[galaxy-commits] commit/galaxy-central: 4 new changesets

30 Nov 2012

4 new commits in galaxy-central:


https://bitbucket.org/galaxy/galaxy-central/changeset/84022ca3c573/
changeset:   84022ca3c573
user:        carlfeberhard
date:        2012-11-30 02:23:14
summary:     history panel: remove IE-incompatible console statements
affected #:  3 files

diff -r 2aae11d62620b6c839b513d68a06d2cc57c5fa21 -r 84022ca3c5733277d8666a999edcb11381f40394 static/scripts/mvc/history/history-model.js

--- a/static/scripts/mvc/history/history-model.js
+++ b/static/scripts/mvc/history/history-model.js
@@ -187,9 +187,9 @@
             // if not interruption by iframe reload
             //TODO: remove when iframes are removed
             if( !( ( xhr.readyState === 0 ) && ( xhr.status === 0 ) ) ){
-                if( console && console.warn ){
-                    console.warn( 'Error getting history updates from the server:', xhr, status, error );
-                }
+                //if( console && console.warn ){
+                //    console.warn( 'Error getting history updates from the server:', xhr, status, error );
+                //}
                 alert( _l( 'Error getting history updates from the server.' ) + '\n' + error );
             }
         });


diff -r 2aae11d62620b6c839b513d68a06d2cc57c5fa21 -r 84022ca3c5733277d8666a999edcb11381f40394 static/scripts/packed/mvc/history/history-model.js
--- a/static/scripts/packed/mvc/history/history-model.js
+++ b/static/scripts/packed/mvc/history/history-model.js
@@ -1,1 +1,1 @@
-var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",diskSize:0,deleted:false,annotation:null,message:null},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b&&b.length){this.hdas.reset(b);this.checkForUpdates()}},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.trigger("loaded:user",e[0]);b.trigger("loaded",d[0])}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.hdaIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();b.trigger("loaded:hdas",d);if(c){callback(b)}})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.hdas.update(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},4000)}else{c.trigger("ready")}}).error(function(f,d,e){if(!((f.readyState===0)&&(f.status===0))){if(console&&console.warn){console.warn("Error getting history updates from the server:",f,d,e)}alert(_l("Error getting history updates from the server.")+"\n"+e)}})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"});
\ No newline at end of file
+var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",diskSize:0,deleted:false,annotation:null,message:null},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b&&b.length){this.hdas.reset(b);this.checkForUpdates()}},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.trigger("loaded:user",e[0]);b.trigger("loaded",d[0])}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.hdaIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();b.trigger("loaded:hdas",d);if(c){callback(b)}})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.hdas.update(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},4000)}else{c.trigger("ready")}}).error(function(f,d,e){if(!((f.readyState===0)&&(f.status===0))){alert(_l("Error getting history updates from the server.")+"\n"+e)}})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"});
\ No newline at end of file


diff -r 2aae11d62620b6c839b513d68a06d2cc57c5fa21 -r 84022ca3c5733277d8666a999edcb11381f40394 templates/root/alternate_history.mako
--- a/templates/root/alternate_history.mako
+++ b/templates/root/alternate_history.mako
@@ -304,11 +304,11 @@
     Galaxy.historyFrame = window;
 
     // ostensibly, this is the App
-    if( console && console.debug ){
-        //if( console.clear ){ console.clear(); }
-        console.pretty = function( o ){ $( '<pre/>' ).text( JSON.stringify( o, null, ' ' ) ).appendTo( 'body' ); }
-        top.storage = jQuery.jStorage
-    }
+    //if( console && console.debug ){
+    //    //if( console.clear ){ console.clear(); }
+    //    console.pretty = function( o ){ $( '<pre/>' ).text( JSON.stringify( o, null, ' ' ) ).appendTo( 'body' ); }
+    //    top.storage = jQuery.jStorage
+    //}
 
 
     // LOAD INITIAL DATA IN THIS PAGE - since we're already sending it...
@@ -330,7 +330,7 @@
     var historyPanel = new HistoryPanel({
         model           : new History( history, hdas ),
         urlTemplates    : galaxy_paths.attributes,
-        logger          : console,
+        //logger          : console,
         // is page sending in show settings? if so override history's
         show_deleted    : ${ 'true' if show_deleted == True else ( 'null' if show_deleted == None else 'false' ) },
         show_hidden     : ${ 'true' if show_hidden  == True else ( 'null' if show_hidden  == None else 'false' ) }



https://bitbucket.org/galaxy/galaxy-central/changeset/c08a5d0d2a4f/
changeset:   c08a5d0d2a4f
user:        natefoo
date:        2012-11-30 03:33:01
summary:     Metadata detection would never complete if setting externally.
affected #:  1 file

diff -r 84022ca3c5733277d8666a999edcb11381f40394 -r c08a5d0d2a4fd1f97943174ed677e8ae17566647 lib/galaxy/jobs/handler.py
--- a/lib/galaxy/jobs/handler.py
+++ b/lib/galaxy/jobs/handler.py
@@ -133,7 +133,7 @@
                     .join(model.HistoryDatasetAssociation) \
                     .join(model.Dataset) \
                     .filter(and_((model.Job.state == model.Job.states.NEW),
-                                 or_((model.HistoryDatasetAssociation._state != None),
+                                 or_((model.HistoryDatasetAssociation._state == model.HistoryDatasetAssociation.states.FAILED_METADATA),
                                      (model.HistoryDatasetAssociation.deleted == True ),
                                      (model.Dataset.state != model.Dataset.states.OK ),
                                      (model.Dataset.deleted == True)))).subquery()



https://bitbucket.org/galaxy/galaxy-central/changeset/f364d992270c/
changeset:   f364d992270c
user:        natefoo
date:        2012-11-30 16:42:50
summary:     Prevent waiting jobs from circumventing limits upon server startup.
affected #:  1 file

diff -r c08a5d0d2a4fd1f97943174ed677e8ae17566647 -r f364d992270c6201a748249c819b5cc41ed95cfb lib/galaxy/jobs/handler.py
--- a/lib/galaxy/jobs/handler.py
+++ b/lib/galaxy/jobs/handler.py
@@ -87,8 +87,11 @@
             if job.tool_id not in self.app.toolbox.tools_by_id:
                 log.warning( "(%s) Tool '%s' removed from tool config, unable to recover job" % ( job.id, job.tool_id ) )
                 JobWrapper( job, self ).fail( 'This tool was disabled before the job completed.  Please contact your Galaxy administrator.' )
-            elif job.job_runner_name is None:
-                log.debug( "(%s) No job runner assigned and job still in '%s' state, adding to the job handler queue" % ( job.id, job.state ) )
+            elif job.job_runner_name is None or (job.job_runner_name is not None and job.job_runner_external_id is None):
+                if job.job_runner_name is None:
+                    log.debug( "(%s) No job runner assigned and job still in '%s' state, adding to the job handler queue" % ( job.id, job.state ) )
+                else:
+                    log.debug( "(%s) Job runner assigned but no external ID recorded, adding to the job handler queue" % job.id )
                 if self.track_jobs_in_database:
                     job.state = model.Job.states.NEW
                 else:



https://bitbucket.org/galaxy/galaxy-central/changeset/88aba66bb813/
changeset:   88aba66bb813
user:        natefoo
date:        2012-11-30 16:54:58
summary:     Merge back dist changes
affected #:  2 files

diff -r 7bfce80911c3a628710ebaaad0119ee46ea9e532 -r 88aba66bb81351cbd625ca7fb9ed39874016b36a lib/galaxy/jobs/handler.py
--- a/lib/galaxy/jobs/handler.py
+++ b/lib/galaxy/jobs/handler.py
@@ -87,8 +87,11 @@
             if job.tool_id not in self.app.toolbox.tools_by_id:
                 log.warning( "(%s) Tool '%s' removed from tool config, unable to recover job" % ( job.id, job.tool_id ) )
                 JobWrapper( job, self ).fail( 'This tool was disabled before the job completed.  Please contact your Galaxy administrator.' )
-            elif job.job_runner_name is None:
-                log.debug( "(%s) No job runner assigned and job still in '%s' state, adding to the job handler queue" % ( job.id, job.state ) )
+            elif job.job_runner_name is None or (job.job_runner_name is not None and job.job_runner_external_id is None):
+                if job.job_runner_name is None:
+                    log.debug( "(%s) No job runner assigned and job still in '%s' state, adding to the job handler queue" % ( job.id, job.state ) )
+                else:
+                    log.debug( "(%s) Job runner assigned but no external ID recorded, adding to the job handler queue" % job.id )
                 if self.track_jobs_in_database:
                     job.state = model.Job.states.NEW
                 else:
@@ -133,7 +136,7 @@
                     .join(model.HistoryDatasetAssociation) \
                     .join(model.Dataset) \
                     .filter(and_((model.Job.state == model.Job.states.NEW),
-                                 or_((model.HistoryDatasetAssociation._state != None),
+                                 or_((model.HistoryDatasetAssociation._state == model.HistoryDatasetAssociation.states.FAILED_METADATA),
                                      (model.HistoryDatasetAssociation.deleted == True ),
                                      (model.Dataset.state != model.Dataset.states.OK ),
                                      (model.Dataset.deleted == True)))).subquery()

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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[galaxy-commits] commit/galaxy-central: 4 new changesets

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