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Merge 16.01 into 16.04

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carlfeberhard
2016-04-14 14:49:07 -04:00
parent f013cf2021 68ce6ce49c
commit 8b49814859
8 changed files with 36 additions and 23 deletions
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client/galaxy/scripts/mvc/citation/citation-model.js
+23 -11
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@@ -14,28 +14,40 @@ var logNamespace = 'citation';
* @name Citation
* @augments Backbone.Model
*/
var Citation = Backbone.Model.extend( baseMVC.LoggableMixin ).extend( {
var Citation = Backbone.Model.extend( baseMVC.LoggableMixin ).extend({
_logNamespace : logNamespace,
initialize: function() {
var bibtex = this.get( 'content' );
var entry = parseBibtex(bibtex).entries[0];
this.entry = entry;
var bibtex = this.attributes.content;
var parsed = BibtexParser( bibtex );
// bibtex returns successfully parsed in .entries and any parsing errors in .errors
if( parsed.errors.length ){
// the gen. form of these errors seems to be [ line, col, char, error message ]
var errors = parsed.errors.reduce( function( all, current ){ return all + '; ' + current; });
// throw new Error( 'Error parsing bibtex: ' + errors );
this.log( 'Error parsing bibtex: ' + errors );
}
this._fields = {};
var rawFields = entry.Fields;
for(var key in rawFields) {
var value = rawFields[ key ];
var lowerKey = key.toLowerCase();
this._fields[ lowerKey ] = value;
this.entry = _.first( parsed.entries );
if( this.entry ){
var rawFields = this.entry.Fields;
for( var key in rawFields ){
var value = rawFields[ key ];
var lowerKey = key.toLowerCase();
this._fields[ lowerKey ] = value;
}
}
},
entryType: function() {
return this.entry.EntryType;
return this.entry? this.entry.EntryType : undefined;
},
fields: function() {
return this._fields;
}
} );
});
//==============================================================================
/** @class Backbone collection of citations.
lib/galaxy/web/framework/middleware/remoteuser.py
+7 -5
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@@ -76,7 +76,12 @@ class RemoteUser( object ):
# seems improbable that an attacker with access to the server hosting
# Galaxy would not have access to Galaxy itself, and be attempting to
# attack the system
if self.config_secret_header is not None:
if path_info.startswith( '/api/' ):
# The API handles its own authentication via keys
# Check for API key before checking for header
return self.app( environ, start_response )
elif self.config_secret_header is not None:
if environ.get('HTTP_GX_SECRET') is None:
title = "Access to Galaxy is denied"
message = """
@@ -91,7 +96,7 @@ class RemoteUser( object ):
"""
return self.error( start_response, title, message )
if not safe_str_cmp(environ.get('HTTP_GX_SECRET'), self.config_secret_header):
if not safe_str_cmp(environ.get('HTTP_GX_SECRET', ''), self.config_secret_header):
title = "Access to Galaxy is denied"
message = """
Galaxy is configured to authenticate users via an external
@@ -161,9 +166,6 @@ class RemoteUser( object ):
"""
return self.error( start_response, title, message )
return self.app( environ, start_response )
elif path_info.startswith( '/api/' ):
# The API handles its own authentication via keys
return self.app( environ, start_response )
else:
log.debug("Unable to identify user. %s not found" % self.remote_user_header)
for k, v in environ.iteritems():
static/maps/mvc/citation/citation-model.js.map
+1 -1
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@@ -1 +1 @@
{"version":3,"file":"citation-model.js","sources":["../../../src/mvc/citation/citation-model.js"],"names":["define","parseBibtex","baseMVC","window","BibtexParser","logNamespace","Citation","Backbone","Model","extend","LoggableMixin","_logNamespace","initialize","bibtex","this","get","entry","entries","_fields","rawFields","Fields","key","value","lowerKey","toLowerCase","entryType","EntryType","fields","BaseCitationCollection","Collection","urlRoot","Galaxy","root","partial","model","HistoryCitationCollection","url","history_id","ToolCitationCollection","tool_id"],"mappings":"AAAAA,QACI,cACA,eACA,sBACD,SAAUC,EAAaC,GAI1BD,EAAcA,GAAeE,OAAOC,YAEpC,IAAIC,GAAe,WAMfC,EAAWC,SAASC,MAAMC,OAAQP,EAAQQ,eAAgBD,QAC1DE,cAAgBN,EAEhBO,WAAY,WACR,GAAIC,GAASC,KAAKC,IAAK,WACnBC,EAAQf,EAAYY,GAAQI,QAAQ,EACxCH,MAAKE,MAAQA,EACbF,KAAKI,UACL,IAAIC,GAAYH,EAAMI,MACtB,KAAI,GAAIC,KAAOF,GAAW,CACtB,GAAIG,GAAQH,EAAWE,GACnBE,EAAWF,EAAIG,aACnBV,MAAKI,QAASK,GAAaD,IAGnCG,UAAW,WACP,MAAOX,MAAKE,MAAMU,WAEtBC,OAAQ,WACJ,MAAOb,MAAKI,WAOhBU,EAAyBrB,SAASsB,WAAWpB,OAAQP,EAAQQ,eAAgBD,QAC7EE,cAAgBN,EAGhByB,QAAUC,OAAOC,KAAO,MACxBC,SAAU,EACVC,MAAQ5B,IAGR6B,EAA4BP,EAAuBnB,QAEnD2B,IAAM,WACF,MAAOtB,MAAKgB,QAAU,cAAgBhB,KAAKuB,WAAa,gBAI5DC,EAAyBV,EAAuBnB,QAEhD2B,IAAM,WACF,MAAOtB,MAAKgB,QAAU,UAAYhB,KAAKyB,QAAU,cAErDN,SAAU,GAKd,QACI3B,SAAWA,EACX6B,0BAA6BA,EAC7BG,uBAAwBA"}
{"version":3,"file":"citation-model.js","sources":["../../../src/mvc/citation/citation-model.js"],"names":["define","parseBibtex","baseMVC","window","BibtexParser","logNamespace","Citation","Backbone","Model","extend","LoggableMixin","_logNamespace","initialize","bibtex","this","attributes","content","parsed","errors","length","reduce","all","current","log","_fields","entry","_","first","entries","rawFields","Fields","key","value","lowerKey","toLowerCase","entryType","EntryType","undefined","fields","BaseCitationCollection","Collection","urlRoot","Galaxy","root","partial","model","HistoryCitationCollection","url","history_id","ToolCitationCollection","tool_id"],"mappings":"AAAAA,QACI,cACA,eACA,sBACD,SAAUC,EAAaC,GAI1BD,EAAcA,GAAeE,OAAOC,YAEpC,IAAIC,GAAe,WAMfC,EAAWC,SAASC,MAAMC,OAAQP,EAAQQ,eAAgBD,QAC1DE,cAAgBN,EAEhBO,WAAY,WAER,GAAIC,GAASC,KAAKC,WAAWC,QACzBC,EAASb,aAAcS,EAE3B,IAAII,EAAOC,OAAOC,OAAQ,CAEtB,GAAID,GAASD,EAAOC,OAAOE,OAAQ,SAAUC,EAAKC,GAAW,MAAOD,GAAM,KAAOC,GAEjFR,MAAKS,IAAK,yBAA2BL,GAKzC,GAFAJ,KAAKU,WACLV,KAAKW,MAAQC,EAAEC,MAAOV,EAAOW,SACzBd,KAAKW,MAAO,CACZ,GAAII,GAAYf,KAAKW,MAAMK,MAC3B,KAAK,GAAIC,KAAOF,GAAW,CACvB,GAAIG,GAAQH,EAAWE,GACnBE,EAAWF,EAAIG,aACnBpB,MAAKU,QAASS,GAAaD,KAIvCG,UAAW,WACP,MAAOrB,MAAKW,MAAOX,KAAKW,MAAMW,UAAYC,QAE9CC,OAAQ,WACJ,MAAOxB,MAAKU,WAQhBe,EAAyBhC,SAASiC,WAAW/B,OAAQP,EAAQQ,eAAgBD,QAC7EE,cAAgBN,EAGhBoC,QAAUC,OAAOC,KAAO,MACxBC,SAAU,EACVC,MAAQvC,IAGRwC,EAA4BP,EAAuB9B,QAEnDsC,IAAM,WACF,MAAOjC,MAAK2B,QAAU,cAAgB3B,KAAKkC,WAAa,gBAI5DC,EAAyBV,EAAuB9B,QAEhDsC,IAAM,WACF,MAAOjC,MAAK2B,QAAU,UAAY3B,KAAKoC,QAAU,cAErDN,SAAU,GAKd,QACItC,SAAWA,EACXwC,0BAA6BA,EAC7BG,uBAAwBA"}
static/scripts/bundled/analysis.bundled.js
+2 -2
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static/scripts/bundled/analysis.bundled.js.map
+1 -1
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static/scripts/bundled/libs.bundled.js.map
+1 -1
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static/scripts/mvc/citation/citation-model.js
+1 -1
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@@ -1,2 +1,2 @@
define(["libs/bibtex","mvc/base-mvc","utils/localization"],function(a,b){a=a||window.BibtexParser;var c="citation",d=Backbone.Model.extend(b.LoggableMixin).extend({_logNamespace:c,initialize:function(){var b=this.get("content"),c=a(b).entries[0];this.entry=c,this._fields={};var d=c.Fields;for(var e in d){var f=d[e],g=e.toLowerCase();this._fields[g]=f}},entryType:function(){return this.entry.EntryType},fields:function(){return this._fields}}),e=Backbone.Collection.extend(b.LoggableMixin).extend({_logNamespace:c,urlRoot:Galaxy.root+"api",partial:!0,model:d}),f=e.extend({url:function(){return this.urlRoot+"/histories/"+this.history_id+"/citations"}}),g=e.extend({url:function(){return this.urlRoot+"/tools/"+this.tool_id+"/citations"},partial:!1});return{Citation:d,HistoryCitationCollection:f,ToolCitationCollection:g}});
define(["libs/bibtex","mvc/base-mvc","utils/localization"],function(a,b){a=a||window.BibtexParser;var c="citation",d=Backbone.Model.extend(b.LoggableMixin).extend({_logNamespace:c,initialize:function(){var a=this.attributes.content,b=BibtexParser(a);if(b.errors.length){var c=b.errors.reduce(function(a,b){return a+"; "+b});this.log("Error parsing bibtex: "+c)}if(this._fields={},this.entry=_.first(b.entries),this.entry){var d=this.entry.Fields;for(var e in d){var f=d[e],g=e.toLowerCase();this._fields[g]=f}}},entryType:function(){return this.entry?this.entry.EntryType:void 0},fields:function(){return this._fields}}),e=Backbone.Collection.extend(b.LoggableMixin).extend({_logNamespace:c,urlRoot:Galaxy.root+"api",partial:!0,model:d}),f=e.extend({url:function(){return this.urlRoot+"/histories/"+this.history_id+"/citations"}}),g=e.extend({url:function(){return this.urlRoot+"/tools/"+this.tool_id+"/citations"},partial:!1});return{Citation:d,HistoryCitationCollection:f,ToolCitationCollection:g}});
//# sourceMappingURL=../../../maps/mvc/citation/citation-model.js.map
templates/webapps/galaxy/galaxy.panels.mako
-1
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@@ -144,7 +144,6 @@
## Scripts can be loaded later since they progressively add features to
## the panels, but do not change layout
<script type="text/javascript">
## configure left panel
%if self.galaxy_config['left_panel']:
var lp = new panels.LeftPanel({ el: '#left' });