Merge 97d93c4 into a748c94

.travis.yml

@@ -17,11 +17,8 @@ install:
   - pip install .
 script:
   - qiita_env make_test_env
-  - nosetests --with-doctest
+  - nosetests --with-doctest --with-coverage --cover-package=coveralls
   - pep8 qiita_db qiita_core qiita_pet setup.py
-  # we need to run the test suite from setup.py for coveralls to grab the info
-  - coverage run setup.py test
-  - coverage report -m
 services:
   - redis-server
 after_success:

qiita_pet/handlers/analysis_handlers.py

@@ -1,3 +1,16 @@
+r"""
+Qitta analysis handlers for the Tornado webserver.
+
+"""
+# -----------------------------------------------------------------------------
+# Copyright (c) 2014--, The Qiita Development Team.
+#
+# Distributed under the terms of the BSD 3-clause License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# -----------------------------------------------------------------------------
+from __future__ import division
+
 from tornado.web import authenticated
 from collections import defaultdict
 
@@ -7,6 +20,7 @@
 from qiita_db.study import Study
 from qiita_db.data import ProcessedData
 from qiita_db.metadata_template import SampleTemplate
+from qiita_db.job import Job
 # login code modified from https://gist.github.com/guillaumevincent/4771570
 
 
@@ -78,3 +92,47 @@ def post(self):
                 samples = [(processed_data[data_type], sid) for sid in
                            sample_ids]
                 analysis.add_samples(samples)
+
+
+class AnalysisWaitHandler(BaseHandler):
+    @authenticated
+    def get(self, analysis_id):
+        analysis = Analysis(analysis_id)
+        commands = []
+        for job in analysis.jobs:
+            jobject = Job(job)
+            commands.append("%s:%s" % (jobject.datatype, jobject.command[0]))
+
+        self.render("analysis_waiting.html", user=self.get_current_user(),
+                    aid=analysis_id, aname=analysis.name,
+                    commands=commands)
+
+    @authenticated
+    def post(self, analysis_id):
+        command_args = self.get_arguments("commands")
+        split = [x.split("#") for x in command_args]
+        analysis = Analysis(analysis_id)
+
+        commands = []
+        for data_type, command in split:
+            job = Job.create(data_type, command, {}, analysis)
+            commands.append("%s:%s" % (data_type, command))
+
+        self.render("analysis_waiting.html", user=self.get_current_user(),
+                    aid=analysis_id, aname=analysis.name,
+                    commands=commands)
+        # fire off analysis run here
+
+
+class AnalysisResultsHandler(BaseHandler):
+    @authenticated
+    def get(self, aid):
+        analysis = Analysis(aid)
+        jobres = defaultdict(list)
+        for job in analysis.jobs:
+            jobject = Job(job)
+            jobres[jobject.datatype].append((jobject.command[0],
+                                             jobject.results))
+
+        self.render("analysis_results.html", user=self.get_current_user(),
+                    jobres=jobres, aname=analysis.name)

qiita_pet/handlers/websocket_handlers.py

@@ -1,25 +1,22 @@
 # adapted from
 # https://github.com/leporo/tornado-redis/blob/master/demos/websockets
+from time import sleep
 
-from redis import Redis
-from tornadoredis import Client
 from tornado.websocket import WebSocketHandler
-import tornado.gen
+from tornado.gen import engine, Task
 from json import loads
 
 # all messages are in json format. They must have the following format:
-# 'job': jobname
+# 'analysis': analysis_id
 # 'msg': message to print
-# 'analysis': what analysis this is from in format datatype:analysis
-# 'results': list of files created if any
+# 'command': what command this is from in format datatype#command
 
 
 class MessageHandler(WebSocketHandler):
     def __init__(self, *args, **kwargs):
         super(MessageHandler, self).__init__(*args, **kwargs)
-        self.r_server = Redis()
-        self.redis = Client()
-        self.redis.connect()
+        # self.redis = Client()
+        # self.redis.connect()
 
     def get_current_user(self):
         user = self.get_secure_cookie("user")
@@ -32,33 +29,22 @@ def on_message(self, msg):
         msginfo = loads(msg)
         # listens for handshake from page
         if "user:" in msginfo['msg']:
-            self.channel = msginfo['msg'].split(':')[1]
+            self.aid = msginfo['msg'].split()[0]
+            self.channel = msginfo['msg'].split()[1].split(':')[1]
             # need to split the rest off to new func so it can be asynchronous
             self.listen()
 
     # decorator turns the function into an asynchronous generator object
-    @tornado.gen.engine
+    @engine
     def listen(self):
-        # runs task given, with the yield required to get returned value
-        # equivalent of callback/wait pairing from tornado.gen
-        yield tornado.gen.Task(self.redis.subscribe, self.channel)
-        if not self.redis.subscribed:
-            self.write_message('ERROR IN SUBSCRIPTION')
-        # listen from tornadoredis makes the listen object asynchronous
-        # if using standard redis lib, it blocks while listening
-        self.redis.listen(self.callback)
-        # fight race condition by loading from redis after listen started
-        # need to use std redis lib because tornadoredis is in subscribed state
-        oldmessages = self.r_server.lrange(self.channel + ':messages', 0, -1)
-        if oldmessages is not None:
-            for message in oldmessages:
-                self.write_message(message)
+        sleep(5)
+        self.write_message({"analysis": self.aid, "msg": "allcomplete"})
 
     def callback(self, msg):
         if msg.kind == 'message':
             self.write_message(str(msg.body))
 
-    @tornado.gen.engine
+    @engine
     def on_close(self):
-        yield tornado.gen.Task(self.redis.unsubscribe, self.channel)
+        yield Task(self.redis.unsubscribe, self.channel)
         self.redis.disconnect()

qiita_pet/static/css/style.css

@@ -1,4 +1,5 @@
 #template-content{
   padding: 20px;
+  height: 100%;
 }
 

qiita_pet/templates/analysis_results.html

@@ -0,0 +1,37 @@
+{% extends sitebase.html%}
+
+{%block head%}
+
+
+{%end%}
+
+{%block content%}
+<div class="container">
+<div class="row">
+<h1>Analysis {{aname}}</h1>
+</div>
+  <div class="row">
+    <div class="col-md-2">
+      <div class="panel-group" id="accordion">
+        {% for data_type, jobs in jobres.items() %}
+          <div class="panel panel-default">
+            <div class="panel-heading">
+              <h3 class="panel-title"><a data-toggle="collapse" data-parent="#accordion" href="#{{data_type}}">{{data_type}}</a></h3>
+            </div>
+            <div id="{{data_type}}" class="panel-collapse collapse">
+              {% for job, result in jobs%}
+                <div class="panel-body">
+                  <a href="/results/{{result}}" target="resframe">{{job}}</a>
+                </div>
+              {% end %}
+            </div>
+          </div>
+        {% end %}
+      </div>
+    </div>
+    <div class="col-md-10">
+        <iframe id="resframe" name="resframe" width="100%" height="900" frameBorder=0></iframe>
+    </div>
+  </div>
+</div>
+{%end%}

qiita_pet/templates/waiting.html → qiita_pet/templates/analysis_waiting.html

@@ -9,15 +9,15 @@
         noerror = true;
 
         websocket.onopen = function() {
-            websocket.send(JSON.stringify({'msg': 'user:{{user}}'}));
-            console.log(JSON.stringify({'msg': 'user:{{user}}'}));
+            websocket.send(JSON.stringify({'msg': '{{aid}} user:{{user}}'}));
+            console.log(JSON.stringify({'msg':'{{aid}} user:{{user}}'}));
         };
         websocket.onmessage = function(evt) {
             console.log(evt.data);
             message = JSON.parse(evt.data);
-            if(message.job == '{{job}}') {
+            if(message.analysis == '{{aid}}') {
                 if(noerror && message.msg == 'allcomplete') { 
-                    window.location.replace("/completed/{{job}}");
+                    window.location.replace("/analysis/results/{{aid}}");
                 }
                 list = document.getElementById(message.analysis);
                 if(message.msg.indexOf("ERROR") != -1) {
@@ -30,11 +30,7 @@
                 else {
                   list.style.color="Blue"; 
                 }
-                list.innerHTML = message.msg + '<br />';
-                for(var i=0; i<message.results.length; i++) {
-                    list.innerHTML += '<a class="link" target="_blank" href="../' + 
-                    message.results[i] + '">Plot ' + (i+1) + '</a><br />';
-                }
+                list.innerHTML = message.msg;
             }
         };
         websocket.onerror = function(evt) { };
@@ -52,24 +48,12 @@
 {% end %}
 
 {% block content %}
-<table width='100%'>
-  <tr>
-    <td width=180 valign='top'>
-      1) Choose studies<br />
-      2) Select analyses<br />
-      3) Set analysis options<br />
-      4) Review analysis<br />
-      <b>5) Running analysis</b><br />
-      6) Analysis results<br />
-    </td>
-    <td>
-<h1>Analysis {{job}}</h1>
-  {% for analysis in analyses %}
+<h1>Analysis {{aname}}</h1>
+  {% for command in commands%}
     <p>
-    {{analysis}}: <span id='{{analysis}}'>Queued</span>
+    {{command}}: <span id='{{command}}'>Queued</span>
     </p>
   {% end %}
-</td></tr></table>
 <div id='error'></div>
 
 {% end %}

qiita_pet/templates/select_commands.html

@@ -19,8 +19,7 @@ <h1>Select Commands</h1>
   {% end %}
 </ul>
 
-<form role="form" action="/analysis/wait/" method="post">
-  <input type="hidden" name="analysis-id" value="{{aid}}">
+<form role="form" action="/analysis/wait/{{aid}}" method="post">
   <div class="tab-content" style="height:300px">
     {% for data_type in data_types %}
       <div class="tab-pane" id="{{ data_type }}">

qiita_pet/templates/sitebase.html

@@ -13,7 +13,7 @@
 
     {% block head %}{% end %}
   </head>
-  <body style="padding-top: 65px;">
+  <body style="padding-top: 65px; height: 100%">
     <div class="navbar navbar-inverse navbar-fixed-top" role="navigation">
       <div class="container">
         <div class="navbar-header">

qiita_pet/webserver.py

@@ -17,7 +17,9 @@
 from qiita_pet.handlers.auth_handlers import (
     AuthCreateHandler, AuthLoginHandler, AuthLogoutHandler, AuthVerifyHandler)
 from qiita_pet.handlers.analysis_handlers import (
-    CreateAnalysisHandler, SelectStudiesHandler, SelectCommandsHandler)
+    CreateAnalysisHandler, SelectStudiesHandler, SelectCommandsHandler,
+    AnalysisWaitHandler, AnalysisResultsHandler)
+from qiita_pet.handlers.websocket_handlers import MessageHandler
 
 define("port", default=8888, help="run on the given port", type=int)
 
@@ -43,6 +45,9 @@ def __init__(self):
             (r"/analysis/1", CreateAnalysisHandler),
             (r"/analysis/2", SelectStudiesHandler),
             (r"/analysis/3", SelectCommandsHandler),
+            (r"/analysis/wait/(.*)", AnalysisWaitHandler),
+            (r"/analysis/results/(.*)", AnalysisResultsHandler),
+            (r"/consumer/", MessageHandler),
             (r"/mockup/", MockupHandler),
             # 404 PAGE MUST BE LAST IN THIS LIST!
             (r".*", NoPageHandler)