1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/963fb2afb6d2/
Changeset: 963fb2afb6d2
User: guerler
Date: 2014-11-24 19:31:19+00:00
Summary: ToolForm: Adjust batch mode for collections
Affected #: 3 files
diff -r 4efb0741cdb40f52100b36605be9b84f505c3a29 -r 963fb2afb6d2876e0e9f1a2b7021dce18e6ef0d4 client/galaxy/scripts/mvc/tools/tools-select-content.js
--- a/client/galaxy/scripts/mvc/tools/tools-select-content.js
+++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js
@@ -190,7 +190,7 @@
// prepare result dict
var result = {
- batch : !this.options.multiple && id_list.length > 1,
+ batch : !this.options.multiple && (this.current == 'collection' || id_list.length > 1),
values : []
}
diff -r 4efb0741cdb40f52100b36605be9b84f505c3a29 -r 963fb2afb6d2876e0e9f1a2b7021dce18e6ef0d4 static/scripts/mvc/tools/tools-select-content.js
--- a/static/scripts/mvc/tools/tools-select-content.js
+++ b/static/scripts/mvc/tools/tools-select-content.js
@@ -190,7 +190,7 @@
// prepare result dict
var result = {
- batch : !this.options.multiple && id_list.length > 1,
+ batch : !this.options.multiple && (this.current == 'collection' || id_list.length > 1),
values : []
}
diff -r 4efb0741cdb40f52100b36605be9b84f505c3a29 -r 963fb2afb6d2876e0e9f1a2b7021dce18e6ef0d4 static/scripts/packed/mvc/tools/tools-select-content.js
--- a/static/scripts/packed/mvc/tools/tools-select-content.js
+++ b/static/scripts/packed/mvc/tools/tools-select-content.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(!g.multiple){this.current="single"}else{this.current="multiple"}if(!g.multiple){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"};j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"};this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1||this.options.multiple){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple&&j.length>1,values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(!g.multiple){this.current="single"}else{this.current="multiple"}if(!g.multiple){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"};j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"};this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1||this.options.multiple){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple&&(this.current=="collection"||j.length>1),values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/4efb0741cdb4/
Changeset: 4efb0741cdb4
User: guerler
Date: 2014-11-24 18:36:24+00:00
Summary: ToolForm: Adjust batch mode submission
Affected #: 3 files
diff -r 104537c5219c83b8124956f237caedeb07c7164e -r 4efb0741cdb40f52100b36605be9b84f505c3a29 client/galaxy/scripts/mvc/tools/tools-select-content.js
--- a/client/galaxy/scripts/mvc/tools/tools-select-content.js
+++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js
@@ -190,7 +190,7 @@
// prepare result dict
var result = {
- batch : !this.options.multiple,
+ batch : !this.options.multiple && id_list.length > 1,
values : []
}
diff -r 104537c5219c83b8124956f237caedeb07c7164e -r 4efb0741cdb40f52100b36605be9b84f505c3a29 static/scripts/mvc/tools/tools-select-content.js
--- a/static/scripts/mvc/tools/tools-select-content.js
+++ b/static/scripts/mvc/tools/tools-select-content.js
@@ -190,7 +190,7 @@
// prepare result dict
var result = {
- batch : !this.options.multiple,
+ batch : !this.options.multiple && id_list.length > 1,
values : []
}
diff -r 104537c5219c83b8124956f237caedeb07c7164e -r 4efb0741cdb40f52100b36605be9b84f505c3a29 static/scripts/packed/mvc/tools/tools-select-content.js
--- a/static/scripts/packed/mvc/tools/tools-select-content.js
+++ b/static/scripts/packed/mvc/tools/tools-select-content.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(!g.multiple){this.current="single"}else{this.current="multiple"}if(!g.multiple){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"};j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"};this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1||this.options.multiple){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple,values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(!g.multiple){this.current="single"}else{this.current="multiple"}if(!g.multiple){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"};j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"};this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1||this.options.multiple){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple&&j.length>1,values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/104537c5219c/
Changeset: 104537c5219c
User: martenson
Date: 2014-11-24 18:26:24+00:00
Summary: add logging when password reset fails; stop retreving message form the request - we never need it
Affected #: 1 file
diff -r 7d97ff9d4bef1a92adf5be7e61c5b4a3007a76fd -r 104537c5219c83b8124956f237caedeb07c7164e lib/galaxy/webapps/galaxy/controllers/user.py
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -1119,22 +1119,22 @@
"""Reset the user's password. Send an email with the new password."""
if trans.app.config.smtp_server is None:
return trans.show_error_message( "Mail is not configured for this Galaxy instance. Please contact your local Galaxy administrator." )
- message = util.sanitize_text( util.restore_text( kwd.get( 'message', '' ) ) )
+ message = ''
status = 'done'
if kwd.get( 'reset_password_button', False ):
reset_user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).first()
user = trans.get_user()
if reset_user:
if user and user.id != reset_user.id:
- message = "You may only reset your own password"
+ message = "You may only reset your own password."
status = 'error'
else:
chars = string.letters + string.digits
new_pass = ""
reset_password_length = getattr( trans.app.config, "reset_password_length", 15 )
- for i in range(reset_password_length):
- new_pass = new_pass + random.choice(chars)
- host = trans.request.host.split(':')[0]
+ for i in range( reset_password_length ):
+ new_pass = new_pass + random.choice( chars )
+ host = trans.request.host.split( ':' )[ 0 ]
if host == 'localhost':
host = socket.getfqdn()
body = 'Your password on %s has been reset to:\n\n %s\n' % ( host, new_pass )
@@ -1148,10 +1148,11 @@
trans.log_event( "User reset password: %s" % email )
message = "Password has been reset and emailed to: %s. <a href='%s'>Click here</a> to return to the login form." % ( email, web.url_for( controller='user', action='login', noredirect='true' ) )
except Exception, e:
+ status = 'error'
message = 'Failed to reset password: %s' % str( e )
- status = 'error'
+ log.exception( 'Unable to reset password: ' + str( e ) )
elif email is not None:
- message = "The specified user does not exist"
+ message = "The specified user does not exist."
status = 'error'
elif email is None:
email = ""
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/6cc3b0c515bc/
Changeset: 6cc3b0c515bc
User: guerler
Date: 2014-11-24 17:30:29+00:00
Summary: ToolForm: Allow 1 to n selection for batch mode fields
Affected #: 3 files
diff -r ebceda0721f3f3215447c19f94525f06f164afd1 -r 6cc3b0c515bce43786031f750bf4bd98d7fc9fed client/galaxy/scripts/mvc/tools/tools-jobs.js
--- a/client/galaxy/scripts/mvc/tools/tools-jobs.js
+++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js
@@ -145,12 +145,14 @@
}
// check number of inputs
- if (batch_n === -1) {
- batch_n = n;
- } else {
- if (batch_n !== n) {
- this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.');
- return false;
+ if (n > 1) {
+ if (batch_n === -1) {
+ batch_n = n;
+ } else {
+ if (batch_n !== n) {
+ this._foundError(input_id, 'Please make sure that you select the same number or a single input for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.');
+ return false;
+ }
}
}
}
diff -r ebceda0721f3f3215447c19f94525f06f164afd1 -r 6cc3b0c515bce43786031f750bf4bd98d7fc9fed static/scripts/mvc/tools/tools-jobs.js
--- a/static/scripts/mvc/tools/tools-jobs.js
+++ b/static/scripts/mvc/tools/tools-jobs.js
@@ -145,12 +145,14 @@
}
// check number of inputs
- if (batch_n === -1) {
- batch_n = n;
- } else {
- if (batch_n !== n) {
- this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.');
- return false;
+ if (n > 1) {
+ if (batch_n === -1) {
+ batch_n = n;
+ } else {
+ if (batch_n !== n) {
+ this._foundError(input_id, 'Please make sure that you select the same number or a single input for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.');
+ return false;
+ }
}
}
}
diff -r ebceda0721f3f3215447c19f94525f06f164afd1 -r 6cc3b0c515bce43786031f750bf4bd98d7fc9fed static/scripts/packed/mvc/tools/tools-jobs.js
--- a/static/scripts/packed/mvc/tools/tools-jobs.js
+++ b/static/scripts/packed/mvc/tools/tools-jobs.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f]);break}}else{console.debug(e);c.app.modal.show({title:"Job submission failed",body:a.error(d),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(!l||!j||!e){console.debug("tools-jobs::_validation - Retrieving input objects failed.");continue}if(!j.optional&&e.validate&&!e.validate()){this._foundError(l);return false}if(f&&f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this._foundError(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g){this._foundError(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})});
\ No newline at end of file
+define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f]);break}}else{console.debug(e);c.app.modal.show({title:"Job submission failed",body:a.error(d),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(!l||!j||!e){console.debug("tools-jobs::_validation - Retrieving input objects failed.");continue}if(!j.optional&&e.validate&&!e.validate()){this._foundError(l);return false}if(f&&f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this._foundError(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(g>1){if(m===-1){m=g}else{if(m!==g){this._foundError(l,"Please make sure that you select the same number or a single input for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</b>.");return false}}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/ebceda0721f3/
Changeset: ebceda0721f3
User: jmchilton
Date: 2014-11-24 17:24:21+00:00
Summary: Allow passing extra parameter to docker run command in job_conf.xml.
As request in the following thread http://dev.list.galaxyproject.org/more-control-over-the-quot-docker-quot-co….
Affected #: 3 files
diff -r 3edc85f4761bbcde996470590cc002828ce21d03 -r ebceda0721f3f3215447c19f94525f06f164afd1 config/job_conf.xml.sample_advanced
--- a/config/job_conf.xml.sample_advanced
+++ b/config/job_conf.xml.sample_advanced
@@ -204,6 +204,9 @@
remote job user. Leave empty to not use the -u argument with
Docker. --><!-- <param id="docker_set_user">$UID</param> -->
+ <!-- Pass extra arguments to the docker run command not covered by the
+ above options (e.g. --link server:server) -->
+ <!-- <param id="docker_run_extra_arguments"></param> --><!-- Following command can be used to tweak docker command. --><!-- <param id="docker_cmd">/usr/local/custom_docker/docker</param> --><!-- Following can be used to connect to docke server in different
diff -r 3edc85f4761bbcde996470590cc002828ce21d03 -r ebceda0721f3f3215447c19f94525f06f164afd1 lib/galaxy/tools/deps/containers.py
--- a/lib/galaxy/tools/deps/containers.py
+++ b/lib/galaxy/tools/deps/containers.py
@@ -245,6 +245,7 @@
net=prop("net", "none"), # By default, docker instance has networking disabled
auto_rm=asbool(prop("auto_rm", docker_util.DEFAULT_AUTO_REMOVE)),
set_user=prop("set_user", docker_util.DEFAULT_SET_USER),
+ run_extra_arguments=prop("run_extra_arguments", docker_util.DEFAULT_RUN_EXTRA_ARGUMENTS),
**docker_host_props
)
return "%s\n%s" % (cache_command, run_command)
diff -r 3edc85f4761bbcde996470590cc002828ce21d03 -r ebceda0721f3f3215447c19f94525f06f164afd1 lib/galaxy/tools/deps/docker_util.py
--- a/lib/galaxy/tools/deps/docker_util.py
+++ b/lib/galaxy/tools/deps/docker_util.py
@@ -11,6 +11,7 @@
DEFAULT_VOLUMES_FROM = None
DEFAULT_AUTO_REMOVE = True
DEFAULT_SET_USER = "$UID"
+DEFAULT_RUN_EXTRA_ARGUMENTS = None
class DockerVolume(object):
@@ -116,6 +117,7 @@
working_directory=DEFAULT_WORKING_DIRECTORY,
name=None,
net=DEFAULT_NET,
+ run_extra_arguments=DEFAULT_RUN_EXTRA_ARGUMENTS,
docker_cmd=DEFAULT_DOCKER_COMMAND,
sudo=DEFAULT_SUDO,
sudo_cmd=DEFAULT_SUDO_COMMAND,
@@ -148,6 +150,8 @@
command_parts.extend(["--net", net])
if auto_rm:
command_parts.append("--rm")
+ if run_extra_arguments:
+ command_parts.append(run_extra_arguments)
if set_user:
user = set_user
if set_user == DEFAULT_SET_USER:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/c1a9ed13d5f7/
Changeset: c1a9ed13d5f7
Branch: next-stable
User: BjoernGruening
Date: 2014-11-24 16:28:25+00:00
Summary: getstring() does not exist, use get() instead
Affected #: 1 file
diff -r 475716a95133cdeb443f38bbd7fcb7a8291e6069 -r c1a9ed13d5f71deb671ab83ed262c0a861c469d2 lib/galaxy/web/base/interactive_environments.py
--- a/lib/galaxy/web/base/interactive_environments.py
+++ b/lib/galaxy/web/base/interactive_environments.py
@@ -77,7 +77,7 @@
}
if self.attr.viz_config.has_option("docker", "galaxy_url"):
- conf_file['galaxy_url'] = self.attr.viz_config.getstring("docker", "galaxy_url")
+ conf_file['galaxy_url'] = self.attr.viz_config.get("docker", "galaxy_url")
elif self.attr.galaxy_config.galaxy_infrastructure_url_set:
conf_file['galaxy_url'] = self.attr.galaxy_config.galaxy_infrastructure_url.rstrip('/') + '/'
else:
https://bitbucket.org/galaxy/galaxy-central/commits/428cd34786bd/
Changeset: 428cd34786bd
User: jmchilton
Date: 2014-11-24 16:59:13+00:00
Summary: Merge next-stable.
Affected #: 0 files
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/c433a83d85cc/
Changeset: c433a83d85cc
User: jmchilton
Date: 2014-11-24 16:57:42+00:00
Summary: Merged in BjoernGruening/galaxy-central-1/fix_galaxy_url_parsing (pull request #572)
Fix bug in IE config parsing.
Affected #: 1 file
diff -r dd2d0b244a27460ad15df5f12eaf243702086044 -r c433a83d85cc9296b04a51b3cc1225d031ea1b16 lib/galaxy/web/base/interactive_environments.py
--- a/lib/galaxy/web/base/interactive_environments.py
+++ b/lib/galaxy/web/base/interactive_environments.py
@@ -77,7 +77,7 @@
}
if self.attr.viz_config.has_option("docker", "galaxy_url"):
- conf_file['galaxy_url'] = self.attr.viz_config.getstring("docker", "galaxy_url")
+ conf_file['galaxy_url'] = self.attr.viz_config.get("docker", "galaxy_url")
elif self.attr.galaxy_config.galaxy_infrastructure_url_set:
conf_file['galaxy_url'] = self.attr.galaxy_config.galaxy_infrastructure_url.rstrip('/') + '/'
else:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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