Initial commit

main.py

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+import tornado.ioloop
+import tornado.web
+import tornado.gen as gen
+import tornado.escape as escape
+import tornado.websocket as websocket
+from tornado.web import URLSpec, asynchronous
+import os
+import sys
+import StringIO
+import jinja2
+import mimetypes
+import rpy2.robjects as robjects
+import json
+
+# Fake r initialization
+robjects.globalenv['A'] = robjects.r.matrix(robjects.IntVector(range(10)), nrow=5)
+robjects.globalenv['B'] = robjects.r.matrix(robjects.IntVector(range(10,0,-1)), nrow=5)
+
+# Jinja setup
+jinja_env = jinja2.Environment(loader=jinja2.PackageLoader('pyr',
+                                                           'templates'))
+
+def url_for(handler_name, *args):
+    return application.reverse_url(handler_name, *args)
+
+class RPYRequestHandler(tornado.web.RequestHandler):
+    def render_template_to_string(self, filename, **args):
+        # Make some custom functions accessible from the template
+        args['url_for'] = url_for
+        args['static_url'] = self.static_url
+
+        template = jinja_env.get_template(filename)
+        return template.render(**args)
+
+    def render_template(self, filename, **args):
+        self.write(self.render_template_to_string(filename, **args))
+        self.finish()
+
+    def send_file(self, data, mimetype):
+        self.set_header('Content-Type', mimetype)
+        self.write(data)
+        self.finish()
+
+    def send_json(self, data):
+        self.set_header('Content-Type', 'application/json')
+        # http://www.tornadoweb.org/documentation/_modules/tornado/escape.html
+        self.write(escape.json_encode(data))
+        self.finish()
+
+    def send_plot(self, fig):
+        imgdata = StringIO.StringIO()
+        fig.savefig(imgdata, format='png')
+        imgdata.seek(0)
+        self.send_file(imgdata.read(), 'image/png')
+
+def list_workspace():
+    matrices = {}
+    strobjs = {}
+
+    for name in robjects.r.ls(robjects.globalenv):
+        print name
+        obj = robjects.r[name]
+        if isinstance(obj, robjects.vectors.Matrix):
+            matrices[name] = {'cmajordata' : list(obj),
+                          'nrow' : obj.nrow,
+                          'ncol' : obj.ncol}
+        else:
+            strobjs[name] = obj.r_repr()
+
+    return {'matrices':matrices, 'strobjs':strobjs}
+
+## Handlers
+# Websocket
+# http://blog.kagesenshi.org/2011/10/simple-websocket-push-server-using.html
+class RSocket(websocket.WebSocketHandler):
+    def open(self):
+        print 'WebSocket opened'
+
+    def send_refresh_workspace(self):
+        wsdict = list_workspace()
+        response = {
+            'type': 'workspace',
+            'data' : wsdict
+        }
+        self.write_message(escape.json_encode(response))
+
+    def send_reval_result(self, command):
+        try:
+            result = str(robjects.r(command))
+        except Exception as e:
+            result = str(e)
+
+        response = {
+            'type': 'evalresult',
+            'data':result
+        }
+        self.write_message(escape.json_encode(response))
+
+    def on_message(self, message):
+        msg = escape.json_decode(message)
+        print msg
+        if msg['type'] == 'refreshws':
+            self.send_refresh_workspace()
+        elif msg['type'] == 'submit':
+            data = msg['data']
+            self.send_reval_result(data)
+            self.send_refresh_workspace()
+
+    def on_close(self):
+        print 'WebSocket closed'
+
+# Standard handlers
+class ListRWorkspace(RPYRequestHandler):
+    def get(self):
+        self.send_json(list_workspace())
+
+class IndexPage(RPYRequestHandler):
+    def get(self):
+        self.render_template('index.html')
+
+
+#class IndexPage(RPYRequestHandler):
+    #def do_plot(self, seqname, segname, segidx, callback):
+        #seq = get_sequence(seqname)
+        #segmentation = seq.load_segmentation(segname)
+        #segment = segmentation.get_segment(segidx)
+
+        ## plot
+        #fig = Figure()
+        #canvas = FigureCanvas(fig)
+        #ax = fig.add_subplot(111)
+        #ax.plot(segment.data)
+        #ax.set_title("%s/%s/%i" % (seqname, segname, segidx))
+        #ax.set_xlabel('Sample index (segment-based)')
+        #ax.set_ylabel('Value')
+        #ax.set_xlim(0, segment.data.shape[0])
+        #callback(fig)
+
+    #@asynchronous
+    #@gen.engine
+    #def get(self, seqname, segname, segidx):
+        #segidx = int(segidx)
+        #fig = yield gen.Task(self.do_plot, seqname, segname, segidx)
+        #self.send_plot(fig)
+
+settings = {
+    'static_path': os.path.join(os.path.dirname(__file__), 'static'),
+    'debug': True,
+}
+
+application = tornado.web.Application([
+        URLSpec(r"/", IndexPage, name='index'),
+        URLSpec(r"/rworkspace",
+                ListRWorkspace, name='rworkspace'),
+        URLSpec(r"/rsocket",
+                RSocket, name='rsocket')
+
+        #URLSpec(r"/seq/(?P<seqname>\w+)",
+                #SequenceHandler, name='sequence'),
+        #URLSpec(r"/seq/(?P<seqname>\w+)/seg/(?P<segname>\w+)/dataplot",
+                #SequenceDataplotHandler, name='sequence_dataplot'),
+        #URLSpec(r"/seq/(?P<seqname>\w+)/seg/(?P<segname>\w+)",
+                #SequenceSegmentationHandler, name="sequence_segmentation"),
+        #URLSpec(r"/seq/(?P<seqname>\w+)/seg/(?P<segname>\w+)/(?P<segidx>\d+)/dataplot",
+                #SequenceSegmentDataPlotHandler, name='sequence_segment_dataplot'),
+        #URLSpec(r"/seq/(?P<seqname>\w+)/seg/(?P<segname>\w+)/(?P<segidx>\d+)/medimage",
+                #SequenceSegmentMedimageHandler, name='sequence_segment_medimage'),
+        #URLSpec(r"/seq/(?P<seqname>\w+)/seg/(?P<segname>\w+)/segments",
+                #SequenceSegmentsPlotHandler, name='sequence_segments_plots')
+    ],
+    **settings)
+
+
+if __name__ == '__main__':
+    port = 8888
+    application.listen(port, address='0.0.0.0')
+    print 'Listening on port ', port
+    tornado.ioloop.IOLoop.instance().start()
+

run.sh

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+#!/bin/sh
+PYTHONPATH=../:$PYTHONPATH python -m tornado.autoreload -m pyr.main