--FX Launcher-->
-        <dependency>
-            <groupId>no.tornado</groupId>
-            <artifactId>fxlauncher</artifactId>
-            <version>1.0.8</version>
-        </dependency>
-
-        <!-- Airavata Dependencies-->
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-data-models</artifactId>
-            <version>${airavata.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-model-utils</artifactId>
-            <version>${airavata.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-api-stubs</artifactId>
-            <version>${airavata.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-client-configuration</artifactId>
-            <version>${airavata.version}</version>
-        </dependency>
-
-        <!-- UI Dialogs-->
-        <dependency>
-            <groupId>org.controlsfx</groupId>
-            <artifactId>controlsfx</artifactId>
-            <version>8.40.10</version>
-        </dependency>
-
-        <!--OAuth Dependencies-->
-        <dependency>
-            <groupId>org.codehaus.jackson</groupId>
-            <artifactId>jackson-mapper-asl</artifactId>
-            <version>1.8.5</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.oltu.oauth2</groupId>
-            <artifactId>org.apache.oltu.oauth2.client</artifactId>
-            <version>1.0.0</version>
-        </dependency>
-
-
-        <!-- Apache Commons -->
-        <dependency>
-            <groupId>commons-lang</groupId>
-            <artifactId>commons-lang</artifactId>
-            <version>2.6</version>
-        </dependency>
-        <dependency>
-            <groupId>commons-collections</groupId>
-            <artifactId>commons-collections</artifactId>
-            <version>3.2.2</version>
-        </dependency>
-
-        <!-- JSch Dependency-->
-        <dependency>
-            <groupId>com.jcraft</groupId>
-            <artifactId>jsch</artifactId>
-            <version>0.1.53</version>
-        </dependency>
-
-
-        <!-- Google Guava -->
-        <dependency>
-            <groupId>com.google.guava</groupId>
-            <artifactId>guava</artifactId>
-            <version>18.0</version>
-        </dependency>
-
-        <!--Jogl dependencies for legacy GAMESS editor-->
-        <dependency>
-            <groupId>org.jogamp.gluegen</groupId>
-            <artifactId>gluegen-rt-main</artifactId>
-            <version>2.0-rc11</version>
-        </dependency>
-        <dependency>
-            <groupId>org.jogamp.jogl</groupId>
-            <artifactId>jogl-all-main</artifactId>
-            <version>2.0-rc11</version>
-        </dependency>
-
-
-        <!-- Logging  -->
-        <dependency>
-            <groupId>org.slf4j</groupId>
-            <artifactId>slf4j-api</artifactId>
-            <version>1.6.1</version>
-        </dependency>
-        <dependency>
-            <groupId>org.slf4j</groupId>
-            <artifactId>jcl-over-slf4j</artifactId>
-            <version>1.6.1</version>
-        </dependency>
-        <dependency>
-            <groupId>org.slf4j</groupId>
-            <artifactId>slf4j-log4j12</artifactId>
-            <version>1.6.1</version>
-        </dependency>
-        <dependency>
-            <groupId>log4j</groupId>
-            <artifactId>log4j</artifactId>
-            <version>1.2.16</version>
-        </dependency>
-    <dependency>
-      <groupId>junit</groupId>
-      <artifactId>junit</artifactId>
-      <version>3.8.1</version>
-      <scope>test</scope>
-    </dependency>
-  </dependencies>
-   <repositories>
-        <repository>
-            <id>apache.snapshots</id>
-            <name>Apache Snapshot Repository</name>
-            <url>http://repository.apache.org/snapshots</url>
-            <releases>
-                <enabled>false</enabled>
-            </releases>
-        </repository>
-    </repositories>
-</project>

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-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
- */
-package org.airavata.xbaya;
-
-import javafx.application.Application;
-import javafx.fxml.FXMLLoader;
-import javafx.scene.Parent;
-import javafx.scene.Scene;
-import javafx.stage.Stage;
-
-public class App {
-
-
-}

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-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
- */
-package org.airavata.xbaya.ui.home;
-
-import javafx.application.Application;
-import javafx.fxml.FXMLLoader;
-import javafx.scene.Parent;
-import javafx.scene.Scene;
-import javafx.stage.Stage;
-
-public class HomeWindow extends Application {
-
-    @Override
-    public void start(Stage primaryStage) throws Exception{
-    	Parent root = FXMLLoader.load(getClass().getResource("/views/home.fxml"));    
-    	primaryStage.setTitle("XBaya GUI");
-        primaryStage.setScene(new Scene(root, 1060, 600));
-        primaryStage.show();
-    }
-
-    public static void main(String[] args) {
-        launch(args);
-    }
-}
\ No newline at end of file

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