Release candidate November 1st, 2017

.gitignore

@@ -57,7 +57,3 @@ gg_13_8-*
 
 # sphinx documentation
 qiita_pet/static/doc/
-
-# moi static files
-qiita_pet/static/vendor/js/moi.js
-qiita_pet/static/vendor/js/moi_list.js

INSTALL.md

@@ -140,7 +140,6 @@ Set your `QIITA_CONFIG_FP` environment variable to point to that file (into `.ba
 
 ```bash
   echo "export QIITA_CONFIG_FP=$HOME/.qiita_config_test.cfg" >> ~/.bashrc
-  echo "export MOI_CONFIG_FP=$HOME/.qiita_config_test.cfg" >> ~/.bashrc
   source ~/.bashrc
   # Re-enable conda environment for qiita
   source activate qiita

qiita_pet/static/js/qiita.js

@@ -240,3 +240,100 @@ function change_artifact_name(portal_dir, artifact_id, new_name, on_success_func
     }
   });
 }
+
+/**
+ * Taken from https://goo.gl/KkQ1S4
+ *
+ * Original script information:
+ * @author Daniel McDonald
+ * @copyright Copyright 2014, biocore
+ * @credits Daniel McDonald, Joshua Shorenstein, Jose Navas
+ * @license BSD
+ * @version 0.1.0-dev
+ * @maintainer Daniel McDonald
+ * @email mcdonadt@colorado.edu
+ * @status Development
+ *
+ *
+ * @name qiita_websocket
+ *
+ * @class manages WebSocket for job information
+ *
+ */
+
+var qiita_websocket = new function () {
+    var
+      /* the server end of the websocket */
+      host = null,
+      /* the websocket */
+      ws = null,
+
+      /* registered callbacks */
+      callbacks = {},
+
+      /* the encode and decode methods used for communication */
+      encode = JSON.stringify,
+      decode = JSON.parse;
+
+    /**
+     *
+     * Registers a callback method for a given action
+     *
+     * @param {action} The associated action verb, str.
+     * @param {func} The associated function, function. This function must
+     * accept an object. Any return is ignored.
+     *
+     */
+    this.add_callback = function(action, func) { callbacks[action] = func; };
+
+    /**
+     *
+     * Packages data into an object, and passes an encoded version of the
+     * object to the websocket.
+     *
+     * @param {action} The associated action to send, str.
+     * @param {data} The data to send, str or Array of str.
+     */
+    this.send = function(action, data) {
+        to_send = {};
+        to_send[action] = data;
+        ws.send(encode(to_send));
+    };
+
+    /**
+     *
+     * Verify the browser supports websockets, and if so, initialize the
+     * websocket. On construction, this method will send a message over the
+     * socket to get all known job information associated with this client.
+     *
+     * @param {host} The URL for the websocket, minus the ws:// header, or null
+     * to use the default qiita_websocket-ws.
+     * @param {on_close} Optional function for action when websocket is closed.
+     * @param {on_error} Optional function for action when websocket errors.
+     */
+    this.init = function(host, on_close, on_error) {
+        if (!("WebSocket" in window)) {
+            alert("Your browser does not appear to support websockets!");
+            return;
+        }
+        //check if we need regular or secure websocket
+        socket = window.location.protocol == "https:" ? 'wss://' : 'ws://';
+        ws = new WebSocket(socket + host);
+
+        // retrive all messages
+        var on_open_message = [];
+
+        ws.onopen = function(){};
+        ws.onclose = on_close;
+        ws.onerror = on_error;
+
+        ws.onmessage = function(evt) {
+            message = decode(evt.data);
+            for(var action in message) {
+                if(action in callbacks) {
+                    callbacks[action](message[action]);
+                }
+            }
+        };
+    };
+};

qiita_pet/templates/analysis_selected.html

@@ -2,7 +2,6 @@
 {% block head %}
 {% from future.utils import viewitems %}
 {% from itertools import chain %}
-<script src="{% raw qiita_config.portal_dir %}/static/vendor/js/moi.js"></script>
 <script type="text/javascript">
 
 function error(evt) { $('#ws-error').html("<b>Server communication error. Sample removal will not be recorded. Please try again later.</b>"); };
@@ -16,7 +15,7 @@
 
 function clear() {
   if(confirm('Are you sure you want to remove all samples?')) {
-    moi.send('clear', {'pids': {% raw [int(p) for p in chain.from_iterable(pid.keys() for sid, pid in viewitems(sel_data))] %} });
+    qiita_websocket.send('clear', {'pids': {% raw [int(p) for p in chain.from_iterable(pid.keys() for sid, pid in viewitems(sel_data))] %} });
   }
 }
 
@@ -27,7 +26,7 @@
 
 function remove_proc_data(pid, sid) {
   if(confirm('Are you sure you want to remove all samples for this processed data?')) {
-    moi.send('remove_pd', {'proc_data': pid, 'samples': [], 'sid': sid});
+    qiita_websocket.send('remove_pd', {'proc_data': pid, 'samples': [], 'sid': sid});
   }
 }
 
@@ -41,7 +40,7 @@
     check_empty();
 }
 
-function remove_sample(sid, pid, sample) { moi.send('remove_sample', {'proc_data': pid, 'samples': [sample], 'sid': sid}); }
+function remove_sample(sid, pid, sample) { qiita_websocket.send('remove_sample', {'proc_data': pid, 'samples': [sample], 'sid': sid}); }
 
 function remove_sample_from_html(data) {
     pid = data.proc_data;
@@ -58,10 +57,10 @@
     check_empty();
 }
 $(document).ready(function() {
-      moi.init(null, window.location.host + '{% raw qiita_config.portal_dir %}/analysis/selected/socket/', function(){}, error, error);
-      moi.add_callback('remove_pd', remove_pd_from_html);
-      moi.add_callback('remove_sample', remove_sample_from_html);
-      moi.add_callback('clear', clear_from_html);
+      qiita_websocket.init(window.location.host + '{% raw qiita_config.portal_dir %}/analysis/selected/socket/', error, error);
+      qiita_websocket.add_callback('remove_pd', remove_pd_from_html);
+      qiita_websocket.add_callback('remove_sample', remove_sample_from_html);
+      qiita_websocket.add_callback('clear', clear_from_html);
       $('#clear-button').on('click', clear);
       {% if sel_data %}$('#no-selected').hide(){% end %}
     });

qiita_pet/templates/analysis_waiting.html

@@ -1,8 +1,6 @@
 {% extends sitebase.html%}
 
 {%block head%}
-<script src="{% raw qiita_config.portal_dir %}/static/vendor/js/moi.js"></script>
-<script src="{% raw qiita_config.portal_dir %}/static/vendor/js/moi_list.js"></script>
 <script type="text/javascript">
     $(document).ready(function() {
       moi_list.init("{{group_id}}", undefined, window.location.host + '{% raw qiita_config.portal_dir %}/moi-ws/');

qiita_pet/templates/artifact_ajax/artifact_summary.html

@@ -89,6 +89,14 @@
   function validate_new_name() {
     $("#update-name-btn").prop('disabled', $("#new-artifact-name").val() === "");
   }
+
+  $(document).ready(function() {
+    // Set the focus on the text input when the modal to change the artifact
+    // name is shown
+    $('#update-artifact-name').on('shown.bs.modal', function() {
+      $('#new-artifact-name').focus();
+    });
+  });
 </script>
 <div class='row'>
   <div class='col-md-12'>

qiita_pet/templates/list_studies.html

@@ -4,7 +4,6 @@
 <link rel="stylesheet" href="{% raw qiita_config.portal_dir %}/static/vendor/css/jquery.dataTables.min.css" type="text/css">
 <link rel="stylesheet" href="{% raw qiita_config.portal_dir %}/static/vendor/css/select2.min.css" type="text/css">
 
-<script src="{% raw qiita_config.portal_dir %}/static/vendor/js/moi.js"></script>
 <script src="{% raw qiita_config.portal_dir %}/static/vendor/js/select2.min.js"></script>
 <script src="{% raw qiita_config.portal_dir %}/static/js/sharing.js"></script>
 <script src="{% raw qiita_config.portal_dir %}/static/vendor/js/tag-it.min.js" type="text/javascript" charset="utf-8"></script>
@@ -21,7 +20,7 @@
   $.get('/artifact/samples/', {ids:aids})
     .done(function ( data ) {
       if (data['status']=='success') {
-        moi.send('sel', data['data']);
+        qiita_websocket.send('sel', data['data']);
         button.value = 'Added';
         $(button).removeClass("btn-info");
       } else {
@@ -80,8 +79,8 @@
   });
 
   $("#search-waiting").hide();
-  moi.init(null, window.location.host + '{% raw qiita_config.portal_dir %}/study/list/socket/', function(){}, error, error);
-  moi.add_callback('sel', show_alert);
+  qiita_websocket.init(window.location.host + '{% raw qiita_config.portal_dir %}/study/list/socket/', error, error);
+  qiita_websocket.add_callback('sel', show_alert);
   function format_biom_rows(data, row) {
     var proc_data_table = '<table class="table" cellpadding="0" cellspacing="0" border="0" style="padding-left:0px;width:95%">';
     proc_data_table += '<tr>';

scripts/qiita-env

@@ -8,8 +8,6 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-from sys import exit
-
 import click
 
 import qiita_db as qdb
@@ -89,44 +87,13 @@ def test(runner):
     """Test the environment
 
     Check to make sure that basic services are up and working. These include
-    connectivity to postgres, redis, and the ability to submit jobs through
-    moi.
+    connectivity to postgres, and redis.
 
     Tests are performed both on localhost and ipengines.
     """
     _test(runner)
 
 
-@env.command()
-@click.option('--job', required=True, type=str, help='The job ID')
-def job_details(job):
-    """Pretty print moi job details"""
-    from json import loads
-    from redis.exceptions import ResponseError
-    from qiita_core.qiita_settings import r_client
-
-    try:
-        data = r_client.get(job)
-    except ResponseError:
-        click.echo("ID does not appear to be a job")
-        exit(1)
-
-    if data is None:
-        click.echo("Job cannot be found")
-    else:
-        data = loads(data)
-        for k in sorted(data):
-            value = data[k]
-
-            if k == 'result':
-                if isinstance(value, list):
-                    value = ''.join(value)
-                else:
-                    value = str(value)
-
-            click.echo("%s : %s" % (k, value))
-
-
 @env.command(name="create-portal")
 @click.argument('portal', required=True, type=str)
 @click.argument('description', required=True, type=str)