Apollo golr server change

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Apollo golr server change

nathandunn

If you are using the GO annotation lookup with Apollo 1.0.0 or 2.0.0 you’ll need to change the GOLR server as follows and re-deploy.   

The next release of Apollo (2.0.1) will provide an automated proxy and the correct URL, making further server changes to redeployment un-necessary. 

Please let us know if you have any questions.

Nathan


Apollo 2.0.0

% git diff
diff --git a/client/apollo/js/View/Track/AnnotTrack.js b/client/apollo/js/View/Track/AnnotTrack.js
index 98dba80..e258e85 100644
--- a/client/apollo/js/View/Track/AnnotTrack.js
+++ b/client/apollo/js/View/Track/AnnotTrack.js
@@ -2819,8 +2819,8 @@ define([
                                                     }
                                                 }
                                             });
-                                            //var gserv = 'http://golr.berkeleybop.org/';
-                                            var gserv = 'http://golr.geneontology.org/solr/';
+                                            var gserv = 'http://golr.berkeleybop.org/solr/';
+                                            //var gserv = 'http://golr.geneontology.org/solr/';
                                             var gconf = new bbop.golr.conf(amigo.data.golr);
                                             var args = {
                                                 label_template: '{{annotation_class_label}} [{{annotation_class}}]',


Apollo 1.0.4 (and prior):


% git diff
diff --git a/client/apollo/js/View/Track/AnnotTrack.js b/client/apollo/js/View/Track/AnnotTrack.js
index b1904c3..150a9a8 100644
--- a/client/apollo/js/View/Track/AnnotTrack.js
+++ b/client/apollo/js/View/Track/AnnotTrack.js
@@ -2814,8 +2814,8 @@ var AnnotTrack = declare( DraggableFeatureTrack,
                                         }
                                     });
                                     // replaced with valid GOLR URL in build.xml file during copy process #148
-                                    //var gserv = 'http://golr.berkeleybop.org/';
-                                    var gserv = 'http://golr.geneontology.org/solr/';
+                                    var gserv = 'http://golr.berkeleybop.org/solr/';
+                                    //var gserv = 'http://golr.geneontology.org/solr/';



Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Apollo GO annotation lookup server update

nathandunn

This is a follow-up to this for those doing GO annotations with your apollo instance.  We had experienced some down-time with the production server.

The Permanent GOLR long-term GO URL:


The backup GOLR URL:

http://golr.berkeleybop.org/  (some regularly scheduled downtime)


URL’s maintained for backwards compatibility (will be pulled sometime in the New Year):

http://golr.geneontology.org/solr/        (will maintain 1.0.X compatibility)
http://golr.berkeleybop.org/solr/          (was used as a temporary stop-gap)


To check if a particular server is up (they are all up as of this writing):



I updated the fixes  to reflect this (below). 

In 2.0.1 (when released . . hopefully *before* the New Year, but we are unsure) you’ll be able to do this (if EVER necessary or you want to use another GOLR server) from an admin panel.


So, if you have to make any changes you have until the New Year to make them.


Nathan

On Nov 19, 2015, at 11:27 AM, Nathan Dunn <[hidden email]> wrote:


If you are using the GO annotation lookup with Apollo 1.0.0 or 2.0.0 you’ll need to change the GOLR server as follows and re-deploy.   

The next release of Apollo (2.0.1) will provide an automated proxy and the correct URL, making further server changes to redeployment un-necessary. 

Please let us know if you have any questions.

Nathan


Apollo 2.0.0

% git diff
diff --git a/client/apollo/js/View/Track/AnnotTrack.js b/client/apollo/js/View/Track/AnnotTrack.js
index 98dba80..e258e85 100644
--- a/client/apollo/js/View/Track/AnnotTrack.js
+++ b/client/apollo/js/View/Track/AnnotTrack.js
@@ -2819,8 +2819,8 @@ define([
                                                     }
                                                 }
                                             });
-                                            var gserv = 'http://golr.geneontology.org/solr/';
+                                            var gserv = 'http://golr.geneontology.org/';
                                             var args = {
                                                 label_template: '{{annotation_class_label}} [{{annotation_class}}]',


Apollo 1.0.4 (and prior):


% git diff
diff --git a/client/apollo/js/View/Track/AnnotTrack.js b/client/apollo/js/View/Track/AnnotTrack.js
index b1904c3..150a9a8 100644
--- a/client/apollo/js/View/Track/AnnotTrack.js
+++ b/client/apollo/js/View/Track/AnnotTrack.js
@@ -2814,8 +2814,8 @@ var AnnotTrack = declare( DraggableFeatureTrack,
                                         }
                                     });
                                     // replaced with valid GOLR URL in build.xml file during copy process #148
-                                    var gserv = 'http://golr.geneontology.org/solr/';
+                                    var gserv = 'http://golr.geneontology.org/';



Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.