def structure(self,**kwargs):
print_out(str(kwargs))
if "current_doc" not in kwargs:
return '<script>document.location.href="open";</script>'
elif "screenshot" in kwargs:
cherrypy.response.headers['Content-Type'] = "image/png"
cherrypy.response.headers['Content-Disposition'] = 'attachment; filename="' + kwargs["current_doc"] + '.png"'
if sys.version_info[0] == 2:
return file_generator(StringIO(structure_main("local", "3", 'local', **kwargs)))
else:
return file_generator(BytesIO(b64decode(structure_main("local", "3", 'local', **kwargs))))
else:
return structure_main("local","3",'local',**kwargs)
def key(self, url, headers=None):
r = self.make_request(url, True, headers)[1]
buffer = StringIO.StringIO()
for chunk in r.iter_content(16):
buffer.write(chunk)
buffer.seek(0)
return file_generator(buffer)
def index(self):
im = getRPiCameraImage()
im_data = StringIO.StringIO()
im.save(im_data, format="JPEG")
im_data.seek(0)
cherrypy.response.headers['Content-Type'] = "image/jpeg"
return file_generator(im_data)
def GET(self, *args, **kwargs):
if len(args) < 1:
raise cherrypy.HTTPError(403, 'Directory Listing Denied')
from PIL import Image
fileName, fileExtension = os.path.splitext(args[0])
if fileExtension=='.jpg':
#path = os.path.join(self._basePath, args[0])
data = Image.open(os.path.join(self._basePath, args[0]))
img = {
'data': None,
'meta': {
'type': '',
'name': ''
}
}
else:
img = self._dao.getBinary(args[0])
if img['data'] == None:
path = os.path.join(self._basePath, args[0])
if os.path.exists(path):
data = io.FileIO(path)
else:
raise cherrypy.HTTPError(404)
else:
data = io.BytesIO(img['data'])
cherrypy.response.headers['Content-Type'] = mimetypes.guess_type(img['meta']['name'] + '.' + img['meta']['type'])[0]
return file_generator(data)
def __set__(self, obj, value):
# Convert the given value to an iterable object.
if py3k and isinstance(value, str):
raise ValueError(self.unicode_err)
if isinstance(value, basestring):
# strings get wrapped in a list because iterating over a single
# item list is much faster than iterating over every character
# in a long string.
if value:
value = [value]
else:
# [''] doesn't evaluate to False, so replace it with [].
value = []
elif py3k and isinstance(value, list):
# every item in a list must be bytes...
for i, item in enumerate(value):
if isinstance(item, str):
raise ValueError(self.unicode_err)
# Don't use isinstance here; io.IOBase which has an ABC takes
# 1000 times as long as, say, isinstance(value, str)
elif hasattr(value, "read"):
value = file_generator(value)
elif value is None:
value = []
obj._body = value
def GET(self, *args, **kwargs):
#if len(args) < 1:
#raise cherrypy.HTTPError(403, 'Directory Listing Denied')
mp = MapProcessor(self._emptyMap)
sensors = self._sr.resolveStates(self._dao.findSensors())
#sensors = self._sr.appendSensorMetadata(sensors, self._emptyMap) #adds location and type
cob = self._dao.getRobotByName(self._robotName)
robot = {
'icon':self._dao.sensors.getSensorIconByName('robot')['id'],
'name':cob['robotName'],
'xCoord': cob['xCoord'],
'yCoord': cob['yCoord'],
'orientation': '%sd' % cob['orientation'],
'id':'r%s' % (cob['robotId'])
}
elements = []
elements.extend(sensors)
#important to put robot last as z-order is determined by render order in svg and we want the robot icon
#to always be on top
elements.append(robot)
img = mp.buildMap(elements)
data = io.BytesIO(img)
cherrypy.response.headers['Content-Type'] = mimetypes.guess_type('img.svg')[0]
return file_generator(data)
def export_participants(self, id):
"""Exports xlsx file with event participants
Args:
id (int): event id
"""
id = int(id)
req = cherrypy.request
orm_session = req.orm_session
# Retrieve event object
event = api.find_event_by_id(orm_session, id)
if event is None:
raise HTTPError(404)
# Set appropriate headers
filename = re.compile(r'[^\w-]').sub('', event.title.replace(' ', '_'))
cherrypy.response.headers['Content-Type'] = (
'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet'
)
cherrypy.response.headers['Content-Disposition'] = (
'attachment; filename={}-{}-{}-participants.xlsx'.format(
event.id, filename, event.date,
)
)
# Retrieve participation data
participations = api.find_participants_by_event(orm_session, event)
return file_generator(gen_participants_xlsx(participations))
def __set__(self, obj, value):
# Convert the given value to an iterable object.
if py3k and isinstance(value, str):
raise ValueError(self.unicode_err)
if isinstance(value, basestring):
# strings get wrapped in a list because iterating over a single
# item list is much faster than iterating over every character
# in a long string.
if value:
value = [value]
else:
# [''] doesn't evaluate to False, so replace it with [].
value = []
elif py3k and isinstance(value, list):
# every item in a list must be bytes...
for i, item in enumerate(value):
if isinstance(item, str):
raise ValueError(self.unicode_err)
# Don't use isinstance here; io.IOBase which has an ABC takes
# 1000 times as long as, say, isinstance(value, str)
elif hasattr(value, 'read'):
value = file_generator(value)
elif value is None:
value = []
obj._body = value
def index(self):
im = getRPiCameraImage()
im_data = StringIO.StringIO()
im.save(im_data, format="JPEG")
im_data.seek(0)
cherrypy.response.headers['Content-Type'] = "image/jpeg"
return file_generator(im_data)
def GET(self, *args, **kwargs):
#if len(args) < 1:
#raise cherrypy.HTTPError(403, 'Directory Listing Denied')
mp = MapProcessor(self._emptyMap)
sensors = self._sr.resolveStates(self._dao.findSensors())
#sensors = self._sr.appendSensorMetadata(sensors, self._emptyMap) #adds location and type
cob = self._dao.getRobotByName(self._robotName)
robot = {
'icon':self._dao.sensors.getSensorIconByName('robot')['id'],
'name':cob['robotName'],
'xCoord': cob['xCoord'],
'yCoord': cob['yCoord'],
'orientation': '%sd' % cob['orientation'],
'id':'r%s' % (cob['robotId'])
}
elements = []
elements.extend(sensors)
#important to put robot last as z-order is determined by render order in svg and we want the robot icon
#to always be on top
elements.append(robot)
img = mp.buildMap(elements)
data = io.BytesIO(img)
cherrypy.response.headers['Content-Type'] = mimetypes.guess_type('img.svg')[0]
cherrypy.response.headers['Cache-Control'] = "max-age=0, no-cache, must-revalidate"
cherrypy.response.headers['Pragma'] = "no-cache"
# In the past to prevent browser caching
cherrypy.response.headers['Expires'] = (datetime.datetime.utcnow() - datetime.timedelta(hours=1)).strftime('%a, %d %b %Y %H:%M:%S GMT')
return file_generator(data)
def GET(self, *args, **kwargs):
#if len(args) < 1:
#raise cherrypy.HTTPError(403, 'Directory Listing Denied')
mp = MapProcessor()
sensors = self._sr.resolveStates(self._dao.findSensors())
sensors = self._sr.appendSensorMetadata(
sensors) #adds location and type
cob = self._dao.getRobotByName(self._robotName)
robot = {
'type':
'robot',
'name':
cob['robotName'],
'location':
(cob['xCoord'], cob['yCoord'], '%sd' % (cob['orientation'] * -1)
), #svg rotates opposite of our cooridnate system
'id':
'r%s' % (cob['robotId'])
}
elements = []
elements.extend(sensors)
#important to put robot last as z-order is determined by render order in svg and we want the robot icon
#to always be on top
elements.append(robot)
img = mp.buildMap(elements)
data = io.BytesIO(img)
cherrypy.response.headers['Content-Type'] = mimetypes.guess_type(
'img.svg')[0]
return file_generator(data)
def export_participants(self, id):
"""Exports xlsx file with event participants
Args:
id (int): event id
"""
id = int(id)
req = cherrypy.request
orm_session = req.orm_session
# Retrieve event object
event = api.find_event_by_id(orm_session, id)
if event is None:
raise HTTPError(404)
# Set appropriate headers
filename = re.compile(r'[^\w-]').sub('', event.title.replace(' ', '_'))
cherrypy.response.headers['Content-Type'] = (
'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet'
)
cherrypy.response.headers['Content-Disposition'] = (
'attachment; filename={}-{}-{}-participants.xlsx'.format(
event.id,
filename,
event.date,
))
# Retrieve participation data
participations = api.find_participants_by_event(orm_session, event)
return file_generator(gen_participants_xlsx(participations))
def GET(self, *args, **kwargs):
if os.path.isfile(self._file):
f = open(self._file, 'rb')
cherrypy.response.headers['Content-Type'] = mimetypes.guess_type(self._file)[0]
return file_generator(f)
else:
raise cherrypy.HTTPError(404)
def GET(self, *args, **kwargs):
# if len(args) < 1:
# raise cherrypy.HTTPError(403, 'Directory Listing Denied')
mp = MapProcessor()
sensors = self._sr.resolveStates(self._dao.findSensors())
sensors = self._sr.appendSensorMetadata(sensors) # adds location and type
cob = self._dao.getRobotByName(self._robotName)
robot = {
"type": "robot",
"name": cob["robotName"],
"location": (
cob["xCoord"],
cob["yCoord"],
"%sd" % (cob["orientation"] * -1),
), # svg rotates opposite of our cooridnate system
"id": "r%s" % (cob["robotId"]),
}
elements = []
elements.extend(sensors)
# important to put robot last as z-order is determined by render order in svg and we want the robot icon
# to always be on top
elements.append(robot)
img = mp.buildMap(elements)
data = io.BytesIO(img)
cherrypy.response.headers["Content-Type"] = mimetypes.guess_type("img.svg")[0]
return file_generator(data)
def guest_list_report(self):
guests = m.Guest.query.order_by(m.Guest.name).all()
csv_data = []
header = ['Guest','Party Size','RSVPd','Attending','Comment',
'Guests Requested', 'Guests Allowed',
'Guests Attending','Total']
for guest in guests:
d = []
d.append(guest.name)
d.append(guest.party_size)
d.append('1' if guest.rsvpd else '0')
d.append('1' if guest.attending else '0')
d.append(guest.comment or '')
d.append(guest.guests_requested)
d.append(guest.guests_allowed)
d.append(guest.guests_coming)
if guest.rsvpd:
d.append(guest.party_size + guest.guests_coming)
else:
d.append(0)
csv_data.append(d)
csv_buffer = StringIO.StringIO()
csv_report = csv.writer(csv_buffer)
# csv_report.writeheader(header)
csv_report.writerow(header)
csv_report.writerows(csv_data)
csv_buffer.seek(0)
cherrypy.response.headers['Content-type'] = 'application/xls'
cherrypy.response.headers['Content-Disposition'] = 'attachment; filename="guest_list.csv"'
return file_generator(csv_buffer)
def barcode(self, data, scale=4):
""" """
cherrypy.response.headers['Content-Type'] = "image/png"
buffer = StringIO.StringIO()
code = pyqrcode.create(data)
code.png(buffer, scale=scale)
buffer.seek(0)
return file_generator(buffer)
def GET(self, *args, **kwargs):
if os.path.isfile(self._file):
f = open(self._file, 'rb')
cherrypy.response.headers['Content-Type'] = mimetypes.guess_type(
self._file)[0]
return file_generator(f)
else:
raise cherrypy.HTTPError(404)
def plot_graph(self, data, urlparams):
line_data = []
pie_data = []
limit = int(urlparams.limit)
if urlparams.graphtype == 'pie' and len(data) > limit and limit > 1: # formulate an artificial 'other' group with values > 'limit'
sum = 0L
for k, v in data[limit-1:]:
sum += v
data[limit-1:] = [('Other', sum)]
if urlparams.output_format == 'graph':
if urlparams.graphtype == 'line':
line_data = fill_timeline_holes(data, urlparams.graphbucket, urlparams.db_uniq)
line_data = [(int(time.mktime(p[0].timetuple()) * 1000), p[1]) for p in line_data]
line_data = json.dumps(line_data)
elif urlparams.graphtype == 'pie':
for d in data:
pie_data.append({'label': str(d[0]), 'data': [d[1]]})
pie_data = json.dumps(pie_data)
tmpl = env.get_template('graph.html')
return tmpl.render(line_data=line_data, pie_data=pie_data, graph_type=urlparams.graphtype, table=urlparams.table,
graph_key=urlparams.graphkey, graph_bucket=urlparams.graphbucket)
elif urlparams.output_format == 'png':
chart = None
if urlparams.graphtype == 'line':
line_data = fill_timeline_holes(data, urlparams.graphbucket, urlparams.db_uniq)
import pygal
chart = pygal.Line(width=1000)
chart.title = 'Counts of {} over 1{} slots'.format(urlparams.graphkey, urlparams.graphbucket)
labels = []
mod_constant = 10 if len(line_data) < 100 else (30 if len(line_data) < 1000 else 1000)
for i, d in enumerate(line_data):
if i == 0 or i == len(line_data)-1:
labels.append(d[0].strftime('%m-%d %H:%M'))
continue
if i % mod_constant == 0:
labels.append(d[0].strftime('%m-%d %H:%M'))
chart.x_labels = labels
chart.add('Count', [v for t, v in line_data])
elif urlparams.graphtype == 'pie':
import pygal
chart = pygal.Pie()
chart.title = 'Distribution of {} values'.format(urlparams.graphkey)
for key, count in data:
chart.add(str(key), count)
random_file_path = '/tmp/pgzebra{}.png'.format(random.random())
chart.render_to_png(random_file_path)
output = StringIO.StringIO(open(random_file_path).read()) # should be possible to skip this step also?
os.unlink(random_file_path)
cherrypy.response.headers['Content-Type'] = 'image/png'
return file_generator(output)
def __set__(self, obj, value):
if isinstance(value, basestring):
if value:
value = [value]
else:
value = []
elif hasattr(value, 'read'):
value = file_generator(value)
elif value is None:
value = []
obj._body = value
def __set__(self, obj, value):
if isinstance(value, basestring):
if value:
value = [value]
else:
value = []
elif hasattr(value, 'read'):
value = file_generator(value)
elif value is None:
value = []
obj._body = value
def __call__(self, *args, **kwargs):
response = cherrypy.serving.response
self.body = self.oldhandler(*args, **kwargs)
if isinstance(self.body, basestring):
# strings get wrapped in a list because iterating over a single
# item list is much faster than iterating over every character
# in a long string.
if self.body:
self.body = [self.body]
else:
# [''] doesn't evaluate to False, so replace it with [].
self.body = []
elif hasattr(self.body, 'read'):
self.body = file_generator(self.body)
elif self.body is None:
self.body = []
ct = response.headers.elements("Content-Type")
if self.debug:
cherrypy.log('Content-Type: %r' % [str(h) for h in ct],
'TOOLS.ENCODE')
if ct:
ct = ct[0]
if self.text_only:
if ct.value.lower().startswith("text/"):
if self.debug:
cherrypy.log(
'Content-Type %s starts with "text/"' % ct,
'TOOLS.ENCODE')
do_find = True
else:
if self.debug:
cherrypy.log(
'Not finding because Content-Type %s does '
'not start with "text/"' % ct, 'TOOLS.ENCODE')
do_find = False
else:
if self.debug:
cherrypy.log('Finding because not text_only',
'TOOLS.ENCODE')
do_find = True
if do_find:
# Set "charset=..." param on response Content-Type header
ct.params['charset'] = self.find_acceptable_charset()
if self.add_charset:
if self.debug:
cherrypy.log('Setting Content-Type %s' % ct,
'TOOLS.ENCODE')
response.headers["Content-Type"] = str(ct)
return self.body
def getImage(self):
cherrypy.response.headers['Content-Type'] = "image/jpeg"
self.startCamera()
stream = BytesIO()
#stream = StringIO.StringIO()
try:
self.camera.capture(stream, format='jpeg')
stream.seek(0)
except:
self.log("Could not get an image from camera.", 0)
return file_generator(stream)
def __call__(self, *args, **kwargs):
response = cherrypy.serving.response
self.body = self.oldhandler(*args, **kwargs)
if isinstance(self.body, text_or_bytes):
# strings get wrapped in a list because iterating over a single
# item list is much faster than iterating over every character
# in a long string.
if self.body:
self.body = [self.body]
else:
# [''] doesn't evaluate to False, so replace it with [].
self.body = []
elif hasattr(self.body, 'read'):
self.body = file_generator(self.body)
elif self.body is None:
self.body = []
ct = response.headers.elements('Content-Type')
if self.debug:
cherrypy.log('Content-Type: %r' % [str(h)
for h in ct], 'TOOLS.ENCODE')
if ct and self.add_charset:
ct = ct[0]
if self.text_only:
if ct.value.lower().startswith('text/'):
if self.debug:
cherrypy.log(
'Content-Type %s starts with "text/"' % ct,
'TOOLS.ENCODE')
do_find = True
else:
if self.debug:
cherrypy.log('Not finding because Content-Type %s '
'does not start with "text/"' % ct,
'TOOLS.ENCODE')
do_find = False
else:
if self.debug:
cherrypy.log('Finding because not text_only',
'TOOLS.ENCODE')
do_find = True
if do_find:
# Set "charset=..." param on response Content-Type header
ct.params['charset'] = self.find_acceptable_charset()
if self.debug:
cherrypy.log('Setting Content-Type %s' % ct,
'TOOLS.ENCODE')
response.headers['Content-Type'] = str(ct)
return self.body
def structure(self, **kwargs):
print_out(str(kwargs))
if "current_doc" not in kwargs:
return '<script>document.location.href="open";</script>'
elif "screenshot" in kwargs:
cherrypy.response.headers['Content-Type'] = "image/png"
cherrypy.response.headers[
'Content-Disposition'] = 'attachment; filename="' + kwargs[
"current_doc"] + '.png"'
if sys.version_info[0] == 2:
return file_generator(
StringIO(structure_main("local", "3", 'local', **kwargs)))
else:
return file_generator(
BytesIO(
b64decode(
structure_main("local", "3", 'local', **kwargs))))
else:
CORS(
) # This should not be necessary since the function is registered
# as cherrypy's 'before_handler', but for some reason the CORS
# header does not get set unless this is called explicitly.
return structure_main("local", "3", 'local', **kwargs)
def GET(self, *args, **kwargs):
path = ''
for arg in args:
path = os.path.join(path, arg)
if path == '':
raise cherrypy.HTTPError(403, 'Directory Listing Denied')
ospath = os.path.join(self._root, path)
if os.path.isfile(ospath):
f = open(ospath, 'rb')
cherrypy.response.headers['Content-Type'] = mimetypes.guess_type(ospath)[0]
return file_generator(f)
else:
raise cherrypy.HTTPError(404, ospath)
def GET(self, *args, **kwargs):
if len(args) < 1:
raise cherrypy.HTTPError(403, 'Directory Listing Denied')
key = args[0]
sensorHist = self._dao.getSensorHistory(key)
if len(sensorHist) > 0:
mp = MapProcessor()
s = StateResolver()
sensors = s.resolveStates(sensorHist)
img = mp.buildMap(sensors)
data = io.BytesIO(img)
cherrypy.response.headers['Content-Type'] = mimetypes.guess_type('img.svg')[0]
return file_generator(data)
def __set__(self, obj, value):
# Convert the given value to an iterable object.
if isinstance(value, basestring):
# strings get wrapped in a list because iterating over a single
# item list is much faster than iterating over every character
# in a long string.
if value:
value = [value]
else:
# [''] doesn't evaluate to False, so replace it with [].
value = []
elif isinstance(value, types.FileType):
value = file_generator(value)
elif value is None:
value = []
obj._body = value
def GET(self, *args, **kwargs):
path = ''
for arg in args:
path = os.path.join(path, arg)
if path == '':
raise cherrypy.HTTPError(403, 'Directory Listing Denied')
ospath = os.path.join(self._root, path)
if os.path.isfile(ospath):
f = open(ospath, 'rb')
cherrypy.response.headers['Content-Type'] = mimetypes.guess_type(
ospath)[0]
return file_generator(f)
else:
raise cherrypy.HTTPError(404)
def __set__(self, obj, value):
# Convert the given value to an iterable object.
if isinstance(value, basestring):
# strings get wrapped in a list because iterating over a single
# item list is much faster than iterating over every character
# in a long string.
if value:
value = [value]
else:
# [''] doesn't evaluate to False, so replace it with [].
value = []
elif isinstance(value, types.FileType):
value = file_generator(value)
elif value is None:
value = []
obj._body = value
def GET(self, *args, **kwargs):
if len(args) < 1:
raise cherrypy.HTTPError(403, 'Directory Listing Denied')
key = args[0]
sensorHist = self._dao.getSensorHistory(key)
if len(sensorHist) > 0:
mp = MapProcessor()
s = StateResolver()
sensors = s.resolveStates(sensorHist)
#[{'id': sensor['sensorId'], 'value': sensor['value'], 'state':'on'},]
sensors = s.appendSensorMetadata(sensors) #adds location and type
img = mp.buildMap(sensors)
data = io.BytesIO(img)
cherrypy.response.headers['Content-Type'] = mimetypes.guess_type('img.svg')[0]
return file_generator(data)
def GET(self, *args, **kwargs):
if len(args) < 1:
raise cherrypy.HTTPError(403, 'Directory Listing Denied')
img = self._dao.getBinary(args[0])
if img['data'] == None:
path = os.path.join(self._basePath, args[0])
if os.path.exists(path):
data = io.FileIO(path)
else:
raise cherrypy.HTTPError(404)
else:
data = io.BytesIO(img['data'])
cherrypy.response.headers['Content-Type'] = mimetypes.guess_type(img['meta']['name'] + '.' + img['meta']['type'])[0]
return file_generator(data)
def wav(self,engine=None,voice=None,rate=None,pitch=None,volume=None,text=None):
TTS.setEngine(engine,True)
TTS.setVoice(voice)
TTS.setRate(rate)
TTS.setPitch(pitch)
TTS.setVolume(volume)
TTS.update()
wav = TTS.getWavStream(text)
if not wav:
if not text:
raise cherrypy.HTTPError(status=400)
else:
raise cherrypy.HTTPError(status=500)
util.LOG('[{0}] {1} - WAV: {2}'.format(cherrypy.request.remote.ip,TTS.backend.provider,text.decode('utf-8')))
wav.seek(0)
cherrypy.response.headers['Content-Type'] = "audio/x-wav"
return file_generator(wav)
def __set__(self, obj, value):
# Convert the given value to an iterable object.
if isinstance(value, basestring):
# strings get wrapped in a list because iterating over a single
# item list is much faster than iterating over every character
# in a long string.
if value:
value = [value]
else:
# [''] doesn't evaluate to False, so replace it with [].
value = []
# Don't use isinstance here; io.IOBase which has an ABC takes
# 1000 times as long as, say, isinstance(value, str)
elif hasattr(value, 'read'):
value = file_generator(value)
elif value is None:
value = []
obj._body = value
def GET(self, *args, **kwargs):
if len(args) < 1:
raise cherrypy.HTTPError(403, 'Directory Listing Denied')
img = self._dao.getBinary(args[0])
if img['data'] == None:
path = os.path.join(self._basePath, args[0])
if os.path.exists(path):
data = io.FileIO(path)
else:
raise cherrypy.HTTPError(404)
else:
data = io.BytesIO(img['data'])
cherrypy.response.headers['Content-Type'] = mimetypes.guess_type(
img['meta']['name'] + '.' + img['meta']['type'])[0]
return file_generator(data)
def GET(self, *args, **kwargs):
if len(args) < 1:
raise cherrypy.HTTPError(403, 'Directory Listing Denied')
key = args[0]
sensorHist = self._dao.getSensorHistory(key)
if len(sensorHist) > 0:
mp = MapProcessor()
s = StateResolver()
sensors = s.resolveStates(sensorHist)
#[{'id': sensor['sensorId'], 'value': sensor['value'], 'state':'on'},]
sensors = s.appendSensorMetadata(sensors) #adds location and type
img = mp.buildMap(sensors)
data = io.BytesIO(img)
cherrypy.response.headers['Content-Type'] = mimetypes.guess_type(
'img.svg')[0]
return file_generator(data)
def __call__(self, *args, **kwargs):
response = cherrypy.serving.response
self.body = self.oldhandler(*args, **kwargs)
if isinstance(self.body, basestring):
if self.body:
self.body = [self.body]
else:
self.body = []
elif hasattr(self.body, 'read'):
self.body = file_generator(self.body)
elif self.body is None:
self.body = []
ct = response.headers.elements('Content-Type')
if self.debug:
cherrypy.log('Content-Type: %r' % [str(h) for h in ct],
'TOOLS.ENCODE')
if ct:
ct = ct[0]
if self.text_only:
if ct.value.lower().startswith('text/'):
if self.debug:
cherrypy.log(
'Content-Type %s starts with "text/"' % ct,
'TOOLS.ENCODE')
do_find = True
else:
if self.debug:
cherrypy.log(
'Not finding because Content-Type %s does not start with "text/"'
% ct, 'TOOLS.ENCODE')
do_find = False
else:
if self.debug:
cherrypy.log('Finding because not text_only',
'TOOLS.ENCODE')
do_find = True
if do_find:
ct.params['charset'] = self.find_acceptable_charset()
if self.add_charset:
if self.debug:
cherrypy.log('Setting Content-Type %s' % ct,
'TOOLS.ENCODE')
response.headers['Content-Type'] = str(ct)
return self.body
def prepare_iter(value):
"""
Ensure response body is iterable and resolves to False when empty.
"""
if isinstance(value, text_or_bytes):
# strings get wrapped in a list because iterating over a single
# item list is much faster than iterating over every character
# in a long string.
if value:
value = [value]
else:
# [''] doesn't evaluate to False, so replace it with [].
value = []
# Don't use isinstance here; io.IOBase which has an ABC takes
# 1000 times as long as, say, isinstance(value, str)
elif hasattr(value, 'read'):
value = file_generator(value)
elif value is None:
value = []
return value
def default(self, attr=''):
if os.path.isfile(NEW_MAIN_IMAGE_PATH):
log('New main image')
try:
os.remove(MAIN_IMAGE_PATH)
except:
pass
os.rename(NEW_MAIN_IMAGE_PATH, MAIN_IMAGE_PATH)
self._im = None
if not self._im:
log('Load main image')
try:
self._im = load_main_image(MAIN_IMAGE_PATH)
except:
self._im = None
if self._im:
cherrypy.response.headers['Content-type'] = 'image/png'
return file_generator(image_stream(self._im))
return 'Oops!'
def prepare_iter(value):
"""
Ensure response body is iterable and resolves to False when empty.
"""
if isinstance(value, text_or_bytes):
# strings get wrapped in a list because iterating over a single
# item list is much faster than iterating over every character
# in a long string.
if value:
value = [value]
else:
# [''] doesn't evaluate to False, so replace it with [].
value = []
# Don't use isinstance here; io.IOBase which has an ABC takes
# 1000 times as long as, say, isinstance(value, str)
elif hasattr(value, 'read'):
value = file_generator(value)
elif value is None:
value = []
return value
def __call__(self, *args, **kwargs):
response = cherrypy.serving.response
self.body = self.oldhandler(*args, **kwargs)
if isinstance(self.body, basestring):
if self.body:
self.body = [self.body]
else:
self.body = []
elif hasattr(self.body, 'read'):
self.body = file_generator(self.body)
elif self.body is None:
self.body = []
ct = response.headers.elements('Content-Type')
if self.debug:
cherrypy.log('Content-Type: %r' % [ str(h) for h in ct ], 'TOOLS.ENCODE')
if ct:
ct = ct[0]
if self.text_only:
if ct.value.lower().startswith('text/'):
if self.debug:
cherrypy.log('Content-Type %s starts with "text/"' % ct, 'TOOLS.ENCODE')
do_find = True
else:
if self.debug:
cherrypy.log('Not finding because Content-Type %s does not start with "text/"' % ct, 'TOOLS.ENCODE')
do_find = False
else:
if self.debug:
cherrypy.log('Finding because not text_only', 'TOOLS.ENCODE')
do_find = True
if do_find:
ct.params['charset'] = self.find_acceptable_charset()
if self.add_charset:
if self.debug:
cherrypy.log('Setting Content-Type %s' % ct, 'TOOLS.ENCODE')
response.headers['Content-Type'] = str(ct)
return self.body
def render_figure(self, probeset, fig_type, format, r=None):
if fig_type == "scatter":
probeset = urllib.unquote_plus(probeset)
# generate figure
fig = Figure()
fig.set_size_inches(16, 6)
ax_cp73 = fig.add_subplot(121)
ax_cp101 = fig.add_subplot(122)
if r == "a": # auto range
xlim = None
elif r == "f": # full range
xlim = (0, 15)
pda.plotProbe(pd_all, pd_covar, probeset, "CP73", ax_cp73, legend=False, xlim=xlim)
pda.plotProbe(pd_all, pd_covar, probeset, "CP101", ax_cp101, legend=True, xlim=xlim)
fig.tight_layout(rect=[0, 0, 0.7, 1], h_pad=0.5)
fig.set_facecolor('w')
canvas = FigureCanvas(fig)
# render
if fig_type == "boxplot":
probeset = urllib.unquote_plus(probeset)
fig = Figure()
fig.set_size_inches(15, 8)
ax_cp73 = fig.add_subplot(121)
ax_cp101 = fig.add_subplot(122)
cp73_groups = [("ASC / chronic saline", ss.ss_cp73_ascorbate_saline.filenames),
("OHDA / chronic saline", ss.cp73_chronic_saline.filenames),
("OHDA / acute saline", ss.ss_cp73_acuteSaline.filenames),
("OHDA / acute High L-DOPA", ss.ss_cp73_acuteHigh.filenames),
("OHDA / chronic Low L-DOPA", ss.ss_cp73_chronicLow.filenames),
("OHDA / chronic High L-DOPA", ss.ss_cp73_chronicHigh.filenames)
]
cp101_groups = [("ASC / chronic saline", ss.ss_cp101_ascorbate_saline.filenames),
("OHDA / chronic saline", ss.cp101_chronic_saline.filenames),
("OHDA / chronic Low L-DOPA", ss.ss_cp101_chronicLow.filenames),
("OHDA / chronic High L-DOPA", ss.ss_cp101_chronicHigh.filenames)
]
pda.probe_boxPlots(probeset, pd_all, cp73_groups, "CP73", ax_cp73)
pda.probe_boxPlots(probeset, pd_all, cp101_groups, "CP101", ax_cp101)
fig.tight_layout(rect=[0, 0, 0.7, 1], h_pad=0.5)
fig.set_facecolor('w')
canvas = FigureCanvas(fig)
if format == "png":
cherrypy.response.headers['Content-Type'] = "image/png"
buffer = StringIO.StringIO()
canvas.print_png(buffer)
buffer.seek(0)
return file_generator(buffer)
def photo(self, mathematician_id):
session = DBSession()
mathematician = session.query(Mathematician).get(mathematician_id)
return file_generator(io.BytesIO(mathematician.image))
def result_table(self, result_set, format="HTML", sort_field=0, sort_dir="DESC", rows=100, dimlist=None, page=0, cell_type=None, contrast=None):
if result_set == "cp73":
s = cp73_wide_info
elif result_set == "cp101":
s = cp101_wide_info
elif result_set == "t2_up":
s = t2_up[cell_type][contrast]
elif result_set == "t2_down":
s = t2_down[cell_type][contrast]
if sort_dir == "ASC":
sort_asc = True
else:
sort_asc = False
if sort_field is not None:
s = s.sort([s.columns.values[int(sort_field)]], ascending=sort_asc)
else:
s = s
if format == "txt":
cherrypy.response.headers['Content-Type'] = "application/octet-stream"
filename = "PDAIMS_2013_%s_%s_%s.txt" % (result_set, cell_type, contrast)
cherrypy.response.headers["Content-Disposition"] = "attachment; filename=%s" % filename
buffer = StringIO.StringIO()
s.to_csv(buffer, sep="\t")
buffer.seek(0)
return file_generator(buffer)
s["probe_img"] = ["<img width=350 src='/probeset/figure/%s/scatter/png'/>" % urllib.quote_plus(probe_id) for probe_id in s.probe_id]
s["probe_id"] = ["<a target='_detail' href='/probeset/%s'>%s</a>" % (urllib.quote_plus(probe_id), probe_id) for probe_id in s.probe_id]
s["symbol"] = ["<a target='_ncbi' href='http://www.ncbi.nlm.nih.gov/gene/?term=%s'>%s</a>" % (sym, sym) for sym in s.symbol]
# c = [s.columns[-1]]
# c.extend(s.columns[0:-1])
# s = s[c]
row_start = int(page) * 100
#print
t = tl.get_template("result_table.html")
if dimlist is None:
dimarray = range(0, len(s.columns)-1)
dimlist = ",".join([str(q) for q in dimarray])
else:
dimarray = [int(i) for i in dimlist.split(",")]
dimarray.sort()
if dimarray is not None:
column_list = s.columns[dimarray]
else:
column_list = s.columns
return t.render_unicode( fulltable = s.ix[s.index[row_start:row_start + 100],:],
displaytable = s.ix[s.index[row_start:row_start + 100], column_list],
page=int(page),
col_widths={"gene_name" : "300px"},
sort_field=int(sort_field),
sort_dir=sort_dir,
dimlist=dimlist,
dimarray=dimarray,
dim_descriptions=dim_descriptions,
result_set=result_set,
cell_type=cell_type,
contrast=contrast)
def render_figure(self, probeset, fig_type, format, r=None):
if fig_type == "scatter":
probeset = urllib.unquote_plus(probeset)
# generate figure
fig = Figure()
fig.set_size_inches(16, 6)
ax_cp73 = fig.add_subplot(121)
ax_cp101 = fig.add_subplot(122)
if r == "a": # auto range
xlim = None
elif r == "f": # full range
xlim = (0, 15)
pda.plotProbe(pd_all,
pd_covar,
probeset,
"CP73",
ax_cp73,
legend=False,
xlim=xlim)
pda.plotProbe(pd_all,
pd_covar,
probeset,
"CP101",
ax_cp101,
legend=True,
xlim=xlim)
fig.tight_layout(rect=[0, 0, 0.7, 1], h_pad=0.5)
fig.set_facecolor('w')
canvas = FigureCanvas(fig)
# render
if fig_type == "boxplot":
probeset = urllib.unquote_plus(probeset)
fig = Figure()
fig.set_size_inches(15, 8)
ax_cp73 = fig.add_subplot(121)
ax_cp101 = fig.add_subplot(122)
cp73_groups = [
("ASC / chronic saline",
ss.ss_cp73_ascorbate_saline.filenames),
("OHDA / chronic saline", ss.cp73_chronic_saline.filenames),
("OHDA / acute saline", ss.ss_cp73_acuteSaline.filenames),
("OHDA / acute High L-DOPA", ss.ss_cp73_acuteHigh.filenames),
("OHDA / chronic Low L-DOPA", ss.ss_cp73_chronicLow.filenames),
("OHDA / chronic High L-DOPA",
ss.ss_cp73_chronicHigh.filenames)
]
cp101_groups = [("ASC / chronic saline",
ss.ss_cp101_ascorbate_saline.filenames),
("OHDA / chronic saline",
ss.cp101_chronic_saline.filenames),
("OHDA / chronic Low L-DOPA",
ss.ss_cp101_chronicLow.filenames),
("OHDA / chronic High L-DOPA",
ss.ss_cp101_chronicHigh.filenames)]
pda.probe_boxPlots(probeset, pd_all, cp73_groups, "CP73", ax_cp73)
pda.probe_boxPlots(probeset, pd_all, cp101_groups, "CP101",
ax_cp101)
fig.tight_layout(rect=[0, 0, 0.7, 1], h_pad=0.5)
fig.set_facecolor('w')
canvas = FigureCanvas(fig)
if format == "png":
cherrypy.response.headers['Content-Type'] = "image/png"
buffer = StringIO.StringIO()
canvas.print_png(buffer)
buffer.seek(0)
return file_generator(buffer)
def result_table(self,
result_set,
format="HTML",
sort_field=0,
sort_dir="DESC",
rows=100,
dimlist=None,
page=0,
cell_type=None,
contrast=None):
if result_set == "cp73":
s = cp73_wide_info
elif result_set == "cp101":
s = cp101_wide_info
elif result_set == "t2_up":
s = t2_up[cell_type][contrast]
elif result_set == "t2_down":
s = t2_down[cell_type][contrast]
if sort_dir == "ASC":
sort_asc = True
else:
sort_asc = False
if sort_field is not None:
s = s.sort([s.columns.values[int(sort_field)]], ascending=sort_asc)
else:
s = s
if format == "txt":
cherrypy.response.headers[
'Content-Type'] = "application/octet-stream"
filename = "PDAIMS_2013_%s_%s_%s.txt" % (result_set, cell_type,
contrast)
cherrypy.response.headers[
"Content-Disposition"] = "attachment; filename=%s" % filename
buffer = StringIO.StringIO()
s.to_csv(buffer, sep="\t")
buffer.seek(0)
return file_generator(buffer)
s["probe_img"] = [
"<img width=350 src='/probeset/figure/%s/scatter/png'/>" %
urllib.quote_plus(probe_id) for probe_id in s.probe_id
]
s["probe_id"] = [
"<a target='_detail' href='/probeset/%s'>%s</a>" %
(urllib.quote_plus(probe_id), probe_id) for probe_id in s.probe_id
]
s["symbol"] = [
"<a target='_ncbi' href='http://www.ncbi.nlm.nih.gov/gene/?term=%s'>%s</a>"
% (sym, sym) for sym in s.symbol
]
# c = [s.columns[-1]]
# c.extend(s.columns[0:-1])
# s = s[c]
row_start = int(page) * 100
#print
t = tl.get_template("result_table.html")
if dimlist is None:
dimarray = range(0, len(s.columns) - 1)
dimlist = ",".join([str(q) for q in dimarray])
else:
dimarray = [int(i) for i in dimlist.split(",")]
dimarray.sort()
if dimarray is not None:
column_list = s.columns[dimarray]
else:
column_list = s.columns
return t.render_unicode(
fulltable=s.ix[s.index[row_start:row_start + 100], :],
displaytable=s.ix[s.index[row_start:row_start + 100], column_list],
page=int(page),
col_widths={"gene_name": "300px"},
sort_field=int(sort_field),
sort_dir=sort_dir,
dimlist=dimlist,
dimarray=dimarray,
dim_descriptions=dim_descriptions,
result_set=result_set,
cell_type=cell_type,
contrast=contrast)