From ebb41225bef68042d7725bbff2f75721f23f0e66 Mon Sep 17 00:00:00 2001
From: shiltemann <s.hiltemann@erasmusmc.nl>
Date: Tue, 2 Feb 2016 11:08:31 +0100
Subject: [PATCH 1/4] added Phinch interactive environment

---
 .../phinch/config/phinch.ini.sample           | 21 ++++++++
 .../phinch/config/phinch.xml                  | 15 ++++++
 .../phinch/static/js/phinch.js                | 44 +++++++++++++++++
 .../phinch/templates/phinch.mako              | 49 +++++++++++++++++++
 4 files changed, 129 insertions(+)
 create mode 100644 config/plugins/interactive_environments/phinch/config/phinch.ini.sample
 create mode 100644 config/plugins/interactive_environments/phinch/config/phinch.xml
 create mode 100644 config/plugins/interactive_environments/phinch/static/js/phinch.js
 create mode 100644 config/plugins/interactive_environments/phinch/templates/phinch.mako

diff --git a/config/plugins/interactive_environments/phinch/config/phinch.ini.sample b/config/plugins/interactive_environments/phinch/config/phinch.ini.sample
new file mode 100644
index 00000000000..66adc27dc92
--- /dev/null
+++ b/config/plugins/interactive_environments/phinch/config/phinch.ini.sample
@@ -0,0 +1,21 @@
+[main]
+# Unused
+
+[docker]
+# Command to execute docker. For example `sudo docker` or `docker-lxc`.
+command = docker {docker_args}
+
+# The docker image name that should be started.
+image = shiltemann/docker-phinch-galaxy:v1
+
+# Additional arguments that are passed to the `docker run` command.
+#command_inject = --sig-proxy=true -e DEBUG=false
+
+# URL to access the Galaxy API with from the spawn Docker container, if empty
+# this falls back to galaxy.ini's galaxy_infrastructure_url and finally to the
+# Docker host of the spawned container if that is also not set.
+#galaxy_url =
+
+# The Docker hostname. It can be useful to run the Docker daemon on a different
+# host than Galaxy.
+#docker_hostname = localhost
diff --git a/config/plugins/interactive_environments/phinch/config/phinch.xml b/config/plugins/interactive_environments/phinch/config/phinch.xml
new file mode 100644
index 00000000000..3af1eee586b
--- /dev/null
+++ b/config/plugins/interactive_environments/phinch/config/phinch.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE interactive_environment SYSTEM "../../interactive_environments.dtd">
+<interactive_environment name="Phinch">
+    <data_sources>
+        <data_source>
+            <model_class>HistoryDatasetAssociation</model_class>
+            <test type="isinstance" test_attr="datatype" result_type="datatype">Biom1</test>
+            <to_param param_attr="id">dataset_id</to_param>
+        </data_source>
+    </data_sources>
+    <params>
+        <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
+    </params>
+    <entry_point entry_point_type="mako">phinch.mako</entry_point>
+</interactive_environment>
\ No newline at end of file
diff --git a/config/plugins/interactive_environments/phinch/static/js/phinch.js b/config/plugins/interactive_environments/phinch/static/js/phinch.js
new file mode 100644
index 00000000000..e91c8983007
--- /dev/null
+++ b/config/plugins/interactive_environments/phinch/static/js/phinch.js
@@ -0,0 +1,44 @@
+function load_notebook(url){
+    $( document ).ready(function() {
+        test_ie_availability(url, function(){
+            append_notebook(url)
+        });
+    });
+}
+
+function keep_alive(notebook_access_url){
+    /**
+    * This is needed to keep the container alive. If the user leaves this site
+    * this function is not constantly pinging the container, the container will
+    * terminate itself.
+    */
+
+    var request_count = 0;
+    interval = setInterval(function(){
+        $.ajax({
+            url: notebook_access_url,
+            xhrFields: {
+                withCredentials: true
+            },
+            type: "GET",
+            timeout: 500,
+            success: function(){
+                console.log("Connected to IE, returning");
+            },
+            error: function(jqxhr, status, error){
+                request_count++;
+                console.log("Request " + request_count);
+                if(request_count > 30){
+                    clearInterval(interval);
+                    clear_main_area();
+                    toastr.error(
+                        "Could not connect to IE, contact your administrator",
+                        "Error",
+                        {'closeButton': true, 'timeOut': 20000, 'tapToDismiss': false}
+                    );
+                }
+            }
+        });
+    }, 10000);
+}
+
diff --git a/config/plugins/interactive_environments/phinch/templates/phinch.mako b/config/plugins/interactive_environments/phinch/templates/phinch.mako
new file mode 100644
index 00000000000..e6308f6f0a7
--- /dev/null
+++ b/config/plugins/interactive_environments/phinch/templates/phinch.mako
@@ -0,0 +1,49 @@
+<%namespace name="ie" file="ie.mako" />
+<%
+
+import os
+
+# Sets ID and sets up a lot of other variables
+ie_request.load_deploy_config()
+
+# Define a volume that will be mounted into the container.
+# This is a useful way to provide access to large files in the container,
+# if the user knows ahead of time that they will need it.
+user_file = ie_request.volume(hda.file_name, '/home/Phinch/data/'+os.path.basename(hda.file_name)+'.biom', how='ro')
+
+# Launch the IE. This builds and runs the docker command in the background.
+ie_request.launch(
+    volumes=[user_file]
+)
+
+# Only once the container is launched can we template our URLs. The ie_request
+# doesn't have all of the information needed until the container is running.
+url = ie_request.url_template('${PROXY_URL}/phinch/')
+
+
+%>
+<html>
+<head>
+${ ie.load_default_js() }
+</head>
+<body>
+<script type="text/javascript">
+${ ie.default_javascript_variables() }
+var url = '${ url }';
+${ ie.plugin_require_config() }
+
+// Keep container running
+requirejs(['interactive_environments', 'plugin/phinch'], function(){
+    keep_alive(url);
+});
+
+// Load notebook
+requirejs(['interactive_environments', 'plugin/phinch'], function(){
+    load_notebook(url);
+});
+
+</script>
+<div id="main" style="width: 100%; height: 5000px;">
+</div>
+</body>
+</html>

From 87b5ba458fe574deb8c6200d8f12a8c329af98a1 Mon Sep 17 00:00:00 2001
From: shiltemann <s.hiltemann@erasmusmc.nl>
Date: Wed, 3 Feb 2016 10:41:55 +0100
Subject: [PATCH 2/4] changed docker tag to fit with Galaxy release

---
 .../interactive_environments/phinch/config/phinch.ini.sample    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/plugins/interactive_environments/phinch/config/phinch.ini.sample b/config/plugins/interactive_environments/phinch/config/phinch.ini.sample
index 66adc27dc92..be08cb60848 100644
--- a/config/plugins/interactive_environments/phinch/config/phinch.ini.sample
+++ b/config/plugins/interactive_environments/phinch/config/phinch.ini.sample
@@ -6,7 +6,7 @@
 command = docker {docker_args}
 
 # The docker image name that should be started.
-image = shiltemann/docker-phinch-galaxy:v1
+image = shiltemann/docker-phinch-galaxy:16.04
 
 # Additional arguments that are passed to the `docker run` command.
 #command_inject = --sig-proxy=true -e DEBUG=false

From 1b04ba3833597f2ebdc2e4f527044906ab7a4e7d Mon Sep 17 00:00:00 2001
From: Saskia Hiltemann <zazkia@gmail.com>
Date: Thu, 4 Feb 2016 11:02:11 +0100
Subject: [PATCH 3/4] use bioblend for dataset import instead of mount

---
 .../phinch/templates/phinch.mako                      | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/config/plugins/interactive_environments/phinch/templates/phinch.mako b/config/plugins/interactive_environments/phinch/templates/phinch.mako
index e6308f6f0a7..3b139ba311d 100644
--- a/config/plugins/interactive_environments/phinch/templates/phinch.mako
+++ b/config/plugins/interactive_environments/phinch/templates/phinch.mako
@@ -6,15 +6,12 @@ import os
 # Sets ID and sets up a lot of other variables
 ie_request.load_deploy_config()
 
-# Define a volume that will be mounted into the container.
-# This is a useful way to provide access to large files in the container,
-# if the user knows ahead of time that they will need it.
-user_file = ie_request.volume(hda.file_name, '/home/Phinch/data/'+os.path.basename(hda.file_name)+'.biom', how='ro')
 
 # Launch the IE. This builds and runs the docker command in the background.
-ie_request.launch(
-    volumes=[user_file]
-)
+ie_request.launch(env_override={
+    'dataset_hid': hda.hid,
+    'dataset_filename': hda.file_name
+})
 
 # Only once the container is launched can we template our URLs. The ie_request
 # doesn't have all of the information needed until the container is running.

From 674bf530c65c05fea3e77a82404a77dc03f645ca Mon Sep 17 00:00:00 2001
From: Saskia Hiltemann <zazkia@gmail.com>
Date: Fri, 5 Feb 2016 10:51:47 +0100
Subject: [PATCH 4/4] fix window height issue

---
 .../interactive_environments/phinch/static/js/phinch.js    | 7 +++++++
 .../interactive_environments/phinch/templates/phinch.mako  | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/config/plugins/interactive_environments/phinch/static/js/phinch.js b/config/plugins/interactive_environments/phinch/static/js/phinch.js
index e91c8983007..1b4c993e554 100644
--- a/config/plugins/interactive_environments/phinch/static/js/phinch.js
+++ b/config/plugins/interactive_environments/phinch/static/js/phinch.js
@@ -6,6 +6,13 @@ function load_notebook(url){
     });
 }
 
+function append_notebook(url){
+    clear_main_area();
+    $('#main').append('<iframe frameBorder="0" seamless="seamless" style="width: 100%; height: 100%; overflow:auto;" scrolling="yes" src="'+ url +'"></iframe>'
+    );
+}
+
+
 function keep_alive(notebook_access_url){
     /**
     * This is needed to keep the container alive. If the user leaves this site
diff --git a/config/plugins/interactive_environments/phinch/templates/phinch.mako b/config/plugins/interactive_environments/phinch/templates/phinch.mako
index 3b139ba311d..c446bf7d6e5 100644
--- a/config/plugins/interactive_environments/phinch/templates/phinch.mako
+++ b/config/plugins/interactive_environments/phinch/templates/phinch.mako
@@ -40,7 +40,7 @@ requirejs(['interactive_environments', 'plugin/phinch'], function(){
 });
 
 </script>
-<div id="main" style="width: 100%; height: 5000px;">
+<div id="main" style="width: 100%; height: 100%; overflow:hidden;">
 </div>
 </body>
 </html>