From 53b13d8af4c8538af607616866ada007ba1695d7 Mon Sep 17 00:00:00 2001
From: Joseph Balsamo <joseph.balsamo@stonybrook.edu>
Date: Thu, 10 May 2018 20:25:56 +0000
Subject: [PATCH 1/3] Alert added for no finalized data

---
 js/annotationtoolslymph/osdAnnotationTools_Lymph.js | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/js/annotationtoolslymph/osdAnnotationTools_Lymph.js b/js/annotationtoolslymph/osdAnnotationTools_Lymph.js
index e16753387..5d0b52133 100644
--- a/js/annotationtoolslymph/osdAnnotationTools_Lymph.js
+++ b/js/annotationtoolslymph/osdAnnotationTools_Lymph.js
@@ -3339,7 +3339,9 @@ annotools.prototype.loadChangeUsername = function()
                         }
                     }
                 }
-            }
+            } else {
+		container.append('<blockquote><h5><span class="glyphicon glyphicon-alert red"> There are no users with finalized data to view!  Instruct the users to set weight thresholds and click finalize to make them available.</h5></blockquote>');
+	    }
         } catch (e){
             console.log('ERROR');
             console.log(e);

From 0af5dc7839a59bc9596d102d9c4c75c4153badfb Mon Sep 17 00:00:00 2001
From: Joseph Balsamo <joseph.balsamo@stonybrook.edu>
Date: Fri, 11 May 2018 17:10:05 +0000
Subject: [PATCH 2/3] removed Delete annotations from Lymph app

---
 .../geoJSONHandler_Lymph.js                   | 78 ++++++++++---------
 1 file changed, 42 insertions(+), 36 deletions(-)

diff --git a/js/annotationtoolslymph/geoJSONHandler_Lymph.js b/js/annotationtoolslymph/geoJSONHandler_Lymph.js
index e3f6bac2b..830f8d3da 100644
--- a/js/annotationtoolslymph/geoJSONHandler_Lymph.js
+++ b/js/annotationtoolslymph/geoJSONHandler_Lymph.js
@@ -690,13 +690,18 @@ annotools.prototype.generateSVG = function (annotations) {
                 content += line;
             }
 
-            if (ctrl)
-                content += "<button class='btn-danger btn' id='deleteAnnot'><a href='#confirmDelete' rel='modal:open'>Delete</a></button>";
-            else if (alt)
+ //  Section commented to disable Annotation deletion as per 
+//      bug SBU-BMI/quip_distro#268 by Joe Balsamo
+//           if (ctrl)
+//                content += "<button class='btn-danger btn' id='deleteAnnot'><a href='#confirmDelete' rel='modal:open'>Delete</a></button>";
+//            else  **When working join next line to this one again.
+	    if (alt)
                 content += "<button class='btn-danger btn' id='featureScape'>FeatureScape</button>";
 
 
-            content += "<button class='btn-danger btn' id='deleteAnnot'><a href='#confirmDelete' rel='modal:open'>Delete</a></button>";
+ //  Section commented to disable Annotation deletion as per 
+//      bug SBU-BMI/quip_distro#268 by Joe Balsamo
+//           content += "<button class='btn-danger btn' id='deleteAnnot'><a href='#confirmDelete' rel='modal:open'>Delete</a></button>";
             content += "<button class='btn' id='cancelPanel'>Cancel</button>";
             content += "</div>";
             var cancel = function () {
@@ -711,38 +716,39 @@ annotools.prototype.generateSVG = function (annotations) {
             jQuery("#cancelPanel").click(function () {
                 cancel();
             });
-
-            if (ctrl) { // Ctrl key for deletion of human generated annotation
-
-                jQuery("#deleteAnnot").click(function (e) {
-
-                    //$("#confirmDelete").css(
-                    //console.log(data.provenance.analysis.source);
-                    if (data.provenance.analysis.source == "human") {
-                        jQuery("#confirmDeleteButton").click(function () {
-                            var secret = jQuery("#deleteSecret").val();
-                            var payload = {
-                                "id": id,
-                                "secret": secret
-                            };
-
-                            jQuery.ajax({
-                                //url: 'api/Data/getProperties.php?id=' + id,
-                                url: 'api/Data/getPropertiesClone.php?id=' + id,
-                                type: 'DELETE',
-                                data: (payload),
-                                success: function (data) {
-                                    console.log(data);
-                                    jQuery("#panel").hide("slide");
-                                    self.getMultiAnnot();
-                                }
-                            });
-                        });
-                    } else {
-                        alert("Can't delete computer generated segments");
-                    }
-                });
-            }
+//  Section commented to disable Annotation deletion as per 
+//      bug SBU-BMI/quip_distro#268 by Joe Balsamo
+//            if (ctrl) { // Ctrl key for deletion of human generated annotation
+//
+//                jQuery("#deleteAnnot").click(function (e) {
+//
+//                    //$("#confirmDelete").css(
+//                    //console.log(data.provenance.analysis.source);
+//                    if (data.provenance.analysis.source == "human") {
+//                        jQuery("#confirmDeleteButton").click(function () {
+//                            var secret = jQuery("#deleteSecret").val();
+//                            var payload = {
+//                                "id": id,
+//                                "secret": secret
+//                            };
+//
+//                            jQuery.ajax({
+//                                //url: 'api/Data/getProperties.php?id=' + id,
+//                                url: 'api/Data/getPropertiesClone.php?id=' + id,
+//                                type: 'DELETE',
+//                                data: (payload),
+//                                success: function (data) {
+//                                    console.log(data);
+//                                    jQuery("#panel").hide("slide");
+//                                    self.getMultiAnnot();
+//                                }
+//                            });
+//                        });
+//                    } else {
+//                        alert("Can't delete computer generated segments");
+//                    }
+//                });
+//            }
 
         });
 

From 3463debad825110564ecf9aadea0ab1cfa938dc5 Mon Sep 17 00:00:00 2001
From: Joseph Balsamo <joseph.balsamo@stonybrook.edu>
Date: Fri, 11 May 2018 17:15:54 +0000
Subject: [PATCH 3/3] Fixed panel display at start of app.

---
 osdCamicroscope.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/osdCamicroscope.php b/osdCamicroscope.php
index c1b28a170..aa7837851 100644
--- a/osdCamicroscope.php
+++ b/osdCamicroscope.php
@@ -32,7 +32,7 @@
 <div id="container">
 
     <div id="tool"></div>
-    <div id="panel"></div>
+    <div id="panel" hidden></div>
     <!-- div id="bookmarkURLDiv"></div -->
     <div id="algosel">
         <div id="tree"></div>