1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/6ebb0a47a2a3/
Changeset: 6ebb0a47a2a3
User: jmchilton
Date: 2014-08-06 18:36:27
Summary: Fix more BibTeX problems caught by @peterjc.
See https://bitbucket.org/galaxy/galaxy-central/commits/3e8dfd372918c90ee4b3726….
Thanks Peter!
Affected #: 1 file
diff -r 3e8dfd372918c90ee4b37267f0b7c03a291acb54 -r 6ebb0a47a2a3088ba9ed313d8f323d7e1f5c9bb6 tools/phenotype_association/lps.xml
--- a/tools/phenotype_association/lps.xml
+++ b/tools/phenotype_association/lps.xml
@@ -308,12 +308,16 @@
journal = {Journal of Machine Learning Research},
year = {2007},
volume = {8},
- pages = {1519-1555},
+ pages = {1519--1555},
}</citation>
- <citation type="bibtex">@MISC{Shi08lasso-patternsearchalgorithm,
+ <citation type="bibtex">@ARTICLE{Shi08lasso-patternsearchalgorithm,
author = {Weiliang Shi and Grace Wahba and Stephen Wright and Kristine Lee and Ronald Klein and Barbara Klein},
- title = { LASSO-Patternsearch Algorithm with Application to Ophthalmology and Genomic Data},
- year = {2008}
+ title = {LASSO-Patternsearch Algorithm with Application to Ophthalmology and Genomic Data},
+ journal= {Stat Interface},
+ year = {2008},
+ volume = {1},
+ number = {1},
+ pages = {137--153}
}</citation></citations></tool>
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/3e8dfd372918/
Changeset: 3e8dfd372918
User: jmchilton
Date: 2014-08-06 18:31:50
Summary: Fix citation problem in 39c9831 caught by @peterjc.
Affected #: 1 file
diff -r 0e9c220ff8cd619c902aca574a07f208a2a30a21 -r 3e8dfd372918c90ee4b37267f0b7c03a291acb54 tools/phenotype_association/lps.xml
--- a/tools/phenotype_association/lps.xml
+++ b/tools/phenotype_association/lps.xml
@@ -307,7 +307,8 @@
title = {An interior-point method for large-scale l1-regularized logistic regression},
journal = {Journal of Machine Learning Research},
year = {2007},
- volume = {2007}
+ volume = {8},
+ pages = {1519-1555},
}</citation><citation type="bibtex">@MISC{Shi08lasso-patternsearchalgorithm,
author = {Weiliang Shi and Grace Wahba and Stephen Wright and Kristine Lee and Ronald Klein and Barbara Klein},
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/a57767f4ae8f/
Changeset: a57767f4ae8f
Branch: next-stable
User: dannon
Date: 2014-08-06 16:16:22
Summary: Fix for conditionally using bucket_default in cloudlaunch.
Affected #: 1 file
diff -r 283f3be266eab2951f04cda8204fc24af22983ca -r a57767f4ae8f5e45ed04a123aae5be53c69ebe91 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
--- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
+++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
@@ -70,10 +70,18 @@
cfg = cloudman.CloudManConfig(key_id, secret, cluster_name, ami,
instance_type, password, placement=zone)
cml = cloudman.launch.CloudManLauncher(key_id, secret)
- result = cml.launch(cluster_name, ami, instance_type, password,
- cfg.kernel_id, cfg.ramdisk_id, cfg.key_name,
- cfg.security_groups, cfg.placement,
- bucket_default=bucket_default)
+ # This should probably be handled better on the bioblend side, but until
+ # an egg update can be made, this needs to conditionally include the
+ # parameter or not, even if the value is None.
+ if bucket_default:
+ result = cml.launch(cluster_name, ami, instance_type, password,
+ cfg.kernel_id, cfg.ramdisk_id, cfg.key_name,
+ cfg.security_groups, cfg.placement,
+ bucket_default=bucket_default)
+ else:
+ result = cml.launch(cluster_name, ami, instance_type, password,
+ cfg.kernel_id, cfg.ramdisk_id, cfg.key_name,
+ cfg.security_groups, cfg.placement)
# result is a dict with sg_names, kp_name, kp_material, rs, and instance_id
if not result['rs']:
trans.response.status = 400
https://bitbucket.org/galaxy/galaxy-central/commits/3976f4d59bc0/
Changeset: 3976f4d59bc0
Branch: next-stable
User: dannon
Date: 2014-08-06 17:25:12
Summary: Merge.
Affected #: 3 files
diff -r a57767f4ae8f5e45ed04a123aae5be53c69ebe91 -r 3976f4d59bc0d7b65575e7573f13fb7470c9bf53 lib/galaxy/managers/citations.py
--- a/lib/galaxy/managers/citations.py
+++ b/lib/galaxy/managers/citations.py
@@ -157,8 +157,8 @@
if self.raw_bibtex is DoiCitation.BIBTEX_UNSET:
return """@MISC{%s,
- DOI = '%s',
- note = 'Failed to fetch BibTeX for DOI.'
+ DOI = {%s},
+ note = {Failed to fetch BibTeX for DOI.}
}""" % (self.__doi, self.__doi)
else:
return self.raw_bibtex
diff -r a57767f4ae8f5e45ed04a123aae5be53c69ebe91 -r 3976f4d59bc0d7b65575e7573f13fb7470c9bf53 static/scripts/mvc/citation/citation-view.js
--- a/static/scripts/mvc/citation/citation-view.js
+++ b/static/scripts/mvc/citation/citation-view.js
@@ -94,7 +94,7 @@
return info + ".";
},
_asSentence: function(str) {
- return str ? str + ". " : "";
+ return (str && str.trim()) ? str + ". " : "";
}
});
diff -r a57767f4ae8f5e45ed04a123aae5be53c69ebe91 -r 3976f4d59bc0d7b65575e7573f13fb7470c9bf53 static/scripts/packed/mvc/citation/citation-view.js
--- a/static/scripts/packed/mvc/citation/citation-view.js
+++ b/static/scripts/packed/mvc/citation/citation-view.js
@@ -1,1 +1,1 @@
-define(["mvc/base-mvc","mvc/citation/citation-model","utils/localization"],function(a,d,c){var b=Backbone.View.extend({tagName:"div",className:"citations",render:function(){this.$el.append("<p>"+this.formattedReference()+"</p>");return this},formattedReference:function(){var j=this.model;var i=j.entryType();var k=j.fields();var g="";var n=this._asSentence((k.author?k.author:"")+(k.year?(" ("+k.year+")"):""))+" ";var m=k.title||"";var h=k.pages?("pp. "+k.pages):"";var o=k.address;if(i=="article"){g=n+this._asSentence(m)+(k.journal?("In <em>"+k.journal+", "):"")+(k.volume?k.volume:"")+(k.number?("("+k.number+"), "):", ")+this._asSentence(h)+this._asSentence(k.address)+"</em>"}else{if(i=="inproceedings"||i=="proceedings"){g=n+this._asSentence(m)+(k.booktitle?("In <em>"+k.booktitle+", "):"")+(h?h:"")+(o?", "+o:"")+".</em>"}else{if(i=="mastersthesis"||i=="phdthesis"){g=n+this._asSentence(m)+(k.howpublished?k.howpublished+". ":"")+(k.note?k.note+".":"")}else{if(i=="techreport"){g=n+". "+this._asSentence(m)+this._asSentence(k.institution)+this._asSentence(k.number)+this._asSentence(k.type)}else{if(i=="book"||i=="inbook"||i=="incollection"){g=this._asSentence(n)+" "+this._formatBookInfo(k)}else{g=this._asSentence(n)+" "+this._asSentence(m)+this._asSentence(k.howpublished)+this._asSentence(k.note)}}}}}var l="";if(k.DOI){l="http://dx.doi.org/"+k.DOI;g+='[<a href="'+l+'">doi:'+k.DOI+"</a>]"}var f=k.url||l;if(f){g+='[<a href="'+f+'">Link</a>]'}return g},_formatBookInfo:function(f){var g="";if(f.chapter){g+=f.chapter+" in "}if(f.title){g+="<em>"+f.title+"</em>"}if(f.editor){g+=", Edited by "+f.editor+", "}if(f.publisher){g+=", "+f.publisher}if(f.pages){g+=", pp. "+f.pages+""}if(f.series){g+=", <em>"+f.series+"</em>"}if(f.volume){g+=", Vol."+f.volume}if(f.issn){g+=", ISBN: "+f.issn}return g+"."},_asSentence:function(f){return f?f+". ":""}});var e=Backbone.View.extend({el:"#citations",initialize:function(){this.listenTo(this.collection,"add",this.renderCitation)},events:{"click .citations-to-bibtex":"showBibtex","click .citations-to-formatted":"showFormatted"},renderCitation:function(g){var f=new b({model:g});this.$(".citations-formatted").append(f.render().el);var h=this.$(".citations-bibtex-text");h.val(h.val()+"\n\r"+g.attributes.content)},render:function(){this.$el.html(this.citationsElement());this.collection.each(function(f){this.renderCitation(f)},this);this.showFormatted()},showBibtex:function(){this.$(".citations-to-formatted").show();this.$(".citations-to-bibtex").hide();this.$(".citations-bibtex").show();this.$(".citations-formatted").hide();this.$(".citations-bibtex-text").select()},showFormatted:function(){this.$(".citations-to-formatted").hide();this.$(".citations-to-bibtex").show();this.$(".citations-bibtex").hide();this.$(".citations-formatted").show()},partialWarningElement:function(){if(this.collection.partial){return['<div style="padding:5px 10px">',"<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',"</div>",].join("")}else{return""}},citationsElement:function(){return['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>',' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">',this.partialWarningElement(),'<span class="citations-formatted"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")}});return{CitationView:b,CitationListView:e}});
\ No newline at end of file
+define(["mvc/base-mvc","mvc/citation/citation-model","utils/localization"],function(a,d,c){var b=Backbone.View.extend({tagName:"div",className:"citations",render:function(){this.$el.append("<p>"+this.formattedReference()+"</p>");return this},formattedReference:function(){var j=this.model;var i=j.entryType();var k=j.fields();var g="";var n=this._asSentence((k.author?k.author:"")+(k.year?(" ("+k.year+")"):""))+" ";var m=k.title||"";var h=k.pages?("pp. "+k.pages):"";var o=k.address;if(i=="article"){g=n+this._asSentence(m)+(k.journal?("In <em>"+k.journal+", "):"")+(k.volume?k.volume:"")+(k.number?("("+k.number+"), "):", ")+this._asSentence(h)+this._asSentence(k.address)+"</em>"}else{if(i=="inproceedings"||i=="proceedings"){g=n+this._asSentence(m)+(k.booktitle?("In <em>"+k.booktitle+", "):"")+(h?h:"")+(o?", "+o:"")+".</em>"}else{if(i=="mastersthesis"||i=="phdthesis"){g=n+this._asSentence(m)+(k.howpublished?k.howpublished+". ":"")+(k.note?k.note+".":"")}else{if(i=="techreport"){g=n+". "+this._asSentence(m)+this._asSentence(k.institution)+this._asSentence(k.number)+this._asSentence(k.type)}else{if(i=="book"||i=="inbook"||i=="incollection"){g=this._asSentence(n)+" "+this._formatBookInfo(k)}else{g=this._asSentence(n)+" "+this._asSentence(m)+this._asSentence(k.howpublished)+this._asSentence(k.note)}}}}}var l="";if(k.DOI){l="http://dx.doi.org/"+k.DOI;g+='[<a href="'+l+'">doi:'+k.DOI+"</a>]"}var f=k.url||l;if(f){g+='[<a href="'+f+'">Link</a>]'}return g},_formatBookInfo:function(f){var g="";if(f.chapter){g+=f.chapter+" in "}if(f.title){g+="<em>"+f.title+"</em>"}if(f.editor){g+=", Edited by "+f.editor+", "}if(f.publisher){g+=", "+f.publisher}if(f.pages){g+=", pp. "+f.pages+""}if(f.series){g+=", <em>"+f.series+"</em>"}if(f.volume){g+=", Vol."+f.volume}if(f.issn){g+=", ISBN: "+f.issn}return g+"."},_asSentence:function(f){return(f&&f.trim())?f+". ":""}});var e=Backbone.View.extend({el:"#citations",initialize:function(){this.listenTo(this.collection,"add",this.renderCitation)},events:{"click .citations-to-bibtex":"showBibtex","click .citations-to-formatted":"showFormatted"},renderCitation:function(g){var f=new b({model:g});this.$(".citations-formatted").append(f.render().el);var h=this.$(".citations-bibtex-text");h.val(h.val()+"\n\r"+g.attributes.content)},render:function(){this.$el.html(this.citationsElement());this.collection.each(function(f){this.renderCitation(f)},this);this.showFormatted()},showBibtex:function(){this.$(".citations-to-formatted").show();this.$(".citations-to-bibtex").hide();this.$(".citations-bibtex").show();this.$(".citations-formatted").hide();this.$(".citations-bibtex-text").select()},showFormatted:function(){this.$(".citations-to-formatted").hide();this.$(".citations-to-bibtex").show();this.$(".citations-bibtex").hide();this.$(".citations-formatted").show()},partialWarningElement:function(){if(this.collection.partial){return['<div style="padding:5px 10px">',"<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',"</div>",].join("")}else{return""}},citationsElement:function(){return['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>',' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">',this.partialWarningElement(),'<span class="citations-formatted"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")}});return{CitationView:b,CitationListView:e}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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