Merge b250d16 into 58b1e81

knimin/handlers/barcode_util.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 from tornado.web import authenticated
+from tornado.escape import json_encode
 from knimin.handlers.base import BaseHandler
 from datetime import datetime
 
@@ -172,8 +173,35 @@ def _build_email(self, login_user, barcode, email_type,
         return subject, body_message
 
 
+@set_access(['Scan Barcodes'])
+class PushQiitaHandler(BaseHandler):
+    @authenticated
+    def get(self):
+        barcodes = db.get_unsent_barcodes_from_qiita_buffer()
+        status = db.get_send_qiita_buffer_status()
+        dat = {'status': status, "barcodes": barcodes}
+        self.write(json_encode(dat))
+        self.finish()
+
+    @authenticated
+    def post(self):
+        barcodes = db.get_unsent_barcodes_from_qiita_buffer()
+        db.set_send_qiita_buffer_status("Pushing...")
+
+        try:
+            print("Sending: %s" % str(barcodes))
+        except:
+            db.set_send_qiita_buffer_status("Failed!")
+        else:
+            db.mark_barcodes_sent_to_qiita(barcodes)
+            db.set_send_qiita_buffer_status("Idle")
+
+        self.finish()
+
+
 @set_access(['Scan Barcodes'])
 class BarcodeUtilHandler(BaseHandler, BarcodeUtilHelper):
+
     @authenticated
     def get(self):
         barcode = self.get_argument('barcode', None)
@@ -293,9 +321,12 @@ def post(self):
 
             new_proj, parent_project = db.getBarcodeProjType(barcode)
         if parent_project == 'American Gut':
+            db.push_barcode_to_qiita_buffer(barcode)
+
             email_msg, ag_update_msg = self.update_ag_barcode(
                 barcode, login_user, login_email, email_type, sent_date,
                 send_mail, sample_date, sample_time, other_text)
+
         self.render("barcode_util.html", div_and_msg=None,
                     barcode_projects=[],
                     parent_project=None,

knimin/lib/data_access.py

@@ -1402,6 +1402,60 @@ def getAGKitDetails(self, supplied_kit_id):
         else:
             return {}
 
+    def push_barcode_to_qiita_buffer(self, barcode):
+        """Adds barcode to the qiita buffer
+
+        Parameters
+        ----------
+        barcode : str
+            The identifier to stage
+        """
+        sql = """SELECT barcode
+                 FROM project_qiita_buffer"""
+        present = {i[0] for i in self._con.execute_fetchall(sql)}
+
+        if barcode in present:
+            return "Barcode in queue or already sent to Qiita"
+
+        else:
+            sql = """INSERT INTO project_qiita_buffer (barcode)
+                     VALUES (%s)"""
+            self._con.execute(sql, [barcode])
+            return "Barcode inserted"
+
+    def get_send_qiita_buffer_status(self):
+        """Obtain the present status of the Qiita submission buffer"""
+        sql = """SELECT state FROM project_qiita_buffer_status"""
+        return self._con.execute_fetchone(sql)
+
+    def set_send_qiita_buffer_status(self, state):
+        """Obtain the present status of the Qiita submission buffer"""
+        sql = """UPDATE project_qiita_buffer_status
+                 SET state = %s
+                 WHERE id = 0"""
+        self._con.execute(sql, [state])
+
+    def get_unsent_barcodes_from_qiita_buffer(self):
+        """Extract the barcodes that have not been sent to Qiita"""
+        sql = """SELECT barcode
+                 FROM project_qiita_buffer
+                 WHERE pushed_to_qiita='N'"""
+        return [i[0] for i in self._con.execute_fetchall(sql)]
+
+    def mark_barcodes_sent_to_qiita(self, barcodes):
+        """Mark the provided barcodes as sent
+
+        Parameters
+        ----------
+        barcodes : list of str
+            The identifiers to mark a successfully sent to qiita
+        """
+        if barcodes:
+            sql = """UPDATE project_qiita_buffer
+                     SET pushed_to_qiita = 'Y'
+                     WHERE barcode IN %s"""
+            self._con.execute(sql, [tuple(barcodes)])
+
     def add_barcodes_to_kit(self, ag_kit_id, num_barcodes=1):
         """Attaches barcodes to an existing american gut kit
 

knimin/static/css/qiime.css

@@ -45,6 +45,21 @@ html, body {
 	width: 200px;
 }
 
+#qiita_buffer_window {
+    position: fixed;
+    top: 8px;
+    right: 8px;
+	margin: 8px;
+	background: #fff;
+	opacity: 0.8;
+	padding: 8px;
+	border: 2px black solid;
+	border-radius: 5px;
+	font: 15px normal Arial, Helvetica, sans-serif;
+    word-wrap: break-word;
+	width: 300px;
+}
+
 .login {
 	float:left;
 	margin: 8px;
@@ -294,6 +309,11 @@ h2.verification_text{
 	width: 100%;
 }
 
+h3.qiita_buffer_warning_text{
+    font-style: italic;
+	width: 100%;
+}
+
 #invalid_barcode {
   background-color: #f00;
 }

knimin/templates/barcode_util.html

@@ -15,6 +15,51 @@
       }
     });
   });
+
+function update_qiita_buffer(data, status) {
+    // update the buffer sending status and the buffer level
+    document.getElementById("qiita_buffer_status").innerHTML = "Send status: " + data['status'];
+    document.getElementById("qiita_buffer_level").innerHTML = "Samples queued: " + data['barcodes'].length;
+    console.log(status);
+}
+
+function immediate_update_qiita_buffer() {
+    // immediate update of buffer and status
+    $.get("/notify-qiita/", function(data, status) {
+        data = JSON.parse(data);
+        update_qiita_buffer(data, status);
+	} );
+}
+
+function submit_qiita_buffer() {
+    // issue a request to the knimin server to push data to qiita
+    $.post("/notify-qiita/", function(data, status) {
+        console.log("POST /notify-qiita/");
+        console.log(data);
+        console.log(status);
+	} );
+    immediate_update_qiita_buffer();
+}
+
+(function poll() {
+    // poll for buffer and submission status on a 5 second interval
+    setTimeout(function() {
+        $.ajax({
+            url: "/notify-qiita/",
+            type: "GET",
+            success: function(data, status) {
+                console.log("polling");
+                update_qiita_buffer(data, status);
+            },
+            dataType: "json",
+            complete: poll,
+            timeout: 5000
+        })
+    }, 5000);
+})();
+
+immediate_update_qiita_buffer();
+
 </script>
 {% end %}
 
@@ -42,7 +87,16 @@ <h3>Barcode Scanner </h3>
         document.check_barcode.barcode.focus()
     </script>
 </form>
-<div>
+</div>
+
+<div id="qiita_buffer_window">
+	<h3 id="qiita_buffer_level">Samples queued: refreshing...</h3>
+    <h3 id="qiita_buffer_status">Send status: refreshing...</h3>
+	<h3 class="qiita_buffer_warning_text">
+		Note: queued samples will be inaccessible to LabControl <br>
+	</h3>
+	<button onClick="submit_qiita_buffer()">Send to Qiita</button>
+</div>
 
 {% if barcode is not None%}
 <div id="{{div_and_msg[0]}}" class="verification_color">

knimin/webserver.py

@@ -12,7 +12,7 @@
 from knimin.handlers.auth_handlers import AuthLoginHandler, AuthLogoutHandler
 from knimin.handlers.ag_search import AGSearchHandler
 from knimin.handlers.logged_in_index import LoggedInIndexHandler
-from knimin.handlers.barcode_util import BarcodeUtilHandler
+from knimin.handlers.barcode_util import BarcodeUtilHandler, PushQiitaHandler
 from knimin.handlers.ag_stats import AGStatsHandler
 from knimin.handlers.ag_edit_participant import AGEditParticipantHandler
 from knimin.handlers.ag_new_kit import AGNewKitHandler, AGNewKitDLHandler
@@ -53,6 +53,7 @@ def __init__(self):
             (r"/logged_in_index/", LoggedInIndexHandler),
             (r"/ag_search/", AGSearchHandler),
             (r"/barcode_util/", BarcodeUtilHandler),
+            (r"/notify-qiita/", PushQiitaHandler),
             (r"/ag_add_barcode_kit/", AGAddBarcodeKitHandler),
             (r"/ag_stats/", AGStatsHandler),
             (r"/ag_edit_participant/", AGEditParticipantHandler),