def __init__(self, *args, **kwargs):
self._console_listener = kwargs.pop('console_listener')
self._handler = kwargs.pop('handler')
self._event_listener = EventListener(lambda command: self._handle_command(command))
if not self._console_listener is None:
self._console_listener.on_command_received().add_listener(self._event_listener)
super(EpiVizPyEndpoint, self).__init__(*args, **kwargs)
def __init__(self, *args, **kwargs):
self._console_listener = kwargs.pop('console_listener')
self._measurements = kwargs.pop('measurements')
self._measurements_lock = kwargs.pop('measurements_lock')
self._event_listener = EventListener(lambda command: self._handle_command(command))
if not self._console_listener is None:
self._console_listener.on_command_received().add_listener(self._event_listener)
# Used to keep track of callbacks for responses
self._callback_map = {}
self._charts = []
self._current_location = None
super(EpiVizPyEndpoint, self).__init__(*args, **kwargs)
class EpiVizPyEndpoint(tornado.websocket.WebSocketHandler):
def __init__(self, *args, **kwargs):
self._console_listener = kwargs.pop('console_listener')
self._handler = kwargs.pop('handler')
self._event_listener = EventListener(lambda command: self._handle_command(command))
if not self._console_listener is None:
self._console_listener.on_command_received().add_listener(self._event_listener)
super(EpiVizPyEndpoint, self).__init__(*args, **kwargs)
def check_origin(self, origin):
return True
def open(self):
print 'new connection'
def on_message(self, json_message):
print 'message received %s' % json_message
# message = simplejson.loads(json_message)
self._handle_request(json_message)
def on_close(self):
if not self._console_listener is None:
self._console_listener.on_command_received().remove_listener(self._event_listener.id())
print 'connection closed'
def send_request(self, request):
'''
:param request: Request
'''
def _handle_request(self, json_message):
response = self._handler(json_message)
print 'sending response %s' % response
self.write_message(response)
class EpiVizPyEndpoint(tornado.websocket.WebSocketHandler):
def __init__(self, *args, **kwargs):
self._console_listener = kwargs.pop('console_listener')
self._measurements = kwargs.pop('measurements')
self._measurements_lock = kwargs.pop('measurements_lock')
self._event_listener = EventListener(lambda command: self._handle_command(command))
if not self._console_listener is None:
self._console_listener.on_command_received().add_listener(self._event_listener)
# Used to keep track of callbacks for responses
self._callback_map = {}
self._charts = []
self._current_location = None
super(EpiVizPyEndpoint, self).__init__(*args, **kwargs)
def check_origin(self, origin):
return True
def open(self):
print 'new connection'
def on_message(self, json_message):
print 'message received %s' % json_message
message = simplejson.loads(json_message)
if message['type'] == 'request':
request = Request.from_raw_object(message)
self._handle_request(request)
if message['type'] == 'response':
if message['requestId'] in self._callback_map:
callback = self._callback_map[message['requestId']]
self._callback_map.pop(message['requestId'])
callback(message['data'])
def on_close(self):
if not self._console_listener is None:
self._console_listener.on_command_received().remove_listener(self._event_listener.id())
print 'connection closed'
def send_request(self, request):
'''
:param request: Request
'''
def _handle_request(self, request):
action = request.get('action')
# switch(action)
response = {
Request.Action.GET_MEASUREMENTS: lambda: self._get_measurements(request.id()),
Request.Action.GET_ROWS: lambda: self._get_rows(request.id(), request.get('datasource'), request.get('chr'), request.get('start'), request.get('end'), request.get('metadata')),
Request.Action.GET_VALUES: lambda: self._get_values(request.id(), request.get('measurement'), request.get('datasource'), request.get('chr'), request.get('start'), request.get('end')),
Request.Action.GET_SEQINFOS: lambda: self._get_seqinfos(request.id()),
Request.Action.SEARCH: lambda: self._search(request.id(), request.get('q'), request.get('maxResults'))
}[action]()
message = response.to_json()
self.write_message(message)
# Request handlers
def _get_measurements(self, request_id):
'''
Returns Response
'''
self._measurements_lock.acquire()
data = {'id': [], 'name': [], 'type': [], 'datasourceId': [], 'datasourceGroup': [],
'defaultChartType': [], 'annotation': [], 'minValue': [], 'maxValue': [], 'metadata': [] }
for i in range(len(self._measurements)):
for key, value in self._measurements[i].iteritems():
data[key].append(value)
self._measurements_lock.release()
return Response(request_id, data)
def _get_rows(self, request_id, datasource, seq_name, start, end, metadata):
'''
:param datasource: string
:param seq_name: string
:param start: number
:param end: number
:param metadata: string[] A list of column names for which to retrieve the values
Returns response
'''
# Return a genomic range of 100 base pairs every 1000 base pairs
step, width = 1000, 100
globalStartIndex = math.floor((start - 1) / step) + 1
firstStart = globalStartIndex * step + 1
firstEnd = firstStart + width
if firstEnd < start:
firstStart += step
firstEnd += step
if firstStart >= end:
# Nothing to return
return Response(request_id, {
'values': { 'id': [], 'start': [], 'end': [], 'strand': [], 'metadata': { 'py_metadata': [] } },
'globalStartIndex': None,
'useOffset': False
})
ids = []
starts = []
ends = []
strands = '*'
py_metadata = []
globalIndex = globalStartIndex
s = firstStart
while s < end:
ids.append(globalIndex)
starts.append(s)
ends.append(s + width)
py_metadata.append(self._random_str(5)) # Random string
globalIndex += 1
s += step
return Response(request_id, {
'values': { 'id': ids, 'start': starts, 'end': ends, 'strand': strands, 'metadata':{ 'py_metadata': py_metadata } },
'globalStartIndex': globalStartIndex,
'useOffset': False
})
def _get_values(self, request_id, measurement, datasource, seq_name, start, end):
'''
:param measurement: string, column name in the datasource that contains requested values
:param datasource: string
:param seq_name: string
:param start: number
:param end: number
Returns response
'''
# Return a genomic range of 100 base pairs every 1000 base pairs
step, width = 1000, 100
globalStartIndex = math.floor((start - 1) / step) + 1
firstStart = globalStartIndex * step + 1
firstEnd = firstStart + width
if firstEnd < start:
firstStart += step
firstEnd += step
if firstStart >= end:
# Nothing to return
return Response(request_id, {
'values': [],
'globalStartIndex': None,
})
values = []
globalIndex = globalStartIndex
s = firstStart
while s < end:
v = random.random() * 30 - 5
values.append(v)
globalIndex += 1
s += step
return Response(request_id, {
'values': values,
'globalStartIndex': globalStartIndex
})
def _get_seqinfos(self, request_id):
'''
Returns response
'''
return Response(request_id, [['chr1', 1, 248956422], ['pyChr', 1, 1000000000]])
def _search(self, request_id, query, max_results):
'''
:param query: string
:param max_results: number
Returns response
'''
return Response(request_id, [])
def _handle_command(self, command):
# switch(action)
request = {
Request.Action.ADD_MEASUREMENTS: lambda: self._add_measurements(),
Request.Action.REMOVE_MEASUREMENTS: lambda: self._remove_measurements(),
Request.Action.ADD_SEQINFOS: lambda: self._add_seqinfos(),
Request.Action.REMOVE_SEQNAMES: lambda: self._remove_seqnames(),
Request.Action.ADD_CHART: lambda: self._add_chart(),
Request.Action.REMOVE_CHART: lambda: self._remove_chart(),
Request.Action.CLEAR_DATASOURCE_GROUP_CACHE: lambda: self._clear_datasource_group_cache(),
Request.Action.FLUSH_CACHE: lambda: self._flush_cache(),
Request.Action.NAVIGATE: lambda: self._navigate(),
Request.Action.REDRAW: lambda: self._redraw(),
Request.Action.GET_CURRENT_LOCATION: lambda: self._get_current_location()
}[command]()
if request is None:
print '**unable to make request**'
return
message = request.to_json()
self.write_message(message)
def _add_measurements(self):
mid = self._random_str(5)
m = {
'id': 'python_ms_%s' % mid,
'name': 'Python Measurement %s' % mid,
'type': 'feature',
'datasourceId': 'py_datasource',
'datasourceGroup': 'py_datasourcegroup',
'defaultChartType': 'Line Track',
'annotation': None,
'minValue':-5,
'maxValue': 25,
'metadata': ['py_metadata']
}
self._measurements_lock.acquire()
self._measurements.append(m)
self._measurements_lock.release()
return Request.add_measurements([m])
def _remove_measurements(self):
if len(self._measurements) == 0:
return None
self._measurements_lock.acquire()
m = self._measurements.pop()
self._measurements_lock.release()
return Request.remove_measurements([m])
def _add_seqinfos(self):
return None
def _add_chart(self):
if len(self._measurements) == 0:
return None
ms = [self._measurements[0]]
if (len(self._measurements) > 1):
ms.append(self._measurements[1])
request = Request.add_chart('epiviz.plugins.charts.LineTrack', ms)
self._callback_map[request.id()] = lambda data: self._chart_added(data)
return request
def _chart_added(self, data):
if not data['success']:
print '**Adding chart failed: %s**' % data['errorMessage']
return
self._charts.append(data['value']['id'])
print 'Added chart successfully: %s' % data['value']['id']
def _remove_chart(self):
if len(self._charts) == 0:
return None
chart_id = self._charts.pop()
return Request.remove_chart(chart_id)
def _redraw(self):
return Request.redraw()
def _flush_cache(self):
return Request.flush_cache()
def _clear_datasource_group_cache(self):
return Request.clear_datasource_group_cache('py_datasourcegroup')
def _get_current_location(self):
request = Request.get_current_location()
self._callback_map[request.id()] = lambda data: self._current_location_retrieved(data)
return request
def _current_location_retrieved(self, data):
if not data['success']:
print '**Current location retrieval failed: %s**' % data['errorMessage']
return
self._current_location = data['value']
print 'Current location: %s:%s-%s' % (data['value']['seqName'], data['value']['start'], data['value']['end'])
def _navigate(self):
if self._current_location is None:
return None
width = self._current_location['end'] - self._current_location['start']
start = self._current_location['start'] + width * 0.2
end = start + width
self._current_location = { 'seqName': self._current_location['seqName'], 'start': start, 'end': end }
return Request.navigate(self._current_location)
def _random_str(self, size):
chars = '0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
result = ''
for _ in range(size):
result += chars[random.randint(0, len(chars) - 1)]
return result