Merge remote-tracking branch 'erasche/ie-updates2' into pr229

Conflicts:
	config/plugins/interactive_environments/ipython/config/ipython.ini.sample

config/plugins/interactive_environments/ipython/config/ipython.ini.sample

@@ -12,10 +12,10 @@
 command = docker
 
 # The docker image name that should be started.
-image = bgruening/docker-ipython-notebook:0.2
+image = bgruening/docker-ipython-notebook:dev
 
 # Additional arguments that are passed to the `docker run` command.
-command_inject = --sig-proxy=true
+command_inject = --sig-proxy=true -e DEBUG=false
 
 # URL to access the Galaxy API with from the spawn Docker containter, if empty
 # this falls back to galaxy.ini's galaxy_infrastructure_url and finally to the

config/plugins/interactive_environments/ipython/templates/ipython.mako

@@ -11,8 +11,10 @@ ie_request.load_deploy_config()
 ie_request.attr.docker_port = 6789
 # Create tempdir in galaxy
 temp_dir = os.path.abspath( tempfile.mkdtemp() )
-# Write out conf file...needs work
-ie_request.write_conf_file(temp_dir)
+
+# Get all configurations
+conf = ie_request.get_conf_dict()
+ENV = ' '.join(['-e "%s=%s"' % (key.upper(), item) for key, item in conf.items()])
 
 ## IPython Specific
 # Prepare an empty notebook
@@ -34,9 +36,12 @@ else:
 notebook_access_url = ie_request.url_template('${PROXY_URL}/ipython/${PORT}/notebooks/ipython_galaxy_notebook.ipynb')
 notebook_login_url = ie_request.url_template('${PROXY_URL}/ipython/${PORT}/login?next=%2Fipython%2F${PORT}%2Ftree')
 
-docker_cmd = ie_request.docker_cmd(temp_dir)
+
+# Add all environment variables collected from Galaxy's IE infrastructure
+docker_cmd = ie_request.docker_cmd(temp_dir).replace('run', 'run %s' % ENV)
 ie_request.log.info("Starting IPython docker container with command [%s]" % docker_cmd)
 subprocess.call(docker_cmd, shell=True)
+
 %>
 <html>
 <head>

config/plugins/interactive_environments/ipython/templates/notebook.ipynb

@@ -20,7 +20,7 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "You can access your data via the dataset number. For example, ``handle = get(42)``.",
+      "You can access your data via the dataset number. For example, ``handle = open(get(42), 'r')``.",
       "To save data, write your data to a file, and then call ``put('filename.txt')``. The dataset will then be available in your galaxy history.",
       "Notebooks can be saved to Galaxy by clicking the large green button at the top right of the IPython interface.<br>",
       "More help and informations can be found on the project [website](https://github.com/bgruening/galaxy-ipython)."

lib/galaxy/web/base/interactive_environments.py

@@ -6,9 +6,6 @@ import random
 
 from galaxy.util.bunch import Bunch
 from galaxy import web
-from galaxy import eggs
-eggs.require("PyYAML")
-import yaml
 from galaxy.managers import api_keys
 
 import logging
@@ -68,9 +65,9 @@ class InteractiveEnviornmentRequest(object):
         self.attr.APACHE_URLS = _boolean_option("apache_urls")
         self.attr.SSL_URLS = _boolean_option("ssl")
 
-    def write_conf_file(self, output_directory, extra={}):
+    def get_conf_dict(self, extra={}):
         """
-            Build up a configuration file that is standard for ALL IEs.
+            Build up a configuration dictionary that is standard for ALL IEs.
 
             TODO: replace hashed password with plaintext.
         """
@@ -92,7 +89,9 @@ class InteractiveEnviornmentRequest(object):
         else:
             conf_file['galaxy_url'] = request.application_url.rstrip('/') + '/'
             web_port = self.attr.galaxy_config.galaxy_infrastructure_web_port
-            conf_file['galaxy_paster_port'] = web_port or self.attr.galaxy_config.guess_galaxy_port()
+            conf_file['galaxy_web_port'] = web_port or self.attr.galaxy_config.guess_galaxy_port()
+            # Galaxy paster port is deprecated
+            conf_file['galaxy_paster_port'] = conf_file['galaxy_web_port']
 
         if self.attr.PASSWORD_AUTH:
             # Generate a random password + salt
@@ -110,9 +109,7 @@ class InteractiveEnviornmentRequest(object):
             conf_file[extra_key] = extra[extra_key]
 
         self.attr.notebook_pw = notebook_pw
-        # Write conf
-        with open( os.path.join( output_directory, 'conf.yaml' ), 'wb' ) as handle:
-            handle.write( yaml.dump(conf_file, default_flow_style=False) )
+        return conf_file
 
     def generate_hex(self, length):
         return ''.join(random.choice('0123456789abcdef') for _ in range(length))

lib/galaxy/web/proxy/js/lib/proxy.js

@@ -36,6 +36,23 @@ var DynamicProxy = function(options) {
 };
 
 DynamicProxy.prototype.rewriteRequest = function(request) {
+    if(request.url.indexOf('rstudio') != -1){
+        var remap = {
+            'content-type': 'Content-Type',
+            'content-length': 'Content-Length',
+        }
+        // RStudio isn't spec compliant and pitches a fit on NodeJS's http module's lowercase HTTP headers
+        for(var i = 0; i<Object.keys(remap).length; i++){
+            var key = Object.keys(remap)[i];
+            if(key in request.headers){
+                request.headers[remap[key]] = request.headers[key];
+                delete request.headers[key];
+            }
+        }
+        if('Content-Type' in request.headers && request.headers['Content-Type'] == 'application/x-www-form-urlencoded; charset=UTF-8'){
+            request.headers['Content-Type'] = 'application/x-www-form-urlencoded';
+        }
+    }
 }
 
 DynamicProxy.prototype.targetForRequest = function(request) {